Microbiol. Mol. Biol. Rev.-2014-Darmon-1-39

10.1128/MMBR.00035-13.
2014, 78(1):1. DOI: Microbiol. Mol. Biol. Rev.

Elise Darmon and David R. F. Leach
Bacterial Genome Instability

http://mmbr.asm.org/content/78/1/1
Updated information and services can be found at:
These include:
REFERENCES
http://mmbr.asm.org/content/78/1/1#ref-list-1 free at:
This article cites 640 articles, 250 of which can be accessed
CONTENT ALERTS
more articles cite this article),
Receive: RSS Feeds, eTOCs, free email alerts (when new
http://journals.asm.org/site/misc/reprints.xhtml Information about commercial reprint orders:
http://journals.asm.org/site/subscriptions/ To subscribe to to another ASM Journal go to:

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

Elise Darmon, David R. F. Leach
Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
SUMMARY. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
INSTABILITY MEDIATED BY SPECIALIZED GENETIC ELEMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
Mobile Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Insertion sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Miniature inverted-repeat transposable elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Repetitive extragenic palindromic sequences and bacterial interspersed mosaic elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Transposons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Transposable bacteriophages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Genomic islands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Inteins, Introns, and Retroelements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Self-splicing elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
(i) Inteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
(ii) Introns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
(iii) Homing endonucleases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Retroelements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
(i) Retrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
(ii) Diversity-generating retroelements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Integrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Genetic Elements Controlling the Stability of Mobile Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Postsegregation killing systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
(i) Toxin-antitoxin systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
(ii) Restriction-modication systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
CRISPR-Cas systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
INSTABILITY MEDIATED BY HOMOLOGOUS AND ILLEGITIMATE RECOMBINATION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Mechanisms of Homologous and Illegitimate Recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Homologous recombination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Illegitimate recombination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Gene Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Genome Instability Due to Recombination at Repeated Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Tandem-repeat deletion or amplication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
(i) Tandem-repeat variation by illegitimate recombination: microsatellite instability and contingency loci. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
(ii) Tandem-repeat variation by homologous recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Hairpin structure-stimulated strand slippage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Control of genomic instability by DNA repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Site-Specic Recombination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Site-specic inversion systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Excision/insertion of DNA elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Developmentally regulated gene rearrangements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
CONSEQUENCES OF GENOME INSTABILITY IN BACTERIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Phase and Antigenic Variation in Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Mechanisms of phase and antigenic variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Roles of phase and antigenic variation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Regulation of phase and antigenic variation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Horizontal Gene Transfer in Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Benets of HGT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Mechanism of HGT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
(i) Agents mediating HGT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
(ii) Natural limitations of HGT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
(iii) Cellular mechanisms to ght HGT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
(continued)
Address correspondence to David R. F. Leach, d.leach@ed.ac.uk.
Copyright 2014, American Society for Microbiology. All Rights Reserved.
doi:10.1128/MMBR.00035-13
March 2014 Volume 78 Number 1 Microbiology and Molecular Biology Reviews p. 139 mmbr.asm.org 1

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

(iv) Mechanisms of propagation of HGT elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
HGT in contemporary organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
(i) Methods used to detect HGT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
(ii) Levels of HGT in contemporary organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
(iii) Genes susceptible to HGT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
(iv) Relationships between HGT and an organisms life-style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
(v) Selshness of mobile elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
HGT and evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
(i) HGT and the beginning of life on Earth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
(ii) HGT and the tree of life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
(iii) HGT and bacterial species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
(iv) HGT, CRISPR-Cas, Lamarckism, and Darwinism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
CONCLUSION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
ACKNOWLEDGMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
SUMMARY
Bacterial genomes are remarkably stable from one generation
to the next but are plastic on an evolutionary time scale, sub-
stantially shaped by horizontal gene transfer, genome rear-
rangement, and the activities of mobile DNA elements. This
implies the existence of a delicate balance between the mainte-
nance of genome stability and the tolerance of genome insta-
bility. In this review, we describe the specialized genetic ele-
ments and the endogenous processes that contribute to
genome instability. We then discuss the consequences of ge-
nome instability at the physiological level, where cells have
harnessed instability to mediate phase and antigenic variation,
and at the evolutionary level, where horizontal gene transfer
has played an important role. Indeed, this ability to share DNA
sequences has played a major part in the evolution of life on
Earth. The evolutionary plasticity of bacterial genomes, cou-
pled with the vast numbers of bacteria on the planet, substan-
tially limits our ability to control disease.
INTRODUCTION
B
acteria are ubiquitous, extremely numerous, and essential
planetary life-forms. It has beenestimated that there are about
5 10
30
bacteria on earth, with the majority residing in oceanic
and terrestrial subsurfaces, the open ocean, and soil (1). Bacteria
canalsobe foundwithinandonthe surfaces of other organisms, as
symbionts or pathogens. Bacteria play important roles in the en-
vironment and the ecology of the planet as well as in the evolution
of living organisms (by their physical interactions with these or-
ganisms and by distributing genetic information by horizontal
gene transfer [HGT]).
Maintaining the right balance between genome integrity and in-
stability is essential for the survival of organisms and their offspring.
Bacterial chromosomes are complex and dynamic, characteristics
that give exibilitytothe genome (2, 3). Genome instabilitycanresult
frompoint mutations or fromgenome rearrangements such as dele-
tions, duplications, amplications, insertions, inversions, or translo-
cations. This review concentrates on instabilities brought about by
genome rearrangements and does not discuss the acquisition of ge-
netic information on whole replicons (such as plasmids). Some of
these mutations can be silent, while others can lead to phenotypic
variation, evolution, and speciation. Deletions, duplications, inser-
tions, and amplications change the amount of information con-
tained in the genome. Inversions, deletions, insertions, and translo-
cations candisrupt genes. Most forms of genome rearrangement also
result in the appearance of new sequences at the sites of the events.
Thesenewjunctions havethepotential toalter thefunctionor expres-
sion of proteins. Finally, rearrangements can inuence the structure
of the chromosome, with indirect effects on phenotype (4). For ex-
ample, a large inversion in the chromosome of Escherichia coli can
have dramatic effects on cell viability (5, 6). Bacteria possess var-
ious mechanisms to repair DNA damage. Some of these repair
mechanisms, such as nonhomologous end joining (NHEJ) and
translesion bypass replication, are mutagenic. Mutagenesis is nec-
essary for adaptation to changing environments and for bacte-
rial evolution, which is signicantly dependent on the potential
for genetic instability and horizontal gene transfer. Additionally,
specic genome instability can be at the origin of regulatory path-
ways, as in the case of phase and antigenic variation. Restriction-
modication (RM) systems and the CRISPR-Cas system (com-
prising clustered regularly interspaced short palindromic repeats
[CRISPR] and CRISPR-associated [Cas] proteins) also use ge-
nome instability toprotect bacteria against invasionby phages and
mobile elements. Genome instability is also used by pathogenic
bacteria to facilitate host infection without being attacked by im-
mune systems. Some instabilities are programmed, whereas oth-
ers are random. They can be the result of specialized genetic ele-
ments and/or of the action of endogenous pathways of DNA
metabolism. This review focuses mainly on natural chromosomal
instability in bacteria. We rst describe specialized genetic ele-
ments that mediate genome instability. We then report how en-
dogenous processes themselves can create genetic instability by
homologous or illegitimate recombination. Finally, we analyze
two remarkable consequences of genetic instability in bacteria:
phase and antigenic variation and horizontal gene transfer.
INSTABILITY MEDIATED BY SPECIALIZED GENETIC
ELEMENTS
There are several kinds of specialized genetic elements playing a role
ingenomic instability. We rst describe a number of mobile elements
(insertionsequences [ISs], miniatureinverted-repeat transposableel-
ements [MITEs], repetitive extragenic palindromic [REP] sequences,
bacterial interspersed mosaic elements [BIMEs], transposons, trans-
posable bacteriophages, andgenomic islands), inteins, introns, retro-
elements, and integrons. We then present two genetic elements that
control the stability of mobile elements: postsegregation killing sys-
tems and the CRISPR-Cas system.
Darmon and Leach
2 mmbr.asm.org Microbiology and Molecular Biology Reviews

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

Mobile Elements
Studies on spontaneous mutations led to the discovery of trans-
posable elements (7). They are found in every kingdomof life, but
in bacteria, they are often more abundant in cells living in extreme
environments (811). Transposable elements are DNA sequences
with dened ends that can move locus within and between ge-
nomes by means of excision and integration reactions that are
independent of homologous recombination. To be mobile, most
transposable elements have short terminal inverted repeats (IRs)
and use transposases that recognize and process the ends of the
elements (Fig. 1). Transposable elements often duplicate the tar-
get sequence in which they integrate, creating a short direct-repeat
sequence called a target site duplication. Selection of the target site
is a function of the transposase and differs at the level of sequence
specicity and stringency. The target sites of some elements are
very specic (as is the case for Tn7 [12]), whereas other elements
display little target specicity (e.g., Tn5 [13]).
Despite their ubiquity, transposable elements are not the
only forms of mobile DNA in bacteria. The characteristics of
these elements can overlap and intertwine, and mobile ele-
ments often invade each other. Therefore, some of these ele-
ments can be difcult to categorize. In addition to plasmids
(which are mobile but are not discussed in this review), there
are various main groups of bacterial elements that are poten-
tially mobile (Fig. 1; see also Fig. 2 and 3): ISs, MITEs, REP
sequences, BIMEs, transposons (including integrative conju-
gative elements [ICEs]), transposable bacteriophages, and, to
some extent, inteins, introns, homing endonucleases, and ret-
roelements (see Inteins, Introns, and Retroelements, below).
All mobile elements need to regulate their mobility to avoid
excessive mutagenesis, which would be detrimental for the cell.
Insertion sequences. An IS is a relatively small (0.7- to 2.5-kb)
DNAsegment. It contains one or two openreading frames (ORFs)
encoding only proteins responsible for functions involved in its
mobility (a transposase) and is bounded by short terminal IR se-
quences (Fig. 1A) (1416). Insertion of an IS will always change
the host genome, whereas excision of an IS can either restore the
chromosome to its original state or create a mutation. Table 1 lists
some examples of IS-mediated alterations in bacterial genomes.
Insertion of an IS in a chromosome changes the genome of the
host organism, as it adds the transposase gene(s) and often dupli-
cates a target sequence, creating a direct repeat. Additionally, in-
sertion of an IS can modify the expression of some host genes. The
disruption of a gene or its regulatory sequence can lead to gene
inactivation. Depending on the gene that is inactivated, the direct
or indirect cellular consequences of the IS insertion can vary from
advantageous to deleterious. On the other hand, an IS inserting
upstream of a gene can activate the expression of this gene in any
FIG 1 Schematic organization of different transposable elements inserted into a genome. (A) Organization of a typical IS (represented as a rectangle). It
contains a single open reading frame (sometimes two), encoding the transposase, that extends within the right inverted repeat (IRR). The transposase
promoter (P) is partially localized in the left inverted repeat (IRL). DR is the target fragment that has been duplicated to become a direct repeat following
the insertion of the IS. (B) Organization of a typical MITE. (C) Organization of a typical transposon. Long terminal inverted repeated (IR) sequences
surround function modules of genes. (D) Organization of a typical composite transposon. A chromosomal sequence is transposed together with two IS
elements that surround it (here ISs are in a direct orientation, but they can be inverted). At least one of the transposases needs to be active. The internal
DR of the IS elements can be absent. (E) Organization of a typical conjugative transposon (or ICE). The element contains inverted repeats surrounding
various modules of genes for maintenance (recombination), regulation, and dissemination (conjugation) and some accessory proteins. A conjugal origin
of transfer, oriT, is situated in the dissemination module. (F) Schematic organization of Mu, a typical transposable bacteriophage. Mu is delimited by
inverted repeats. The element contains various modules of genes for regulation, transposition, lysis, and head and tail proteins. The G region is invertible,
enabling the synthesis of different tail ber proteins.
March 2014 Volume 78 Number 1 mmbr.asm.org 3

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

of the several ways described below. Again, the consequences of
this activation can be diverse, from benecial to lethal. Transcrip-
tion of a gene within an IS can carry on outside the IS and tran-
scribe neighboring host genes (17). Alternatively, some ISs con-
tain an outward-facing 35 hexamer promoter motif in or near
their terminal inverted repeats; their integration into the genome
at the correct distance froma 10 promoter sequence changes the
regulation of the downstream gene(s) (18). An IS might also con-
tain an entire outward-facing promoter in or near its inverted
repeats (19). Upon insertion of the IS, this promoter can activate
downstream host genes. Furthermore, insertion of an IS can
change the topology of the DNA into which it is inserted and can
sometimes introduce or disrupt a regulatory binding sequence,
affecting the regulation of the downstreamgene(s) (2024). Inter-
estingly, the transposition of some ISs can be regulated by certain
natural conditions required to activate the transcription of other-
wise silent operons (25). An IS can also induce phase variation by
alternating insertion and precise excision at a specic locus within
a gene (see Excision/insertion of DNA elements, below) (26).
The distribution of ISs in the genome is not random, as there are
more ISs where they are less disturbing, in the intergenic regions
between convergently oriented genes (27). This distribution sug-
gests that detrimental insertions outnumber benecial insertions.
Incorrect excisions of ISs are mostly consequences of the action
of some host proteins, mainly but not exclusively DNAreplication
or repair proteins, andresult inthe introductionof mutations into
the host chromosome (see also Genome Instability Due to Re-
combination at Repeated Sequences, below). After a nearly pre-
cise excision, some IS DNA remains in the host chromosome,
resulting in an insertion (28), whereas an imprecise excision re-
moves some host DNA, resulting in a deletion (28, 29).
The interaction of an IS with another DNA molecule with
which it shares identical sequences, either another copy of the
same IS, a different transposable element, or some genomic DNA,
TABLE 1 Examples of prokaryotic genomic rearrangements induced by natural transposable elements
a
Rearrangement
Element(s) (reference[s])
IS MITE Transposon
Composite
transposon
Conjugative
or mobilizable
transposon Bacteriophage
Change upon insertion of the element
Addition of genetic material IS1186 (601) BOX (44) Tn6061 (602) Tn2922 (603) Tn916 (604) D3112 (605)
Inactivation of genes IS629, ISEc8 (29) RUP, BOX (44) Tn551 (606) Tn4001(607) Tn916 (608) Mu (86)
Creation of gene fusion RPE (53) Tn916 (609)
Activation of genes by addition of a
35 sequence
IS2 (18) Tn4652 (610)
Activation of genes due to the presence
of an outward promoter
IS6110 (19) Correia (52) Gamma delta
(611)
Tn10 (IS10)
(612)
Activation of genes by leakage of
promoter from genes inside the
element
ISTosp1 (17) Tn1000 (613)
Change due to perturbation of gene
regulation
IS1 (21, 23) Tn315 (614)
Change of DNA topology around
insertion site that impacts gene
expression
IS1 and IS5 (20, 22) ERIC (615)
Addition of a binding site that impacts
gene expression
IS5 (24) Correia (616) Tn4652 (617)
Change of mRNA properties of genes
adjacent to insertion site
ERIC (618)
Change upon excision of the element
Nucleotide substitution Tn916 (619)
Nearly precise excision (DNA insertion) IS629 (28) Tn10 (620) Tn916 (621)
Imprecise excision (DNA deletion) IS629 (28, 29) Tn7 (622) Tn5, Tn10
(622)
Mu (622)
Change involving another DNA molecule
Adjacent deletion (in which the element
is not deleted)
IS629 (28) Tn3 (623) Tn10 (624) Mucts62 (625)
Large deletion IS407A, ISBma2
(626)
Correia (627) Tn5 (IS50)
(628)
Tn5386-
Tn916
(629)
Mu (630)
Large duplication IS200 (631) Tn4651 (632) Tn10 (633)
Inversion IS905 (634) Tn2660 (635) Tn10 (622) CampMu (636)
Large genomic rearrangement IS407A, ISBma2
(626)
MITE (41) DEH (637) Mu (638)
Replicon fusion or cointegrate IS21 (639) Tn4430 (640) Tn4400 (641) NBU1 (642) D108 (643)
a
The list is nonexhaustive.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

can result in more important genomic rearrangements. Under
these circumstances, there are two possible mechanisms leading to
genome instability (30). The rst mechanism is direct and in-
volves the actionof the transposase andthe ends of different trans-
posable elements (or similar sequences) in an alternative transpo-
sition process. The second mechanism is indirect and relies on
host proteins, as it uses the host homologous or illegitimate re-
combination systems (see Instability Mediated by Homologous
and Illegitimate Recombination, below). Overall, these two pro-
cesses induce IS-dependent genome instability, such as adjacent
deletions, in which DNA connected to one end of the element is
deleted without affecting the element itself, large-scale deletions,
duplications, insertions, and chromosomal rearrangements. Re-
combination of two elements displaying the same orientation
would lead to a deletion, whereas recombination of two elements
of opposite orientations would result in an inversion of the inter-
vening sequence. Importantly, ISs can insert into plasmids or bac-
teriophages as well as intochromosomes. Recombinationbetween
two ISs on different DNA molecules or a failure to resolve struc-
tures during transposition can lead to replicon fusions or cointe-
grates. This includes the formation of Hfr strains if the recombi-
nation event is between ISs on a chromosome and a conjugative
plasmid such as F (31). Such events enable the transfer of chro-
mosomal DNA by conjugation (32, 33).
An IS is a small DNAmolecule, but its insertion or excision can
cause important genome instability in its host, especially when it
involves recombination or transposition with other DNA se-
quences. ISs can be considered selsh parasites or symbiotic se-
quences helping their hosts to evolve (see Horizontal Gene
Transfer in Prokaryotes, below).
Miniature inverted-repeat transposable elements. MITEs are
small, AT-rich DNAsequences (0.1 to 0.5 kb) containing terminal
inverted repeats, often displaying a TA dinucleotide motif at their
extremities and being surrounded by target-site duplications (Fig.
1B) (4, 34, 35). They often possess the recognition sequences nec-
essary for their mobility but do not encode a transposase. MITEs
are widespread in eukaryotic genomes, where they can achieve
high transposition activity using transposases encoded by other
autonomous elements (36). Mobilization of MITEs has also been
shown in bacteria (37). The study of MITEs in prokaryotes began
recently, and they have not yet been well dened. As a conse-
quence, distinctive MITE-like sequences have been classed and
named differently in various organisms. They are referred to as
MITEs in several bacteria but also as Correia elements (CE/
NEMIS/CREE/SRE) in Neisseria; RUP, BOX, and SPRITE in
Streptococcus; RPE in Rickettsia; CIR in Caulobacter and Brucella;
Nezha in cyanobacteria; ISM854-1 in Microcystis; and RU-1
(ERIC/IRU), RU-2 (YPAL), or RU-3 in enterobacteria (11, 35,
3844; for a more complete list, see reference 4).
Examples of MITE-induced genome instability in prokaryotes
are listed in Table 1. As for ISs, MITE insertion can add genetic
material, including functional ORFs (45); inactivate a gene; or
modulate the transcription of neighboring genes by introducing
an outward-facing promoter or a regulatory binding site or by
changing the DNAtopology at the insertionsite. Additionally, two
MITEs can recombine, leading to the formation of large deletions
or other chromosomal rearrangements (46, 47). Strikingly, due to
their small size, two main types of MITE-specic genome insta-
bility can also occur. Frequently, a MITE encodes one or several
ORFs, and its insertion into a host gene can result in an in-frame
gene fusion and the formation of a new protein (48). Sometimes,
aninserted ORF encodes a specic motif that will change the func-
tion or the localization of the protein. MITEs can also have an
effect on the regulation or the stability of mRNAs generated by
genes surrounding their insertion sites (35). For example, Correia
elements can be cotranscribed with their adjacent genes and be
targeted for cleavage by RNase III, changing the stability level of
these transcripts and therefore gene expression levels (49, 50). The
same element can also act as a transcriptional terminator (51) and
maybe as a noncoding regulatory RNA (52).
MITEs have denite actions on the genome of their host, from
slightly detrimental to maybe benecial (48, 53). Further studies
of MITEs in bacteria may reveal their origins and intrinsic cellular
functions.
Repetitive extragenic palindromic sequences and bacterial
interspersed mosaic elements. REP sequences were rst discov-
ered to be distributed throughout the chromosomes of enteric
bacteria (they have also been called PUs, for palindromic units)
(34, 54, 55). REP-like sequences have now been widely found in
other bacteria but seem to be absent from extrachromosomal el-
ements. The E. coli chromosome contains nearly 600 REP se-
quences, which corresponds to 1% of its genome. They are highly
repeated imperfect palindromes of 20 to 40 nucleotides that are
generally in extragenic but transcribed genomic regions. About
25%of E. coli transcription units harbor REP sequences. They can
be found as single occurrences but are more often organized in
pairs or inclusters. ABIMEis a pair of REPsequences inaninverse
orientation separated by a short linker sequence containing other
conserved sequence motifs (56, 57). The E. coli chromosome con-
tains 250 BIMEs, mostly in GC-rich genomic regions.
REP sequences can inuence the expression or the regulation
of genes or operons. After transcription, some REP sequences can
fold into stable RNA structures that protect upstream mRNAs
from degradation by 3=-to-5= exonucleases (58, 59). Therefore,
REP sequences can control differential gene expression in an
operon by modulating the stability of the different mRNA seg-
ments. Additionally, some BIMEs are involved in transcription
attenuation using a Rho-dependent mechanism (57), and a sub-
class of REP sequences can act as transcription terminators (60).
Strikingly, BIMEs have also been found to specically interact
with a number of proteins, which might indicate a role of these
repetitive elements inDNAtopology and/or inthe organizationor
the structure of the bacterial nucleoid. BIMEs of one category are
bound by the integration host factor (IHF); these structures have
been called RIBs (reiterative ihf BIMEs) (61) or RIPs (repetitive
IHF-binding palindromic elements) (62). Additionally, DNA
gyrase binds and cleaves some BIMEs (56, 6365). DNApolymer-
ase I (Pol I) alsobinds certainBIMEs (56, 66). Finally, the nucleoid
protein HU might interact with these repetitive elements (67).
Notably, REP sequences have been shown to stimulate the innate
immune system of mammalian cells (68).
The number and the location of BIMEs and REP sequences are
variable as a function of the bacterial strain and species (69). A
REP-associated transposase was found, suggesting that BIMEs
might be nonautonomous mobilizable transposable elements
(70). However, alternative mechanisms have been proposed re-
cently to explain the apparent mobility of BIMEs (71).
BIMEs and REP sequences seemto have an important effect on
genome instability, bacterial evolution, and speciation. They are
hot spots for specic transpositions (7275), and they have been

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

found at the junctions of RecA-dependent and RecA-independent
duplications (76, 77).
Transposons. Transposons generally range in size from 2.5 to
60 kb and usually possess long terminal inverted repeats and one
or several accessory genes that confer an advantageous phenotype
to their bacterial host, such as antibiotic, heavy metal, or phage
resistance; catabolic, vitamin, or antimicrobial compoundsynthe-
sis pathways; or nitrogen xation (Fig. 1C to E). Transposons
comprise functional modules, dened as regions devoted to indi-
vidual functions (Fig. 1C). Complex transposons have been clas-
sied according to their structures and properties. Acomposite or
compound transposon is anked on both sides by similar or iden-
tical ISs, at least one of which one encodes a functional trans-
posase, permitting their transposition together with the sequence
that separates them(Fig. 1D) (78). Aconjugative transposon, also
named an ICE, can transpose intracellularly or excise to transfer
intercellularly by conjugation (Fig. 1E) (7982). These elements
have phage, plasmid, and transposon characteristics (e.g., ICEs
can integrate and excise using an integrase enzyme) and are trans-
missible among bacteria. Mobilizable transposons or plasmids can
be mobilized by conjugative elements but are not self-transmissi-
ble (83). Recently, a conjugative transposon from Bacillus subtilis
was also shown to mobilize plasmids that did not have the usual
characteristics of mobilizable plasmids (84).
Most transposon-induced genome instabilities are similar to
genome instabilities that originate from ISs (Table 1). Some ele-
ments, such as the conjugative transposon Tn5397, have strong
insertion site preferences (85). Upon insertion, a transposon can
disrupt a gene or modify the regulation of neighboring genes. As a
consequence, transposons became useful tools for mutagenesis.
Transposons can also induce genomic rearrangements, such as
deletions, duplications, or inversions, or the formation of cointe-
grates. However, an important change caused by natural trans-
posons but not by ISs is the addition of accessory genetic material
into the host chromosome, as described above.
Transposable bacteriophages. Transposable bacteriophages
are viruses that can transpose their DNA into a bacterial chromo-
some, plasmid, or prophage, often duplicating the sequence sur-
rounding their insertion site during this process (Fig. 1F) (8688).
These temperate phages can stay in their host genomes as latent
prophages (lysogenic cycle) or replicate actively (lytic cycle). They
are mutator elements, as their integration into their host genome
is nearly random (Mu phages). Therefore, transposable bacterio-
phages are useful tools to identify genes involved indifferent path-
ways by mutagenesis. Examples of the effect of bacteriophage
transpositions on the bacterial genome are listed in Table 1. Inser-
tionof this kind of element into a gene (or its regulatory sequence)
might result in inactivation of the gene. Importantly, mutations
created by these elements have a polar effect, so the downstream
genes in the same operon will also be inactivated (89). Addition-
ally, transposable bacteriophages can induce the formation of dif-
ferent genomic rearrangements: various sizes of deletions or in-
versions or the formation of cointegrates. Finally, these
bacteriophages can stimulate the mobility of other bacteriophages
or induce recombination between transposable elements (90, 91).
Genomic islands. Genomic islands (GIs) or chromosomal is-
lands are large DNAsequences specically present in the genomes
of certain bacterial strains but not in the genomes of their most
closely related variants (92103). They are generally integrated
within a bacterial chromosome, but they can also be found on
plasmids or in phages. Some ICEs, integrated plasmids, or pro-
phages have been considered GIs. These islands usually encode a
number of accessory genes offering a selective advantage to the
cell, which enhances the bacteriums chances of survival or of
colonization of a newniche. Introduction of a newGI can result in
a total change of phenotype, behavior, or life-style of the receiving
organism. Depending on the provided phenotypic advantages, a
GI can be a pathogenicity island (such as Salmonella pathogenicity
island 1 [SPI1] [104]), a tness island (such as E. coli acid tness
island [AFI] [105]), a metabolic island (such as the Xanthomonas
xanthan gum production island [106]), a resistance island (to an-
tibiotics) (such as AbaR7 in Acinetobacter baumannii [107]), a
symbiosis island (such as the Mesorhizobium loti strain R7A sym-
biosis island [108]), a saprophytic island (like the island encoding
adhesins in some E. coli strains [94]), an ecological island (such as
an island permitting phenol degradation in Pseudomonas putida
[94, 109]), or a defense island (as in Shewanella sp. strain ANA-3
[110]). Strikingly, similar GIs may show distinct functions in dif-
ferent bacteria or under specic ecological conditions or life-
styles. A bacterium can contain various GIs in its genome.
AGI is usually between10 and200 kb inlength; smaller regions
with similar characteristics have been called genomic islets. They
often show evidence of horizontal gene transfer even though this
capacity might have beenlost. They are usually inserted into tRNA
gene loci, which often act as integration sites for foreign DNA,
mainly prophages. They are anked by directly repeated se-
quences consisting of a few to more than a hundred nucleotides.
These repeated sequences may have been generated during the
chromosomal integration of the GI or of some mobile elements by
recombination or by transposition. Additionally, the percentage
of GC content, the frequency of small repeats, and the codon
usage of a GI are generally different from the rest of the chromo-
some, indicating that these sequences were imported by horizon-
tal gene transfer. This hypothesis is consistent withthe fact that the
same GI can be found in distantly related bacterial species. Finally,
most GIs encode functional or degenerated mobile elements
(phage or plasmid genes, ISs, integrases, transposases, or restric-
tion-modication or toxin-antitoxin [TA] gene complexes).
These mobility genes can be involved in the formation, rearrange-
ment, integration, deletion, and mobility of GIs. Some of these
islands have mosaic-like structures, suggesting an evolution that
required multiple acquisitions fromvarious donors. Most GIs can
excise by homologous recombination at the direct repeats or with
the help of a GI-encoded integrase or IS elements. Sometimes a GI
excises together with a part of or all of its surrounding tRNA,
leading to the loss of this coding sequence (93). Interestingly, spe-
cic parts or a whole pathogenicity island can excise at a precise
point of a pathological process to facilitate the next stage of an
infection (as in Salmonella enterica serovar Enteritidis [111]). Fol-
lowing its excision, a GI can integrate into a different locus of the
same chromosome or be transmitted to another cell by horizontal
gene transfer (such as the 89K pathogenicity island in Streptococ-
cus suis serotype 2 [112]). The bacterial background and its envi-
ronment have a great impact on the transferability of GIs, which
can increase under stress conditions (113) [see also Mechanism
of HGT. (ii) Natural limitations of HGT, below].
GIs generally encode proteins playing novel roles in transport,
DNA binding and modication, cell motility, cell defense, the cell
surface, and pathogenicity (114). Regulators encoded on a GI can
control the expression of genes anywhere on the host genome. Simi-
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

larly, GI genes can be regulated by proteins encoded by the same GI,
another GI, or the bacterial host genome, indicating that GIs are well
adapted to their hosts. Therefore, GI genes can be regulated by some
environmental signals, such as pH(115), osmolarity (116), tempera-
ture (117), cell density (118), or the concentration of specic ele-
ments (116, 119121).
To summarize, with or without the help of plasmids or bacte-
riophages, mobile elements can move between organisms belong-
ing to different species or genera. Additionally, they can incorpo-
rate intoeachother, whichis anefcient methodfor accumulating
resistance genes and improving their characteristics (122). Inte-
gration of an IS into a transposon may change the expression of
genes in this transposon, and recombination at IS sites within or
between transposons creates new elements. Importantly, inser-
tions, fusions, andrearrangements betweenmobile elements seem
to be at the origin of genomic islands, of the assembling and ex-
pressionpatterns of the arrays of genes carriedby them, andsome-
times of their transfer within or between organisms (15, 123).
Therefore, transposable elements have an essential role in hori-
zontal gene transfer and the spread of antibiotic resistance and
pathogenicity determinants.
Inteins, Introns, and Retroelements
An intein is a mobile element encoding a peptide that splices out
froma host protein after its translation. An intron is an intragenic
element encoding an RNA that splices out after its transcription.
There are two types of introns in bacteria: group I introns and
group II introns. They are both transposable elements, and group
II introns are also retroelements. Aretroelement encodes a reverse
transcriptase and functions through an RNA intermediate. There
are three mainretroelements inbacteria: group II introns, retrons,
and diversity-generating retroelements (DGRs).
Self-splicing elements. Inteins and introns encode self-splicing
proteins and RNAs, respectively. Usually, self-splicing elements
integrate into their new host at the exact inteinless or intronless
DNA locus, using a process named homing (or retrohoming for
group II introns). Alternatively, they can occasionally recombine,
reverse splice, or retrotranspose into a new DNA locus. Full ele-
ments encode homing endonucleases, which are responsible for
their mobility.
(i) Inteins. Inteins are widespread in bacteria (124136). They
are peptides of 134 to 608 amino acids encoded in frame within
host proteins. One host protein can contain several inteins. By
posttranslational processing, an intein self-catalyzes its precise ex-
cision and the concomitant ligation of its anking regions, result-
ing in the formation of a mature functional host protein. Inteins
do not require cofactors or accessory proteins for protein splicing.
They often encode a homing endonuclease domain that is essen-
tial only for their mobility. This domain is also encoded in frame
with the intein and the host protein. Interestingly, a protein con-
taining an intein can be encoded by two partial genes localized in
different places in a genome (137, 138). Each gene encodes a part
of the protein fused to a part of the intein so that the original gene
is disrupted within the intein element. After translation, the intein
fuses the two halves of the protein by trans-splicing, resulting in
the formation of an active whole protein. Inteins were hypothe-
sized to have a role in cell development or in the regulation of
protein expression or activity. Since their discovery, inteins be-
came very useful biotechnological tools (as self-cleavable afnity
tags for proteinpuricationor toligate expressedproteinby trans-
splicing [131]).
Inteins generally interrupt the conserved regions of essential
proteins. They can be found in proteins involved in DNA or RNA
metabolism and biosynthesis (such as a ribonucleotide reductase
in Anabaena [139]); cell division (such as an ATPase involved in
chromatin remodeling in Deinococcus radiodurans [140]); tran-
scription (such as the GyrA gyrase in mycobacteria [141]); and
DNA replication (such as DnaX, the DNA polymerase subunit, in
Synechocystis and the DnaB helicase in Rhodothermus marinus
[142, 143]), repair, and recombination (such as RecAin mycobac-
teria [144]). There are several nonexclusive hypotheses for their
localization. By choosing conserved sequences, inteins would in-
crease their chances of mobility and of not being counterselected
(as imprecise excisions of these elements will probably result in
nonfunctional host proteins). On the other hand, expression of
inteins at the same time as DNA repair and recombination pro-
teins wouldhelpthe cell to recover fromDNAcleavage (unwanted
cleavage or during the homing process).
Bacterial intein-like domains (BILs) also posttranslationally
self-process their host proteins (145, 146). They are domains of
130 to 165 amino acids found in proteobacteria, actinobacteria,
and the Bacillus-Clostridium group. Interestingly, the number of
BILs per species is very variable, probably due to gene duplica-
tions, as BILs were not shown to be mobile elements. These do-
mains can be present in nonconserved regions of hypervariable
bacterial proteins such as secreted proteins (such as the FhaB-like
protein in Pseudomonas syringae, FhaB being a secreted lamen-
tous hemagglutinin [145]). BILs might have a role in generating
protein diversity, cell development, and host microevolution.
(ii) Introns. In bacteria, group I and group II introns are small
mobile elements (0.2 to 1 kb and 0.7 to 3 kb, respectively) that are
transcribed into self-splicing RNAs (147, 148). These introns are
widespread within the bacterial kingdom but not very abundant.
(a) Group I introns. A group I intron is transcribed into a struc-
turedself-splicing RNAwith10 helices cappedby loops andjoined
by junctions (149). The site-specic homing endonuclease, which
is used by the intron to invade another DNAmolecule, is generally
encoded within a terminal loop. Group I introns frequently lose
this gene, limiting their mobility. They often insert into bacterio-
phages. In the bacterial chromosome, they are found in tRNAs,
rRNAs, or essential genes. Importantly, in bacteriophage T4, a
group I intron inserting into a newlocus leads to the coconversion
of the exons at the newinsertionsite (150). This actionchanges the
sequences surrounding the newintron, with repercussions for the
encoded protein or RNA. Furthermore, some group I introns can-
not splice out, whichmay have consequences oncell growth(151).
(b) Group II introns. Group II introns behave more as retroele-
ments than as introns (152, 153). They are transcribed into highly
structured RNAs with six distinct double-helical domains, which
provide the catalytic activity for splicing. Additionally, they en-
code in their fourth domain a protein showing endonuclease, re-
verse transcriptase, and RNA maturase activities, providing mo-
bility to the intron (154). Bacterial group II introns are often
fragmented, meaning that part of the intron is missing or mixed
with DNA from another origin (155). However, they mostly inte-
grate into mobile elements, which increases their chances of pro-
liferation. Their rare integrations into host genes inactivate a tar-
geted gene only when the intron cannot splice out (155).
Surprisingly, for bacteria, a group II intron can also undergo al-

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

ternative splicing, which alters the sequence of the host protein
(156). These introns might also be at the origin of gene conversion
events (157). Finally, they can induce deletions, inversions, or
other chromosomal rearrangements intheir host genome, as is the
case in Wolbachia bacterial endosymbionts (155, 157).
(iii) Homing endonucleases. Homing endonucleases are con-
sidered to be the real mobile elements encoded within introns and
inteins, but they can also be freestanding in intergenic regions
(129, 133, 136, 158166). A homing endonuclease would bring
mobility to a splicing element in exchange for the capacity to tar-
get conserved genes without being detrimental to the host bacte-
rium. A splicing element avoids being counterselected, as it does
not disturb the function of its host protein. Furthermore, deletion
of the element may be counterselected, as imprecise excision is
likely to damage the host gene. Therefore, this association in-
creases the chances of the homing endonuclease and the splicing
element being maintained in a population and invading other
bacteria by horizontal gene transfer. During the homing process,
the endonuclease cleaves the target DNA. Gene conversion then
occurs during the DNA repair process, when the splicing element
is copied into the previously empty allele. Insertion of the splicing
element disrupts the recognition site of the homing endonuclease,
preventing new cleavage. Additionally, the splicing element can
insert into a new target gene by illegitimate recombination.
Homing endonucleases are usually encoded by short genes
(1 kb). They recognize specic DNA sequences of 12 to 44 res-
idues, allowing a few single-base-pair changes within this target
sequence, which is often present only once by genome. This rare-
cutting characteristic helps maximizing their mobility while min-
imizing nonspecic cleavage and makes them excellent biological
tools. Some homing endonucleases need associated proteins to
regulate their activity. Finally, certain homing endonucleases also
encode a maturase activity (helping intron RNAsplicing) and/or a
reverse transcriptase activity (for the retrohoming of group II in-
trons).
Retroelements. (i) Retrons. Retrons are rare retroelements of
about 2 kb that are inserted into prophages and a wide variety of
bacterial chromosomes (167169). They are composed of at least
three ORFs, encoding a reverse transcriptase and a peculiar DNA/
RNAhybridmolecule that has beendescribedas multicopy single-
stranded DNA (msDNA) (Fig. 2). Usually, msDNA is a small,
single-stranded cDNA molecule covalently bound to an RNA
molecule, which folds together into a stable secondary structure.
This molecule accumulates abundantly in its host, up to 1,000
molecules per cell.
So far, there has been no proof that retrons are mobile ele-
ments. However, truncated copies of msDNAs can be found in-
serted into some bacterial genomes (170, 171). Upon integration,
retrons seem to replace various sizes of sequences of the host
genomic DNA (172174). Strikingly, overexpression of some
msDNAs increases the number of frameshift andbase substitution
mutations in E. coli (175, 176). This increased mutagenic level
results fromthe binding of most cellular mismatch repair proteins
to the mismatches on msDNAmolecules. Similarly, the frequency
of recombination between donor and recipient DNA sequences
during matings of Salmonella and E. coli cells increases when some
msDNAs are overexpressed, as the interspecic recombination
frequency is normally reduced by the action of mismatch repair
proteins (177). The function of msDNA molecules is still un-
FIG 2 Schematic diagram describing the synthesis of msDNA. The retron element (represented as a rectangle) is transcribed, and the retron-specic reverse
transcriptase (RT) is produced, whereas the part of the mRNA containing the transcription product of the msr and msd genes folds into a particular secondary
structure. Thanks to this structure, the 2=-OHgroup of a specic branching guanosine residue (G) becomes the primer permitting the reverse transcription of the
msd gene, while RNase H cleaves the mRNA template. Transcription stops at a xed point, resulting in the msDNA molecule: an RNA and a cDNA molecule
covalently linked. (Based on references 167169.)
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

known, but they could be involved in helping bacteria to increase
their mutation rates when needed for survival.
(ii) Diversity-generating retroelements. Diversity-generating
retroelements (DGRs) rely on reverse transcription to create di-
versity in DNAsequences that encode proteins involved in ligand-
receptor interactions, mainly extracellular, cell wall, or membrane
proteins. The main studied example is in the BPP-1 bacteriophage
of Bordetella species, but DGR sequence patterns have been found
in a wide range of bacterial prophages, plasmids, and chromo-
somes (178184). DGRs are usually composed of two repeats of
about 150 bp and two ORFs (Fig. 3). The rst repeat forms the 3=
end of a gene and is the variable repeat (VR), as its sequence can
undergo nucleotide substitutions at variable hotspots. Generally,
downstreamof the gene containing the VRare the template repeat
(TR), which has an invariant sequence, and the ORFs, one of them
encoding a reverse transcriptase. Strikingly, mutations in the se-
quence of the variable repeat always exchange a dATP for a ran-
dom deoxyribonucleotide. The mechanism creating this directed
mutagenesis involves the reverse transcriptase and a unidirec-
tional transfer of information from the TR to the VR. A DGR
induces at a low frequency a very high variability in the sequence
of the protein encoded by the targeted gene. The fact that a num-
ber of DGRs are found in surface proteins, such as the LdtA lipo-
protein in Legionella, led to the suggestion that DGRs may play an
important role in the interaction that a bacterium has with its
environment (184).
More groups of bacterial retroelements have been identied
only recently (185, 186). Future studies might reveal some un-
known effects of these elements on genome instability.
Integrons
Integrons are relatively common non-self-transferable genetic el-
ements that capture and rearrange single promoterless ORFs into
an operon, allowing the appropriate expression of these genes
(Fig. 4) (187190). They are composed of a stable platform into
which various gene cassettes that encode accessory functions are
integrated. The stable part of the integron is generally composed
of the intI gene and its associated promoter, a primary attI recom-
bination site upstreamof the promoter of intI, and a P
c
promoter,
located in the intI gene or the attI site (Fig. 4A). The intI gene
encodes a site-specic tyrosine recombinase. The gene cassettes
are free circular DNAmolecules generally containing a single pro-
moterless ORF and an attC recombination site (also called a 59-
base element but with a size varying from 57 bp to 141 bp). The
attC recombination site is a cassette-specic imperfect inverted
repeat, variable in length and sequence, that can form secondary
structures through self-pairing of the DNAstrands (191). The IntI
integrase recognizes the secondary structure of the bottom strand
of the single-stranded attC site on the gene cassette and recom-
bines it with the attI site in the integron (191193), inserting the
gene cassette just behind the P
c
promoter in an orientation that
usually results in the expression of the newly integrated gene. In-
tegration of a single-stranded product may favor events following
DNA transfer of a single strand via conjugation (i.e., in an inter-
cellular event). Importantly, the next gene introduced into the
integron will also be inserted at the attI site and will therefore be
between the promoter and the previously integrated gene. Succes-
sive integrations result in the formation of an array of gene cas-
settes, which is the variable part of the integron. The further a gene
is from the P
c
promoter, the lower its chances are to be tran-
scribed. IntI can also promote the excision of a gene cassette, per-
mitting the mobility of a gene within the array in order to stimu-
late its expression (Fig. 4B) (194). Additional cassettes can also be
acquired by horizontal gene transfer. A newly integrated cassette
will be maintained in the integron if it confers an advantageous
phenotype on the cell.
There are two main forms of integrons: mobile integrons (or
resistance integrons) and superintegrons (or chromosomal inte-
grons). Mobile integrons are carried by conjugative plasmids,
transposons, or other mobile elements (46, 195, 196). In their
array, gene cassettes have variable attC sites and encode a few
proteins often involved in antibiotic resistance. Superintegrons
are nonmobile and located in their host chromosome. Their very
large numbers of cassettes have similar attC sites and express pro-
teins involved in the cells interactions with its environment or in
undened functions. These integrons can represent a signicant
fraction of the genome of their host (up to 3%). Importantly, the
FIG 3 Schematic organization of a diversity-generating retroelement (DGR). A DGR (represented as a rectangle) is generally composed of two repeated
sequences and one or two ORFs. VR is the variable repeat, which is at the 3= end of a variable gene. TR is the template repeat, and its sequence is invariable. orf2
is not always present and differs in the function of the system. It is sometimes named atd (accessory tropism determinant) or hrdC (helicase and RNase D C
terminal). The order of these elements is changeable. The template repeat is transcribed and integrated at the place of the variable repeat by a reverse transcription
process that also exchanges some adenines for random nucleotides. RT is the reverse transcriptase.

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

P
c
promoter cannot control the expression of all genes present in
a superintegron, andthe expressionof the IntI integrase is induced
by cellular stress, especially DNA damage (via the SOS system
[197]). These characteristics indicate that only the rst few genes
downstreamof P
c
are expressed and that the subsequent genes are
silent, constituting a pool of information that the cell can rear-
range, select, and use when necessary (Fig. 4B). However, a recent
study demonstrated that some cassettes within the array can in-
clude a promoter that controls the transcription of several genes
(198). To be able to maintain such large numbers of unused genes,
superintegrons containpostsegregationkilling systems (see Post-
segregation killing systems, below).
Recombination generally occurs between an attI site and an
attC site in a free gene cassette (199). However, two attC sites (or
attI and attC) in an array can recombine to generate a cassette
(200), and there are rare events of two attI sites in different inte-
grons recombining, which leads to chromosomal rearrangements
(201). A gene cassette can also occasionally integrate into another
locus rather than within an integron, inducing the formation of a
replicon fusion (202205). Importantly, a cassette integrated into
a nonspecic site cannot excise, becoming a permanent feature of
its hosts genome. The inserted gene will be transcribed only when
placed downstream of a promoter. Finally, recombination, dele-
tion, or duplication can occur between closely related or adjacent
cassettes, leading to the formation of new gene cassettes (196).
Superintegrons add a large number of genes to the genomes of
their hosts. They encode proteins that are essential for cell survival
under specic conditions. Mobile integrons are easily transmitted
between hosts and are at the origin of the rise of multidrug resis-
tance in some bacteria. Finally, integrons are often associated with
other mobile elements (190, 206).
Genetic Elements Controlling the Stability of Mobile
Elements
Two different genetic elements can bring genome variability as
well as control the stability of mobile elements (including bacte-
riophages and plasmids). Postsegregation killing systems can sta-
bilize the mobile elements and integrons that they are associated
with and attack other foreign DNA. Clustered regularly inter-
spaced short palindromic repeats (CRISPR) and CRISPR-associ-
ated (Cas) proteins (CRISPR-Cas systems) can protect their host
cells against invasion by bacteriophages or plasmids.
Postsegregation killing systems. Postsegregation killing sys-
tems are also called addiction modules because their loss leads to
the death of their host bacterium. There are two essential compo-
nents in a postsegregation killing system. The rst element can
attack the host organismor an invading agent, whereas the second
element protects its host from attacks mediated by the rst com-
ponent. Upon integration into a new host, this system is tightly
regulated so that protection occurs before any attack is possible,
resulting in the survival of the new host. Following the loss of
genes encoding a postsegregation killing system, attack elements
override the protection elements, which is usually lethal for the
previously hosting bacterium. Two kinds of postsegregation kill-
ing systems are widely present in prokaryotes: toxin-antitoxin
(TA) systems and restriction-modication (RM) systems. Many
FIG 4 Schematic organization of an active integron. An integron (represented as a rectangle) is constituted of a stable platform and a variable part. The stable
platform is integrated into the host genome or a plasmid. It is composed of a site-specic recombinase gene (intI) and its promoter (P
intI
) as well as a primary
recombination site, attI, upstream of the intI gene and the P
c
promoter, located in the intI gene or the attI site. The variable part is formed by cassettes, each
containing a gene and an attCrecombination site. (A) Integration of gene cassettes into the stable platformof the integron. IntI mediates recombination between
the attC site of the incoming cassette and the attI site of the integron so that the gene cassette integrates behind the P
c
promoter, allowing gene expression.
Successive integrations permit the formation of an array of gene cassettes, with the newly integrated cassette being nearest P
c
. (B) Excision and reinsertion of a
gene cassette. A gene in a cassette that is too far from P
c
is not expressed anymore. IntI can mediate the excision of any gene cassette in the integron by
recombination between the two attC sites surrounding the gene and its reinsertion in attI behind the P
c
promoter. Therefore, the integron contains a reservoir
of genes that can be rearranged and used by the cell under selective environments.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

postsegregation killing systems are mobile. Remarkably, some
postsegregation killing systems have been perfectly coordinated
with host development, cell biology, evolution, and speciation.
(i) Toxin-antitoxin systems. TA systems are small mobile ge-
netic modules found in bacterial chromosomes, viruses, and mo-
bile elements (207223). They are generally composed of two
closely linked genes encoding a stable toxin and an unstable anti-
toxin. These genes are often autoregulated. Toxins are always
small proteins (130 amino acids), whereas antitoxins can be
proteins or RNAs. Depending on the type of TA system, an anti-
toxin can either sequester its cognate toxin in a complex to stop its
activity or inhibit its translation. Loss of a TAsystemby exclusion,
segregation, recombination, or mutationcanresult incell deathor
cell growth arrest, as the stable toxin outlives the unstable anti-
toxin and attacks the host cell. There are often multiple TA sys-
tems in a bacterial cell; some accumulate mutations which inacti-
vate them. Toxin proteins can act differently on their host
organism. They can impede cell division (224), stop DNAreplica-
tion (225), cleave mRNAs (226), inhibit transcription (227) or
translation (228), attack the cell membrane (229), stop cell wall
biosynthesis (230), or decrease ATP synthesis (222).
Various roles have beenproposed for TAsystems; some are not
exclusive, and others can be specic to certain TAsystems. At rst,
these systems were found to participate in the maintenance of
other mobile elements (plasmids, prophages, ICEs, integrons, or
genomic islands), as their loss results in cell death, and they can
exclude competitor elements (some toxins can attack invading
elements [231] or act as abortive infection systems [232] or as
antiaddictive modules, if the invading element bears a similar
toxin [233], or the exclusion can be the result of plasmid-plasmid
competition [234]). In the chromosome, they can stabilize large
dispensable DNA regions that could otherwise be deleted (235).
They have also been reported to be selsh elements that promote
only their own survival or to be junk DNA from ancient mobile
elements that will slowly be lost by the cell. On the other hand, TA
systems also protect their host cell against attacks fromphages and
other mobile elements (233). Remarkably, some TA systems are
completely integrated into their host regulatory network and now
play a central role in prokaryotic cell biology. They have been
shown to be involved in the development or the behavior of cer-
tain bacteria. For example, they can control cell death during
fruiting body formation in Myxococcus xanthus or motility in E.
coli (236). Some TAsystems might also play roles in pathogenicity
(219). Additionally, TA systems can have important functions in
regulating the physiological states of bacterial populations and in
stress responses (237). Under various stress stimuli (DNA dam-
age, starvation, the presence of antibiotics or free radicals in the
environment, high temperature, oxidative or osmotic shock, en-
trance into stationary phase, quorum sensing, or infecting
phages), the toxins can be activated, often as a result of the degra-
dation of antitoxins by stress-induced proteases or of the induc-
tion of toxin transcription. Depending on the nature of the stress
and of the activated TA system(s), toxins can provoke altruistic
programmed cell death to either release nutrients for other cells
(226) or stop an infection (232), induce biolm formation (221),
arrest cell growth until improvement of the environmental con-
ditions (238), or differentiate a subpopulation of cells into persist-
ers (multidrug-resistant bacteria in a dormant state) (239). These
stress responses can be determined by TA systems controlling
DNA replication or the regulation of global or specic gene ex-
pression (240, 241). Finally, some toxins have a role in recycling
damaged RNA to decrease cellular stress and release essential
compounds for cell survival. Altogether, TA systems can have
multiple roles and be perfectly integrated into the bacterial regu-
lation system.
(ii) Restriction-modication systems. Essentially, an RM sys-
tem encodes a restriction endonuclease and its cognate modica-
tion activity, most often a methyltransferase (242250). When
several proteins are needed to perform these activities, their genes
are usually located together on the bacterial chromosome, a virus,
or a mobile element. Numerous chromosomal RM systems have
been inactivated by insertions, deletions, or point mutations. The
nuclease and the modication activities recognize and act upon a
highly specic DNA sequence, different from one system to an-
other. Modication of this sequence protects the genomic DNA
from cleavage by the nuclease. A mutation in the modication
activity or the loss of the whole system is often lethal for the host,
as the bacterial DNA would then not be protected from the nu-
clease activity.
So far, several roles have been attributed to RM systems. First,
these systems have been considered host defense mechanisms
against invasions of phages, foreign DNA, and mobile elements.
They attack invading elements that do not display the correct
modications, and no other competing genetic element can elim-
inate them without resulting in the death of the host cell (251,
252). According to the need of a bacterium, inactivation of a DNA
restriction-modicationsystemcanenable anincrease inthe cells
capacity to incorporate foreign DNA into its genome, whereas
activation of this system can protect the cell against a phage or
DNAinvasion. Atemperate phage infection might be detrimental
for an individual bacterium but useful at the population level, as
lysogenization increases cellular genetic information, while lysis
provides nutrients for the rest of the population. It has been
hypothesized that DNA restriction enzymes from intracellular
bacteria might also digest their host DNA to obtain precursor
molecules for their own use (253). Second, these systems can sta-
bilize other mobile elements in the cell population. RM genes are
often linked to sequences resembling or being mobile genetic ele-
ments (within plasmids [254], bacteriophages [255], transposons
[256], ICEs [257], integrons [242], or genomic islands [258] or
near transposases [259], resolvases [259], invertases [260], inte-
grases [261], topoisomerases [247], or phage-related sequences
[262]). Third, they have been described as selsh elements that
promote mainly their own survival. As well as using mobile ele-
ments as transporters, RMsystems can move by themselves, prob-
ably as a result of their DNA cleavage activity. Following DNA
restriction, anRMsystemcantranspose into the locationwhere its
host repairs the break. Additionally, the death of their hosts re-
leases DNAfragments encoding the RMsystems into the environ-
ment, from where they can invade new competent cells. Fourth,
they can increase bacterial diversity and phase and antigenic vari-
ation by inducing genomic rearrangement and homologous re-
combination during break repair or with incoming foreign DNA
(restriction of the invading DNA might help separate benecial
and deleterious mutations) (243, 244). Fifth, they have been hy-
pothesized to monitor the epigenetic DNA methylation level of
their host in order to eliminate cells with unusual levels of meth-
ylation (248).
RMsystems canbe at the originof various genome instabilities.
DNA methylation may locally increase the DNA mutation level

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

(263). Additionally, the action of an endonuclease can induce the
SOS response system, which can increase mutagenesis in the host
cell. Furthermore, repair after DNA restriction or during the in-
sertion of an RMsystemcan result in genomic rearrangement and
phase or antigenic variation. An RM system can transpose into a
new locus (264). It can simply insert into an operon-like gene
cluster (like in the pur operon in Streptococcus suis [265]) or insert
with a short or long and variable target duplication (such as an
8-bp sequence when type II RM genes insert into Xanthomonas
oryzae pv. oryzae [247] or a 506-bp-long direct duplication after
insertion of a type IIS system in Helicobacter pylori [266]). These
long direct repeats can induce the formation of sequence ampli-
cation (like BamHI in Bacillus [267]) or of gene fusion, which can
generate novel proteins (like the formation of an active type II M
gene in H. pylori [247]). An RM system can also integrate by sub-
stitution (such as two type III RMhomologues in H. pylori [266]).
Insertions and substitutions may be associated with neighboring
inversions (as in Pyrococcus [264]). Finally, a more complicated
form of genomic rearrangement arising from the insertion of RM
systems is the association of a substitution, an inversion, and a
deletion (or insertion) next to each other (as in two RMsystems in
H. pylori [266]).
CRISPR-Cas systems. CRISPR-Cas systems have been identi-
ed recently and studied intensively over the last decade (268
284). The mainknownrole of these systems is to protect the cell by
providing adaptive and hereditary immunity against previously
encountered bacteriophages and plasmids. CRISPR-Cas systems
have been found in the chromosomes of about half of the se-
quenced bacteria and nearly all archaea; they can also be found on
plasmids, phages, and mobile elements. Around half of these ge-
nomes carry more than one CRISPR-Cas system (up to 18). Sev-
eral systems present in the same organism can be similar or very
different. A basic CRISPR-Cas system is composed of a leader
sequence immediately followed by a CRISPR array and in the
proximity of a group of cas genes (Fig. 5). Leader sequences and
CRISPR arrays do not contain ORFs. A leader sequence is usually
several hundred nucleotides in length with a large proportion of
adenines and thymines. A CRISPR array is formed of a succession
of short identical direct repeats (21 to 50 bp) separated by unique
highly variable sequences of similar sizes, named spacers (20 to 84
bp). Importantly, spacer sequences can be identical to some bac-
teriophage, plasmid, or chromosomal sequences. These spacers
encode the immunological memory of the system. The sequence
of the leader and the sequence and number of repeats vary greatly
FIG 5 Schematic organization and mechanism of action of a basic CRISPR-Cas system (represented as an open rectangle). A CRISPR-Cas system is usually
composed of cas genes (maroon arrows) and a leader sequence (blue rectangle) containing a promoter on the 5= end of a CRISPRarray, formed by short identical
direct repeats (DR) (blue triangles) alternating with unique sequences (spacers) (colored octagons). (A) Adaptation is the rst step of CRISPR-Cas immunity. A
plasmid or bacteriophage DNAinvades the bacterium. In rare cases, Cas proteins recognize this DNAas a threat (often thanks to a PAMsequence) (dashed open
squares) and introduce a new repeat and spacer sequence into the CRISPR array between the leader sequence and the rst repeat. This spacer corresponds to the
protospacer in the foreign DNA(colored diamonds), a sequence near the PAMmotif, if present. (B) The promoter in the leader sequence allows the transcription
of the CRISPR array into a pre-crRNA (pre-CRISPR RNA). Cas proteins cleave the pre-crRNA into crRNAs, each containing a part of a repeat and a spacer. (C)
Cas proteins and a specic crRNA target and inactivate the foreign DNA previously encountered, if present again in the cell. Some cellular proteins might help
the Cas proteins in any of all these different stages.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

between organisms or CRISPR-Cas systems (from two to several
hundred repeats per array, but most loci have around 50 repeats).
Similarly, the number of cas genes and the nature of the proteins
which they encode are also dependent on the CRISPR-Cas system
(generally 4 to 20 different genes). Usually, a specic CRISPR
array is encountered with a cognate set of cas genes in differing
genomic locations, gene orders, orientations, and groupings. Oc-
casionally, some cas genes are at a different locus in the chromo-
some, but they would be present only when there is a CRISPR
array in the genome. Cas is a large family of proteins carrying
diverse but specic functional domains, such as integrase, endo-
nuclease, exonuclease, RNase, helicase, polymerase, transcrip-
tional regulator, or RNA- and DNA-binding domains.
There are three steps in the CRISPR-Cas immunity process:
adaptation, crRNA (CRISPR RNA) expression, and interference
(Fig. 5). Adaptation comprises the recognition and assimilation of
a foreign DNAsequence by the CRISPR-Cas system. Cas proteins,
with the potential help of the leader sequence and host proteins,
can target and process the DNA of an invading plasmid or bacte-
riophage. They identify a specic sequence within this DNA,
called the protospacer, and add it to the CRISPR array as a new
oriented spacer. Most CRISPR-Cas systems recognize a very short
sequence in the vicinity of the protospacer, named the proto-
spacer-adjacent motif (PAM) (2 to 5 bp). Spacer integration gen-
erally occurs between the leader sequence and the rst repeat of
the CRISPR array and is accompanied by the duplication of a
repeat. Occasionally, several protospacers from one foreign DNA
sequence can be added into the CRISPR array, each with its own
repeat sequence. This multiple acquisition increases the cells level
of resistance to a new invasion by this element (285). In a process
called priming, a spacer already present in a CRISPR array before
an infection with a virus containing the corresponding proto-
spacer leads to a rapid acquisition of additional spacers recogniz-
ing this foreign element (286, 287). In the second step of this
immunity pathway, the CRISPR array is generally transcribed
froma promoter inthe leader sequence, resulting inthe formation
of a nontranslated RNA, the pre-crRNA. Cas proteins and/or cel-
lular ribonucleases process the pre-crRNA into xed-sized
crRNAs (35 to 46 bp), each containing a part of a repeat on its 5=
side, a part or all the spacer, and sometimes also a part of a repeat
on the 3= side. For this restriction step, certain CRISPR-Cas sys-
tems also use a trans-encoded transcript named trans-activating
crRNA (tracrRNA). Finally, interference happens when the same
foreign DNA sequence tries to invade anew the same cell or its
offspring. The specic crRNA guides Cas proteins to the proto-
spacer sequence on the invading DNA. The Cas-crRNA complex
then inactivates this DNA by silencing or degradation. Notably, a
specic group of Cas proteins, the Cmr proteins, seems to attack
RNA and not DNA (288, 289). Cmr proteins are present in about
70% of archaea and 15% of bacteria. Importantly, to escape the
cell defense mechanismprovided by CRISPR-Cas systems, viruses
constantly mutate their genomes by point mutation, deletion, or
recombination(290, 291). Additionally, some bacterial prophages
might encode their own defense system, for example, by using a
protein that specically binds and opens the DNAstructure of the
repeated sequences in the CRISPR array (268, 292) or by express-
ing an anti-CRISPR gene (293). Finally, CRISPR-Cas systems can
also be inactivated by the action of mobile elements (280).
To be efcient, the CRISPR-Cas system must be kept under
control. The size of a CRISPR array is restricted by occasional
deletions of old repeat spacer units, which might be the result of
homologous recombination between identical direct repeats
(294). Furthermore, to avoid an autoimmune response, CRISPR-
Cas systems need a way to distinguish foreign DNAfromthe DNA
sequences of the CRIPSR arrays themselves. So far, two different
strategies of DNA identication have been suggested. In some
CRISPR-Cas systems, DNA cleavage of the chromosome is inhib-
ited by the presence of the repeat sequence adjoining the spacer
(295). Alternatively, CRISPR-Cas systems may recognize in the
foreign DNA the presence of the PAM sequence at a set distance
from the protospacer (281, 296, 297). As the genome does not
carry PAMsequences, it is not regarded as a threat and therefore is
not targeted. Remarkably, the expression of CRISPR-Cas systems
can be regulated by some cellular transcription factors, such as the
heat-stable nucleoid structuring protein (H-NS) and its antago-
nist LeuOin E. coli and Salmonella enterica (276, 298300). More-
over, certain cellular factors and pathways can control the activa-
tion of some CRISPR-Cas systems. In Thermus thermophilus,
phage infections induce the transcriptionof cas genes and CRISPR
arrays by a sensing mechanism using the cells cyclic AMP recep-
tor proteins (301, 302). Stress, such as phage infection, the accu-
mulation of misfolded proteins in the E. coli membrane, or the
absence of ClpP in Streptococcus mutans, can also activate the ex-
pression of certain Cas proteins (303, 304).
CRISPR-Cas systems can be located in specialized regions of
the genome encoding proteins involved in defense and stress re-
sponse mechanisms (defense islands) (305). Even though the
highly dynamic evolution pattern of cas genes would agree with a
function of CRISPR-Cas systems in cell immunity (306), previous
phylogenetic studies suggested that this might not be their main
role and that these systems may have other cellular roles (307,
308). An important proportion of CRISPR array spacers corre-
spond to bacterial chromosomal sequences, probably originating
from immunity accidents (296). Eighteen percent of the organ-
isms encoding a CRIPSR-Cas system display at least one self-tar-
geting spacer. However, about half of these protospacers are lo-
cated in elements that were probably introduced into the host
genome by horizontal gene transfer (prophages, transposons, and
plasmids). Other self-targeting spacers seem to be unstable in the
array and can be deleted. Moreover, the presence of some self-
targeting spacers can also result in mutations inactivating part of
or the full CRISPR-Cas system or steer the evolution of the host
genome. For example, a CRISPR spacer corresponding to the his-
tidyl-tRNAsynthetase (hisS) gene in Pelobacter carbinolicus might
have induced the disappearance in this bacteriumof genes encod-
ing proteins with multiple closely spaced histidines (309). How-
ever, some self-targeting spacers might be used by CRISPR-Cas
systems to regulate endogenous functions by controlling the ex-
pression of specic genes. In Pseudomonas aeruginosa cells con-
taining a CRISPR-Cas system, the presence of a lysogenic bacte-
riophage results in the inhibition of biolm formation and
bacterial swarming, probably to avoid the propagation of the
phage (310). In M. xanthus, the formation of fruiting bodies fol-
lowing starvation involves Cas proteins (311, 312). Moreover, in
E. coli, one of the most conserved Cas proteins is a nuclease that
physically interacts with DNA repair proteins (313). This protein
and its CRISPR array have been proposed to have an important
role in DNArepair and chromosomal segregation following DNA
damage. Finally, repeats present in CRISPR arrays can be at the
origin of large genomic rearrangements, which are evolutionarily

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

important (314). Additional studies should determine whether all
these activities of CRISPR-Cas systems are part of a defense mech-
anism or represent separate cellular roles.
Nowadays, CRISPR-Cas systems are becoming useful tools for
a number of applications. Spoligotyping is based on differences
between CRISPR-Cas systems to identify bacterial strains (315).
This technique helps investigations of evolution and geographical
and/or historical studies (316, 317) and permits the identication
of microbial populations (318) or the analysis of pathogen out-
breaks (319). Newspacer repeat units are insertedin5= extremities
of CRISPR arrays, which provide information on recent infec-
tions. On the other hand, 3= extremities of CRISPR arrays corre-
spond to older infections and are more conserved in evolution. As
a consequence, studies of CRISPR arrays can reveal the sequence
and identity of viruses that are new or difcult to access other-
wise as well as information on the evolution of a population of
viruses and/or bacteria in a studied environment and on the co-
evolutionary dynamics between viruses and their hosts. Addition-
ally, industries using bacteria are domesticating CRISPR-Cas sys-
tems to naturally generate phage-resistant strains. This is
particularly interesting for foodindustries, where there is a needto
ght phage infections without genetically modifying the organ-
ism. The fact that CRISPR-Cas systems encoding Cmr proteins
can target RNA has been used to design a system permitting the
cleavage or silencing of a desiredRNAtarget, creating a newway of
impeding the expression of specic proteins in a cell (289).
CRISPR-Cas systems can also become customized restriction en-
zymes for genome engineering (320322).
The singularity of this system resides in the fact that cells ac-
quire resistance to a specic foreign DNA that can be inherited by
their offspring. Furthermore, CRISPR-Cas systems can be trans-
mitted to other species by horizontal gene transfer, as they canalso
be present on plasmids or prophages (323, 324).
INSTABILITY MEDIATED BY HOMOLOGOUS AND
ILLEGITIMATE RECOMBINATION
DNA replication, repair, and homologous recombination nor-
mally maintain genome stability. However, these processes can
also induce genome instability and chromosomal rearrangement
(325). Related and repeated sequences within the chromosome or
specialized genetic elements play important roles in genome in-
stability mediated by homologous or illegitimate recombination.
Related sequences can be substrates for gene conversion. Recom-
bination between inverted repeated sequences can lead to DNA
sequence inversion, whereas recombination between directly re-
peated sequences can lead to duplication, amplication, or dele-
tion. Finally, a deleted fragment can potentially reinsert at another
locus in a genome, generating a translocation.
Mechanisms of Homologous and Illegitimate
Recombination
Homologous recombination. Homologous recombination is the
exchange of genetic information between DNAmolecules of iden-
tical or near-identical sequence (326328). These homologous
DNAsequences can be near or far apart on the chromosome or on
different molecules. The minimal homology necessary for this
process has been estimated to be between 20 and 100 bp (329).
Imperfections in the homologous sequence dramatically decrease
the recombination rate. Homologous recombination contributes
both to the maintenance of genome stability and to genetic insta-
bility, as recombination can repair DNA damage and can reassort
genetic information. Furthermore, it is an essential process for the
integration of numerous horizontally transferred genes into their
new host chromosome. Therefore, homologous recombination
has a double role in the cell: it helps cell survival by maintaining
genome integrity while promoting genome rearrangement that
leads to diversity, evolution, and speciation.
In bacteria, homologous recombination has been studied most
extensively inE. coli. Two principal pathways have beenidentied:
the RecBCD-RecA pathway for double-strand break repair and
the RecFOR-RecA pathway for single-strand gap repair. In both
pathways, the RecA protein plays a central role. RecA binds to
single-stranded DNA, forming a spiral lament that catalyzes a
strand-exchange reaction with double-stranded DNA of identical
or near-identical sequence. The binding of RecAstretches the sin-
gle-stranded DNA molecule to 1.5 times the length of its equiva-
lent double-stranded DNA. However, X-ray crystallography re-
cently indicated that the stretching occurs between triplets of
bases that retain the normal separation found in B-type DNA
(330). It is presumably these triplets bound to the RecA lament
that probe the structure of the double-stranded DNA molecule to
nd sequence identity. When it is found, strand exchange occurs
within the RecAlament, generating a postsynaptic structure that
remains stretched between normally separated triplets of base
pairs. The process by which sequence identity is found (homology
searching) remains mysterious. However, a recent single-mole-
cule study has shownthat the reactionis dramatically enhanced by
a random-coil conguration (as opposed to a stretched-out con-
guration) of the targeted double-stranded DNA. This study has
revealed that the RecAsingle-stranded DNA lament makes
multiple heterologous contacts with the random coil, leading to
the discovery and stabilization of interactions that are homolo-
gous (331). In the RecBCD-RecA pathway, the RecBCD helicase-
nuclease is responsible for generating single-stranded DNA and
loading the RecA protein (327). In the RecFOR-RecA pathway,
the RecF, RecO, and RecR proteins work together to facilitate the
loading of the RecA protein onto single-stranded DNA via the
displacement of single-strand-binding (SSB) protein (326).
Illegitimate recombination. Illegitimate recombination refers
to a collection of different reactions generally occurring at closely
spaced DNA sequences that share little or no homology (332
335). This process is RecA independent and takes place when
DNA strands anneal in aberrant congurations following a prob-
lem in DNA processing (Fig. 6). Stretches of a few base pairs of
microhomology generally play a critical role in the efciency of
illegitimate recombination, as they promote DNA strand anneal-
ing at DNA ends formed either during DNA synthesis (strand
slippage) or following DNA strand breakage (single-strand an-
nealing). Illegitimate recombination events occurring by strand
slippage or the annealing of DNA ends can be difcult or impos-
sible to distinguish from the substrate and product structures.
Illegitimate recombination occurring during DNA synthesis can
be responsible for local sequence conversion, deletion, or dupli-
cation. It can arise during DNA replication (336, 337), transposi-
tion (91, 338), or gyrase- and topoisomerase I-mediated strand
cleavage (339341); as a consequence of UVor gamma irradiation
(342344); or following the transformation of cells with linear
DNA sequences under circumstances where homologous recom-
bination is not possible (345, 346). Single-strand annealing fol-
lowing a DNA break can occur after DNA degradation, leading to
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

a local deletion. Mutations in the DNA Pol III or the mismatch
repair system increase the rates of illegitimate recombination
(347, 348). Some bacteria (e.g., B. subtilis, Mycobacterium tuber-
culosis, Mycobacterium smegmatis, and P. aeruginosa) encode a
bona de nonhomologous end-joining (NHEJ) system (349
353). This system consists of the Ku and LigD proteins, which act
together to rejoin DNAends at DNAsequences containing micro-
homologies. Bacterial NHEJ is thought to be particularly impor-
tant inthese bacteria to repair DNA, whena homologous template
is not present to enable DNA double-strand break repair to occur
by homologous recombination.
Gene Conversion
Gene conversion is a widespread mechanism of unidirectional
transfer of genetic information that can occur as a consequence
of homologous recombination when two related but different
DNA sequences nd themselves in the same cell (354, 355). The
presence of these sequences can be the result of a gene transfer
mechanism, or the cell can carry diverged copies of specic
gene sequences. Gene conversion following gene transfer is re-
sponsible for the generation of combinations of alleles not
originally present in the same cell, which accelerates genome
divergence through evolution (see HGT and evolution, be-
low). Intracellular gene conversions can mediate controlled
variations at specic DNA sequences, called cassettes, resulting
in phase or antigenic variation (356, 357) (see Phase and An-
tigenic Variation in Bacteria, below). The level of diversity
introduced by gene conversion depends on the number of cas-
settes and their sequence variability. Gene conversion is some-
times accompanied by crossing-over, which can lead to a chro-
mosomal inversion. Gene conversion seems to occur more
frequently in pathogenic bacteria than in nonpathogenic bac-
teria (358). Gene conversion rates are inuenced by the bacte-
rial cell cycle, the presence of the mismatch repair system, and
the level of iron in the environment (354).
Pilin antigenic variation in Neisseria species exemplies how
gene conversion can be used to facilitate the controlled replacement
of one expressed gene sequence with DNAsequences stored at silent
loci (357, 359). This exchange is mediated by a unidirectional gene
conversionreaction, where informationexpressedfromthe pilEgene
is replaced with that present in one of several silent pilS genes. This
reactionretains the informationat the pilS locus andis accomplished
bya gaprepair reactionmediatedbya RecOR-RecApathway(there is
noRecF proteininNeisseria). ADNAsequence adjacent to the pilE
gene is required for the reaction to proceed. This sequence, G
3
TG
3
T
2
G
3
TG
3
, on the lagging-strand template, has the potential to
fold into a G-quadruplex structure. It is likely that the establish-
ment of this quadruplex structure is required for the formation of
single-stranded DNA at the pilE locus, which both initiates the
reaction and marks pilE as the recipient of genetic information
during this gene conversion (360).
FIG6 Twoclasses of illegitimate recombinationevents. (A) Strandslippage. Strandannealing at regions of DNAmicrohomology (indicatedby blackarrows) canoccur
during DNAsynthesis, resulting in deletions, duplications, and other rearrangements. This gure depicts the formation of a deletion by strand slippage. (B) Annealing
of DNA ends. Strand annealing can also occur at DNA ends following resection and the formation of single-stranded regions. Microhomologies (indicated by black
arrows) facilitate annealing. Importantly, the deletion events depicted here are identical whether produced by strand slippage or by annealing of DNAends.

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

Genome Instability Due to Recombination at Repeated
Sequences
Tandem-repeat deletion or amplication. Deletions and ampli-
cations of almost any bacterial gene can occur at tandem-re-
peated sequences by homologous or illegitimate recombination,
leading to changes in gene copy numbers. Tandemduplications of
large chromosomal sections have been detected in many bacterial
genomes, including those of B. subtilis, E. coli, Haemophilus inu-
enzae, Klebsiella aerogenes, S. enterica, Salmonella Typhimurium,
Streptococcus pneumoniae, and Streptomyces coelicolor. When they
have been determined, tandem-duplication frequencies of ap-
proximately 10
3
to 10
4
per cell are common (361). Duplica-
tions can be further amplied by homologous recombination
(Fig. 7) (362). The same sequence can be amplied up to 100
times. Unless selected for, these events are mostly undetected and
revert to the unduplicated state without any noticeable conse-
quence. However, they provide a fertile ground for selection to act
upon in situations where gene dosage provides a growth advan-
tage, for example, to increase bacterial resistance to a specic an-
tibiotic (363). Gene amplications bring solutions to selective
problems by providing the population with more time and more
cells necessary to facilitate further genetic adaptations. A substan-
tial body of work onthe nature of tandem-repeat duplications and
their consequences was carried out in the 1970s. An excellent re-
view of this early work was written by Anderson and Roth (361),
where they described how these duplications can usually be toler-
ated because they preserve all the existing DNA sequences of the
unduplicated part of the chromosome, while they may contain
FIG 7 Two possible mechanisms for the formation of a tandem duplication and its subsequent amplication or reduction. (A) A tandem duplication can be
formed by a strand slippage mechanism where a DNA sequence is copied and microhomology is then used to reinvade and copy the same DNA sequence again.
This process generates a novel junction sequence (NJ) between the two repeated copies of DNA sequence. The duplicated sequence can then be amplied or
reduced by RecA-mediated homologous recombination. (B) A tandem duplication can occur by homologous recombination between repetitive sequences such
as insertion sequences (ISs). This reaction does not generate novel junction sequences. Again, the duplicated sequence can then be amplied or reduced by
RecA-mediated homologous recombination. (C) DIR/TIDstructures can be formed by strand slippage during DNAreplication or DNArepair. These structures
consist of two overlapping DNApalindromes and may not be stable enough to persist for long. Symmetric deletions that reduce the symmetry of the palindrome
centers have been documented, which may occur via subsequent rounds of strand slippage.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

single novel junctions at their centers. These novel junctions can
alter the nature of an expressed protein or the transcription level
or control of a neighboring gene. Tandem-repeat instability varies
as a function of the DNAsequence and the number of repeats (for
example, CAG repeats are more instable than CTG repeats, and
longer repeats are more instable [364]), their distance (365), their
location in the genome (instability between repeats on the same
molecules or on different molecules will result in different out-
comes), and the cellular pathway leading to their instability (366).
Additionally, the rate of tandem-repeat instability increases fol-
lowing DNA damage (367). Misalignment of repeated sequences
might occur during DNA replication between the nascent strand
and a second site onits template, onthe nascent strand itself, or on
the other sister chromosome. Tandem-repeat instability canresult
from illegitimate recombination, by strand-slippage or single-
strand annealing, from homologous recombination between dis-
persed regions of homology such as IS elements, or by nonequal
recombination between sister chromosomes or rolling-circle rep-
lication (Fig. 6 and 7) (for more details, see references 325, 333,
335, 362, 366, and 368). Importantly, illegitimate events create
novel junction sequences, whereas the misaligned homologous
recombination events do not (77).
(i) Tandem-repeat variation by illegitimate recombination:
microsatellite instability and contingency loci. Microsatellites
are repetitive sequences composedof small repeatedunits (usually
1 to 5 bp in length). These sequences have been shown to be
unstable in bacteria, where their expansion and contraction prob-
ably result from strand slippage (364, 366, 369, 370). The muta-
tion frequency in microsatellites is around 10
4
. The rates of mi-
crosatellite instability can be modulated by different cellular
processes using DNA synthesis, such as DNA replication, recom-
bination, and repair. Furthermore, it has been shown recently that
mismatch repair at these sequences can stimulate strand slippage
at a longer directly repeated sequence located several kilobases
away (367). Microsatellites occur naturally in numerous bacteria,
and their expansions and contractions can regulate specic gene
expression or alter coding sequences, resulting in phase or anti-
genic variation (see Phase and Antigenic Variation in Bacteria,
below). This is particularly important for the control of expression
at contingency loci, where gene expression can be reversibly acti-
vated and inactivated in a way that is benecial for a pathogenic
bacterium as it attempts to evade the defense strategies of its host
(371). Two well-studied examples of contingency loci are anti-
genic variations at the mbrial genes hifAand hifBof H. inuenzae
and at the opaE adhesin-invasin opacity locus of Neisseria gonor-
rhoeae (371, 372). In the case of the mbriae of H. inuenzae, a
dinucleotide repeat sequence, (TA)
n
, lies between the 10 and
35 recognitionsequences of overlapping divergent promoters of
the hifA and hifB genes. Expansions and contractions of the TA
repeat number alternate optimal spacing for the promoters of hifA
and hifB, controlling mbrial phase variation (373). In the case of
the opacity genes of N. gonorrhoeae, the opaE genes carry multiple
copies of the pentameric sequence CTCTT in the leader region of
their ORF. Variations in the number of CTCTTrepeats determine
whether or not a particular copy of the gene is translated. In this
way, the bacterium ensures a changing pattern of expression of
different opacity variants (374).
(ii) Tandem-repeat variation by homologous recombination.
It is likely that the majority of tandemduplications are initiated by
illegitimate events, but the phenomenon of resistance transfer fac-
tor transitioning in E. coli is a good example of an event initiated
by homologous recombination at directly repeated sequences
(e.g., ISs) (368, 375). The r-determinant part of a plasmid encod-
ing antibiotic resistance can be amplied under selection for in-
creased drug resistance and returned to a single copy when the
selection is relaxed. There is substantial evidence that in all situa-
tions of large tandem duplication, amplication, or reduction,
reactions are mediated by RecA-catalyzed homologous recombi-
nation (Fig. 7) (376). Over the past decade or more, there has been
an active debate regarding whether the amplication reaction is
stimulated when cells are held in the stationary phase for pro-
longed periods of time (377379).
Hairpin structure-stimulated strand slippage. DNA palin-
dromes are sequences that are identical when read forwards and
backwards. They promote illegitimate recombination by strand
slippage by forming hairpin structures in single-stranded DNA
that bring together sequences sharing microhomology. Deletions
of palindromes by strand slippage preferentially occur on the lag-
ging strand of the replication fork, consistent with the formation
of DNAhairpins in the single-stranded regions generated between
the Okazaki fragments (380, 381). Importantly, SbcCD is a nu-
clease that can cleave these hairpins and channel the DNA down
the repair pathway of homologous recombination that is faithful
and accurate (382, 383). However, it appears that if the palin-
drome is anked by directly repeated sequences, its cleavage by
SbcCD can also stimulate genomic instability mediated by a
strand-annealing pathway, resulting mainly in deletions (384). A
similar stimulation of instability through the action of SbcCD has
been observed in E. coli in the presence of CAG/CTGtrinucleotide
repeats (364).
Palindromes and other closely spaced inverted-repeat se-
quences (quasipalindromes) can also stimulate the formation of a
particular tandem duplication that consists of both direct and
inverted repeats (DIRs) (385), also described as a tandem inver-
sion duplication (TID) (Fig. 7C) (77). Models for howthese struc-
tures can be generated have been proposed and involve various
strand slippage reactions during DNAreplication and DNArepair
(77, 385, 386). The structure formed consists of two overlapping
DNA palindromes and is itself likely to be prone to hairpin struc-
ture-stimulated strand slippage that reduces the symmetry of the
palindrome centers. This mechanism of symmetry reduction via
strand slippage within palindromes has been documented previ-
ously (381).
Control of genomic instability by DNA repair. Homologous
recombination contributes to genome stability, as unrepaired
DNA double-strand breaks are a potential source of aberrant re-
actions that can lead to the formation of new DNA junctions and
chromosomal rearrangements by illegitimate events. One such
reaction is the formation of inverted chromosome dimers at the
site of a palindromic sequence in E. coli recAsbcDCmutants (387).
In the presence of SbcCD and RecA, homologous recombination
repairs breaks in a way that avoids the formation of these inverted
chromosome dimers. Moreover, DNA palindromes are hot spots
for deletion formation by illegitimate recombination (see Hair-
pin structure-stimulated strand slippage, above). However,
SbcCD and homologous recombination may limit the frequency
of these deletions (388). Supporting this hypothesis are the facts
that RecBCD and SbcCD decrease the level of homology-facili-
tated illegitimate recombination in Acinetobacter baylyi (389) and

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

that rates of illegitimate inversions are elevated in E. coli sbcC
mutants (390).
Recombination has a dual cellular function. It protects the ge-
nome and maintains genome stability as well as increases genome
instability, leading to deletion, duplication, amplication, inver-
sion, and translocation. These instabilities develop diversity
through phase and antigenic variation and induce speciation and
evolution. The role of recombination in genome instability is
highly dependent on related or repeated sequences, which are var-
ious and numerous in a bacterial genome.
Site-Specic Recombination
Site-specic recombination generally uses a dened recombinase
to recognize and recombine rare specic sites carried at the ex-
tremities of a DNAsequence element. This type of recombination
requires a precise and oriented proximity of the recombination
sites and is conservative (no loss or gain of DNA). The relative
orientation of the recombination sites within a genome deter-
mines the outcome of this process. Recombination of a molecule
containing inverted repeated sites results in an inversion of the
internal DNA sequence element. On the other hand, recombina-
tion within one DNA molecule carrying directly repeated sites
results in the formation of two separate molecules, whereas re-
combination of two DNAmolecules carrying similar sites leads to
the fusion of these molecules. There are three main site-specic
recombinationsystems inbacteria: site-specic inversionsystems,
excision or insertion of DNA elements, and developmentally reg-
ulated gene rearrangements.
Site-specic inversion systems. Site-specic inversion systems
are widely spread in bacterial chromosomes, plasmids, and phages
(391395). Their sizes differ from a little more than a hundred
base pairs to 35 kb. They play important roles in the synthesis and
regulation of cell surface proteins (pili, agella, surface layer pro-
teins, and variable surface antigens) as well as type I restriction-
modication systems. They bring a selective advantage to their
hosts by increasing the adaptability of the organism, which might
permit cell survival in differing environments, changes in patho-
genicity levels, escape from an immune system, or protection
against viruses. At a frequency of generally 10
3
to 10
5
per cell
per generation, an invertase (or recombinase) recognizes and in-
verts sequences bracketed by two terminal inverted repeats that
delimit the element (Fig. 8). The invertase gene can be located
within the inverted fragment, in its vicinity, or somewhere else in
the chromosome. The genotypic and phenotypic consequences of
a site-specic inversiondepend onthe positionand characteristics
of the element (Fig. 8). In the following examples, the termgene
is used to represent a gene or several genes in the same operon.
Some site-specic inversion elements can, in one orientation, add
a transcriptional terminator between a gene and its promoter,
hindering the transcription of this gene and resulting in phase
variation (396). Additionally, numerous invertible elements en-
compass an outward-facing promoter. One of these elements sit-
FIG 8 Schematic organization of various examples of site-specic inversion systems. Inversion of the element results in the activation or inactivation of the
transcription of the neighboring gene (A); the expression of either the a or the b gene (B); the expression of the a, b, or c gene selectively (C); the expression of a
short or a longer protein (D); or the transcription of a gene encoding a protein with a different carboxyl-terminal domain (E).
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

uated upstream of a gene can act as an on/off transcription switch
for this region (Fig. 8A) (397). When located between two genes,
this element can allowthe alternate transcription of one of the two
genes selectively (Fig. 8B) (398), inducing antigenic variation by
the formationof different encoded proteins. Acluster of invertible
segments can also be found, permitting the relative mobility of a
promoter sequence upstream of various genes (Fig. 8C) (399).
Site-specic inversion elements can also be located within a cod-
ing region, where their inversion results in the substitution of part
of the gene (generally the 3= end) (Fig. 8D and E) (400). Here
again, a cluster of invertible segments recombining individually or
in groups can lead to the formation of numerous variable proteins
(401). Importantly, site-specic inversion elements can also indi-
rectly change the cell phenotype by controlling the transcription
of regulatory proteins (402). Several invertases canact onthe same
site-specic inversion element (403). Some invertases can pro-
mote only one direction of the reaction (for example, to promote
the switch from on to off but not off to on) (404), can control the
inversion levels of various site-specic inversion elements (405),
or canbe transcriptionally or posttranscriptionally regulated(406,
407). Strikingly, inversion levels can be modulated by host regu-
latory proteins or external factors (408). In summary, site-specic
inversion elements help bacterial survival by permitting the pres-
ence of different individual cell phenotypes withinone clonal pop-
ulation (see Phase and Antigenic Variation in Bacteria, below).
Excision/insertion of DNA elements. Some transposable ele-
ments, bacteriophages, and plasmids use site-specic recombina-
tion to change location or state (409). In some cases, excision and
specic reintegration of an element can control phase variation in
its host. For example, in Pseudomonas atlantica, the presence of an
unstable IS492 element in its chromosome inactivates the synthe-
sis of extracellular polysaccharides, whereas its precise excision as
an independent circular molecule allows the production of these
polysaccharides (26, 410412). Therefore, the frequency of exci-
sion and insertion of IS492 directly regulates the production of
these molecules, which are important in biolm formation. Sim-
ilarly, the formation of a specic lipopolysaccharide in Legionella
pneumophila depends on the presence of a 30-kb unstable genetic
element in its chromosome (413). This element probably origi-
nates from a phage and can excise as a replicating plasmid, conse-
quently stopping its hosts production of lipopolysaccharide.
Developmentally regulated gene rearrangements. In bacteria,
several developmentally regulated gene rearrangements result
from site-specic recombination events (414418). These rear-
rangements can occur in the mother cell during the sporulation
process in B. subtilis and Clostridium difcile or during the forma-
tionof heterocysts, whichare cells specializedfor nitrogenxation
in lamentous cyanobacteria. In each case, a DNAelement (with a
size of between 4 kb and 55 kb) interrupts a coding sequence that
is essential for cell specialization. Environmental signals and cell
regulationinduce the activity of a site-specic recombinase, which
catalyzes a gene rearrangement by excising the element to form a
nonreplicating circular DNAmolecule and ligating the ends of the
previously interrupted chromosomal gene. This excision is non-
reversible, but these specialized cells (mother cells or heterocysts)
cannot divide, so the loss of DNA does not affect another genera-
tion. Interestingly, these inserted elements seem to have a phage
origin (416, 419). Their mechanismof action is reminiscent of the
response of a lysogenic lambda phage when its host is under
threat, which is to enter a lytic cycle by excising its DNA from the
host chromosome (414). Remarkably, in B. subtilis, excision of the
inserted element simply removes a block to the formation of mol-
ecules essential for sporulation, whereas in C. difcile, the excision
of this element is an indispensable step in the sporulation process,
as a strain in which this element is already deleted cannot sporu-
late (416).
Site-specic recombination is a simple but efcient form of
genome rearrangement. Because it can lead to phase and antigenic
variation, the consequences of this process are very diverse and
can be essential for cell survival (see Phase and Antigenic Varia-
tion in Bacteria, below).
CONSEQUENCES OF GENOME INSTABILITY IN BACTERIA
Phase and Antigenic Variation in Bacteria
Phase and antigenic variation involves several programmed ge-
netic or epigenetic processes found in numerous bacteria living in
various environments (see references 371, 391393, 395, and 420
426 and references therein). It induces specic, heritable, and re-
versible changes in the cell phenotype at rates higher than those of
random mutation (10
1
to 10
5
events per cell per generation,
depending on the system). Phase variation can modulate the level
of expression of a gene or an operon (often in an on/off manner
but sometimes gradually), whereas antigenic variation results in
the production of a number of alternative proteins. Phase varia-
tion of several genes can create antigenic variation. Phase and
antigenic variation can lead to the appearance of one or several
different subpopulations. When required, the ability to combine
the variation of several genes or exchange different parts of a gene
leads to the possibility of formation of a very large number of
phenotypes.
Mechanisms of phase andantigenic variation. Various genetic
processes can be at the origin of phase and antigenic variation
(395, 424, 425). A rst class of mechanisms is dependent on the
cellular DNAreplication, recombination, andrepair systems (354,
362, 366). For example, at contingency loci, the number of short
repeated sequences within a promoter or an ORF can vary follow-
ing strand slippage during DNA replication or repair, leading to a
transcriptional or translational switch in the expression of this
gene or operon(335, 371) [see Tandem-repeat variation. (i) Tan-
dem-repeat variation by illegitimate recombination: microsatel-
lite instability and contingency loci, above]. Additionally, gene
conversion or allele replacement permits the expression of one
interchangeable gene (or part of a gene) out of a pool of silent
genes, resulting mainly in antigenic variation (354) (see Gene
Conversion, above). Multiple MITEs encoding outward-facing
promoters of different strengths can recombine within a genome
and induce phase variation (52). A gene can be duplicated or am-
plied by illegitimate and/or homologous recombination, which
changes the level of expression of the gene product (362, 376) (see
Tandem-repeat deletion and amplication, above). When not
selected for, the duplication can be deleted by recombination at
repeated sequences such as ISs. On the other hand, site-specic
inversion systems control phase and antigenic variation indepen-
dently of the cellular DNA replication, recombination, and repair
pathways (see Site-specic inversion systems, above). Similarly,
ISs, prophages, and other elements, such as a plasmid containing
prophage genes, induce phase variation by excision and specic
reintegration (25, 410, 413, 427) (see Excision/insertion of DNA
elements, above). Finally, DGRs use their encoded reverse trans-

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

criptase to create antigenic variation [see Retroelements. (ii) Di-
versity-generating retroelements, above]. Notably, bacterial spe-
cies generally have their preferred variation mechanisms.
Roles of phase and antigenic variation. Most phase- and anti-
genic-variable proteins have important roles in mediating inter-
actions between bacteria and their environments (393, 395). They
control the formation of the capsule (428), the pili (429), agella
(430), adhesins (431), antifungal metabolites (432), iron acquisi-
tion factors (433), and other surface-exposed molecules (432,
434), sometimes affecting motility (432) or colony morphology
(434) and opacity (374). Nevertheless, these proteins can also be
involved in general cellular pathways, such as DNA restriction-
modication (435), gene regulation (436), or metabolism (437).
Phase and antigenic variation is thought to be essential for com-
mensal, symbiotic, and pathogenic bacteria, as these processes can
play anactive role during the invasion(438) and infection(439) of
an organism and help these bacteria to face the challenges raised
by their hosts (440). However, this variation is also happening in
bacteria that are not host associated. Alteration of the cell surface
structure can change the capacity of adhesion of a bacterium, per-
mitting the colonization of different environments (different or-
ganisms, tissues, or habitats, in or outside a host) and biolm
formation or detachment. Importantly, the level of virulence of
some pathogenic bacteria is determined by phase or antigenic
variation (441). Moreover, thanks to this variation, bacteria resid-
ing in an organism can evade host innate and acquired immune
mechanisms (442) and avoid being targeted by cross-immunity
(443). These escapes increase the duration of infection and, hence,
the chances of spreading the bacteria to new hosts, as well as facil-
itating chronic infections and allowing several successive coloni-
zation events of the same host by similar bacterial strains. As a
consequence, these bacteria conserve a larger population of hosts
susceptible to infection and increase their chances of exchanging
genetic information with other strains sharing the same host. In
summary, regulation of cell metabolism and gene expression by
phase and antigenic variation (directly or via the control of DNA
methylation) helps the bacteriumto save energy and to respond to
stress signals and can govern some of the cell properties (viru-
lence, biolmformation, colonization, and sensitivity to bacterio-
phage invasions, etc.).
Regulation of phase and antigenic variation. Phase and anti-
genic variation is key to a survival strategy based on heterogeneity.
It generates diverse subpopulations that can be used either to sur-
vive potentially changing and stressful conditions or to give the
opportunity for a few bacteria to colonize a new environment. In
specic surroundings, several of these subpopulations might be
needed to increase the tness of a mixed but stable population.
Importantly, even if a specic variation confers a growth disad-
vantage under the existing conditions, rearrangements constantly
create specic phenotypes so that, when needed, cells with the
right characteristics are always present in the population. Phase
and antigenic variation is mediated by random events, as no pre-
dictioncanbe made regarding which gene inwhich bacteriumwill
vary and when it will happen. However, the resulting phenotype is
not random, since phase and antigenic variation is predictably
encoded within the bacterial genome. The numbers and the roles
of phase or antigenic variationgenes ina bacterial genome are very
different depending on the organism. Moreover, the conse-
quences of variationdependonthe environment andthe nature of
the proteins controlled by this system. The expression of phase-
variable genes and the mechanism of phase variation can be con-
trolled in a complex manner by cellular regulatory proteins (444).
Due to their mechanisms, some variations can happen only at
certain stages of the cell cycle (growing dividing cells or nondivid-
ing cells [391, 392, 426]). Furthermore, depending on the nature
of the system, the level of variation can be controlled by the regu-
lation of the recombination mechanism, recombinase expression,
repair systems, or accessory proteins.
Some environmental or intracellular factors can inuence the
timing and frequencies of this variation, therefore controlling the
level of the appearance of subpopulations when required for sur-
vival (393, 420). These factors are different as a function of the
variation mechanism and can totally repress phase variation. En-
vironmental or intracellular stress conditions that result in DNA
supercoiling can modify phase variation switching frequency
(445). Some systems are regulated by information about the cells
location, outside or within a host or a tissue, that can be given by
the temperature (446, 447) or the composition of the environ-
ment (pH [448], carbon sources [449], oxygen [450] and iron
[451] levels, amino acid concentrations [446], or the presence of
specic elements [452]). Certain mechanisms answer to eukary-
otic host-specic signal molecules, such as the presence of sialic
acid, which is released by the host as a defense mechanism (453).
Therefore, bacteria have evolved a survival system by which, fol-
lowing invasion, they can use the responses of their hosts to mod-
ulate their genome accordingly.
Phase and antigenic variation is essential for bacterial survival
when there is no time or no suitable environmental signal to use
classical regulatory systems. Accordingly, bacteria with a small
genome seem to encode fewer two-component systems and more
variation systems (371).
Horizontal Gene Transfer in Prokaryotes
Horizontal gene transfer (HGT) is a process that brings nonpa-
rental genetic information into a cell. At present, HGT events are
rare and affect only a limited portion of a genome at a time, but
they can have major consequences (454). HGT has been at the
origin of animated scientic and philosophical debates for several
decades (455484).
Benets of HGT. Overall, HGT might be an advantageous pro-
cess, as no cell has yet excluded it by changing its genetic code
(460). Importantly, most HGT events probably have a neutral or
deleterious effect on their new host and are rapidly lost; only an
advantageous HGTevent can be xed in a population (485). HGT
can quickly bring together systems that have already evolved and
are ready to work under various conditions. It is a risky strategy,
but the evolution of new benecial genes is long and rare, so shar-
ing could be better than remaking. In addition, HGT can change
the level of expression of genes (generating higher, lower, consti-
tutive, or different regulation). It can activate the transcription of
cryptic genes, sometimes as part of a regulation process (25).
Cryptic genes might be a genetic reservoir of information ready to
be activated by mutations (486). HGT permits an individual bac-
teriumto maintain a compact genome, whereas a huge number of
accessory genes is available at the population level. Baumdicker
and collaborators have proposed the innitely many genes
model, which is based on the possibility that individual genomes
have access to an unbounded reservoir of novel genes (487). Fur-
thermore, HGT can create chromosomal rearrangement, plasmid
integration, deletion, insertion, novel gene fusion (bringing novel
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

function), or duplicationthat canopennewpossibilities for future
evolution. Through these events, the main role of HGT is in the
initial acquisition of pathways; its role in pathway variation is
small (488).
The benecial effects of HGT are greater when a population
grows in a stressful environment. HGT can facilitate niche adap-
tation and is important for bacterial mutagenesis and the mainte-
nance of genetic heterogeneity. It has an essential role in the evo-
lution and speciation of prokaryotes. Thanks to this process, cells
can gain genetic information and increase their genome plasticity
by the introduction of mobile elements. Remarkably, some ge-
netic variations brought about by HGT might not be totally ran-
dom but can happen with statistical reproducibility (489).
Mechanism of HGT. Genes introduced by HGT can be new to
the host bacterium (or come back after being lost) or can be par-
alogues of existing genes or substitutes for them. These genes
could confer a novel pathway essential for cell survival or coloni-
zation of a new niche or could encode a protein more efcient
than the one originally produced by the cell.
(i) Agents mediating HGT. In bacteria, HGT can be mediated
by various mechanisms: by transformation, conjugation, or trans-
duction or by using gene transfer agents (GTAs), nanotubes, or
membrane vesicles (MVs). Transformation is a process by which a
cell takes up DNA from its environment. It occurs when the re-
cipient bacterium is competent, a particular physiological state
natural to some bacteria. Conjugation permits the direct transfer
of DNA between two cells bridged by a pilus. It requires the pres-
ence of a conjugative plasmid or a chromosomally integrated con-
jugative element (ICE) in the donor cell. Transduction uses bac-
teriophages to transport DNA from one cell to another. GTAs are
natural vectors that convey genomic DNA in a transduction-like
manner (481, 490493). They are host-encoded virus-like ele-
ments that cannot induce cell lysis but package and transport ran-
dom fragments of the host chromosome. So far, GTAs have been
described in proteobacteria and spirochetes. Nanotubes are tubu-
lar protrusions that join neighboring cells grown on solid surfaces
(494). They have been suggested to permit the exchange of cellular
molecules, including nonconjugative plasmids, within and be-
tween species. Finally, extracellular outer MVs are naturally pro-
duced by numerous Gram-negative bacteria (495497). These
spherical vesicles can transport proteins and/or DNA (from the
host chromosome, a plasmid, or a phage) to a new host. Impor-
tantly, in a number of these processes, homologous recombina-
tion is essential for the integration of the horizontally transferred
genes into their new host chromosome.
(ii) Natural limitations of HGT. The existence of many differ-
ent kinds of transfer mechanism ensures that no bacterium is
completely immune to HGT. Nevertheless, the level of HGT de-
pends on the organization of the recipient cell and on its environ-
ment. Agents mediating HGT have restricted ranges. Not all cells
are competent, and phages and plasmids have specic hosts. A
bacteriophage might also destroy its host during HGT. Addition-
ally, HGT efciencies depend on the level of DNA stability pro-
vided by the transport carrier and on the physical distance be-
tween the donor and the recipient cell. Most transfers occur
between cells residing in the same habitats. Furthermore, the ma-
jority of HGTevents will be quickly lost, as the newDNAhas to be
incorporated into the total genome of the recipient cell and be
expressed into a useful product. The genome integration process
can be carried out by homologous recombination, illegitimate in-
corporation at a double-strand break, or specialized genetic ele-
ments, such as mobile elements, MITEs, plasmids, phages, inte-
grons, or genomic islands. Some elements integrate randomly,
whereas others have specic targets. The frequency of recent HGT
correlates linearly with the GC content and the genome and pro-
teome sequence similarities between the transfer donor and the
recipient cells (498). The cells genome size, carbon utilization,
and oxygen tolerance are also important factors (499). Homolo-
gous sequences are necessary to integrate DNA into a new host
genome by homologous recombination. However, if available, the
nonhomologous end-joining pathway seems to be able to help a
bacterium to overcome this sequence similarity barrier (498).
Once integrated into the genome, the regulation, transcription,
and translation apparatus of the new host might not recognize
horizontally transferred genes froma very different organism. For
example, the newDNAmight contain suboptimal codon frequen-
cies that do not t the tRNA pool of the recipient cell. Finally, the
new genetic information should pass the test of natural selection.
A large number of bacterial pseudogenes are horizontally trans-
ferred genes that were not useful at the time of their acquisition
(500). To be xed in a large population, the transferred DNA
might need to bring more advantages than problems. In most
cases, it cannot be toxic or disrupt a gene encoding an important
cellular function when integrating. Often, it must be expressed at
a functional level without decreasing the tness of the cell or hin-
dering the function of other cellular components. The encoded
information usually needs to be new and useful as it is or to be an
improvement on the information previously held by the cell.
Strikingly, some eukaryotic genes can be found in parasitic or
symbiotic bacteria (501), and some hyperthermophilic bacteria
have acquired various genes from archaea (502), demonstrating
that HGTcancross major phylogenetic barriers. Once successfully
in the genome, the transferred sequence slowly acquires the char-
acteristics of its newhost genome, which increases its stability and
might change its expression level or function.
(iii) Cellular mechanisms to ght HGT. Most cells actively ght
HGT by acting against the invasion of agents mediating this process,
suchas viruses, mobile elements, or conjugative plasmids. These var-
ious defense mechanisms include differential recognition by DNA
uptake systems, CRISPR-Cas systems, restriction-modication sys-
tems, toxin-antitoxin systems, endogenous nucleases, and mismatch
repair systems. Paradoxically, most of these systems wouldhave been
introducedintothecell genomebyHGT. Additionally, somecells can
specically silence certainforeigngenes by the bindingof histone-like
nucleotide structuring (H-NS) proteins (503).
(iv) Mechanisms of propagation of HGT elements. An HGT
element can use another HGT element to be transferred. For ex-
ample, an IS element can move into a conjugative plasmid to be
transported into another host. Some HGT elements avoid being
lost by using postsegregation or postdisturbance killing mecha-
nisms (see Postsegregation killing systems, above). Moreover,
the use of certain antibiotics induces the SOS system, which acti-
vates the transfer of bacteriophages and ICEs, resulting in the
spread of antibiotic resistance genes by HGT (504, 505). Some
HGT induces biolm formation, which improves the capacity of
transferring DNA (506). Finally, in order to limit competition,
specic HGT elements, such as phages, restriction-modication
systems (243), toxin-antitoxin systems, CRISPR-Cas systems
(507), or ISs (29), can ght other invading genetic elements.
HGT in contemporary organisms. (i) Methods used to detect

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

HGT. Phylogenetic and/or genomic analyses can be used to deter-
mine whether a gene has been subject to HGT. With these types of
analyses, it might be difcult to determine whether a gene was
introduced into a bacterium by HGT or lost from its closely re-
lated organisms, so a combination of analyses might be more re-
liable (470). Phylogenetic analyses are based on anomalies in gene
tree comparisons, indicating that a gene has a different origin than
the rest of the genome. Genomic analyses rely on specic charac-
teristics of the studied genome (frequencies of nucleotides,
codons, and amino acids and gene distribution patterns). Addi-
tionally, regions adjacent to genes susceptible to have been hori-
zontally transferred can be analyzed for potential relics of se-
quences that helped their integration. Importantly, genomic
analyses can indicate only recent HGT events, as transferred se-
quences will progressively acquire their host characteristics by di-
rectional mutation pressure.
(ii) Levels of HGTincontemporary organisms. Several studies
have concluded that, depending on the bacterial strain, up to 20%
of genes in a prokaryotic genome were recently introduced by
HGT (459, 508, 509). According to Dutta and Pan, these numbers
are underestimates, whereas they are overestimates for Kurland
and collaborators and for Gao and Gupta (464, 483, 510, 511). In
addition, a study of 181 sequenced prokaryotic genomes indicated
that at least 81% of the genes in each of these genomes had been
involved in HGT at one point in their history (512).
(iii) Genes susceptible to HGT. The type and number of genes
acquired by HGTare limited by the environment and the selective
pressures exertedonthe cells. All functional categories of genes are
susceptible to HGT (513). However, some categories of genes are
inherited more often than others, and some genes might be toxic
to their newhost and so cannot be transferred to them. Moreover,
high gene expression levels can result in a tness cost that limits
HGT (514). Lerat and collaborators indicated that single-copy
orthologous genes would be resistant to HGT (515), but this af-
rmation was contested by Bapteste and collaborators (516).
Basically, genes that encode proteins that interact with other cel-
lular molecules are less transferable, unless all the proteins of the
pathway are encoded in a transferable operon (517, 518). There-
fore, a protein with high interactivity can be displaced only by a
similar protein from a closely related organism, whereas a modu-
lar element can be transferred from a phylogenetically more dis-
tant donor. As a consequence, HGT is more frequent for enzymes
involved in peripheral cellular mechanisms than for enzymes in-
volved in reactions central to cell survival. Most genes encoding
molecules involved in replication, transcription, translation, and
housekeeping are rarely acquired by horizontal transfer (519,
520). Conversely, metabolic and regulatory networks are shaped by
HGT that can provide entire genetic pathways (521). However, the
size of a bacterial genome is conned, so a cell that has acquired
genetic material by HGT should lose an equivalent portion of its
genome inthe same HGTevent or by decay andgene loss. Therefore,
to be xed in a population, a transferred gene must bring an advan-
tage to its newhost, which rarely occurs. Examples of newcharacter-
istics that can be introduced by HGT include metabolic properties,
detoxicationof heavymetals, fermentationof exoticcarbonsources,
defense mechanisms, antibiotic resistance, pathogenic functions, vir-
ulence attributes, quorumsensing, aerobic respiration, photosynthe-
sis, thermophily, and halophily.
(iv) Relationships between HGT and an organisms life-style.
The life-style of an organism can determine the amount and ori-
gins of HGT that it will receive. The rates of HGT are higher when
a bacterium is in a biolm community than when it is in a plank-
tonic state (506). Moreover, some pairs of bacterial species were
identied to be linked by a highway of gene sharing, meaning that
numerous different genes were horizontally transferred between
these cells (522). Cyanobacteria living in extreme environments
contain more mobile elements, which increase their genome plas-
ticity and their chances of survival (11).
HGT is a major determinant of the integrity and size of some
prokaryotic genomes. A number of common particularities char-
acterizes genomes of obligate intracellular pathogens and symbi-
onts as well as some extracellular symbionts that are physically
isolated from the rest of the bacterial community (157, 459, 509,
523542). These genomes are much smaller than the genomes of
free-living bacteria (from 4 to almost 30 times smaller than the E.
coli genome), have a strong AT bias, and have very few mobile
elements, regulatory systems, and pseudogenes. Additionally,
these prokaryotes have spontaneous mutation rates at least 10
times higher than those of free-living bacteria (543). Some obli-
gate intracellular bacteria also have a high copy number of their
genome (544). Almost any functional category of gene can be lost
in an obligate intracellular bacterium, but there is a common pat-
tern. These bacteria usually preserve genes involved in essential
processes, such as transcription, translation, and DNA replica-
tion, as well as chaperones and genes devoted to interactions with
their hosts. Conversely, genes that are often lost encode proteins
involved in cell envelope biogenesis, regulatory systems, metabo-
lism (except for proteins needed for survival), and DNA repair
and recombination. Repeated DNA, mobile elements, redundant
pathways, and duplicated genes are almost always lost (545). In-
terestingly, the fact that comparable genome characteristics were
visible in the majority of obligate intracellular symbionts and
pathogens indicates that similar evolutionary forces led these bac-
terial genomes in this direction. Studies of the genomes of numer-
ous bacteria that spent different lengths of time as obligate intra-
cellular microorganisms indicated the dynamics of genome
modulations leading to the speciation of these bacteria. Rapid
evolutionary changes often occur immediately after host restric-
tion. However, the reduction of the genome size and the propor-
tion of AT content in the genome increase with the time of
association between a bacterium and its host. The genome of a
bacteriumthat recently became an obligate intracellular organism
contains a large quantity of mobile elements and pseudogenes.
These mobile elements, along with repeated sequences, inactivate
genes and induce inversions, deletions, and numerous chromo-
somal rearrangements (homologous recombinationdependent or
independent). As the population is small, isolated, and in a stable
and rich environment, the pressure exerted by selection is relaxed,
so transpositions and mutations are not counterselected and be-
come xed in the population, resulting in the proliferation of mo-
bile elements and pseudogenes. These mutations might be bene-
cial (eliminating proteins that could be recognized by the host
immune system), neutral (pathways that are redundant or not
needed anymore), or even slightly deleterious. Once inactivated,
these genes are deleted, as there is a bias toward deletion in bacte-
ria (546). The isolation of these bacteria in a host cell dramatically
reduces their opportunities to gain new genetic material by HGT.
Therefore, gene losses are almost irreversible, and the genome
shrinks. Once some DNA repair genes are inactivated, the muta-
tion rate increases even more, as does the rate of transitions of GC
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

into AT, resulting in an AT-rich genome. Moreover, mutations
in recombination genes decrease further the chances of genetic
exchange. After this rst phase of intense genome reduction, mo-
bile elements themselves undergo inactivation and loss or will
become lethal. Subsequently, there is a gradual gene loss following
gene inactivation by mutation. During this process, genes are
mainly lost, but not shortened, and the size of intergenic regions
principally decreases only in the very small genomes of bacteria
undergoing an ancient association with their host. In summary,
there are two steps that lead to the reduction of the size of these
genomes. First, mobile elements are responsible for a large part of
the deletions and chromosomal rearrangements, resulting in the
shrinking of the genome. Second, the isolation of these organisms
results in the absence of HGT, so the lost DNAcannot be replaced.
Strikingly, despite being small, the genomes of some patho-
genic and parasitic obligate intracellular bacteria have much more
repetitive DNAandmobile elements thanothers (530, 547). These
bacteria can switch hosts or infect host cells that contain other
intracellular microorganisms. Within their hosts, coinfecting bac-
teria can exchange genetic material by HGT (548). Therefore,
these obligate intracellular microorganisms can escape some of
the genetic connement of their ecological niche. Similarly, ge-
nomes of obligate intra-amoebal microorganisms do not seem to
shrink as much as the genomes of other obligate intracellular bac-
teria (549, 550). Here, amoebae act as reservoirs containing large
communities of microorganisms sharing an ecological niche.
They constitute a place where these bacteria can exchange DNAor
acquire DNA from organisms that have been degraded by the
amoebae (551).
(v) Selshness of mobile elements. Mobile elements have been
described as selsh entities or genetic parasites because they usu-
ally survive by invading a host genome without providing a ben-
ecial phenotype to that host (243, 511, 552554). This ability
results from the fact that mobile elements can create copies of
themselves, to spread quicker than the host genes and promote
their own survival within and between cells by HGT. Additionally,
mobile elements often encode postsegregation killing systems,
which are lethal for host cells that eliminate them. To decrease
their chances of inactivation by mutation, some spliceable mobile
elements, such as introns and inteins, insert into or near nucleo-
tide sequences encoding residues that are functionally critical for
host survival. However, some mobile elements may provide short-
or long-term advantages to their host cell. To increase the ef-
ciency of their invasions, some mobile elements carry genes en-
coding phenotypic benets for their host. Postsegregation killing
systems can ght infections by new mobile elements, plasmids, or
phages and can act as part of cell biology pathways or altruistic cell
death strategies (for further examples, see Postsegregation killing
systems, above). Finally, as mutators, mobile elements can in-
duce variation for future evolution. Therefore, mobile elements
should not be considered entirely selsh, but the relationship be-
tween a mobile element and its host might be understood as vary-
ing from extreme parasitism to mutualism (555).
HGT and evolution. The role of HGT in evolution was rst
ignored and then considered to be a minor player as a conse-
quence of rare events. However, in the era of genomics, HGT is
now recognized as a major force in evolution, alongside genomic
mutation, gene loss, gene duplication, and recombinational
events (see references 457, 467, 509, and 556564 as well as refer-
ences cited at the beginning of Horizontal Gene Transfer in Pro-
karyotes, above). HGT is now thought to have been essential for
the origin and development of life on the planet and to still be very
important for the transfer of optimized pathways of genetic infor-
mation, resulting in what has been called evolutionary genetic
quantum leaps, and for increasing genome plasticity, leading to
adaptation, genomic diversication, and speciation. Additionally,
HGT and especially mobile elements provide important mecha-
nisms of evolution of new genes (by bringing small insertions or
deletions, by formation and activation of pseudogenes or new
hybrid genes, by induction of genome duplications forming
paralogous genes, or by genome remodeling following chromo-
somal rearrangements).
(i) HGT and the beginning of life on Earth. HGT might have
had an essential role in the development and evolution of very
early life forms on the planet. The theory of the universal common
ancestor presentedby Woese describes the rst living organisms as
single communal evolutionary units in which HGT and mutation
rates were very high, resulting in high evolution rates (565). These
primitive organisms would have consisted of a pool of constantly
exchanged genes. Evolution was then a communal process; there
was noindividual lineage (460). The genetic code wouldhave been
an innovation of this time (566). All modern organisms would
have descended fromthis universal ancestral community of genes.
Such a theory is hard to conrm or falsify and has been contested
by Poole, who thinks that extreme rates of HGT without barriers
may be disruptive to evolutionary transitions (478).
According to the selsh-operon hypothesis presented by Law-
rence and Roth, HGTwould also be accountable for the formation
of operons, as genes necessary to carry a single pathway increase
their chances of cotransfer when clustered in an operon (567,
568). Alternatively, the formation of operons might be the result
of biophysical constraints (569) or could be driven by random
gene deletions (for conserved genes) (570), or HGT might simply
promote the prevalence of preexisting operons formed when gene
regulation is complex (571). Arguing against a role of HGT in
operon formation, analyses indicate that essential genes are par-
ticularly abundant in E. coli operons, while HGT events exchange
mostly nonessential genes, and that horizontally transferred genes
would have the least chances to be members of an operon (572,
573).
(ii) HGTand the tree of life. Atraditional eukaryotic tree of
life is grounded on vertical inheritance (genes passed directly
from parents to offspring). However, prokaryotic genomes have
been extensively manipulated by HGT, so their histories are dif-
ferent from the histories of all their genes. In other words, it is
problematic to determinate the lineage of an organismwhen most
of its genes have different origins. Therefore, a number of scien-
tists think that origins and relationships between prokaryote spe-
cies cannot be represented as a tree and have proposed various
alternative ways to describe the evolution of bacteria and life, usu-
ally as a forest, a network, or a ring (473, 516, 574581). Con-
versely, numerous scientists think that the universal tree might
still be anappropriate concept and have succeeded inconstructing
a tree of life despite or evenbasedonHGT(468, 483, 511, 518, 561,
582591). Remarkably, as well as being used to construct phylo-
genetic trees, 16S rRNAs were used by microbial ecologists to pre-
dict the ecological functions of a microbe. This methodology is
now thought to be fruitless, as the presence of HGT unlinks the
function and the genotype of bacteria (480, 592).
(iii) HGT and bacterial species. Exchanges of genetic material

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

due to HGT promote microbial diversication and speciation, for
example, by changing the ecological niche of a microorganism.
HGT also contributes to controversies concerning whether bacte-
ria can be divided into species and what would then be the bound-
aries of these species (463, 593597). Traditionally, species are
ecologically distinct organisms that went through an irreversible
divergence and for which diversity is limited by barriers to out-
crossing. For Sonea and Mathieu, the lack of reproductive isola-
tion in prokaryotes results in the absence of bacterial species
(462). Some new microorganism-specic classication systems
have even been proposed (475, 598). However, other scientists
argue that the complexity added by HGT does not impede the
classication of bacteria within species, as the vast majority of a
bacterial genome is still vertically inherited (457, 483).
(iv) HGT, CRISPR-Cas, Lamarckism, and Darwinism. The
CRISPR-Cas system and the process of HGT integrate environ-
mental information into a bacterial genome, permitting inherited
adaptation to an environmental stimulus. For this reason, these
two mechanisms have beenproposedto be Lamarckianandquasi-
Lamarckian, respectively (474, 484, 599, 600). Stress-induced mu-
tagenesis, including that occurring following the activationof mo-
bile elements, has also been suggested to be a quasi-Lamarckian
process. Basically, the theory of Lamarckism states that evolution
is driven primarily by nonrandomly acquired inheritable changes
affected directly by the use of systems. On the other hand, the
theory of Darwinism considers that random mutations provide
evolutionary materials that can be lost or xed by natural selec-
tion, leading to the evolution of organisms that are best adapted to
their environment. According to Koonin and Wolf, evolution
would use a continuum of processes within a range starting from
total randomness up to systems perfectly targeted to specic re-
sponses to the cell environment (484, 599). The CRISPR-Cas sys-
tem, HGT, and stress-induced mutagenesis can still be considered
in accordance with Darwins original ideas of evolution by varia-
tion and selection (484, 591). Furthermore, these processes seem
to be Lamarckian only at the organismal level, as HGT genes
evolve according to Darwinian processes; variations within genes
are random and will be purged by natural selection, regardless of
the origin of these genes (478).
In summary, HGT is the bacterial way of sharing genetic infor-
mation. It is a powerful and complex process that leads to varia-
tion, evolution, and speciation. It might also be at the origin of the
diversity of life on Earth.
CONCLUSION
Bacterial genome integrity is constantly threatened by external
agents, such as mobile elements or phages, as well as by the oper-
ation of their own DNA replication and repair systems at related
or repeated sequences. However, the large number of bacteria
transforms genome instability into a driving force for bacterial
survival, diversication, adaptation, speciation, and evolution. A
growing bacterial population develops a balance between genome
maintenance and instability that depends on the type of bacte-
rium, the cell cycle, and the environment. Furthermore, bacteria
utilize genome instability to increase their gene diversity and con-
trol gene expression and the response to various stresses. Further
studies on these genome instability processes will lead to a better
understanding of their role and action. Over the last 15 years, the
development of genomic technology has allowed the discovery of
several newgenome instability processes, and it would not be sur-
prising if there were more to come.
ACKNOWLEDGMENTS
We thank Meriem El Karoui and Garry Blakely for critical comments on
the manuscript. Bacterial genome instability is a broad subject that has
been studied for numerous years, leading to the publication of countless
excellent articles and reviews. Unfortunately, we could not cite them all,
and we apologize to the deserving colleagues who were not mentioned
here.
We are grateful for funding from the Medical Research Council.
REFERENCES
1. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen
majority. Proc. Natl. Acad. Sci. U. S. A. 95:65786583. http://dx.doi.org
/10.1073/pnas.95.12.6578.
2. Krawiec S, Riley M. 1990. Organization of the bacterial chromosome.
Microbiol. Rev. 54:502539.
3. Saier MH, Jr. 2008. The bacterial chromosome. Crit. Rev. Biochem.
Mol. Biol. 43:89134. http://dx.doi.org/10.1080/10409230801921262.
4. Delihas N. 2011. Impact of small repeat sequences on bacterial genome
evolution. Genome Biol. Evol. 3:959973. http://dx.doi.org/10.1093/gbe
/evr077.
5. Rebollo JE, Francois V, Louarn JM. 1988. Detection and possible role of
two large nondivisible zones on the Escherichia coli chromosome. Proc.
Natl. Acad. Sci. U. S. A. 85:93919395. http://dx.doi.org/10.1073/pnas
.85.24.9391.
6. Esnault E, Valens M, Espli O, Boccard F. 2007. Chromosome struc-
turing limits genome plasticity in Escherichia coli. PLoS Genet. 3:e226.
http://dx.doi.org/10.1371/journal.pgen.0030226.
7. Shapiro JA. 2009. Letting Escherichia coli teach me about genome engi-
neering. Genetics 183:12051214. http://dx.doi.org/10.1534/genetics
.109.110007.
8. Leavis HL, Willems RJ, van Wamel WJ, Schuren FH, Caspers MP,
Bonten MJ. 2007. Insertion sequence-driven diversication creates a
globally dispersed emerging multiresistant subspecies of E. faecium.
PLoS Pathog. 3:e7. http://dx.doi.org/10.1371/journal.ppat.0030007.
9. Bickhart DM, Gogarten JP, Lapierre P, Tisa LS, Normand P, Benson
DR. 2009. Insertion sequence content reects genome plasticity in
strains of the root nodule actinobacterium Frankia. BMC Genomics 10:
468. http://dx.doi.org/10.1186/1471-2164-10-468.
10. Qiu N, He J, Wang Y, Cheng G, Li M, Sun M, Yu Z. 2010. Prevalence
and diversity of insertion sequences in the genome of Bacillus thuringien-
sis YBT-1520 and comparison with other Bacillus cereus group members.
FEMS Microbiol. Lett. 310:916. http://dx.doi.org/10.1111/j.1574-6968
.2010.02033.x.
11. Lin S, Haas S, Zemojtel T, Xiao P, Vingron M, Li R. 2011. Genome-
wide comparison of cyanobacterial transposable elements, potential ge-
netic diversity indicators. Gene 473:139149. http://dx.doi.org/10.1016
/j.gene.2010.11.011.
12. Craig NL. 1991. Tn7: a target site-specic transposon. Mol. Microbiol.
5:25692573. http://dx.doi.org/10.1111/j.1365-2958.1991.tb01964.x.
13. Lodge JK, Weston-Hafer K, Berg DE. 1988. Transposon Tn5 target
specicity: preference for insertion at G/C pairs. Genetics 120:645650.
14. Mahillon J, Chandler M. 1998. Insertion sequences. Microbiol. Mol.
Biol. Rev. 62:725774.
15. Mahillon J, Lonard C, Chandler M. 1999. IS elements as constituents
of bacterial genomes. Res. Microbiol. 150:675687. http://dx.doi.org/10
.1016/S0923-2508(99)00124-2.
16. Siguier P, File J, Chandler M. 2006. Insertion sequences in prokaryotic
genomes. Curr. Opin. Microbiol. 9:526531. http://dx.doi.org/10.1016
/j.mib.2006.08.005.
17. Luque I, Andjar A, Jia L, Zabulon G, de Marsac NT, Flores E,
Houmard J. 2006. Regulated expression of glutamyl-tRNA synthetase is
directed by a mobile genetic element in the cyanobacterium Tolypothrix
sp. PCC 7601. Mol. Microbiol. 60:12761288. http://dx.doi.org/10.1111
/j.1365-2958.2006.05170.x.
18. Bowen SW, Hassan HM. 1993. Characterization of cis-acting regulatory
mutations causing anaerobic expression of the sodA gene in Escherichia
coli. Arch. Biochem. Biophys. 302:372379. http://dx.doi.org/10.1006
/abbi.1993.1226.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

19. Sa H, Barnes PF, Lakey DL, Shams H, Samten B, Vankayalapati R,
Howard ST. 2004. IS6110 functions as a mobile, monocyte-activated
promoter in Mycobacterium tuberculosis. Mol. Microbiol. 52:9991012.
http://dx.doi.org/10.1111/j.1365-2958.2004.04037.x.
20. Reynolds AE, Mahadevan S, LeGrice SF, Wright A. 1986. Enhance-
ment of bacterial gene expression by insertion elements or by mutation
in a CAP-cAMP binding site. J. Mol. Biol. 191:8595. http://dx.doi.org
/10.1016/0022-2836(86)90424-9.
21. Ozawa Y, Mizushima S, Mizuno T. 1990. Osmoregulatory expression of
the ompC gene in Escherichia coli K-12; IS1 insertion in the upstream
regulatory region results in constitutive activation of the promoter.
FEMS Microbiol. Lett. 56:295299.
22. Singh J, Mukerji M, Mahadevan S. 1995. Transcriptional activation of
the Escherichia coli bgl operon: negative regulation by DNA structural
elements near the promoter. Mol. Microbiol. 17:10851092. http://dx
.doi.org/10.1111/j.1365-2958.1995.mmi_17061085.x.
23. Fernndez A, Gil E, Cartelle M, Prez A, Beceiro A, Mallo S, Toms
MM, Prez-Llarena FJ, Villanueva R, Bou G. 2007. Interspecies spread
of CTX-M-32 extended-spectrum beta-lactamase and the role of the in-
sertion sequence IS1 in down-regulating bla CTX-M gene expression.
J. Antimicrob. Chemother. 59:841847. http://dx.doi.org/10.1093/jac
/dkm030.
24. Zhang Z, Saier MH, Jr. 2009. A novel mechanism of transposon-
mediated gene activation. PLoS Genet. 5:e1000689. http://dx.doi.org/10
.1371/journal.pgen.1000689.
25. Hall BG. 1999. Transposable elements as activators of cryptic genes inE. coli.
Genetica 107:181187. http://dx.doi.org/10.1023/A:1003936706129.
26. Perkins-Balding D, Duval-Valentin G, Glasgow AC. 1999. Excision of
IS492 requires anking target sequences andresults incircle formationin
Pseudoalteromonas atlantica. J. Bacteriol. 181:49374948.
27. Plague GR. 2010. Intergenic transposable elements are not randomly
distributed in bacteria. Genome Biol. Evol. 2:584590. http://dx.doi.org
/10.1093/gbe/evq040.
28. Kusumoto M, Ooka T, Nishiya Y, Ogura Y, Saito T, Sekine Y, Iwata
T, Akiba M, Hayashi T. 2011. Insertion sequence-excision enhancer
removes transposable elements frombacterial genomes and induces var-
ious genomic deletions. Nat. Commun. 2:152. http://dx.doi.org/10.1038
/ncomms1152.
29. Ooka T, Ogura Y, Asadulghani M, Ohnishi M, Nakayama K, Terajima
J, Watanabe H, Hayashi T. 2009. Inference of the impact of insertion
sequence (IS) elements on bacterial genome diversication through
analysis of small-size structural polymorphisms in Escherichia coli O157
genomes. Genome Res. 19:18091816. http://dx.doi.org/10.1101/gr
.089615.108.
30. Gray YH. 2000. It takes two transposons to tango: transposable-element-
mediated chromosomal rearrangements. Trends Genet. 16:461468.
http://dx.doi.org/10.1016/S0168-9525(00)02104-1.
31. Virolle MJ, Glugne JP, Bjar S, Bouch JP. 1983. Origin of Escherichia
coli K-12 Hfr B7. J. Bacteriol. 153:610615.
32. Smillie C, Garcilln-Barcia MP, Francia MV, Rocha EP, de la Cruz F.
2010. Mobility of plasmids. Microbiol. Mol. Biol. Rev. 74:434452. http:
//dx.doi.org/10.1128/MMBR.00020-10.
33. Lesic B, Zouine M, Ducos-Galand M, Huon C, Rosso ML, Prvost MC,
Mazel D, Carniel E. 2012. A natural system of chromosome transfer in
Yersinia pseudotuberculosis. PLoS Genet. 8:e1002529. http://dx.doi.org
/10.1371/journal.pgen.1002529.
34. Bachellier S, Clment JM, Hofnung M. 1999. Short palindromic repet-
itive DNAelements in enterobacteria: a survey. Res. Microbiol. 150:627
639. http://dx.doi.org/10.1016/S0923-2508(99)00128-X.
35. Delihas N. 2008. Small mobile sequences in bacteria display diverse
structure/function motifs. Mol. Microbiol. 67:475481. http://dx.doi
.org/10.1111/j.1365-2958.2007.06068.x.
36. Yang G, Nagel DH, Feschotte C, Hancock CN, Wessler SR. 2009.
Tuned for transposition: molecular determinants underlying the hyper-
activity of a Stowaway MITE. Science 325:13911394. http://dx.doi.org
/10.1126/science.1175688.
37. Bardaji L, Anorga M, Jackson RW, Martinez-Bilbao A, Yanguas-Casas
N, Murillo J. 2011. Miniature transposable sequences are frequently
mobilized in the bacterial plant pathogen Pseudomonas syringae pv.
phaseolicola. PLoS One 6:e25773. http://dx.doi.org/10.1371/journal
.pone.0025773.
38. Mennecier S, Servant P, Coste G, Bailone A, Sommer S. 2006. Mutagen-
esis via IS transposition in Deinococcus radiodurans. Mol. Microbiol. 59:
317325. http://dx.doi.org/10.1111/j.1365-2958.2005.04936.x.
39. Xu M, Kong R, Xu X. 2006. A miniature insertion element transposable
in Microcystis sp. FACHB 854. Prog. Nat. Sci. 16:486491. http://dx.doi
.org/10.1080/10020070612330024.
40. Chen Y, Zhou F, Li G, Xu Y. 2008. A recently active miniature inverted-
repeat transposable element, Chunjie, inserted into an operon without
disturbing the operon structure in Geobacter uraniireducens Rf4. Genet-
ics 179:22912297. http://dx.doi.org/10.1534/genetics.108.089995.
41. Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H,
Nakayama K, Toh H, Yoshimura F, Kuhara S, Hattori M, Hayashi T.
2008. Determination of the genome sequence of Porphyromonas gingiva-
lis strain ATCC 33277 and genomic comparison with strain W83 re-
vealed extensive genome rearrangements in P. gingivalis. DNA Res. 15:
215225. http://dx.doi.org/10.1093/dnares/dsn013.
42. Romine MF, Carlson TS, Norbeck AD, McCue LA, Lipton MS. 2008.
Identication of mobile elements and pseudogenes in the Shewanella
oneidensis MR-1 genome. Appl. Environ. Microbiol. 74:32573265. http:
//dx.doi.org/10.1128/AEM.02720-07.
43. Zhou F, Tran T, Xu Y. 2008. Nezha, a novel active miniature inverted-
repeat transposable element in cyanobacteria. Biochem. Biophys. Res.
Commun. 365:790794. http://dx.doi.org/10.1016/j.bbrc.2007.11.038.
44. Croucher NJ, Vernikos GS, Parkhill J, Bentley SD. 2011. Identication,
variation and transcription of pneumococcal repeat sequences. BMC
Genomics 12:120. http://dx.doi.org/10.1186/1471-2164-12-120.
45. De Palmenaer D, Vermeiren C, Mahillon J. 2004. IS231-MIC231 ele-
ments from Bacillus cereus sensu lato are modular. Mol. Microbiol. 53:
457467. http://dx.doi.org/10.1111/j.1365-2958.2004.04146.x.
46. Gillings MR, Labbate M, Sajjad A, Gigure NJ, Holley MP, Stokes
HW. 2009. Mobilization of a Tn402-like class 1 integron with a novel
cassette array via anking miniature inverted-repeat transposable ele-
ment-like structures. Appl. Environ. Microbiol. 75:60026004. http://dx
.doi.org/10.1128/AEM.01033-09.
47. Poirel L, Carrr A, Pitout JD, Nordmann P. 2009. Integron mobiliza-
tion unit as a source of mobility of antibiotic resistance genes. Antimi-
crob. Agents Chemother. 53:24922498. http://dx.doi.org/10.1128/AAC
.00033-09.
48. Delihas N. 2007. Enterobacterial small mobile sequences carry open
reading frames and are found intragenicallyevolutionary implications
for formation of new peptides. Gene Regul. Syst. Biol. 1:191205. http:
//www.ncbi.nlm.nih.gov/pmc/articles/PMC2759123/.
49. Mazzone M, De Gregorio E, Lavitola A, Pagliarulo C, Alifano P, Di
Nocera PP. 2001. Whole-genome organization and functional proper-
ties of miniature DNAinsertionsequences conservedinpathogenic Neis-
seriae. Gene 278:211222. http://dx.doi.org/10.1016/S0378-1119(01)
00725-9.
50. De Gregorio E, Abrescia C, Carlomagno MS, Di Nocera PP. 2003. Ribo-
nuclease III-mediatedprocessing of specic Neisseria meningitidis mRNAs.
Biochem. J. 374:799805. http://dx.doi.org/10.1042/BJ20030533.
51. Francis F, Ramirez-Arcos S, Salimnia H, Victor C, Dillon JR. 2000.
Organizationandtranscriptionof the divisioncell wall (dcw) cluster inNeis-
seria gonorrhoeae. Gene 251:141151. http://dx.doi.org/10.1016/S0378
-1119(00)00200-6.
52. Siddique A, Buisine N, Chalmers R. 2011. The transposon-like Correia
elements encode numerous strong promoters and provide a potential
new mechanism for phase variation in the meningococcus. PLoS Genet.
7:e1001277. http://dx.doi.org/10.1371/journal.pgen.1001277.
53. Abergel C, Blanc G, Monchois V, Renesto P, Sigoillot C, Ogata H,
Raoult D, Claverie JM. 2006. Impact of the excision of an ancient repeat
insertion on Rickettsia conorii guanylate kinase activity. Mol. Biol. Evol.
23:21122122. http://dx.doi.org/10.1093/molbev/msl082.
54. Stern MJ, Ames GF, Smith NH, Robinson EC, Higgins CF. 1984.
Repetitive extragenic palindromic sequences: a major component of the
bacterial genome. Cell 37:10151026. http://dx.doi.org/10.1016/0092
-8674(84)90436-7.
55. Lupski JR, Weinstock GM. 1992. Short, interspersed repetitive DNA
sequences in prokaryotic genomes. J. Bacteriol. 174:45254529.
56. Gilson E, Saurin W, Perrin D, Bachellier S, Hofnung M. 1991. Palin-
dromic units are part of a new bacterial interspersed mosaic element
(BIME). Nucleic Acids Res. 19:13751383. http://dx.doi.org/10.1093
/nar/19.7.1375.
57. Espli O, Moulin L, Boccard F. 2001. Transcription attenuation asso-

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

ciated with bacterial repetitive extragenic BIME elements. J. Mol. Biol.
314:375386. http://dx.doi.org/10.1006/jmbi.2001.5150.
58. Newbury SF, Smith NH, Robinson EC, Hiles ID, Higgins CF. 1987.
Stabilization of translationally active mRNA by prokaryotic REP se-
quences. Cell 48:297310. http://dx.doi.org/10.1016/0092-8674(87)
90433-8.
59. Stern MJ, Prossnitz E, Ames GF. 1988. Role of the intercistronic region
in post-transcriptional control of gene expression in the histidine trans-
port operon of Salmonella typhimurium: involvement of REP sequences.
Mol. Microbiol. 2:141152. http://dx.doi.org/10.1111/j.1365-2958.1988
.tb00015.x.
60. Gilson E, Rousset JP, Clment JM, Hofnung M. 1986. A subfamily of E.
coli palindromic units implicated in transcription termination? Ann.
Inst. Pasteur Microbiol. 137B:259270.
61. Boccard F, Prentki P. 1993. Specic interaction of IHF with RIBs, a class
of bacterial repetitive DNAelements locatedat the 3= endof transcription
units. EMBO J. 12:50195027.
62. Oppenheim AB, Rudd KE, Mendelson I, Teff D. 1993. Integration host
factor binds to a unique class of complex repetitive extragenic DNA
sequences in Escherichia coli. Mol. Microbiol. 10:113122. http://dx.doi
.org/10.1111/j.1365-2958.1993.tb00908.x.
63. Yang Y, Ames GF. 1988. DNA gyrase binds to the family of prokaryotic
repetitive extragenic palindromic sequences. Proc. Natl. Acad. Sci.
U. S. A. 85:88508854. http://dx.doi.org/10.1073/pnas.85.23.8850.
64. Bachellier S, Saurin W, Perrin D, Hofnung M, Gilson E. 1994. Struc-
tural and functional diversity among bacterial interspersed mosaic ele-
ments (BIMEs). Mol. Microbiol. 12:6170. http://dx.doi.org/10.1111/j
.1365-2958.1994.tb00995.x.
65. Espli O, Boccard F. 1997. In vivo cleavage of Escherichia coli BIME-2
repeats by DNA gyrase: genetic characterization of the target and identi-
cation of the cut site. Mol. Microbiol. 26:767777. http://dx.doi.org/10
.1046/j.1365-2958.1997.6121983.x.
66. Gilson E, Perrin D, Hofnung M. 1990. DNA polymerase I and a protein
complex bind specically to E. coli palindromic unit highly repetitive
DNA: implications for bacterial chromosome organization. Nucleic Ac-
ids Res. 18:39413952. http://dx.doi.org/10.1093/nar/18.13.3941.
67. Macvanin M, Edgar R, Cui F, Trostel A, Zhurkin V, Adhya S. 2012.
Noncoding RNAs binding to the nucleoid protein HUin Escherichia coli.
J. Bacteriol. 194:60466055. http://dx.doi.org/10.1128/JB.00961-12.
68. Magnusson M, Tobes R, Sancho J, Pareja E. 2007. Natural DNA
repetitive extragenic sequences from gram-negative pathogens strongly
stimulate TLR9. J. Immunol. 179:3135. http://www.jimmunol.org
/content/179/1/31.long.
69. Bachellier S, Clment JM, Hofnung M, Gilson E. 1997. Bacterial
interspersed mosaic elements (BIMEs) are a major source of sequence
polymorphism in Escherichia coli intergenic regions including specic
associations with a new insertion sequence. Genetics 145:551562.
70. Nunvar J, Huckova T, Licha I. 2010. Identication and characterization
of repetitive extragenic palindromes (REP)-associated tyrosine trans-
posases: implications for REP evolution and dynamics in bacterial ge-
nomes. BMC Genomics 11:44. http://dx.doi.org/10.1186/1471-2164-11
-44.
71. Ton-Hoang B, Siguier P, Quentin Y, Onillon S, Marty B, Fichant G,
Chandler M. 2012. Structuring the bacterial genome: Y1-transposases
associated with REP-BIME sequences. Nucleic Acids Res. 40:35963609.
http://dx.doi.org/10.1093/nar/gkr1198.
72. Clment JM, Wilde C, Bachellier S, Lambert P, Hofnung M. 1999.
IS1397 is active for transposition into the chromosome of Escherichia coli
K-12 and inserts specically into palindromic units of bacterial inter-
spersed mosaic elements. J. Bacteriol. 181:69296936.
73. Wilde C, Bachellier S, Hofnung M, Clment JM. 2001. Transposition
of IS1397 in the family Enterobacteriaceae and rst characterization of
ISKpnI, a new insertion sequence associated with Klebsiella pneumoniae
palindromic units. J. Bacteriol. 183:43954404. http://dx.doi.org/10
.1128/JB.183.15.4395-4404.2001.
74. Wilde C, Escartin F, Kokeguchi S, Latour-Lambert P, Lectard A, Clment
JM. 2003. Transposases are responsible for the target specicity of IS1397
andISKpnI for twodifferent types of palindromicunits (PUs). NucleicAcids
Res. 31:43454353. http://dx.doi.org/10.1093/nar/gkg494.
75. Tobes R, Pareja E. 2006. Bacterial repetitive extragenic palindromic
sequences are DNA targets for insertion sequence elements. BMC
Genomics 7:62. http://dx.doi.org/10.1186/1471-2164-7-62.
76. Shyamala V, Schneider E, Ames GF. 1990. Tandem chromosomal
duplications: role of REP sequences in the recombination event at the
join-point. EMBO J. 9:939946.
77. Reams AB, Kofoid E, Kugelberg E, Roth JR. 2012. Multiple pathways of
duplication formation with and without recombination (RecA) in Sal-
monella enterica. Genetics 192:397415. http://dx.doi.org/10.1534
/genetics.112.142570.
78. Reznikoff WS. 2008. Transposon Tn5. Annu. Rev. Genet. 42:269286.
http://dx.doi.org/10.1146/annurev.genet.42.110807.091656.
79. Salyers AA, Shoemaker NB, Stevens AM, Li LY. 1995. Conjugative
transposons: an unusual and diverse set of integrated gene transfer ele-
ments. Microbiol. Rev. 59:579590.
80. Scott JR, Churchward GG. 1995. Conjugative transposition. Annu. Rev.
Microbiol. 49:367397. http://dx.doi.org/10.1146/annurev.mi.49.100195
.002055.
81. Pembroke JT, MacMahon C, McGrath B. 2002. The role of conjugative
transposons in the Enterobacteriaceae. Cell. Mol. Life Sci. 59:20552064.
http://dx.doi.org/10.1007/s000180200005.
82. Wozniak RA, Waldor MK. 2010. Integrative and conjugative elements:
mosaic mobile genetic elements enabling dynamic lateral gene ow. Nat.
Rev. Microbiol. 8:552563. http://dx.doi.org/10.1038/nrmicro2382.
83. Adams V, Lyras D, Farrow KA, Rood JI. 2002. The clostridial mobil-
isable transposons. Cell. Mol. Life Sci. 59:20332043. http://dx.doi.org
/10.1007/s000180200003.
84. Lee CA, Thomas J, Grossman AD. 2012. The Bacillus subtilis conjuga-
tive transposon ICEBs1 mobilizes plasmids lacking dedicated mobiliza-
tion functions. J. Bacteriol. 194:31653172. http://dx.doi.org/10.1128/JB
.00301-12.
85. Wang H, Smith MC, Mullany P. 2006. The conjugative transposon
Tn5397 has a strong preference for integration into its Clostridium dif-
cile target site. J. Bacteriol. 188:48714878. http://dx.doi.org/10.1128/JB
.00210-06.
86. Taylor AL. 1963. Bacteriophage-induced mutation in Escherichia coli.
Proc. Natl. Acad. Sci. U. S. A. 50:10431051. http://dx.doi.org/10.1073
/pnas.50.6.1043.
87. Bukhari AI. 1976. Bacteriophage Mu as a transposition element.
Annu. Rev. Genet. 10:389412. http://dx.doi.org/10.1146/annurev
.ge.10.120176.002133.
88. Kleckner N. 1981. Transposable elements in prokaryotes. Annu. Rev.
Genet. 15:341404. http://dx.doi.org/10.1146/annurev.ge.15.120181
.002013.
89. Daniell E, Abelson J. 1973. Lac messenger RNA in lacZ gene mutants of
Escherichia coli caused by insertion of bacteriophage Mu. J. Mol. Biol.
76:319322. http://dx.doi.org/10.1016/0022-2836(73)90395-1.
90. Faelen M, Toussaint A, De Lafonteyne J. 1975. Model for the enhance-
ment of lambda-gal integration into partially induced Mu-1 lysogens. J.
Bacteriol. 121:873882.
91. Cameron RK, Ulycznyj PI, DuBow MS. 1995. Mu transposase-
stimulated illegitimate recombination of Tn3kan- and IS101-containing
plasmids. Res. Microbiol. 146:601616. http://dx.doi.org/10.1016/0923
-2508(96)81059-X.
92. Hacker J, Blum-Oehler G, Mhldorfer I, Tschpe H. 1997. Pathoge-
nicity islands of virulent bacteria: structure, function and impact on mi-
crobial evolution. Mol. Microbiol. 23:10891097. http://dx.doi.org/10
.1046/j.1365-2958.1997.3101672.x.
93. Hacker J, Kaper JB. 2000. Pathogenicity islands and the evolution of
microbes. Annu. Rev. Microbiol. 54:641679. http://dx.doi.org/10.1146
/annurev.micro.54.1.641.
94. Hacker J, Carniel E. 2001. Ecological tness, genomic islands and bacterial
pathogenicity. ADarwinian viewof the evolution of microbes. EMBORep.
2:376381. http://dx.doi.org/10.1093/embo-reports/kve097.
95. Hentschel U, Hacker J. 2001. Pathogenicity islands: the tip of the ice-
berg. Microbes Infect. 3:545548. http://dx.doi.org/10.1016/S1286-4579
(01)01410-1.
96. Dobrindt U, Hochhut B, Hentschel U, Hacker J. 2004. Genomic islands
in pathogenic and environmental microorganisms. Nat. Rev. Microbiol.
2:414424. http://dx.doi.org/10.1038/nrmicro884.
97. Schmidt H, Hensel M. 2004. Pathogenicity islands in bacterial patho-
genesis. Clin. Microbiol. Rev. 17:1456. http://dx.doi.org/10.1128/CMR
.17.1.14-56.2004.
98. Gal-Mor O, Finlay BB. 2006. Pathogenicity islands: a molecular toolbox
for bacterial virulence. Cell. Microbiol. 8:17071719. http://dx.doi.org
/10.1111/j.1462-5822.2006.00794.x.
99. Manson JM, Gilmore MS. 2006. Pathogenicity island integrase cross-
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

talk: a potential new tool for virulence modulation. Mol. Microbiol. 61:
555559. http://dx.doi.org/10.1111/j.1365-2958.2006.05262.x.
100. Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW,
Crook DW. 2009. Genomic islands: tools of bacterial horizontal gene
transfer and evolution. FEMS Microbiol. Rev. 33:376393. http://dx.doi
.org/10.1111/j.1574-6976.2008.00136.x.
101. Novick RP, Christie GE, Penads JR. 2010. The phage-related chromo-
somal islands of Gram-positive bacteria. Nat. Rev. Microbiol. 8:541551.
http://dx.doi.org/10.1038/nrmicro2393.
102. Dutta C, Paul S. 2012. Microbial lifestyle and genome signatures. Curr.
Genomics 13:153162. http://dx.doi.org/10.2174/138920212799860698.
103. Daccord A, Ceccarelli D, Rodrigue S, Burrus V. 2013. Comparative
analysis of mobilizable genomic islands. J. Bacteriol. 195:606614. http:
//dx.doi.org/10.1128/JB.01985-12.
104. Que F, Wu S, Huang R. 2013. Salmonella pathogenicity island 1 (SPI-1)
at work. Curr. Microbiol. 66:582587. http://dx.doi.org/10.1007/s00284
-013-0307-8.
105. Mates AK, Sayed AK, Foster JW. 2007. Products of the Escherichia coli
acid tness island attenuate metabolite stress at extremely low pH and
mediate a cell density-dependent acid resistance. J. Bacteriol. 189:2759
2768. http://dx.doi.org/10.1128/JB.01490-06.
106. Lima WC, Paquola AC, Varani AM, Van Sluys MA, Menck CF. 2008.
Laterally transferred genomic islands in Xanthomonadales related to
pathogenicity and primary metabolism. FEMS Microbiol. Lett. 281:87
97. http://dx.doi.org/10.1111/j.1574-6968.2008.01083.x.
107. Sung JY, Koo SH, Cho HH, Kwon KC. 2012. AbaR7, a genomic
resistance island found in multidrug-resistant Acinetobacter baumannii
isolates inDaejeon, Korea. Ann. Lab. Med. 32:324330. http://dx.doi.org
/10.3343/alm.2012.32.5.324.
108. Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD,
Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS,
Weaver JE, Webby RJ, De Bruijn FJ, Ronson CW. 2002. Comparative
sequence analysis of the symbiosis island of Mesorhizobium loti strain
R7A. J. Bacteriol. 184:30863095. http://dx.doi.org/10.1128/JB.184.11
.3086-3095.2002.
109. Ravatn R, Studer S, Springael D, Zehnder AJ, van der Meer JR. 1998.
Chromosomal integration, tandem amplication, and deamplication
in Pseudomonas putida F1 of a 105-kilobase genetic element containing
the chlorocatechol degradative genes fromPseudomonas sp. strain B13. J.
Bacteriol. 180:43604369.
110. Makarova KS, Wolf YI, Snir S, Koonin EV. 2011. Defense islands in
bacterial and archaeal genomes and prediction of novel defense systems.
111. Quiroz TS, Nieto PA, Tobar HE, Salazar-Echegarai FJ, Lizana RJ,
Quezada CP, Santiviago CA, Araya DV, Riedel CA, Kalergis AM,
Bueno SM. 2011. Excision of an unstable pathogenicity island in Salmo-
nella enterica serovar Enteritidis is induced during infection of phago-
cytic cells. PLoS One 6:e26031. http://dx.doi.org/10.1371/journal.pone
.0026031.
112. Li M, Shen X, Yan J, Han H, Zheng B, Liu D, Cheng H, Zhao Y, Rao
X, Wang C, Tang J, Hu F, Gao GF. 2011. GI-type T4SS-mediated
horizontal transfer of the 89K pathogenicity island in epidemic Strepto-
coccus suis serotype 2. Mol. Microbiol. 79:16701683. http://dx.doi.org
/10.1111/j.1365-2958.2011.07553.x.
113. Middendorf B, Hochhut B, Leipold K, Dobrindt U, Blum-Oehler G,
Hacker J. 2004. Instability of pathogenicity islands in uropathogenic
Escherichia coli 536. J. Bacteriol. 186:30863096. http://dx.doi.org/10
.1128/JB.186.10.3086-3096.2004.
114. Merkl R. 2006. A comparative categorization of protein function en-
coded in bacterial or archeal genomic islands. J. Mol. Evol. 62:114. http:
//dx.doi.org/10.1007/s00239-004-0311-5.
115. Scott DR, Marcus EA, Wen Y, Oh J, Sachs G. 2007. Gene expression in
vivo shows that Helicobacter pylori colonizes anacidic niche onthe gastric
surface. Proc. Natl. Acad. Sci. U. S. A. 104:72357240. http://dx.doi.org
/10.1073/pnas.0702300104.
116. Njoroge JW, Gruber C, Sperandio V. 2013. The interacting Cra and
KdpE regulators are involved in the expression of multiple virulence
factors in enterohemorrhagic Escherichia coli. J. Bacteriol. 195:2499
2508. http://dx.doi.org/10.1128/JB.02252-12.
117. Wu DQ, Ye J, Ou HY, Wei X, Huang X, He YW, Xu Y. 2011. Genomic
analysis and temperature-dependent transcriptome proles of the rhizo-
sphere originating strain Pseudomonas aeruginosa M18. BMC Genomics
12:438. http://dx.doi.org/10.1186/1471-2164-12-438.
118. Choi J, Shin D, Ryu S. 2007. Implication of quorum sensing in Salmo-
nella enterica serovar Typhimurium virulence: the luxS gene is necessary
for expression of genes in pathogenicity island 1. Infect. Immun. 75:
48854890. http://dx.doi.org/10.1128/IAI.01942-06.
119. Prouty AM, Gunn JS. 2000. Salmonella enterica serovar Typhimurium
invasion is repressed in the presence of bile. Infect. Immun. 68:6763
6769. http://dx.doi.org/10.1128/IAI.68.12.6763-6769.2000.
120. Ellermeier JR, Slauch JM. 2008. Fur regulates expression of the Salmo-
nella pathogenicity island 1 type III secretion system through HilD. J.
Bacteriol. 190:476486. http://dx.doi.org/10.1128/JB.00926-07.
121. Maddox SM, Coburn PS, Shankar N, Conway T. 2012. Transcriptional
regulator PerA inuences biolm-associated, platelet binding, and met-
abolic gene expression in Enterococcus faecalis. PLoS One 7:e34398. http:
//dx.doi.org/10.1371/journal.pone.0034398.
122. Rice LB. 2002. Association of different mobile elements to generate novel
integrative elements. Cell. Mol. Life Sci. 59:20232032. http://dx.doi.org
/10.1007/s000180200002.
123. Parks AR, Peters JE. 2007. Transposon Tn7 is widespread in diverse
bacteria and forms genomic islands. J. Bacteriol. 189:21702173. http:
//dx.doi.org/10.1128/JB.01536-06.
124. Davis EO, Sedgwick SG, Colston MJ. 1991. Novel structure of the recA
locus of Mycobacterium tuberculosis implies processing of the gene prod-
uct. J. Bacteriol. 173:56535662.
125. Davis EO, Jenner PJ, Brooks PC, Colston MJ, Sedgwick SG. 1992.
Protein splicing in the maturation of M. tuberculosis recA protein: a
mechanism for tolerating a novel class of intervening sequence. Cell 71:
201210. http://dx.doi.org/10.1016/0092-8674(92)90349-H.
126. Cooper AA, Stevens TH. 1993. Protein splicing: excision of intervening
sequences at the protein level. Bioessays 15:667674. http://dx.doi.org
/10.1002/bies.950151006.
127. Colston MJ, Davis EO. 1994. The ins and outs of protein splicing ele-
ments. Mol. Microbiol. 12:359363. http://dx.doi.org/10.1111/j.1365
-2958.1994.tb01025.x.
128. Perler FB, Davis EO, Dean GE, Gimble FS, Jack WE, Neff N, Noren CJ,
Thorner J, Belfort M. 1994. Protein splicing elements: inteins and ex-
teinsa denition of terms and recommended nomenclature. Nucleic
Acids Res. 22:11251127. http://dx.doi.org/10.1093/nar/22.7.1125.
129. Belfort M, Reaban ME, Coetzee T, Dalgaard JZ. 1995. Prokaryotic
introns and inteins: a panoply of form and function. J. Bacteriol. 177:
38973903.
130. Liu XQ. 2000. Protein-splicing intein: genetic mobility, origin, and evo-
lution. Annu. Rev. Genet. 34:6176. http://dx.doi.org/10.1146/annurev
.genet.34.1.61.
131. Paulus H. 2000. Protein splicing and related forms of protein autopro-
cessing. Annu. Rev. Biochem. 69:447496. http://dx.doi.org/10.1146
/annurev.biochem.69.1.447.
132. Pietrokovski S. 2001. Intein spread and extinction in evolution. Trends
Genet. 17:465472. http://dx.doi.org/10.1016/S0168-9525(01)02365-4.
133. Gogarten JP, Senejani AG, Zhaxybayeva O, Olendzenski L, Hilario E.
2002. Inteins: structure, function, and evolution. Annu. Rev. Microbiol. 56:
263287. http://dx.doi.org/10.1146/annurev.micro.56.012302.160741.
134. Paulus H. 2003. Inteins as targets for potential antimycobacterial drugs.
Front. Biosci. 8:s1157s1165. http://dx.doi.org/10.2741/1195.
135. Raghavan R, Minnick MF. 2009. Group I introns and inteins: disparate
origins but convergent parasitic strategies. J. Bacteriol. 191:61936202.
http://dx.doi.org/10.1128/JB.00675-09.
136. Barzel A, Naor A, Privman E, Kupiec M, Gophna U. 2011. Homing
endonucleases residing within inteins: evolutionary puzzles awaiting ge-
netic solutions. Biochem. Soc. Trans. 39:169173. http://dx.doi.org/10
.1042/BST0390169.
137. Wu H, Hu Z, Liu XQ. 1998. Protein trans-splicing by a split intein
encoded in a split DnaE gene of Synechocystis sp. PCC6803. Proc. Natl.
Acad. Sci. U. S. A. 95:92269231. http://dx.doi.org/10.1073/pnas.95.16
.9226.
138. Iwai H, Zger S, Jin J, Tam PH. 2006. Highly efcient protein trans-
splicing by a naturally split DnaE intein from Nostoc punctiforme. FEBS
Lett. 580:18531858. http://dx.doi.org/10.1016/j.febslet.2006.02.045.
139. Gleason FK, Olszewski NE. 2002. Isolation of the gene for the B12-
dependent ribonucleotide reductase fromAnabaena sp. strain PCC7120
and expression in Escherichia coli. J. Bacteriol. 184:65446550. http://dx
.doi.org/10.1128/JB.184.23.6544-6550.2002.
140. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin
EV, Daly MJ. 2001. Genome of the extremely radiation-resistant bacte-

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

rium Deinococcus radiodurans viewed from the perspective of compara-
tive genomics. Microbiol. Mol. Biol. Rev. 65:4479. http://dx.doi.org/10
.1128/MMBR.65.1.44-79.2001.
141. Fsihi H, Vincent V, Cole ST. 1996. Homing events in the gyrA gene of
some mycobacteria. Proc. Natl. Acad. Sci. U. S. A. 93:34103415. http:
//dx.doi.org/10.1073/pnas.93.8.3410.
142. Liu XQ, Hu Z. 1997. Identication and characterization of a cyanobac-
terial DnaX intein. FEBS Lett. 408:311314. http://dx.doi.org/10.1016
/S0014-5793(97)00393-1.
143. Liu XQ, Hu Z. 1997. A DnaB intein in Rhodothermus marinus: indica-
tion of recent intein homing across remotely related organisms. Proc.
Natl. Acad. Sci. U. S. A. 94:78517856. http://dx.doi.org/10.1073/pnas.94
.15.7851.
144. Frischkorn K, Sander P, Scholz M, Teschner K, Prammananan T,
Bttger EC. 1998. Investigation of mycobacterial recA function: protein
introns in the RecA of pathogenic mycobacteria do not affect compe-
tency for homologous recombination. Mol. Microbiol. 29:12031214.
http://dx.doi.org/10.1046/j.1365-2958.1998.01003.x.
145. Amitai G, Belenkiy O, Dassa B, Shainskaya A, Pietrokovski S. 2003.
Distribution and function of new bacterial intein-like protein domains.
Mol. Microbiol. 47:6173. http://dx.doi.org/10.1046/j.1365-2958.2003
.03283.x.
146. Dori-Bachash M, Dassa B, Peleg O, Pineiro SA, Jurkevitch E, Pietrok-
ovski S. 2009. Bacterial intein-like domains of predatory bacteria: a new
domain type characterized in Bdellovibrio bacteriovorus. Funct. Integr.
Genomics 9:153166. http://dx.doi.org/10.1007/s10142-008-0106-7.
147. Tourasse NJ, Kolst AB. 2008. Survey of group I and group II introns in
29 sequenced genomes of the Bacillus cereus group: insights into their
spread and evolution. Nucleic Acids Res. 36:45294548. http://dx.doi
.org/10.1093/nar/gkn372.
148. Edgell DR, Chalamcharla VR, Belfort M. 2011. Learning to live to-
gether: mutualism between self-splicing introns and their hosts. BMC
Biol. 9:22. http://dx.doi.org/10.1186/1741-7007-9-22.
149. Haugen P, Simon DM, Bhattacharya D. 2005. The natural history of
group I introns. Trends Genet. 21:111119. http://dx.doi.org/10.1016/j
.tig.2004.12.007.
150. Mueller JE, Smith D, Belfort M. 1996. Exon coconversion biases ac-
companying intron homing: battle of the nucleases. Genes Dev. 10:
21582166. http://dx.doi.org/10.1101/gad.10.17.2158.
151. Everett KD, Kahane S, Bush RM, Friedman MG. 1999. An unspliced
group I intron in 23S rRNA links Chlamydiales, chloroplasts, and mito-
chondria. J. Bacteriol. 181:47344740.
152. Robart AR, Zimmerly S. 2005. Group II intron retroelements: function
and diversity. Cytogenet. Genome Res. 110:589597. http://dx.doi.org
/10.1159/000084992.
153. Toro N, Jimnez-Zurdo JI, Garca-Rodrguez FM. 2007. Bacterial
group II introns: not just splicing. FEMS Microbiol. Rev. 31:342358.
http://dx.doi.org/10.1111/j.1574-6976.2007.00068.x.
154. Ferat JL, Michel F. 1993. Group II self-splicing introns in bacteria.
Nature 364:358361. http://dx.doi.org/10.1038/364358a0.
155. Dai L, Zimmerly S. 2002. Compilation and analysis of group II intron
insertions in bacterial genomes: evidence for retroelement behavior. Nu-
cleic Acids Res. 30:10911102. http://dx.doi.org/10.1093/nar/30.5.1091.
156. Robart AR, Montgomery NK, Smith KL, Zimmerly S. 2004. Principles
of 3= splice site selection and alternative splicing for an unusual group II
intron from Bacillus anthracis. RNA 10:854862. http://dx.doi.org/10
.1261/rna.5246804.
157. Leclercq S, Giraud I, Cordaux R. 2011. Remarkable abundance and
evolution of mobile group II introns in Wolbachia bacterial endosymbi-
onts. Mol. Biol. Evol. 28:685697. http://dx.doi.org/10.1093/molbev
/msq238.
158. Belfort M. 1991. Self-splicing introns in prokaryotes: migrant fossils?
Cell 64:911. http://dx.doi.org/10.1016/0092-8674(91)90201-9.
159. Belfort M, Roberts RJ. 1997. Homing endonucleases: keeping the house
in order. Nucleic Acids Res. 25:33793388. http://dx.doi.org/10.1093
/nar/25.17.3379.
160. Jurica MS, Stoddard BL. 1999. Homing endonucleases: structure, func-
tion and evolution. Cell. Mol. Life Sci. 55:13041326. http://dx.doi.org
/10.1007/s000180050372.
161. Gimble FS. 2000. Invasion of a multitude of genetic niches by mobile
endonuclease genes. FEMS Microbiol. Lett. 185:99107. http://dx.doi
.org/10.1111/j.1574-6968.2000.tb09046.x.
162. Stoddard BL. 2005. Homing endonuclease structure and function. Q.
Rev. Biophys. 38:4995. http://dx.doi.org/10.1017/S0033583505004063.
163. Gogarten JP, Hilario E. 2006. Inteins, introns, and homing endonu-
cleases: recent revelations about the life cycle of parasitic genetic ele-
ments. BMCEvol. Biol. 6:94. http://dx.doi.org/10.1186/1471-2148-6-94.
164. Barzel A, Obolski U, Gogarten JP, Kupiec M, Hadany L. 2011. Home
and awaythe evolutionary dynamics of homing endonucleases. BMC
Evol. Biol. 11:324. http://dx.doi.org/10.1186/1471-2148-11-324.
165. Hafez M, Hausner G. 2012. Homing endonucleases: DNA scissors on a
mission. Genome 55:553569. http://dx.doi.org/10.1139/g2012-049.
166. Taylor GK, Stoddard BL. 2012. Structural, functional and evolutionary
relationships between homing endonucleases and proteins from their
host organisms. Nucleic Acids Res. 40:51895200. http://dx.doi.org/10
.1093/nar/gks226.
167. Lampson BC, Inouye M, Inouye S. 2005. Retrons, msDNA, and the
bacterial genome. Cytogenet. Genome Res. 110:491499. http://dx.doi
.org/10.1159/000084982.
168. Inouye S, Inouye M. 1995. Structure, function, and evolution of bacte-
rial reverse transcriptase. Virus Genes 11:8194. http://dx.doi.org/10
.1007/BF01728650.
169. Travisano M, Inouye M. 1995. Retrons: retroelements of no known
function. Trends Microbiol. 3:209212. http://dx.doi.org/10.1016
/S0966-842X(00)88924-6.
170. Lampson BC, Rice SA. 1997. Repetitive sequences found in the chro-
mosome of the myxobacterium Nannocystis exedens are similar to
msDNA: a possible retrotransposition event in bacteria. Mol. Microbiol.
23:813823. http://dx.doi.org/10.1046/j.1365-2958.1997.2671627.x.
171. Lampson BC, Xu C, Rice SA, Inouye S. 2002. A partial copy of msDNA
from a new retron element is likely a retrotransposed DNA found in the
myxobacterium Nannocystis exedens. Gene 299:251261. http://dx.doi
.org/10.1016/S0378-1119(02)00977-0.
172. Herzer PJ, Inouye S, Inouye M. 1992. Retron-Ec107 is inserted into the
Escherichia coli genome by replacing a palindromic 34bp intergenic se-
quence. Mol. Microbiol. 6:345354. http://dx.doi.org/10.1111/j.1365
-2958.1992.tb01477.x.
173. Lim D. 1995. Analysis of a retron EC86 and EC67 insertion site in Esche-
richia coli. Plasmid 34:5861. http://dx.doi.org/10.1006/plas.1995.1033.
174. Dodd IB, Egan JB. 1996. The Escherichia coli retrons Ec67 and Ec86
replace DNA between the cos site and a transcription terminator of a
186-related prophage. Virology 219:115124. http://dx.doi.org/10.1006
/viro.1996.0228.
175. Maas WK, Wang C, Lima T, Zubay G, Lim D. 1994. Multicopy
single-stranded DNAs with mismatched base pairs are mutagenic in
Escherichia coli. Mol. Microbiol. 14:437441. http://dx.doi.org/10.1111
/j.1365-2958.1994.tb02178.x.
176. Mao JR, Inouye S, Inouye M. 1996. Enhancement of frame-shift mu-
tation by the overproduction of msDNA in Escherichia coli. FEMS
Microbiol. Lett. 144:109115. http://dx.doi.org/10.1111/j.1574-6968
.1996.tb08516.x.
177. Maas WK, Wang C, Lima T, Hach A, Lim D. 1996. Multicopy single-
stranded DNA of Escherichia coli enhances mutation and recombination
frequencies by titrating MutS protein. Mol. Microbiol. 19:505509. http:
//dx.doi.org/10.1046/j.1365-2958.1996.392921.x.
178. Doulatov S, Hodes A, Dai L, Mandhana N, Liu M, Deora R, Simons
RW, Zimmerly S, Miller JF. 2004. Tropism switching in Bordetella
bacteriophage denes a family of diversity-generating retroelements. Na-
ture 431:476481. http://dx.doi.org/10.1038/nature02833.
179. Medhekar B, Miller JF. 2007. Diversity-generating retroelements. Curr.
Opin. Microbiol. 10:388395. http://dx.doi.org/10.1016/j.mib.2007.06
.004.
180. Guo H, Tse LV, Barbalat R, Sivaamnuaiphorn S, Xu M, Doulatov S,
Miller JF. 2008. Diversity-generating retroelement homing regenerates
target sequences for repeated rounds of codon rewriting and protein
diversication. Mol. Cell 31:813823. http://dx.doi.org/10.1016/j
.molcel.2008.07.022.
181. Guo H, Tse LV, Nieh AW, Czornyj E, Williams S, Oukil S, Liu VB,
Miller JF. 2011. Target site recognition by a diversity-generating retro-
element. PLoS Genet. 7:e1002414. http://dx.doi.org/10.1371/journal
.pgen.1002414.
182. Schillinger T, Lis M, Chi J, Cullum J, Zingler N. 2012. Analysis of a
comprehensive dataset of diversity generating retroelements generated
by the program DiGReF. BMC Genomics 13:430. http://dx.doi.org/10
.1186/1471-2164-13-430.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

183. Schillinger T, Zingler N. 2012. The lowincidence of diversity-generating
retroelements in sequenced genomes. Mob. Genet. Elements 2:287291.
http://dx.doi.org/10.4161/mge.23244.
184. Arambula D, Wong W, Medhekar BA, Guo H, Gingery M, Czornyj E,
Liu M, Dey S, Ghosh P, Miller JF. 2013. Surface display of a massively
variable lipoprotein by a Legionella diversity-generating retroelement.
/pnas.1301366110.
185. Kojima KK, Kanehisa M. 2008. Systematic survey for novel types of
prokaryotic retroelements based on gene neighborhood and protein ar-
chitecture. Mol. Biol. Evol. 25:13951404. http://dx.doi.org/10.1093
/molbev/msn081.
186. Simon DM, Zimmerly S. 2008. A diversity of uncharacterized reverse
transcriptases in bacteria. Nucleic Acids Res. 36:72197229. http://dx
.doi.org/10.1093/nar/gkn867.
187. Mazel D. 2006. Integrons: agents of bacterial evolution. Nat. Rev.
Microbiol. 4:608620. http://dx.doi.org/10.1038/nrmicro1462.
188. Boucher Y, Labbate M, Koenig JE, Stokes HW. 2007. Integrons: mo-
bilizable platforms that promote genetic diversity in bacteria. Trends
Microbiol. 15:301309. http://dx.doi.org/10.1016/j.tim.2007.05.004.
189. Cambray G, Guerout AM, Mazel D. 2010. Integrons. Annu. Rev. Genet.
44:141166. http://dx.doi.org/10.1146/annurev-genet-102209-163504.
190. Domingues S, da Silva GJ, Nielsen KM. 2012. Integrons: vehicles and
pathways for horizontal dissemination in bacteria. Mob. Genet. Ele-
ments 2:211223. http://dx.doi.org/10.4161/mge.22967.
191. Bouvier M, Demarre G, Mazel D. 2005. Integron cassette insertion: a
recombination process involving a folded single strand substrate. EMBO
J. 24:43564367. http://dx.doi.org/10.1038/sj.emboj.7600898.
192. Collis CM, Kim MJ, Stokes HW, Hall RM. 2002. Integron-encoded IntI
integrases preferentially recognize the adjacent cognate attI site in re-
combination with a 59-be site. Mol. Microbiol. 46:14151427. http://dx
.doi.org/10.1046/j.1365-2958.2002.03260.x.
193. Loot C, Ducos-Galand M, Escudero JA, Bouvier M, Mazel D. 2012.
Replicative resolution of integron cassette insertion. Nucleic Acids Res.
40:83618370. http://dx.doi.org/10.1093/nar/gks620.
194. Collis CM, Hall RM. 1992. Gene cassettes from the insert region of
integrons are excised as covalently closed circles. Mol. Microbiol.
195. Liebert CA, Hall RM, Summers AO. 1999. Transposon Tn21, agship of
the oating genome. Microbiol. Mol. Biol. Rev. 63:507522.
196. Partridge SR, Tsafnat G, Coiera E, Iredell JR. 2009. Gene cassettes and
cassette arrays in mobile resistance integrons. FEMS Microbiol. Rev. 33:
757784. http://dx.doi.org/10.1111/j.1574-6976.2009.00175.x.
197. Guerin E, Cambray G, Sanchez-Alberola N, Campoy S, Erill I, Da Re
S, Gonzalez-Zorn B, Barb J, Ploy MC, Mazel D. 2009. The SOS
response controls integron recombination. Science 324:1034. http://dx
.doi.org/10.1126/science.1172914.
198. Michael CA, Labbate M. 2010. Gene cassette transcription in a large
integron-associated array. BMC Genet. 11:82. http://dx.doi.org/10.1186
/1471-2156-11-82.
199. Collis CM, Grammaticopoulos G, Briton J, Stokes HW, Hall RM.
1993. Site-specic insertion of gene cassettes into integrons. Mol. Micro-
biol. 9:4152. http://dx.doi.org/10.1111/j.1365-2958.1993.tb01667.x.
200. Collis CM, Hall RM. 1992. Site-specic deletion and rearrangement of
integron insert genes catalyzed by the integron DNA integrase. J. Bacte-
riol. 174:15741585.
201. Collis CM, Recchia GD, Kim MJ, Stokes HW, Hall RM. 2001. Ef-
ciency of recombination reactions catalyzed by class 1 integron integrase
IntI1. J. Bacteriol. 183:25352542. http://dx.doi.org/10.1128/JB.183.8
.2535-2542.2001.
202. Francia MV, de la Cruz F, Garcia Lobo JM. 1993. Secondary-sites for
integration mediated by the Tn21 integrase. Mol. Microbiol. 10:823
828. http://dx.doi.org/10.1111/j.1365-2958.1993.tb00952.x.
203. Recchia GD, Stokes HW, Hall RM. 1994. Characterisation of specic
and secondary recombination sites recognised by the integron DNA in-
tegrase. Nucleic Acids Res. 22:20712078. http://dx.doi.org/10.1093/nar
/22.11.2071.
204. Recchia GD, Hall RM. 1995. Plasmid evolution by acquisition of mobile
gene cassettes: plasmid pIE723 contains the aadB gene cassette precisely in-
serted at a secondary site in the IncQ plasmid RSF1010. Mol. Microbiol.
205. Francia MV, Garcia Lobo JM. 1996. Gene integration in the Escherichia
coli chromosome mediated by Tn21 integrase (Int21). J. Bacteriol. 178:
894898.
206. Doublet B, Praud K, Weill FX, Cloeckaert A. 2009. Association of
IS26-composite transposons and complex In4-type integrons generates
novel multidrug resistance loci in Salmonella genomic island 1. J. Anti-
microb. Chemother. 63:282289. http://dx.doi.org/10.1093/jac/dkn500.
207. Engelberg-Kulka H, Glaser G. 1999. Addiction modules and pro-
grammed cell death and antideath in bacterial cultures. Annu. Rev.
Microbiol. 53:4370. http://dx.doi.org/10.1146/annurev.micro.53.1.43.
208. Hayes F. 2003. Toxins-antitoxins: plasmid maintenance, programmed
cell death, and cell cycle arrest. Science 301:14961499. http://dx.doi.org
/10.1126/science.1088157.
209. Gerdes K, Christensen SK, Lbner-Olesen A. 2005. Prokaryotic toxin-
antitoxin stress response loci. Nat. Rev. Microbiol. 3:371382. http://dx
.doi.org/10.1038/nrmicro1147.
210. Pandey DP, Gerdes K. 2005. Toxin-antitoxin loci are highly abundant in
free-living but lost from host-associated prokaryotes. Nucleic Acids Res.
33:966976. http://dx.doi.org/10.1093/nar/gki201.
211. Condon C. 2006. Shutdown decay of mRNA. Mol. Microbiol. 61:573
583. http://dx.doi.org/10.1111/j.1365-2958.2006.05270.x.
212. Gerdes K, Wagner EG. 2007. RNA antitoxins. Curr. Opin. Microbiol.
10:117124. http://dx.doi.org/10.1016/j.mib.2007.03.003.
213. Magnuson RD. 2007. Hypothetical functions of toxin-antitoxin systems.
214. Fozo EM, Hemm MR, Storz G. 2008. Small toxic proteins and the
antisense RNAs that repress them. Microbiol. Mol. Biol. Rev. 72:579
589. http://dx.doi.org/10.1128/MMBR.00025-08.
215. Makarova KS, Wolf YI, Koonin EV. 2009. Comprehensive compara-
tive-genomic analysis of type 2 toxin-antitoxin systems and related mo-
bile stress response systems in prokaryotes. Biol. Direct 4:19. http://dx
.doi.org/10.1186/1745-6150-4-19.
216. Van Melderen L, Saavedra De Bast M. 2009. Bacterial toxin-antitoxin
systems: more than selsh entities? PLoS Genet. 5:e1000437. http://dx
.doi.org/10.1371/journal.pgen.1000437.
217. Van Melderen L. 2010. Toxin-antitoxin systems: why so many, what for?
Curr. Opin. Microbiol. 13:781785. http://dx.doi.org/10.1016/j.mib
.2010.10.006.
218. Blower TR, Salmond GP, Luisi BF. 2011. Balancing at survivals edge: the
structure and adaptive benets of prokaryotic toxin-antitoxin partners.
Curr. Opin. Struct. Biol. 21:109118. http://dx.doi.org/10.1016/j.sbi.2010
.10.009.
219. Bukowski M, Rojowska A, Wladyka B. 2011. Prokaryotic toxin-
antitoxin systemsthe role in bacterial physiology and application in
molecular biology. Acta Biochim. Pol. 58:19. http://www.actabp.pl/pdf
/1_2011/1.pdf.
220. Guglielmini J, Van Melderen L. 2011. Bacterial toxin-antitoxin systems:
translation inhibitors everywhere. Mob. Genet. Elements 1:283290.
http://dx.doi.org/10.4161/mge.18477.
221. Wang X, Wood TK. 2011. Toxin-antitoxin systems inuence biolm
and persister cell formation and the general stress response. Appl. Envi-
ron. Microbiol. 77:55775583. http://dx.doi.org/10.1128/AEM.05068
-11.
222. Yamaguchi Y, Park JH, Inouye M. 2011. Toxin-antitoxin systems in
bacteria and archaea. Annu. Rev. Genet. 45:6179. http://dx.doi.org/10
.1146/annurev-genet-110410-132412.
223. Schuster CF, Bertram R. 2013. Toxin-antitoxin systems are ubiquitous
and versatile modulators of prokaryotic cell fate. FEMS Microbiol. Lett.
340:7385. http://dx.doi.org/10.1111/1574-6968.12074.
224. Tan Q, Awano N, Inouye M. 2011. YeeV is an Escherichia coli toxin that
inhibits cell division by targeting the cytoskeleton proteins, FtsZ and
MreB. Mol. Microbiol. 79:109118. http://dx.doi.org/10.1111/j.1365
-2958.2010.07433.x.
225. Gurout AM, Iqbal N, Mine N, Ducos-Galand M, Van Melderen L,
Mazel D. 2013. Characterization of the phd-doc and ccd toxin-antitoxin
cassettes from Vibrio superintegrons. J. Bacteriol. 195:22702283. http:
//dx.doi.org/10.1128/JB.01389-12.
226. Ramisetty BC, Natarajan B, Santhosh RS. 25 June 2013. mazEF-
mediated programmed cell death in bacteria: What is this? Crit. Rev.
Microbiol. http://dx.doi.org/10.3109/1040841X.2013.804030.
227. Robson J, McKenzie JL, Cursons R, Cook GM, Arcus VL. 2009. The
vapBCoperon fromMycobacteriumsmegmatis is an autoregulated toxin-
antitoxin module that controls growth via inhibition of translation. J.
Mol. Biol. 390:353367. http://dx.doi.org/10.1016/j.jmb.2009.05.006.

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

228. Liu M, Zhang Y, Inouye M, Woychik NA. 2008. Bacterial addiction
module toxin Doc inhibits translation elongation through its association
with the 30S ribosomal subunit. Proc. Natl. Acad. Sci. U. S. A. 105:5885
5890. http://dx.doi.org/10.1073/pnas.0711949105.
229. Unoson C, Wagner EG. 2008. A small SOS-induced toxin is targeted
against the inner membrane in Escherichia coli. Mol. Microbiol. 70:258
270. http://dx.doi.org/10.1111/j.1365-2958.2008.06416.x.
230. Mutschler H, Gebhardt M, Shoeman RL, Meinhart A. 2011. A novel
mechanismof programmed cell death in bacteria by toxin-antitoxin sys-
tems corrupts peptidoglycan synthesis. PLoS Biol. 9:e1001033. http://dx
.doi.org/10.1371/journal.pbio.1001033.
231. Blower TR, Fineran PC, Johnson MJ, Toth IK, Humphreys DP,
Salmond GP. 2009. Mutagenesis and functional characterization of the
RNA and protein components of the toxIN abortive infection and toxin-
antitoxinlocus of Erwinia. J. Bacteriol. 191:60296039. http://dx.doi.org
/10.1128/JB.00720-09.
232. Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond
GP. 2009. The phage abortive infection system, ToxIN, functions as a
protein-RNA toxin-antitoxin pair. Proc. Natl. Acad. Sci. U. S. A. 106:
233. Saavedra De Bast M, Mine N, Van Melderen L. 2008. Chromosomal
toxin-antitoxin systems may act as antiaddiction modules. J. Bacteriol.
190:46034609. http://dx.doi.org/10.1128/JB.00357-08.
234. Cooper TF, Heinemann JA. 2000. Postsegregational killing does not
increase plasmid stability but acts to mediate the exclusion of competing
plasmids. Proc. Natl. Acad. Sci. U. S. A. 97:1264312648. http://dx.doi
.org/10.1073/pnas.220077897.
235. Christensen-Dalsgaard M, Gerdes K. 2006. Two higBA loci in the Vibrio
cholerae superintegronencode mRNAcleaving enzymes and canstabilize
plasmids. Mol. Microbiol. 62:397411. http://dx.doi.org/10.1111/j.1365
-2958.2006.05385.x.
236. Gonzlez Barrios AF, Zuo R, Hashimoto Y, Yang L, Bentley WE,
Wood TK. 2006. Autoinducer 2 controls biolm formation in Esche-
richia coli through a novel motility quorum-sensing regulator (MqsR,
B3022). J. Bacteriol. 188:305316. http://dx.doi.org/10.1128/JB.188.1
.305-316.2006.
237. Christensen SK, Pedersen K, Hansen FG, Gerdes K. 2003. Toxin-
antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK
cleave translated RNAs and are counteracted by tmRNA. J. Mol. Biol.
332:809819. http://dx.doi.org/10.1016/S0022-2836(03)00922-7.
238. Yamaguchi Y, Inouye M. 2011. Regulation of growth and death in
Escherichia coli by toxin-antitoxin systems. Nat. Rev. Microbiol. 9:779
790. http://dx.doi.org/10.1038/nrmicro2651.
239. Rotem E, Loinger A, Ronin I, Levin-Reisman I, Gabay C, Shoresh N,
Biham O, Balaban NQ. 2010. Regulation of phenotypic variability by a
threshold-based mechanism underlies bacterial persistence. Proc. Natl.
Acad. Sci. U. S. A. 107:1254112546. http://dx.doi.org/10.1073/pnas
.1004333107.
240. Yamaguchi Y, Inouye M. 2009. mRNA interferases, sequence-specic en-
doribonucleases from the toxin-antitoxin systems. Prog. Mol. Biol. Transl.
Sci. 85:467500. http://dx.doi.org/10.1016/S0079-6603(08)00812-X.
241. Kim Y, Wang X, Zhang XS, Grigoriu S, Page R, Peti W, Wood TK.
2010. Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin
CspD. Environ. Microbiol. 12:11051121. http://dx.doi.org/10.1111/j
.1462-2920.2009.02147.x.
242. Kobayashi I, Nobusato A, Kobayashi-Takahashi N, Uchiyama I. 1999.
Shaping the genomerestriction-modication systems as mobile ge-
netic elements. Curr. Opin. Genet. Dev. 9:649656. http://dx.doi.org/10
.1016/S0959-437X(99)00026-X.
243. Kobayashi I. 2001. Behavior of restriction-modication systems as self-
ish mobile elements and their impact on genome evolution. Nucleic Ac-
ids Res. 29:37423756. http://dx.doi.org/10.1093/nar/29.18.3742.
244. Blumenthal RM, Cheng X. 2002. Restriction-modication systems, p
177225. In Streips UN, Yasbin RE (ed), Modern microbial genetics, 2nd
ed. Wiley-Liss, Inc., New York, NY.
245. Kobayashi I. 2002. Life cycle of restriction-modication gene com-
plexes, powers in genome evolution. Int. Congr. Ser. 1246:191200. http:
//dx.doi.org/10.1016/S0531-5131(02)01142-1.
246. Tock MR, Dryden DT. 2005. The biology of restriction and anti-
restriction. Curr. Opin. Microbiol. 8:466472. http://dx.doi.org/10
.1016/j.mib.2005.06.003.
247. Furuta Y, Abe K, Kobayashi I. 2010. Genome comparison and context
analysis reveals putative mobile forms of restriction-modication sys-
tems and related rearrangements. Nucleic Acids Res. 38:24282443.
http://dx.doi.org/10.1093/nar/gkp1226.
248. Ishikawa K, Fukuda E, Kobayashi I. 2010. Conicts targeting epigenetic
systems and their resolution by cell death: novel concepts for methyl-
specic and other restriction systems. DNA Res. 17:325342. http://dx
.doi.org/10.1093/dnares/dsq027.
249. Furuta Y, Kobayashi I. 2013. Restriction-modication systems as mo-
bile epigenetic elements, p 85103. In Roberts AP, Mullany P (ed), Bac-
terial integrative mobile genetic elements. Landes Bioscience, Austin,
TX.
250. Vasu K, Nagaraja V. 2013. Diverse functions of restriction-modication
systems in addition to cellular defense. Microbiol. Mol. Biol. Rev. 77:53
251. Naito Y, Naito T, Kobayashi I. 1998. Selsh restriction modication
genes: resistance of a resident R/Mplasmid to displacement by anincom-
patible plasmid mediated by host killing. Biol. Chem. 379:429436. http:
//dx.doi.org/10.1515/bchm.1998.379.4-5.429.
252. Nakayama Y, Kobayashi I. 1998. Restriction-modication gene com-
plexes as selsh gene entities: roles of a regulatory system in their estab-
lishment, maintenance, and apoptotic mutual exclusion. Proc. Natl.
Acad. Sci. U. S. A. 95:64426447. http://dx.doi.org/10.1073/pnas.95.11
.6442.
253. Gumulak-Smith J, Teachman A, Tu AH, Simecka JW, Lindsey JR,
Dybvig K. 2001. Variations in the surface proteins and restriction en-
zyme systems of Mycoplasma pulmonis in the respiratory tract of infected
rats. Mol. Microbiol. 40:10371044. http://dx.doi.org/10.1046/j.1365
-2958.2001.02464.x.
254. Glatman LI, Moroz AF, Yablokova MB, Rebentish BA, Kcholmina GV.
1980. A novel plasmid-mediated DNA restriction-modication system
in E. coli. Plasmid 4:350351. http://dx.doi.org/10.1016/0147-619X(80)
90072-4.
255. Iida S, Meyer J, Bach B, Stlhammar-Carlemalm M, Schrickel S,
Bickle TA, Arber W. 1983. DNArestriction-modication genes of phage
P1 and plasmid p15B. Structure and in vitro transcription. J. Mol. Biol.
165:118.
256. Rochepeau P, Selinger LB, Hynes MF. 1997. Transposon-like structure
of a newplasmid-encoded restriction-modication systemin Rhizobium
leguminosarum VF39SM. Mol. Gen. Genet. 256:387396. http://dx.doi
.org/10.1007/s004380050582.
257. Balado M, Lemos ML, Osorio CR. 2013. Integrating conjugative ele-
ments of the SXT/R391 family from sh-isolated Vibrios encode restric-
tion-modication systems that confer resistance to bacteriophages.
FEMS Microbiol. Ecol. 83:457467. http://dx.doi.org/10.1111/1574
-6941.12007.
258. Jermyn WS, Boyd EF. 2005. Molecular evolution of Vibrio pathogenic-
ity island-2 (VPI-2): mosaic structure among Vibrio cholerae and Vibrio
mimicus natural isolates. Microbiology 151:311322. http://dx.doi.org
/10.1099/mic.0.27621-0.
259. Brassard S, Paquet H, Roy PH. 1995. A transposon-like sequence
adjacent to the AccI restriction-modication operon. Gene 157:6972.
http://dx.doi.org/10.1016/0378-1119(94)00734-A.
260. Vaivila R, Vilkaitis G, Janulaitis A. 1995. Identication of a gene
encoding a DNA invertase-like enzyme adjacent to the PaeR7I restric-
tion-modication system. Gene 157:8184. http://dx.doi.org/10.1016
/0378-1119(94)00793-R.
261. Lee KF, Shaw PC, Picone SJ, Wilson GG, Lunnen KD. 1998. Sequence
comparison of the EcoHK31I and EaeI restriction-modication systems
suggests an intergenic transfer of genetic material. Biol. Chem. 379:437
441. http://dx.doi.org/10.1515/bchm.1998.379.4-5.437.
262. Chaturvedi D, Chakravorty M. 2003. Restriction-modication system
in bacteriophage MB78. Biochem. Biophys. Res. Commun. 303:884
890. http://dx.doi.org/10.1016/S0006-291X(03)00421-2.
263. Lieb M. 1991. Spontaneous mutation at a 5-methylcytosine hotspot is pre-
vented by very short patch (VSP) mismatch repair. Genetics 128:2327.
264. Chinen A, Uchiyama I, Kobayashi I. 2000. Comparison between Pyro-
coccus horikoshii and Pyrococcus abyssi genome sequences reveals linkage
of restriction-modication genes with large genome polymorphisms.
Gene 259:109121. http://dx.doi.org/10.1016/S0378-1119(00)00459-5.
265. Sekizaki T, Otani Y, Osaki M, Takamatsu D, Shimoji Y. 2001. Evidence
for horizontal transfer of SsuDAT1I restriction-modicationgenes to the
Streptococcus suis genome. J. Bacteriol. 183:500511. http://dx.doi.org
/10.1128/JB.183.2.500-511.2001.
266. Nobusato A, Uchiyama I, Ohashi S, Kobayashi I. 2000. Insertion with
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

long target duplication: a mechanism for gene mobility suggested from
comparison of two related bacterial genomes. Gene 259:99108. http:
//dx.doi.org/10.1016/S0378-1119(00)00456-X.
267. Sadykov M, Asami Y, Niki H, Handa N, Itaya M, Tanokura M,
Kobayashi I. 2003. Multiplication of a restriction-modication gene
complex. Mol. Microbiol. 48:417427. http://dx.doi.org/10.1046/j.1365
-2958.2003.03464.x.
268. Sorek R, Kunin V, Hugenholtz P. 2008. CRISPRa widespread system
that provides acquired resistance against phages in bacteria and archaea.
Nat. Rev. Microbiol. 6:181186. http://dx.doi.org/10.1038/nrmicro1793.
269. van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ. 2009.
CRISPR-based adaptive and heritable immunity in prokaryotes. Trends
Biochem. Sci. 34:401407. http://dx.doi.org/10.1016/j.tibs.2009.05.002.
270. Waters LS, Storz G. 2009. Regulatory RNAs in bacteria. Cell 136:615
628. http://dx.doi.org/10.1016/j.cell.2009.01.043.
271. Deveau H, Garneau JE, Moineau S. 2010. CRISPR/Cas system and its
role in phage-bacteria interactions. Annu. Rev. Microbiol. 64:475493.
http://dx.doi.org/10.1146/annurev.micro.112408.134123.
272. Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of
bacteria and archaea. Science 327:167170. http://dx.doi.org/10.1126
/science.1179555.
273. Karginov FV, Hannon GJ. 2010. The CRISPR system: small RNA-
guided defense in bacteria and archaea. Mol. Cell 37:719. http://dx.doi
.org/10.1016/j.molcel.2009.12.033.
274. Marrafni LA, Sontheimer EJ. 2010. CRISPR interference: RNA-
directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet.
11:181190. http://dx.doi.org/10.1038/nrg2749.
275. Vale PF, Little TJ. 2010. CRISPR-mediated phage resistance and the
ghost of coevolution past. Proc. Biol. Sci. 277:20972103. http://dx.doi
.org/10.1098/rspb.2010.0055.
276. Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T,
Wurm R, Raine A, Mescher M, Van Heereveld L, Mastop M, Wagner
EG, Schnetz K, Van Der Oost J, Wagner R, Brouns SJ. 2010. H-NS-
mediated repression of CRISPR-based immunity in Escherichia coli K12
can be relieved by the transcription activator LeuO. Mol. Microbiol. 77:
13801393. http://dx.doi.org/10.1111/j.1365-2958.2010.07315.x.
277. Al-Attar S, Westra ER, van der Oost J, Brouns SJ. 2011. Clustered
regularly interspaced short palindromic repeats (CRISPRs): the hallmark
of an ingenious antiviral defense mechanismin prokaryotes. Biol. Chem.
392:277289. http://dx.doi.org/10.1515/BC.2011.042.
278. Bhaya D, Davison M, Barrangou R. 2011. CRISPR-Cas systems in bacteria
and archaea: versatile small RNAs for adaptive defense and regulation.
Annu. Rev. Genet. 45:273297. http://dx.doi.org/10.1146/annurev-genet
-110410-132430.
279. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E,
Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost
J, Koonin EV. 2011. Evolution and classication of the CRISPR-Cas
systems. Nat. Rev. Microbiol. 9:467477. http://dx.doi.org/10.1038
/nrmicro2577.
280. Shah SA, Garrett RA. 2011. CRISPR/Cas and Cmr modules, mobility
and evolution of adaptive immune systems. Res. Microbiol. 162:2738.
http://dx.doi.org/10.1016/j.resmic.2010.09.001.
281. Terns MP, Terns RM. 2011. CRISPR-based adaptive immune systems.
Curr. Opin. Microbiol. 14:321327. http://dx.doi.org/10.1016/j.mib
.2011.03.005.
282. Fineran PC, Charpentier E. 2012. Memory of viral infections by
CRISPR-Cas adaptive immune systems: acquisition of new information.
Virology 434:202209. http://dx.doi.org/10.1016/j.virol.2012.10.003.
283. Richter C, Chang JT, Fineran PC. 2012. Function and regulation of
clustered regularly interspaced short palindromic repeats (CRISPR)/
CRISPR associated (Cas) systems. Viruses 4:22912311. http://dx.doi
.org/10.3390/v4102291.
284. Barrangou R. 2013. CRISPR-Cas systems and RNA-guided interference.
Wiley Interdiscip. Rev. RNA 4:267278. http://dx.doi.org/10.1002/wrna
.1159.
285. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau
S, Romero DA, Horvath P. 2007. CRISPR provides acquired resistance
against viruses in prokaryotes. Science 315:17091712. http://dx.doi.org
/10.1126/science.1138140.
286. Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K,
Semenova E. 2012. Molecular memory of prior infections activates the
CRISPR/Cas adaptive bacterial immunity system. Nat. Commun. 3:945.
http://dx.doi.org/10.1038/ncomms1937.
287. Swarts DC, Mosterd C, van Passel MW, Brouns SJ. 2012. CRISPR
interference directs strand specic spacer acquisition. PLoS One
7:e35888. http://dx.doi.org/10.1371/journal.pone.0035888.
288. Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM,
Terns MP. 2009. RNA-guided RNA cleavage by a CRISPR RNA-Cas
proteincomplex. Cell 139:945956. http://dx.doi.org/10.1016/j.cell.2009
.07.040.
289. Hale CR, Majumdar S, Elmore J, Pster N, Compton M, Olson S,
Resch AM, Glover CV, III, Graveley BR, Terns RM, Terns MP. 2012.
Essential features and rational design of CRISPR RNAs that function
with the Cas RAMP module complex to cleave RNAs. Mol. Cell 45:292
302. http://dx.doi.org/10.1016/j.molcel.2011.10.023.
290. Andersson AF, Baneld JF. 2008. Virus population dynamics and ac-
quired virus resistance in natural microbial communities. Science 320:
10471050. http://dx.doi.org/10.1126/science.1157358.
291. Deveau H, Barrangou R, Garneau JE, Labonte J, Fremaux C, Boyaval
P, Romero DA, Horvath P, Moineau S. 2008. Phage response to
CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol.
190:13901400. http://dx.doi.org/10.1128/JB.01412-07.
292. Peng X, Brgger K, Shen B, Chen L, She Q, Garrett RA. 2003. Genus-
specic protein binding to the large clusters of DNArepeats (short regularly
spaced repeats) present in Sulfolobus genomes. J. Bacteriol. 185:2410
2417. http://dx.doi.org/10.1128/JB.185.8.2410-2417.2003.
293. Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR. 2013. Bacte-
riophage genes that inactivate the CRISPR/Cas bacterial immune system.
Nature 493:429432. http://dx.doi.org/10.1038/nature11723.
294. Horvath P, Romero DA, Cot-Monvoisin AC, Richards M, Deveau
H, Moineau S, Boyaval P, Fremaux C, Barrangou R. 2008. Diversity,
activity, and evolution of CRISPR loci in Streptococcus thermophilus. J.
295. Marrafni LA, Sontheimer EJ. 2010. Self versus non-self discrimination
during CRISPR RNA-directed immunity. Nature 463:568571. http:
//dx.doi.org/10.1038/nature08703.
296. Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. 2010. Self-targeting
by CRISPR: gene regulation or autoimmunity? Trends Genet. 26:335
340. http://dx.doi.org/10.1016/j.tig.2010.05.008.
297. Sashital DG, Wiedenheft B, Doudna JA. 2012. Mechanism of foreign
DNAselection in a bacterial adaptive immune system. Mol. Cell 46:606
615. http://dx.doi.org/10.1016/j.molcel.2012.03.020.
298. Pougach K, Semenova E, Bogdanova E, Datsenko KA, Djordjevic M,
Wanner BL, Severinov K. 2010. Transcription, processing and function
of CRISPR cassettes in Escherichia coli. Mol. Microbiol. 77:13671379.
http://dx.doi.org/10.1111/j.1365-2958.2010.07265.x.
299. Pul U, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R. 2010.
Identication and characterization of E. coli CRISPR-cas promoters and
their silencing by H-NS. Mol. Microbiol. 75:14951512. http://dx.doi
.org/10.1111/j.1365-2958.2010.07073.x.
300. Medina-Aparicio L, Rebollar-Flores JE, Gallego-Hernndez AL,
Vzquez A, Olvera L, Gutirrez-Ros RM, Calva E, Hernndez-Lucas
I. 2011. The CRISPR/Cas immune system is an operon regulated by
LeuO, H-NS, and leucine-responsive regulatory protein in Salmonella
enterica serovar Typhi. J. Bacteriol. 193:23962407. http://dx.doi.org/10
.1128/JB.01480-10.
301. Shinkai A, Kira S, Nakagawa N, Kashihara A, Kuramitsu S, Yokoyama
S. 2007. Transcription activation mediated by a cyclic AMP receptor
protein from Thermus thermophilus HB8. J. Bacteriol. 189:38913901.
http://dx.doi.org/10.1128/JB.01739-06.
302. Agari Y, Sakamoto K, Tamakoshi M, Oshima T, Kuramitsu S, Shinkai
A. 2010. Transcription prole of Thermus thermophilus CRISPR systems
after phage infection. J. Mol. Biol. 395:270281. http://dx.doi.org/10
.1016/j.jmb.2009.10.057.
303. Chattoraj P, Banerjee A, Biswas S, Biswas I. 2010. ClpP of Streptococcus
mutans differentially regulates expression of genomic islands, mutacin
production, and antibiotic tolerance. J. Bacteriol. 192:13121323. http:
//dx.doi.org/10.1128/JB.01350-09.
304. Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke
A, DeLisa MP. 2011. Envelope stress is a trigger of CRISPR RNA-
mediated DNAsilencing in Escherichia coli. Mol. Microbiol. 79:584599.
http://dx.doi.org/10.1111/j.1365-2958.2010.07482.x.
305. Koonin EV, Makarova KS. 2009. CRISPR-Cas: an adaptive immunity
system in prokaryotes. F1000 Biol. Rep. 1:95. http://f1000.com/prime
/reports/b/1/95.
306. Takeuchi N, Wolf YI, Makarova KS, Koonin EV. 2012. Nature and

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

intensity of selection pressure on CRISPR-associated genes. J. Bacteriol.
194:12161225. http://dx.doi.org/10.1128/JB.06521-11.
307. Touchon M, Rocha EP. 2010. The small, slow and specialized CRISPR
and anti-CRISPR of Escherichia and Salmonella. PLoS One 5:e11126.
http://dx.doi.org/10.1371/journal.pone.0011126.
308. Touchon M, Charpentier S, Clermont O, Rocha EP, Denamur E,
Branger C. 2011. CRISPR distribution within the Escherichia coli species
is not suggestive of immunity-associated diversifying selection. J. Bacte-
riol. 193:24602467. http://dx.doi.org/10.1128/JB.01307-10.
309. Aklujkar M, Lovley DR. 2010. Interference with histidyl-tRNA synthe-
tase by a CRISPRspacer sequence as a factor inthe evolutionof Pelobacter
carbinolicus. BMC Evol. Biol. 10:230. http://dx.doi.org/10.1186/1471
-2148-10-230.
310. Zegans ME, Wagner JC, Cady KC, Murphy DM, Hammond JH,
OToole GA. 2009. Interaction between bacteriophage DMS3 and host
CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. J.
311. Haft DH, Selengut J, Mongodin EF, Nelson KE. 2005. A guild of 45
CRISPR-associated (Cas) protein families and multiple CRISPR/Cas
subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1:e60. http:
//dx.doi.org/10.1371/journal.pcbi.0010060.
312. Viswanathan P, Murphy K, Julien B, Garza AG, Kroos L. 2007.
Regulation of dev, an operon that includes genes essential for Myxococcus
xanthus development and CRISPR-associated genes and repeats. J. Bac-
teriol. 189:37383750. http://dx.doi.org/10.1128/JB.00187-07.
313. Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B,
Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S,
Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Ed-
wards AM, Yakunin AF. 2011. A dual function of the CRISPR-Cas
systemin bacterial antivirus immunity and DNArepair. Mol. Microbiol.
79:484502. http://dx.doi.org/10.1111/j.1365-2958.2010.07465.x.
314. DeBoy RT, Mongodin EF, Emerson JB, Nelson KE. 2006. Chromo-
some evolution in the Thermotogales: large-scale inversions and strain
diversication of CRISPR sequences. J. Bacteriol. 188:23642374. http:
//dx.doi.org/10.1128/JB.188.7.2364-2374.2006.
315. Mokrousov I, Limeschenko E, Vyazovaya A, Narvskaya O. 2007.
Corynebacterium diphtheriae spoligotyping based on combined use of
two CRISPR loci. Biotechnol. J. 2:901906. http://dx.doi.org/10.1002
/biot.200700035.
316. Vergnaud G, Li Y, Gorg O, Cui Y, Song Y, Zhou D, Grissa I,
Dentovskaya SV, Platonov ME, Rakin A, Balakhonov SV, Neubauer
H, Pourcel C, Anisimov AP, Yang R. 2007. Analysis of the three Yersinia
pestis CRISPR loci provides new tools for phylogenetic studies and pos-
sibly for the investigation of ancient DNA. Adv. Exp. Med. Biol. 603:327
338. http://dx.doi.org/10.1007/978-0-387-72124-8_30.
317. Cui Y, Li Y, Gorg O, Platonov ME, Yan Y, Guo Z, Pourcel C,
Dentovskaya SV, Balakhonov SV, Wang X, Song Y, Anisimov AP,
Vergnaud G, Yang R. 2008. Insight into microevolution of Yersinia pestis
by clustered regularly interspaced short palindromic repeats. PLoS One
3:e2652. http://dx.doi.org/10.1371/journal.pone.0002652.
318. Ginevra C, Jacotin N, Diancourt L, Guigon G, Arquilliere R, Meugnier
H, Descours G, Vandenesch F, Etienne J, Lina G, Caro V, Jarraud S.
2012. Legionella pneumophila sequence type 1/Paris pulsotype subtyping
by spoligotyping. J. Clin. Microbiol. 50:696701. http://dx.doi.org/10
.1128/JCM.06180-11.
319. Sheen P, Couvin D, Grandjean L, Zimic M, Dominguez M, Luna G,
Gilman RH, Rastogi N, Moore DA. 2013. Genetic diversity of Myco-
bacterium tuberculosis in Peru and exploration of phylogenetic associa-
tions withdrug resistance. PLoS One 8:e65873. http://dx.doi.org/10.1371
/journal.pone.0065873.
320. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X,
Jiang W, Marrafni LA, Zhang F. 2013. Multiplex genome engineering
using CRISPR/Cas systems. Science 339:819823. http://dx.doi.org/10
.1126/science.1231143.
321. Jiang W, Bikard D, Cox D, Zhang F, Marrafni LA. 2013. RNA-guided
editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotech-
nol. 31:233239. http://dx.doi.org/10.1038/nbt.2508.
322. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE,
Church GM. 2013. RNA-guided human genome engineering via Cas9.
Science 339:823826. http://dx.doi.org/10.1126/science.1232033.
323. Godde JS, Bickerton A. 2006. The repetitive DNA elements called
CRISPRs and their associated genes: evidence of horizontal transfer
among prokaryotes. J. Mol. Evol. 62:718729. http://dx.doi.org/10.1007
/s00239-005-0223-z.
324. Horvath P, Cot-Monvoisin AC, Romero DA, Boyaval P, Fremaux C,
Barrangou R. 2009. Comparative analysis of CRISPR loci in lactic acid
bacteria genomes. Int. J. Food Microbiol. 131:6270. http://dx.doi.org
/10.1016/j.ijfoodmicro.2008.05.030.
325. Roth JR, Benson N, Galitski T, Haack K, Lawrence JG, Miesel L. 1996.
Rearrangements of the bacterial chromosome: formation and applica-
tions, p 22562276. In Neidhardt FC, Curtiss R, III, Ingraham JL, Lin
ECC, LowKB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Um-
barger HE (ed), Escherichia coli and Salmonella: cellular and molecular
biology, 2nd ed, vol 2. ASM Press, Washington, DC.
326. Michel B, Boubakri H, Baharoglu Z, LeMasson M, Lestini R. 2007.
Recombination proteins and rescue of arrested replication forks. DNA
Repair (Amst.) 6:967980. http://dx.doi.org/10.1016/j.dnarep.2007.02
.016.
327. Dillingham MS, Kowalczykowski SC. 2008. RecBCD enzyme and the
repair of double-stranded DNA breaks. Microbiol. Mol. Biol. Rev. 72:
328. Michel B, Leach D. 11 September 2012. Chapter 7.2.7. Homologous
recombinationenzymes and pathways. In Curtiss R, III, Kaper JB,
Squires CL, Karp PD, Neidhardt FC, Slauch JM(ed), EcoSalEscherichia
coli and Salmonella: cellular and molecular biology. ASM Press, Wash-
ington, DC. http://dx.doi.org/10.1128/ecosalplus.7.2.7.
329. Radding C. 1988. Homologous pairing and strand exchange promoted
by Escherichia coli RecAprotein, p 193229. In Kucherlapati R, Smith GR
(ed), Genetic recombination. AmericanSociety for Microbiology, Wash-
ington, DC.
330. Chen Z, Yang H, Pavletich NP. 2008. Mechanism of homologous
recombination from the RecA-ssDNA/dsDNA structures. Nature 453:
489494. http://dx.doi.org/10.1038/nature06971.
331. Forget AL, Kowalczykowski SC. 2012. Single-molecule imaging of DNA
pairing by RecA reveals a three-dimensional homology search. Nature
482:423427. http://dx.doi.org/10.1038/nature10782.
332. Ehrlich SD, Bierne H, dAlencon E, Vilette D, Petranovic M, Noirot P,
Michel B. 1993. Mechanisms of illegitimate recombination. Gene 135:
161166. http://dx.doi.org/10.1016/0378-1119(93)90061-7.
333. Rocha EP. 2003. An appraisal of the potential for illegitimate recombi-
nation in bacterial genomes and its consequences: from duplications to
genome reduction. Genome Res. 13:11231132. http://dx.doi.org/10
.1101/gr.966203.
334. Ikeda H, Shiraishi K, Ogata Y. 2004. Illegitimate recombination medi-
ated by double-strand break and end-joining in Escherichia coli. Adv.
Biophys. 38:320. http://dx.doi.org/10.1016/S0065-227X(04)80031-5.
335. Lovett ST. 2004. Encoded errors: mutations and rearrangements medi-
ated by misalignment at repetitive DNA sequences. Mol. Microbiol. 52:
12431253. http://dx.doi.org/10.1111/j.1365-2958.2004.04076.x.
336. Michel B, Ehrlich SD. 1986. Illegitimate recombination occurs between
the replication origin of the plasmid pC194 and a progressing replication
fork. EMBO J. 5:36913696.
337. Michel B, Ehrlich SD. 1986. Illegitimate recombination at the replica-
tionoriginof bacteriophage M13. Proc. Natl. Acad. Sci. U. S. A. 83:3386
3390. http://dx.doi.org/10.1073/pnas.83.10.3386.
338. Shapiro JA, Leach D. 1990. Action of a transposable element in coding
sequence fusions. Genetics 126:293299.
339. Ikeda H, Moriya K, Matsumoto T. 1981. In vitro study of illegitimate
recombination: involvement of DNA gyrase. Cold Spring Harb. Symp.
Quant. Biol. 45(Part 1):399408.
340. Shuman S. 1989. Vaccinia DNA topoisomerase I promotes illegitimate
recombination in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 86:3489
341. Ashizawa Y, Yokochi T, Ogata Y, Shobuike Y, Kato J, Ikeda H. 1999.
Mechanism of DNA gyrase-mediated illegitimate recombination: char-
acterization of Escherichia coli gyrA mutations that confer hyper-
recombination phenotype. J. Mol. Biol. 289:447458. http://dx.doi.org
/10.1006/jmbi.1999.2758.
342. Yi TM, Stearns D, Demple B. 1988. Illegitimate recombination in an
Escherichia coli plasmid: modulationby DNAdamage anda newbacterial
gene. J. Bacteriol. 170:28982903.
343. Hanada K, Yamashita T, Shobuike Y, Ikeda H. 2001. Role of DnaB helicase
in UV-induced illegitimate recombination in Escherichia coli. J. Bacteriol.
183:49644969. http://dx.doi.org/10.1128/JB.183.17.4964-4969.2001.
344. Shanado Y, Hanada K, Ikeda H. 2001. Suppression of gamma ray-
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

induced illegitimate recombination in Escherichia coli by the DNA-
binding protein H-NS. Mol. Genet. Genomics 265:242248. http://dx
.doi.org/10.1007/s004380000399.
345. Conley EC, Saunders VA, Jackson V, Saunders JR. 1986. Mechanism of
intramolecular recyclization and deletion formation following transfor-
mation of Escherichia coli with linearized plasmid DNA. Nucleic Acids
Res. 14:89198932. http://dx.doi.org/10.1093/nar/14.22.8919.
346. Chayot R, Montagne B, Mazel D, Ricchetti M. 2010. An end-joining
repair mechanism in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 107:
347. Heale SM, Petes TD. 1995. The stabilization of repetitive tracts of DNA
by variant repeats requires a functional DNA mismatch repair system.
Cell 83:539545. http://dx.doi.org/10.1016/0092-8674(95)90093-4.
348. Saveson CJ, Lovett ST. 1997. Enhanced deletion formation by aberrant
DNA replication in Escherichia coli. Genetics 146:457470.
349. Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, Della M, Devine
SK, Day JP, Wilkinson A, dAdda di Fagagna F, Devine KM, Bowater
RP, Jeggo PA, Jackson SP, Doherty AJ. 2002. Identication of a DNA
nonhomologous end-joining complex in bacteria. Science 297:1686
350. Pitcher RS, Brissett NC, Doherty AJ. 2007. Nonhomologous end-
joining in bacteria: a microbial perspective. Annu. Rev. Microbiol. 61:
351. Shuman S, Glickman MS. 2007. Bacterial DNA repair by non-
homologous end joining. Nat. Rev. Microbiol. 5:852861. http://dx.doi
.org/10.1038/nrmicro1768.
352. Ramsden DA. 2011. Polymerases in nonhomologous end joining: build-
ing a bridge over broken chromosomes. Antioxid. Redox Signal. 14:
25092519. http://dx.doi.org/10.1089/ars.2010.3429.
353. de Vega M. 2013. The minimal Bacillus subtilis nonhomologous end
joining repair machinery. PLoS One 8:e64232. http://dx.doi.org/10.1371
/journal.pone.0064232.
354. Santoyo G, Romero D. 2005. Gene conversion and concerted evolution
in bacterial genomes. FEMS Microbiol. Rev. 29:169183. http://dx.doi
.org/10.1016/j.fmrre.2004.10.004.
355. Palmer GH, Bankhead T, Lukehart SA. 2009. Nothing is permanent
but changeantigenic variation in persistent bacterial pathogens. Cell.
Microbiol. 11:16971705. http://dx.doi.org/10.1111/j.1462-5822.2009
.01366.x.
356. Davidsen T, Tnjum T. 2006. Meningococcal genome dynamics. Nat.
357. Cahoon LA, Seifert HS. 2011. Focusing homologous recombination:
pilin antigenic variation in the pathogenic Neisseria. Mol. Microbiol.
81:11361143. http://dx.doi.org/10.1111/j.1365-2958.2011.07773.x.
358. Morris RT, Drouin G. 2007. Ectopic gene conversions in bacterial ge-
nomes. Genome 50:975984. http://dx.doi.org/10.1139/G07-076.
359. Mehr IJ, Seifert HS. 1998. Differential roles of homologous recombina-
tion pathways in Neisseria gonorrhoeae pilin antigenic variation, DNA
transformation and DNA repair. Mol. Microbiol. 30:697710. http://dx
.doi.org/10.1046/j.1365-2958.1998.01089.x.
360. Cahoon LA, Seifert HS. 2009. An alternative DNA structure is necessary
for pilin antigenic variation in Neisseria gonorrhoeae. Science 325:764
361. Anderson RP, Roth JR. 1977. Tandemgenetic duplications in phage and
bacteria. Annu. Rev. Microbiol. 31:473505. http://dx.doi.org/10.1146
/annurev.mi.31.100177.002353.
362. Andersson DI, Hughes D. 2009. Gene amplication and adaptive evo-
lution in bacteria. Annu. Rev. Genet. 43:167195. http://dx.doi.org/10
.1146/annurev-genet-102108-134805.
363. Ives CL, Bott KF. 1990. Characterization of chromosomal DNA ampli-
cations with associated tetracycline resistance in Bacillus subtilis. J. Bac-
teriol. 172:49364944.
364. Zahra R, Blackwood JK, Sales J, Leach DR. 2007. Proofreading and
secondary structure processing determine the orientation dependence of
CAG CTG trinucleotide repeat instability in Escherichia coli. Genetics
176:2741. http://dx.doi.org/10.1534/genetics.106.069724.
365. Bi X, Liu LF. 1996. A replicational model for DNA recombination
between direct repeats. J. Mol. Biol. 256:849858. http://dx.doi.org/10
.1006/jmbi.1996.0131.
366. Bichara M, Wagner J, Lambert IB. 2006. Mechanisms of tandem repeat
instability in bacteria. Mutat. Res. 598:144163. http://dx.doi.org/10
.1016/j.mrfmmm.2006.01.020.
367. Blackwood JK, Okely EA, Zahra R, Eykelenboom JK, Leach DR. 2010.
DNA tandem repeat instability in the Escherichia coli chromosome is
stimulated by mismatch repair at an adjacent CAG.CTG trinucleotide
repeat. Proc. Natl. Acad. Sci. U. S. A. 107:2258222586. http://dx.doi.org
/10.1073/pnas.1012906108.
368. Peterson BC, Rownd RH. 1985. Recombination sites in plasmid drug
resistance gene amplication. J. Bacteriol. 164:13591361.
369. Kang S, Jaworski A, Ohshima K, Wells RD. 1995. Expansion and
deletionof CTGrepeats fromhumandisease genes are determined by the
direction of replication in E. coli. Nat. Genet. 10:213218. http://dx.doi
.org/10.1038/ng0695-213.
370. Iyer RR, Pluciennik A, Rosche WA, Sinden RR, Wells RD. 2000. DNA
polymerase III proofreading mutants enhance the expansion and dele-
tion of triplet repeat sequences in Escherichia coli. J. Biol. Chem. 275:
21742184. http://dx.doi.org/10.1074/jbc.275.3.2174.
371. Moxon R, Bayliss C, Hood D. 2006. Bacterial contingency loci: the role
of simple sequence DNA repeats in bacterial adaptation. Annu. Rev.
Genet. 40:307333. http://dx.doi.org/10.1146/annurev.genet.40.110405
.090442.
372. Bayliss CD, Field D, Moxon ER. 2001. The simple sequence contin-
gency loci of Haemophilus inuenzae and Neisseria meningitidis. J. Clin.
Invest. 107:657662. http://dx.doi.org/10.1172/JCI12557.
373. van Ham SM, van Alphen L, Mooi FR, van Putten JP. 1993. Phase
variation of H. inuenzae mbriae: transcriptional control of two diver-
gent genes through a variable combined promoter region. Cell 73:1187
1196. http://dx.doi.org/10.1016/0092-8674(93)90647-9.
374. Stern A, Brown M, Nickel P, Meyer TF. 1986. Opacity genes in Neisseria
gonorrhoeae: control of phase and antigenic variation. Cell 47:6171.
http://dx.doi.org/10.1016/0092-8674(86)90366-1.
375. Huffman GA, Rownd RH. 1984. Transition of deletion mutants of
the composite resistance plasmid NR1 in Escherichia coli and Salmo-
nella typhimurium. J. Bacteriol. 159:488498.
376. Tlsty TD, Albertini AM, Miller JH. 1984. Gene amplication in the lac
region of E. coli. Cell 37:217224. http://dx.doi.org/10.1016/0092-8674
(84)90317-9.
377. Foster PL. 1999. Mechanisms of stationary phase mutation: a decade of
adaptive mutation. Annu. Rev. Genet. 33:5788. http://dx.doi.org/10
.1146/annurev.genet.33.1.57.
378. Rosenberg SM, Hastings PJ. 2004. Adaptive point mutation and adap-
tive amplication pathways in the Escherichia coli Lac system: stress re-
sponses producing genetic change. J. Bacteriol. 186:48384843. http:
//dx.doi.org/10.1128/JB.186.15.4838-4843.2004.
379. Quinones-Soto S, Roth JR. 2011. Effect of growth under selection on
appearance of chromosomal mutations in Salmonella enterica. Genetics
189:3753. http://dx.doi.org/10.1534/genetics.111.130187.
380. Trinh TQ, Sinden RR. 1991. Preferential DNA secondary structure
mutagenesis in the lagging strand of replication in E. coli. Nature 352:
544547. http://dx.doi.org/10.1038/352544a0.
381. Pinder DJ, Blake CE, Lindsey JC, Leach DR. 1998. Replication strand
preference for deletions associated with DNA palindromes. Mol. Micro-
biol. 28:719727.
382. Leach DR, Okely EA, Pinder DJ. 1997. Repair by recombination of
DNA containing a palindromic sequence. Mol. Microbiol. 26:597606.
http://dx.doi.org/10.1046/j.1365-2958.1997.6071957.x.
383. Eykelenboom JK, Blackwood JK, Okely E, Leach DR. 2008. SbcCD
causes a double-strand break at a DNApalindrome in the Escherichia coli
chromosome. Mol. Cell 29:644651. http://dx.doi.org/10.1016/j.molcel
.2007.12.020.
384. Bzymek M, Lovett ST. 2001. Evidence for two mechanisms of palin-
drome-stimulated deletion in Escherichia coli: single-strand annealing
and replication slipped mispairing. Genetics 158:527540. http://www
.genetics.org/content/158/2/527.long.
385. Pinder DJ, Blake CE, Leach DR. 1997. DIR: a novel DNArearrangement
associated with inverted repeats. Nucleic Acids Res. 25:523529. http:
//dx.doi.org/10.1093/nar/25.3.523.
386. Brewer BJ, Payen C, Raghuraman MK, Dunham MJ. 2011. Origin-
dependent inverted-repeat amplication: a replication-based model for
generating palindromic amplicons. PLoS Genet. 7:e1002016. http://dx
.doi.org/10.1371/journal.pgen.1002016.
387. Darmon E, Eykelenboom JK, Lincker F, Jones LH, White M, Okely E,
Blackwood JK, Leach DR. 2010. E. coli SbcCD and RecA control chro-
mosomal rearrangement induced by an interrupted palindrome. Mol.
Cell 39:5970. http://dx.doi.org/10.1016/j.molcel.2010.06.011.
388. Leach DR. 1994. Long DNA palindromes, cruciform structures, genetic

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

instability and secondary structure repair. Bioessays 16:893900. http:
//dx.doi.org/10.1002/bies.950161207.
389. Harms K, Wackernagel W. 2008. The RecBCD and SbcCD DNases
suppress homology-facilitatedillegitimate recombinationduring natural
transformation of Acinetobacter baylyi. Microbiology 154:24372445.
http://dx.doi.org/10.1099/mic.0.2008/018382-0.
390. Slupska MM, Chiang JH, Luther WM, Stewart JL, Amii L, Conrad A,
Miller JH. 2000. Genes involved in the determination of the rate of
inversions at short inverted repeats. Genes Cells 5:425437. http://dx.doi
.org/10.1046/j.1365-2443.2000.00341.x.
391. Dybvig K. 1993. DNA rearrangements and phenotypic switching in pro-
karyotes. Mol. Microbiol. 10:465471. http://dx.doi.org/10.1111/j.1365
-2958.1993.tb00919.x.
392. Henderson IR, Owen P, Nataro JP. 1999. Molecular switchesthe ON
and OFF of bacterial phase variation. Mol. Microbiol. 33:919932. http:
//dx.doi.org/10.1046/j.1365-2958.1999.01555.x.
393. van der Woude MW, Bumler AJ. 2004. Phase and antigenic variation
in bacteria. Clin. Microbiol. Rev. 17:581611. http://dx.doi.org/10.1128
/CMR.17.3.581-611.2004.
394. Grindley ND, Whiteson KL, Rice PA. 2006. Mechanisms of site-specic
recombination. Annu. Rev. Biochem. 75:567605. http://dx.doi.org/10
.1146/annurev.biochem.73.011303.073908.
395. Wisniewski-Dy F, Vial L. 2008. Phase and antigenic variation mediated
by genome modications. Antonie Van Leeuwenhoek 94:493515. http:
//dx.doi.org/10.1007/s10482-008-9267-6.
396. Emerson JE, Reynolds CB, Fagan RP, Shaw HA, Goulding D, Fair-
weather NF. 2009. Anovel genetic switch controls phase variable expres-
sion of CwpV, a Clostridium difcile cell wall protein. Mol. Microbiol.
74:541556. http://dx.doi.org/10.1111/j.1365-2958.2009.06812.x.
397. Abraham JM, Freitag CS, Clements JR, Eisenstein BI. 1985. An invert-
ible element of DNA controls phase variation of type 1 mbriae of Esch-
erichia coli. Proc. Natl. Acad. Sci. U. S. A. 82:57245727. http://dx.doi
.org/10.1073/pnas.82.17.5724.
398. Kuwahara T, Yamashita A, Hirakawa H, Nakayama H, Toh H, Okada
N, Kuhara S, Hattori M, Hayashi T, Ohnishi Y. 2004. Genomic analysis
of Bacteroides fragilis reveals extensive DNA inversions regulating cell
surface adaptation. Proc. Natl. Acad. Sci. U. S. A. 101:1491914924. http:
//dx.doi.org/10.1073/pnas.0404172101.
399. Dworkin J, Blaser MJ. 1997. Nested DNA inversion as a paradigm of
programmed gene rearrangement. Proc. Natl. Acad. Sci. U. S. A. 94:985
400. Zhang XL, Morris C, Hackett J. 1997. Molecular cloning, nucleotide
sequence, and function of a site-specic recombinase encoded in the
major pathogenicity island of Salmonella typhi. Gene 202:139146.
http://dx.doi.org/10.1016/S0378-1119(97)00466-6.
401. Cerdeo-Trraga AM, Patrick S, Crossman LC, Blakely G, Abratt V,
Lennard N, Poxton I, Duerden B, Harris B, Quail MA, Barron A,
Clark L, Corton C, Doggett J, Holden MT, Larke N, Line A, Lord A,
Norbertczak H, Ormond D, Price C, Rabbinowitsch E, Woodward J,
Barrell B, Parkhill J. 2005. Extensive DNA inversions in the B. fragilis
genome control variable gene expression. Science 307:14631465. http:
//dx.doi.org/10.1126/science.1107008.
402. Yamamoto S, Kutsukake K. 2006. FljA-mediated posttranscriptional
control of phase 1 agellin expression in agellar phase variation of Sal-
monella enterica serovar Typhimurium. J. Bacteriol. 188:958967. http:
//dx.doi.org/10.1128/JB.188.3.958-967.2006.
403. McClain MS, Blomeld IC, Eisenstein BI. 1991. Roles of mB and mE
in site-specic DNA inversion associated with phase variation of type 1
mbriae in Escherichia coli. J. Bacteriol. 173:53085314.
404. Kulasekara HD, Blomeld IC. 1999. The molecular basis for the speci-
city of mE in the phase variation of type 1 mbriae of Escherichia coli
K-12. Mol. Microbiol. 31:11711181. http://dx.doi.org/10.1046/j.1365
-2958.1999.01257.x.
405. Nakayama-Imaohji H, Hirakawa H, Ichimura M, Wakimoto S, Ku-
hara S, Hayashi T, Kuwahara T. 2009. Identication of the site-specic
DNA invertase responsible for the phase variation of SusC/SusD family
outer membrane proteins in Bacteroides fragilis. J. Bacteriol. 191:6003
6011. http://dx.doi.org/10.1128/JB.00687-09.
406. Olsen PB, Klemm P. 1994. Localization of promoters in the m gene
cluster and the effect of H-NS on the transcription of mB and mE.
FEMS Microbiol. Lett. 116:95100. http://dx.doi.org/10.1111/j.1574
-6968.1994.tb06681.x.
407. Joyce SA, Dorman CJ. 2002. A Rho-dependent phase-variable tran-
scription terminator controls expression of the FimE recombinase in
Escherichia coli. Mol. Microbiol. 45:11071117. http://dx.doi.org/10
.1046/j.1365-2958.2002.03081.x.
408. Blomeld IC, Calie PJ, Eberhardt KJ, McClain MS, Eisenstein BI.
1993. Lrp stimulates phase variation of type 1 mbriation in Escherichia
coli K-12. J. Bacteriol. 175:2736.
409. Campbell AM. 1992. Chromosomal insertion sites for phages and plas-
mids. J. Bacteriol. 174:74957499.
410. Bartlett DH, Silverman M. 1989. Nucleotide sequence of IS492, a novel
insertion sequence causing variation in extracellular polysaccharide pro-
duction in the marine bacterium Pseudomonas atlantica. J. Bacteriol.
171:17631766.
411. Higgins BP, Carpenter CD, Karls AC. 2007. Chromosomal context
directs high-frequency precise excision of IS492 in Pseudoalteromonas
atlantica. Proc. Natl. Acad. Sci. U. S. A. 104:19011906. http://dx.doi.org
/10.1073/pnas.0608633104.
412. Higgins BP, Popkowski AC, Caruana PR, Karls AC. 2009. Site-specic
insertion of IS492 in Pseudoalteromonas atlantica. J. Bacteriol. 191:6408
6414. http://dx.doi.org/10.1128/JB.00771-09.
413. Lneberg E, Mayer B, Daryab N, Kooistra O, Zhringer U, Rohde M,
Swanson J, Frosch M. 2001. Chromosomal insertion and excision of a 30
kb unstable genetic element is responsible for phase variation of lipo-
polysaccharide and other virulence determinants in Legionella pneumo-
phila. Mol. Microbiol. 39:12591271. http://dx.doi.org/10.1111/j.1365
-2958.2001.02314.x.
414. Haselkorn R. 1992. Developmentally regulated gene rearrangements in
prokaryotes. Annu. Rev. Genet. 26:113130. http://dx.doi.org/10.1146
/annurev.ge.26.120192.000553.
415. Carrasco CD, Buettner JA, Golden JW. 1995. Programmed DNA rear-
rangement of a cyanobacterial hupL gene in heterocysts. Proc. Natl.
Acad. Sci. U. S. A. 92:791795. http://dx.doi.org/10.1073/pnas.92.3.791.
416. Haraldsen JD, Sonenshein AL. 2003. Efcient sporulation in Clostrid-
ium difcile requires disruption of the sigmaK gene. Mol. Microbiol. 48:
811821. http://dx.doi.org/10.1046/j.1365-2958.2003.03471.x.
417. Carrasco CD, Holliday SD, Hansel A, Lindblad P, Golden JW. 2005.
Heterocyst-specic excision of the Anabaena sp. strain PCC 7120 hupL
element requires xisC. J. Bacteriol. 187:60316038. http://dx.doi.org/10
.1128/JB.187.17.6031-6038.2005.
418. Henson BJ, Watson LE, Barnum SR. 2005. Characterization of a 4 kb
variant of the nifD element in Anabaena sp. strain ATCC 33047. Curr.
Microbiol. 50:129132. http://dx.doi.org/10.1007/s00284-004-4338-z.
419. Krogh S, OReilly M, Nolan N, Devine KM. 1996. The phage-like
element PBSX and part of the skin element, which are resident at differ-
ent locations on the Bacillus subtilis chromosome, are highly homolo-
gous. Microbiology 142(Part 8):20312040.
420. Hallet B. 2001. Playing Dr Jekyll and Mr Hyde: combined mechanisms of
phase variation in bacteria. Curr. Opin. Microbiol. 4:570581. http://dx
.doi.org/10.1016/S1369-5274(00)00253-8.
421. Frank SA, Barbour AG. 2006. Within-host dynamics of antigenic vari-
ation. Infect. Genet. Evol. 6:141146. http://dx.doi.org/10.1016/j.meegid
.2004.10.005.
422. van der Woude MW. 2006. Re-examining the role and randomnature of
phase variation. FEMS Microbiol. Lett. 254:190197. http://dx.doi.org
/10.1111/j.1574-6968.2005.00038.x.
423. Davidson CJ, Surette MG. 2008. Individuality in bacteria. Annu. Rev.
Genet. 42:253268. http://dx.doi.org/10.1146/annurev.genet.42.110807
.091601.
424. Bayliss CD. 2009. Determinants of phase variation rate and the tness
implications of differing rates for bacterial pathogens and commensals.
FEMS Microbiol. Rev. 33:504520. http://dx.doi.org/10.1111/j.1574
-6976.2009.00162.x.
425. Deitsch KW, Lukehart SA, Stringer JR. 2009. Common strategies for
antigenic variation by bacterial, fungal and protozoan pathogens. Nat.
426. van der Woude MW. 2011. Phase variation: how to create and coordi-
nate population diversity. Curr. Opin. Microbiol. 14:205211. http://dx
.doi.org/10.1016/j.mib.2011.01.002.
427. Scott J, Thompson-Mayberry P, Lahmamsi S, King CJ, McShan WM.
2008. Phage-associated mutator phenotype in group A Streptococcus. J.
428. Bacon DJ, Szymanski CM, Burr DH, Silver RP, Alm RA, Guerry P.
2001. A phase-variable capsule is involved in virulence of Campylobacter
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

jejuni 81-176. Mol. Microbiol. 40:769777. http://dx.doi.org/10.1046/j
.1365-2958.2001.02431.x.
429. Blyn LB, Braaten BA, White-Ziegler CA, Rolfson DH, Low DA. 1989.
Phase-variation of pyelonephritis-associated pili in Escherichia coli: evi-
dence for transcriptional regulation. EMBO J. 8:613620.
430. Liu B, Hu B, Zhou Z, Guo D, Guo X, Ding P, Feng L, Wang L. 2012.
A novel non-homologous recombination-mediated mechanism for
Escherichia coli unilateral agellar phase variation. Nucleic Acids Res.
40:45304538. http://dx.doi.org/10.1093/nar/gks040.
431. Goodwin AC, Weinberger DM, Ford CB, Nelson JC, Snider JD, Hall
JD, Paules CI, Peek RM, Jr, Forsyth MH. 2008. Expression of the
Helicobacter pylori adhesin SabAis controlled via phase variation and the
ArsRS signal transduction system. Microbiology 154:22312240. http:
//dx.doi.org/10.1099/mic.0.2007/016055-0.
432. van den Broek D, Chin-A-Woeng TF, Eijkemans K, Mulders IH,
Bloemberg GV, Lugtenberg BJ. 2003. Biocontrol traits of Pseudomonas
spp. are regulated by phase variation. Mol. Plant Microbe Interact. 16:
10031012. http://dx.doi.org/10.1094/MPMI.2003.16.11.1003.
433. Lewis LA, Gipson M, Hartman K, Ownbey T, Vaughn J, Dyer DW.
1999. Phase variation of HpuAB and HmbR, two distinct haemoglobin
receptors of Neisseria meningitidis DNM2. Mol. Microbiol. 32:977989.
http://dx.doi.org/10.1046/j.1365-2958.1999.01409.x.
434. Rosengarten R, Wise KS. 1990. Phenotypic switching in mycoplasmas:
phase variation of diverse surface lipoproteins. Science 247:315318.
http://dx.doi.org/10.1126/science.1688663.
435. Hoskisson PA, Smith MC. 2007. Hypervariation and phase variation in
the bacteriophage resistome. Curr. Opin. Microbiol. 10:396400. http:
//dx.doi.org/10.1016/j.mib.2007.04.003.
436. Hendrixson DR. 2006. A phase-variable mechanism controlling the
Campylobacter jejuni FlgR response regulator inuences commensalism.
Mol. Microbiol. 61:16461659. http://dx.doi.org/10.1111/j.1365-2958
.2006.05336.x.
437. Iqbal S, Parker G, Davidson H, Moslehi-Rahmani E, Robson RL. 2004.
Reversible phase variation in the phnE gene, which is required for phos-
phonate metabolism in Escherichia coli K-12. J. Bacteriol. 186:6118
6123. http://dx.doi.org/10.1128/JB.186.18.6118-6123.2004.
438. Faulstich M, Bttcher JP, Meyer TF, Fraunholz M, Rudel T. 2013.
Pilus phase variation switches gonococcal adherence to invasion by
caveolin-1-dependent host cell signaling. PLoS Pathog. 9:e1003373. http:
//dx.doi.org/10.1371/journal.ppat.1003373.
439. Lindbck T, Secic I, Rrvik LM. 2011. A contingency locus in prfA in a
Listeria monocytogenes subgroupallows reactivationof the PrfAvirulence
regulator during infection in mice. Appl. Environ. Microbiol. 77:3478
3483. http://dx.doi.org/10.1128/AEM.02708-10.
440. Clark SE, Eichelberger KR, Weiser JN. 2013. Evasion of killing by
human antibody and complement through multiple variations in the
surface oligosaccharide of Haemophilus inuenzae. Mol. Microbiol. 88:
603618. http://dx.doi.org/10.1111/mmi.12214.
441. Gunther NW, IV, Snyder JA, Lockatell V, Blomeld I, Johnson DE,
Mobley HL. 2002. Assessment of virulence of uropathogenic Escherichia
coli type 1 mbrial mutants in which the invertible element is phase-
locked on or off. Infect. Immun. 70:33443354. http://dx.doi.org/10
.1128/IAI.70.7.3344-3354.2002.
442. Clark SE, Snow J, Li J, Zola TA, Weiser JN. 2012. Phosphorylcholine
allows for evasion of bactericidal antibody by Haemophilus inuenzae.
PLoS Pathog. 8:e1002521. http://dx.doi.org/10.1371/journal.ppat
.1002521.
443. Norris TL, Bumler AJ. 1999. Phase variation of the lpf operon is a
mechanism to evade cross-immunity between Salmonella serotypes.
/pnas.96.23.13393.
444. Schwan WR. 2011. Regulation of m genes in uropathogenic Escherichia
coli. World J. Clin. Infect. Dis. 1:1725. http://dx.doi.org/10.5495/wjcid
.v1.i1.17.
445. Dove SL, Dorman CJ. 1994. The site-specic recombination system
regulating expression of the type 1 mbrial subunit gene of Escherichia
coli is sensitive to changes in DNAsupercoiling. Mol. Microbiol. 14:975
446. Gally DL, Bogan JA, Eisenstein BI, Blomeld IC. 1993. Environmental
regulation of the mswitch controlling type 1 mbrial phase variation in
Escherichia coli K-12: effects of temperature and media. J. Bacteriol. 175:
61866193.
447. Ratiner YA. 1999. Temperature-dependent agellar antigen phase vari-
ation in Escherichia coli. Res. Microbiol. 150:457463. http://dx.doi.org
/10.1016/S0923-2508(99)00111-4.
448. Moran AP, Knirel YA, Senchenkova SN, Widmalm G, Hynes SO,
Jansson PE. 2002. Phenotypic variation in molecular mimicry between
Helicobacter pylori lipopolysaccharides and human gastric epithelial cell
surface glycoforms. Acid-induced phase variation in Lewis(x) and
Lewis(y) expression by H. pylori lipopolysaccharides. J. Biol. Chem. 277:
57855795. http://dx.doi.org/10.1074/jbc.M108574200.
449. Stinson RS, Talburt DE. 1978. Antigenic variation and increase in
pathogenicity in Pseudomonas aeruginosa as a result of growth on glucose
or N-hexadecane as sole carbon source. Can. J. Microbiol. 24:675679.
http://dx.doi.org/10.1139/m78-113.
450. Lane MC, Li X, Pearson MM, Simms AN, Mobley HL. 2009. Oxygen-
limiting conditions enrich for mbriate cells of uropathogenic Proteus
mirabilis and Escherichia coli. J. Bacteriol. 191:13821392. http://dx.doi
.org/10.1128/JB.01550-08.
451. Serkin CD, Seifert HS. 2000. Iron availability regulates DNA recombi-
nation in Neisseria gonorrhoeae. Mol. Microbiol. 37:10751086. http://dx
.doi.org/10.1046/j.1365-2958.2000.02058.x.
452. Garrison-Schilling KL, Grau BL, McCarter KS, Olivier BJ, Comeaux
NE, Pettis GS. 2011. Calcium promotes exopolysaccharide phase varia-
tion and biolm formation of the resulting phase variants in the human
pathogen Vibrio vulnicus. Environ. Microbiol. 13:643654. http://dx
.doi.org/10.1111/j.1462-2920.2010.02369.x.
453. Sohanpal BK, El-Labany S, Lahooti M, Plumbridge JA, Blomeld IC.
2004. Integrated regulatory responses of mB to N-acetylneuraminic
(sialic) acid and GlcNAc in Escherichia coli K-12. Proc. Natl. Acad. Sci.
U. S. A. 101:1632216327. http://dx.doi.org/10.1073/pnas.0405821101.
454. Juhas M. 18 July 2013. Horizontal gene transfer in human pathogens.
Crit. Rev. Microbiol. http://dx.doi.org/10.3109/1040841X.2013.804031.
455. Watanabe T. 1963. Infective heredity of multiple drug resistance in bac-
teria. Bacteriol. Rev. 27:87115.
456. Doolittle WF. 1999. Lateral genomics. Trends Cell Biol. 9:M5M8. http:
//dx.doi.org/10.1016/S0962-8924(99)01664-5.
457. Kurland CG. 2000. Something for everyone. Horizontal gene transfer in
evolution. EMBO Rep. 1:9295. http://dx.doi.org/10.1093/embo-reports
/kvd042.
458. Levin BR, Bergstrom CT. 2000. Bacteria are different: observations,
interpretations, speculations, and opinions about the mechanisms of
adaptive evolution in prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 97:
459. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and
the nature of bacterial innovation. Nature 405:299304. http://dx.doi
.org/10.1038/35012500.
460. Woese CR. 2000. Interpreting the universal phylogenetic tree. Proc.
.97.15.8392.
461. Koonin EV, Makarova KS, Aravind L. 2001. Horizontal gene transfer in
prokaryotes: quantication and classication. Annu. Rev. Microbiol. 55:
462. Sonea S, Mathieu LG. 2001. Evolution of the genomic systems of pro-
karyotes andits momentous consequences. Int. Microbiol. 4:6771. http:
//dx.doi.org/10.1007/s101230100015.
463. Cohan FM. 2002. Sexual isolation and speciation in bacteria. Genetica
116:359370. http://dx.doi.org/10.1023/A:1021232409545.
464. Dutta C, Pan A. 2002. Horizontal gene transfer and bacterial diversity. J.
Biosci. 27:2733. http://dx.doi.org/10.1007/BF02703681.
465. Gogarten JP, Doolittle WF, Lawrence JG. 2002. Prokaryotic evolution
in light of gene transfer. Mol. Biol. Evol. 19:22262238. http://dx.doi.org
/10.1093/oxfordjournals.molbev.a004046.
466. Woese CR. 2002. On the evolution of cells. Proc. Natl. Acad. Sci. U. S. A.
99:87428747. http://dx.doi.org/10.1073/pnas.132266999.
467. Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbo
CL, Case RJ, Doolittle WF. 2003. Lateral gene transfer and the origins of
prokaryotic groups. Annu. Rev. Genet. 37:283328. http://dx.doi.org/10
.1146/annurev.genet.37.050503.084247.
468. Brown JR. 2003. Ancient horizontal gene transfer. Nat. Rev. Genet.
469. Lawrence JG, Hendrickson H. 2003. Lateral gene transfer: when will
adolescence end? Mol. Microbiol. 50:739749. http://dx.doi.org/10.1046
/j.1365-2958.2003.03778.x.
470. Gogarten JP, Townsend JP. 2005. Horizontal gene transfer, genome

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

innovation and evolution. Nat. Rev. Microbiol. 3:679687. http://dx.doi
.org/10.1038/nrmicro1204.
471. Pal C, Papp B, Lercher MJ. 2005. Adaptive evolution of bacterial met-
abolic networks by horizontal gene transfer. Nat. Genet. 37:13721375.
http://dx.doi.org/10.1038/ng1686.
472. Susko E, Leigh J, Doolittle WF, Bapteste E. 2006. Visualizing and
assessing phylogenetic congruence of core gene sets: a case study of the
gamma-proteobacteria. Mol. Biol. Evol. 23:10191030. http://dx.doi.org
/10.1093/molbev/msj113.
473. Doolittle WF, Bapteste E. 2007. Pattern pluralism and the Tree of Life
hypothesis. Proc. Natl. Acad. Sci. U. S. A. 104:20432049. http://dx.doi
.org/10.1073/pnas.0610699104.
474. Goldenfeld N, Woese C. 2007. Biologys next revolution. Nature 445:
369. http://dx.doi.org/10.1038/445369a.
475. Bapteste E, Boucher Y. 2008. Lateral gene transfer challenges principles
of microbial systematics. Trends Microbiol. 16:200207. http://dx.doi
.org/10.1016/j.tim.2008.02.005.
476. Koonin EV, Wolf YI. 2008. Genomics of bacteria and archaea: the
emerging dynamic view of the prokaryotic world. Nucleic Acids Res.
36:66886719. http://dx.doi.org/10.1093/nar/gkn668.
477. Doolittle WF, Zhaxybayeva O. 2009. On the origin of prokaryotic species.
Genome Res. 19:744756. http://dx.doi.org/10.1101/gr.086645.108.
478. Poole AM. 2009. Horizontal gene transfer and the earliest stages of the
evolution of life. Res. Microbiol. 160:473480. http://dx.doi.org/10.1016
/j.resmic.2009.07.009.
479. Brigulla M, Wackernagel W. 2010. Molecular aspects of gene transfer
and foreign DNA acquisition in prokaryotes with regard to safety issues.
Appl. Microbiol. Biotechnol. 86:10271041. http://dx.doi.org/10.1007
/s00253-010-2489-3.
480. Case RJ, Boucher Y. 2011. Molecular musings in microbial ecology and
evolution. Biol. Direct 6:58. http://dx.doi.org/10.1186/1745-6150-6-58.
481. Popa O, Dagan T. 2011. Trends and barriers to lateral gene transfer in
prokaryotes. Curr. Opin. Microbiol. 14:615623. http://dx.doi.org/10
.1016/j.mib.2011.07.027.
482. Vogan AA, Higgs PG. 2011. The advantages and disadvantages of hor-
izontal gene transfer and the emergence of the rst species. Biol. Direct
6:1. http://dx.doi.org/10.1186/1745-6150-6-1.
483. Gao B, Gupta RS. 2012. Microbial systematics in the post-genomics era.
Antonie Van Leeuwenhoek 101:4554. http://dx.doi.org/10.1007/s10482
-011-9663-1.
484. Koonin EV, Wolf YI. 2012. Evolution of microbes and viruses: a para-
digm shift in evolutionary biology? Front. Cell. Infect. Microbiol. 2:119.
485. Berg OG, Kurland C. 2002. Evolution of microbial genomes: sequence
acquisition and loss. Mol. Biol. Evol. 19:22652276. http://dx.doi.org/10
.1093/oxfordjournals.molbev.a004050.
486. Hall BG, Yokoyama S, Calhoun DH. 1983. Role of cryptic genes in
microbial evolution. Mol. Biol. Evol. 1:109124.
487. Baumdicker F, Hess WR, Pfaffelhuber P. 2012. The innitely many
genes model for the distributed genome of bacteria. Genome Biol. Evol.
4:443456. http://dx.doi.org/10.1093/gbe/evs016.
488. Francis AR, Tanaka MM. 2012. Evolution of variation in presence and
absence of genes in bacterial pathways. BMC Evol. Biol. 12:55. http://dx
.doi.org/10.1186/1471-2148-12-55.
489. Arber W. 2011. Molecular Darwinism: the contingency of spontaneous
genetic variation. Genome Biol. Evol. 3:10901092. http://dx.doi.org/10
.1093/gbe/evr035.
490. Solioz M, Yen HC, Marris B. 1975. Release and uptake of gene transfer
agent by Rhodopseudomonas capsulata. J. Bacteriol. 123:651657.
491. Lang AS, Beatty JT. 2007. Importance of widespread gene transfer agent
genes in alpha-proteobacteria. Trends Microbiol. 15:5462. http://dx
.doi.org/10.1016/j.tim.2006.12.001.
492. Stanton TB. 2007. Prophage-like gene transfer agentsnovel mecha-
nisms of gene exchange for Methanococcus, Desulfovibrio, Brachyspira,
and Rhodobacter species. Anaerobe 13:4349. http://dx.doi.org/10.1016
/j.anaerobe.2007.03.004.
493. McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH.
2010. High frequency of horizontal gene transfer in the oceans. Science
330:50. http://dx.doi.org/10.1126/science.1192243.
494. Dubey GP, Ben-Yehuda S. 2011. Intercellular nanotubes mediate bac-
terial communication. Cell 144:590600. http://dx.doi.org/10.1016/j
.cell.2011.01.015.
495. Kolling GL, Matthews KR. 1999. Export of virulence genes and Shiga
toxin by membrane vesicles of Escherichia coli O157:H7. Appl. Environ.
Microbiol. 65:18431848.
496. Yaron S, Kolling GL, Simon L, Matthews KR. 2000. Vesicle-mediated
transfer of virulence genes fromEscherichia coli O157:H7 to other enteric
bacteria. Appl. Environ. Microbiol. 66:44144420. http://dx.doi.org/10
.1128/AEM.66.10.4414-4420.2000.
497. Mashburn-Warren LM, Whiteley M. 2006. Special delivery: vesicle traf-
cking in prokaryotes. Mol. Microbiol. 61:839846. http://dx.doi.org
/10.1111/j.1365-2958.2006.05272.x.
498. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. 2011.
Directed networks reveal genomic barriers and DNA repair bypasses to
lateral gene transfer among prokaryotes. Genome Res. 21:599609. http:
//dx.doi.org/10.1101/gr.115592.110.
499. Jain R, Rivera MC, Moore JE, Lake JA. 2003. Horizontal gene transfer
accelerates genome innovation and evolution. Mol. Biol. Evol. 20:1598
1602. http://dx.doi.org/10.1093/molbev/msg154.
500. Liu Y, Harrison PM, Kunin V, Gerstein M. 2004. Comprehensive
analysis of pseudogenes in prokaryotes: widespread gene decay and fail-
ure of putative horizontally transferred genes. Genome Biol. 5:R64. http:
//dx.doi.org/10.1186/gb-2004-5-9-r64.
501. Selman M, Corradi N. 2011. Microsporidia: horizontal gene transfers in
vicious parasites. Mob. Genet. Elements 1:251255. http://dx.doi.org/10
.4161/mge.18611.
502. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH,
Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L,
Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM,
Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J,
Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith
HO, Venter JC, Fraser CM. 1999. Evidence for lateral gene transfer
between archaea and bacteria fromgenome sequence of Thermotoga ma-
ritima. Nature 399:323329. http://dx.doi.org/10.1038/20601.
503. Navarre WW, McClelland M, Libby SJ, Fang FC. 2007. Silencing of
xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria
by a defense system that recognizes foreign DNA. Genes Dev. 21:1456
1471. http://dx.doi.org/10.1101/gad.1543107.
504. Beaber JW, Hochhut B, Waldor MK. 2004. SOS response promotes
horizontal dissemination of antibiotic resistance genes. Nature 427:72
74. http://dx.doi.org/10.1038/nature02241.
505. Hastings PJ, Rosenberg SM, Slack A. 2004. Antibiotic-induced lateral
transfer of antibiotic resistance. Trends Microbiol. 12:401404. http://dx
.doi.org/10.1016/j.tim.2004.07.003.
506. Madsen JS, Burmlle M, Hansen LH, Srensen SJ. 2012. The intercon-
nection between biolm formation and horizontal gene transfer. FEMS
Immunol. Med. Microbiol. 65:183195. http://dx.doi.org/10.1111/j
.1574-695X.2012.00960.x.
507. Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boya-
val P, Fremaux C, Horvath P, Magadan AH, Moineau S. 2010. The
CRISPR/Cas bacterial immune system cleaves bacteriophage and plas-
mid DNA. Nature 468:6771. http://dx.doi.org/10.1038/nature09523.
508. Lawrence JG, Ochman H. 1998. Molecular archaeology of the Esche-
richia coli genome. Proc. Natl. Acad. Sci. U. S. A. 95:94139417. http://dx
.doi.org/10.1073/pnas.95.16.9413.
509. Garcia-Vallve S, Romeu A, Palau J. 2000. Horizontal gene transfer in
bacterial and archaeal complete genomes. Genome Res. 10:17191725.
http://dx.doi.org/10.1101/gr.130000.
510. Kurland CG, Canback B, Berg OG. 2003. Horizontal gene transfer: a
critical view. Proc. Natl. Acad. Sci. U. S. A. 100:96589662. http://dx.doi
.org/10.1073/pnas.1632870100.
511. Kurland CG. 2005. What tangled web: barriers to rampant horizontal gene
transfer. Bioessays 27:741747. http://dx.doi.org/10.1002/bies.20258.
512. Dagan T, Artzy-Randrup Y, Martin W. 2008. Modular networks and
cumulative impact of lateral transfer in prokaryote genome evolution.
Proc. Natl. Acad. Sci. U. S. A. 105:1003910044. http://dx.doi.org/10
.1073/pnas.0800679105.
513. Dagan T, Martin W. 2007. Ancestral genome sizes specify the minimum
rate of lateral gene transfer during prokaryote evolution. Proc. Natl.
Acad. Sci. U. S. A. 104:870875. http://dx.doi.org/10.1073/pnas
.0606318104.
514. Park C, Zhang J. 2012. High expression hampers horizontal gene transfer.
Genome Biol. Evol. 4:523532. http://dx.doi.org/10.1093/gbe/evs030.
515. Lerat E, Daubin V, Moran NA. 2003. From gene trees to organismal
phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS
Biol. 1:E19. http://dx.doi.org/10.1371/journal.pbio.0000019.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

516. Bapteste E, Boucher Y, Leigh J, Doolittle WF. 2004. Phylogenetic
reconstruction and lateral gene transfer. Trends Microbiol. 12:406411.
http://dx.doi.org/10.1016/j.tim.2004.07.002.
517. Cohen O, Gophna U, Pupko T. 2011. The complexity hypothesis revis-
ited: connectivity rather than function constitutes a barrier to horizontal
gene transfer. Mol. Biol. Evol. 28:14811489. http://dx.doi.org/10.1093
/molbev/msq333.
518. Abby SS, Tannier E, Gouy M, Daubin V. 2012. Lateral gene transfer as
a support for the tree of life. Proc. Natl. Acad. Sci. U. S. A. 109:4962
519. Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in
prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102:1433214337. http://dx
.doi.org/10.1073/pnas.0504068102.
520. Homma K, Fukuchi S, Nakamura Y, Gojobori T, Nishikawa K. 2007.
Gene cluster analysis method identies horizontally transferred genes
with high reliability and indicates that they provide the main mechanism
of operon gain in 8 species of gamma-Proteobacteria. Mol. Biol. Evol.
24:805813. http://dx.doi.org/10.1093/molbev/msl206.
521. Maslov S, Krishna S, Pang TY, Sneppen K. 2009. Toolbox model of
evolution of prokaryotic metabolic networks and their regulation. Proc.
.0903206106.
522. Bansal MS, Banay G, Gogarten JP, Shamir R. 2011. Detecting highways
of horizontal gene transfer. J. Comput. Biol. 18:10871114. http://dx.doi
.org/10.1089/cmb.2011.0066.
523. Andersson JO, Andersson SG. 1999. Insights into the evolutionary
process of genome degradation. Curr. Opin. Genet. Dev. 9:664671.
http://dx.doi.org/10.1016/S0959-437X(99)00024-6.
524. Moran NA, Mira A. 2001. The process of genome shrinkage in the obligate
symbiont Buchnera aphidicola. Genome Biol. 2:RESEARCH0054
RESEARCH0054.12. http://dx.doi.org/10.1186/gb-2001-2-12-research0054.
525. Silva FJ, Latorre A, Moya A. 2001. Genome size reduction through
multiple events of gene disintegration in Buchnera APS. Trends Genet.
17:615618. http://dx.doi.org/10.1016/S0168-9525(01)02483-0.
526. Frank AC, Amiri H, Andersson SG. 2002. Genome deterioration: loss of
repeated sequences and accumulation of junk DNA. Genetica 115:112.
http://dx.doi.org/10.1023/A:1016064511533.
527. Moran NA. 2002. Microbial minimalism: genome reduction in bacterial
pathogens. Cell 108:583586. http://dx.doi.org/10.1016/S0092-8674(02)
00665-7.
528. Gomez-Valero L, Latorre A, Silva FJ. 2004. The evolutionary fate of non-
functional DNA in the bacterial endosymbiont Buchnera aphidicola. Mol.
Biol. Evol. 21:21722181. http://dx.doi.org/10.1093/molbev/msh232.
529. Moran NA, Plague GR. 2004. Genomic changes following host restric-
tion in bacteria. Curr. Opin. Genet. Dev. 14:627633. http://dx.doi.org
/10.1016/j.gde.2004.09.003.
530. Bordenstein SR, Reznikoff WS. 2005. Mobile DNA in obligate intracel-
lular bacteria. Nat. Rev. Microbiol. 3:688699. http://dx.doi.org/10
.1038/nrmicro1233.
531. Wernegreen JJ. 2005. For better or worse: genomic consequences of
intracellular mutualismand parasitism. Curr. Opin. Genet. Dev. 15:572
583. http://dx.doi.org/10.1016/j.gde.2005.09.013.
532. Hosokawa T, Kikuchi Y, Nikoh N, Shimada M, Fukatsu T. 2006. Strict
host-symbiont cospeciation and reductive genome evolution in insect
gut bacteria. PLoS Biol. 4:e337. http://dx.doi.org/10.1371/journal.pbio
.0040337.
533. Moran NA, McCutcheon JP, Nakabachi A. 2008. Genomics and evo-
lution of heritable bacterial symbionts. Annu. Rev. Genet. 42:165190.
http://dx.doi.org/10.1146/annurev.genet.41.110306.130119.
534. Moya A, Peret J, Gil R, Latorre A. 2008. Learning how to live together:
genomic insights into prokaryote-animal symbioses. Nat. Rev. Genet.
535. OFallon B. 2008. Population structure, levels of selection, and the evo-
lution of intracellular symbionts. Evolution 62:361373. http://dx.doi
.org/10.1111/j.1558-5646.2007.00289.x.
536. Plague GR, Dunbar HE, Tran PL, Moran NA. 2008. Extensive prolif-
eration of transposable elements in heritable bacterial symbionts. J. Bac-
teriol. 190:777779. http://dx.doi.org/10.1128/JB.01082-07.
537. Feldhaar H, Gross R. 2009. Genome degeneration affects both extracel-
lular and intracellular bacterial endosymbionts. J. Biol. 8:31. http://dx
.doi.org/10.1186/jbiol129.
538. Kikuchi Y, Hosokawa T, Nikoh N, Meng XY, Kamagata Y, Fukatsu T.
2009. Host-symbiont co-speciation and reductive genome evolution in
gut symbiotic bacteria of acanthosomatid stinkbugs. BMCBiol. 7:2. http:
//dx.doi.org/10.1186/1741-7007-7-2.
539. Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D. 2009. Massive
comparative genomic analysis reveals convergent evolution of special-
ized bacteria. Biol. Direct 4:13. http://dx.doi.org/10.1186/1745-6150-4
-13.
540. Newton IL, Bordenstein SR. 2011. Correlations between bacterial ecol-
ogy and mobile DNA. Curr. Microbiol. 62:198208. http://dx.doi.org/10
.1007/s00284-010-9693-3.
541. McCutcheon JP, Moran NA. 2012. Extreme genome reduction in sym-
biotic bacteria. Nat. Rev. Microbiol. 10:1326. http://dx.doi.org/10.1038
/nrmicro2670.
542. Wernegreen JJ. 2012. Strategies of genomic integration within insect-
bacterial mutualisms. Biol. Bull. 223:112122. http://www.biolbull.org
/content/223/1/112.long.
543. Moran NA, McLaughlin HJ, Sorek R. 2009. The dynamics and time
scale of ongoing genomic erosion in symbiotic bacteria. Science 323:
544. Lopez-Sanchez MJ, Neef A, Patino-Navarrete R, Navarro L, Jimenez R,
Latorre A, Moya A. 2008. Blattabacteria, the endosymbionts of cock-
roaches, have small genome sizes and high genome copy numbers. Envi-
ron. Microbiol. 10:34173422. http://dx.doi.org/10.1111/j.1462-2920
.2008.01776.x.
545. Mendonca AG, Alves RJ, Pereira-Leal JB. 2011. Loss of genetic redun-
dancy in reductive genome evolution. PLoS Comput. Biol. 7:e1001082.
http://dx.doi.org/10.1371/journal.pcbi.1001082.
546. Kuo CH, Ochman H. 2009. Deletional bias across the three domains of life.
Genome Biol. Evol. 1:145152. http://dx.doi.org/10.1093/gbe/evp016.
547. Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC,
McGraw EA, Martin W, Esser C, Ahmadinejad N, Wiegand C,
Madupu R, Beanan MJ, Brinkac LM, Daugherty SC, Durkin AS,
Kolonay JF, Nelson WC, Mohamoud Y, Lee P, Berry K, Young MB,
Utterback T, Weidman J, Nierman WC, Paulsen IT, Nelson KE,
Tettelin H, ONeill SL, Eisen JA. 2004. Phylogenomics of the reproduc-
tive parasite Wolbachia pipientis wMel: a streamlined genome overrun by
mobile genetic elements. PLoS Biol. 2:E69. http://dx.doi.org/10.1371
/journal.pbio.0020069.
548. Bordenstein SR, Wernegreen JJ. 2004. Bacteriophage ux in endosym-
bionts (Wolbachia): infection frequency, lateral transfer, and recombina-
tion rates. Mol. Biol. Evol. 21:19811991. http://dx.doi.org/10.1093
/molbev/msh211.
549. Moliner C, Fournier PE, Raoult D. 2010. Genome analysis of microorgan-
isms living in amoebae reveals a melting pot of evolution. FEMS Microbiol.
Rev. 34:281294. http://dx.doi.org/10.1111/j.1574-6976.2009.00209.x.
550. Bertelli C, Greub G. 2012. Lateral gene exchanges shape the genomes of
amoeba-resisting microorganisms. Front. Cell. Infect. Microbiol. 2:110.
http://dx.doi.org/10.3389/fcimb.2012.00110.
551. Lamrabet O, Merhej V, Pontarotti P, Raoult D, Drancourt M. 2012.
The genealogic tree of mycobacteria reveals a long-standing sympatric
life into free-living protozoa. PLoS One 7:e34754. http://dx.doi.org/10
.1371/journal.pone.0034754.
552. Doolittle WF, Sapienza C. 1980. Selsh genes, the phenotype paradigm
and genome evolution. Nature 284:601603. http://dx.doi.org/10.1038
/284601a0.
553. Orgel LE, Crick FH. 1980. Selsh DNA: the ultimate parasite. Nature
284:604607. http://dx.doi.org/10.1038/284604a0.
554. Kobayashi I. 1998. Selshness and death: raison detre of restriction,
recombination and mitochondria. Trends Genet. 14:368374. http://dx
.doi.org/10.1016/S0168-9525(98)01532-7.
555. Kidwell MG, Lisch DR. 2001. Perspective: transposable elements, par-
asitic DNA, and genome evolution. Evolution 55:124. http://dx.doi.org
/10.1111/j.0014-3820.2001.tb01268.x.
556. Lan R, Reeves PR. 1996. Gene transfer is a major factor in bacterial evolu-
tion. Mol. Biol. Evol. 13:4755. http://dx.doi.org/10.1093/oxfordjournals
.molbev.a025569.
557. Doolittle WF. 1999. Phylogenetic classication and the universal tree. Sci-
ence 284:21242129. http://dx.doi.org/10.1126/science.284.5423.2124.
558. Spratt BG, Hanage WP, Feil EJ. 2001. The relative contributions of
recombination and point mutation to the diversication of bacterial
clones. Curr. Opin. Microbiol. 4:602606. http://dx.doi.org/10.1016
/S1369-5274(00)00257-5.
559. Mira A, Klasson L, Andersson SG. 2002. Microbial genome evolution:

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

sources of variability. Curr. Opin. Microbiol. 5:506512. http://dx.doi
.org/10.1016/S1369-5274(02)00358-2.
560. Kunin V, Ouzounis CA. 2003. The balance of driving forces during
genome evolution in prokaryotes. Genome Res. 13:15891594. http://dx
.doi.org/10.1101/gr.1092603.
561. Lerat E, Daubin V, Ochman H, Moran NA. 2005. Evolutionary origins
of genomic repertoires in bacteria. PLoS Biol. 3:e130. http://dx.doi.org
/10.1371/journal.pbio.0030130.
562. Lopez P, Bapteste E. 2009. Molecular phylogeny: reconstructing the
forest. C. R. Biol. 332:171182. http://dx.doi.org/10.1016/j.crvi.2008.07
.003.
563. Olendzenski L, Gogarten JP. 2009. Evolution of genes and organisms:
the tree/web of life in light of horizontal gene transfer. Ann. N. Y. Acad.
Sci. 1178:137145. http://dx.doi.org/10.1111/j.1749-6632.2009.04998.x.
564. Raoult D. 2010. The post-Darwinist rhizome of life. Lancet 375:104
105. http://dx.doi.org/10.1016/S0140-6736(09)61958-9.
565. Woese C. 1998. The universal ancestor. Proc. Natl. Acad. Sci. U. S. A.
95:68546859. http://dx.doi.org/10.1073/pnas.95.12.6854.
566. Vetsigian K, Woese C, Goldenfeld N. 2006. Collective evolution and the
genetic code. Proc. Natl. Acad. Sci. U. S. A. 103:1069610701. http://dx
.doi.org/10.1073/pnas.0603780103.
567. Lawrence JG, Roth JR. 1996. Selsh operons: horizontal transfer may
drive the evolution of gene clusters. Genetics 143:18431860.
568. Ballouz S, Francis AR, Lan R, Tanaka MM. 2010. Conditions for the
evolution of gene clusters in bacterial genomes. PLoS Comput. Biol.
6:e1000672. http://dx.doi.org/10.1371/journal.pcbi.1000672.
569. Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA. 2007.
How gene order is inuenced by the biophysics of transcription regula-
tion. Proc. Natl. Acad. Sci. U. S. A. 104:1394813953. http://dx.doi.org
/10.1073/pnas.0700672104.
570. Fang G, Rocha EP, Danchin A. 2008. Persistence drives gene clustering
in bacterial genomes. BMC Genomics 9:4. http://dx.doi.org/10.1186
/1471-2164-9-4.
571. Price MN, Huang KH, Arkin AP, Alm EJ. 2005. Operon formation is
driven by co-regulation and not by horizontal gene transfer. Genome
Res. 15:809819. http://dx.doi.org/10.1101/gr.3368805.
572. Pal C, Hurst LD. 2004. Evidence against the selsh operon theory.
Trends Genet. 20:232234. http://dx.doi.org/10.1016/j.tig.2004.04.001.
573. Davids W, Zhang Z. 2008. The impact of horizontal gene transfer in
shaping operons and protein interaction networksdirect evidence of
preferential attachment. BMCEvol. Biol. 8:23. http://dx.doi.org/10.1186
/1471-2148-8-23.
574. Feil EJ, Spratt BG. 2001. Recombination and the population structures
of bacterial pathogens. Annu. Rev. Microbiol. 55:561590. http://dx.doi
.org/10.1146/annurev.micro.55.1.561.
575. Rivera MC, Lake JA. 2004. The ring of life provides evidence for a
genome fusion origin of eukaryotes. Nature 431:152155. http://dx.doi
.org/10.1038/nature02848.
576. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. 2005. The net of
life: reconstructing the microbial phylogenetic network. Genome Res.
15:954959. http://dx.doi.org/10.1101/gr.3666505.
577. Zhaxybayeva O, Lapierre P, Gogarten JP. 2005. Ancient gene duplica-
tions and the root(s) of the tree of life. Protoplasma 227:5364. http://dx
.doi.org/10.1007/s00709-005-0135-1.
578. Dagan T, Martin W. 2006. The tree of one percent. Genome Biol. 7:118.
http://dx.doi.org/10.1186/gb-2006-7-10-118.
579. Koonin EV. 2009. Darwinian evolution in the light of genomics. Nucleic
Acids Res. 37:10111034. http://dx.doi.org/10.1093/nar/gkp089.
580. Beauregard-Racine J, Bicep C, Schliep K, Lopez P, Lapointe FJ, Bap-
teste E. 2011. Of woods and webs: possible alternatives to the tree of life
for studying genomic uidity in E. coli. Biol. Direct 6:39. http://dx.doi
.org/10.1186/1745-6150-6-39.
581. Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam
CP, Gogarten JP. 2011. A rooted net of life. Biol. Direct 6:45. http://dx
.doi.org/10.1186/1745-6150-6-45.
582. Snel B, Bork P, Huynen MA. 1999. Genome phylogeny based on gene
content. Nat. Genet. 21:108110. http://dx.doi.org/10.1038/5052.
583. Brochier C, Bapteste E, Moreira D, Philippe H. 2002. Eubacterial
phylogeny based on translational apparatus proteins. Trends Genet. 18:
15. http://dx.doi.org/10.1016/S0168-9525(01)02522-7.
584. Daubin V, Gouy M, Perriere G. 2002. A phylogenomic approach to
bacterial phylogeny: evidence of a core of genes sharing a common his-
tory. Genome Res. 12:10801090. http://dx.doi.org/10.1101/gr.187002.
585. Wolf YI, Rogozin IB, Grishin NV, Koonin EV. 2002. Genome trees and
the Tree of Life. Trends Genet. 18:472479. http://dx.doi.org/10.1016
/S0168-9525(02)02744-0.
586. Daubin V, Moran NA, Ochman H. 2003. Phylogenetics and the cohe-
sion of bacterial genomes. Science 301:829832. http://dx.doi.org/10
.1126/science.1086568.
587. Gu X, Zhang H. 2004. Genome phylogenetic analysis based on extended
gene contents. Mol. Biol. Evol. 21:14011408. http://dx.doi.org/10.1093
/molbev/msh138.
588. Lienau EK, DeSalle R, Rosenfeld JA, Planet PJ. 2006. Reciprocal illu-
mination in the gene content tree of life. Syst. Biol. 55:441453. http://dx
.doi.org/10.1080/10635150600697416.
589. House CH. 2009. The Tree of Life viewed through the contents of ge-
nomes. Methods Mol. Biol. 532:141161. http://dx.doi.org/10.1007/978
-1-60327-853-9_8.
590. Horiike T, Miyata D, Tateno Y, Minai R. 2011. HGT-Gen: a tool for
generating a phylogenetic tree with horizontal gene transfer. Bioinfor-
mation 7:211213. http://dx.doi.org/10.6026/97320630007211.
591. Forterre P. 2012. Darwins goldmine is still open: variation and selection
run the world. Front. Cell. Infect. Microbiol. 2:106. http://dx.doi.org/10
.3389/fcimb.2012.00106.
592. Fox GE, Wisotzkey JD, Jurtshuk P, Jr. 1992. How close is close: 16S rRNA
sequence identity may not be sufcient to guarantee species identity. Int. J.
Syst. Bacteriol. 42:166170. http://dx.doi.org/10.1099/00207713-42-1-166.
593. CohanFM. 2002. What are bacterial species? Annu. Rev. Microbiol. 56:457
594. Doolittle WF, Papke RT. 2006. Genomics and the bacterial species prob-
lem. Genome Biol. 7:116. http://dx.doi.org/10.1186/gb-2006-7-9-116.
595. Konstantinidis KT, Ramette A, Tiedje JM. 2006. The bacterial species
denition in the genomic era. Philos. Trans. R. Soc. Lond. B Biol. Sci.
361:19291940. http://dx.doi.org/10.1098/rstb.2006.1920.
596. Franklin L. 2007. Bacteria, sex, and systematics. Philos. Sci. 74:6995.
http://dx.doi.org/10.1086/519476.
597. Caro-Quintero A, Konstantinidis KT. 2012. Bacterial species may exist,
metagenomics reveal. Environ. Microbiol. 14:347355. http://dx.doi.org
/10.1111/j.1462-2920.2011.02668.x.
598. Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. 2011. Bacterial
community assembly based on functional genes rather than species.
Proc. Natl. Acad. Sci. U. S. A. 108:1428814293. http://dx.doi.org/10
.1073/pnas.1101591108.
599. Koonin EV, Wolf YI. 2009. Is evolution Darwinian or/and Lamarckian?
Biol. Direct 4:42. http://dx.doi.org/10.1186/1745-6150-4-42.
600. Haerter JO, Sneppen K. 2012. Spatial structure and Lamarckian adap-
tation explain extreme genetic diversity at CRISPR locus. mBio 3(4):
e0012612. http://dx.doi.org/10.1128/mBio.00126-12.
601. Podglajen I, Breuil J, Collatz E. 1994. Insertion of a novel DNA se-
quence, IS1186, upstream of the silent carbapenemase gene cA, pro-
motes expression of carbapenem resistance in clinical isolates of Bacte-
roides fragilis. Mol. Microbiol. 12:105114. http://dx.doi.org/10.1111/j
.1365-2958.1994.tb00999.x.
602. Coyne S, Courvalin P, Galimand M. 2010. Acquisition of multidrug
resistance transposon Tn6061 and IS6100-mediated large chromosomal
inversions inPseudomonas aeruginosa clinical isolates. Microbiology 156:
14481458. http://dx.doi.org/10.1099/mic.0.033639-0.
603. Martin C, Gomez-Lus R, Ortiz JM, Garcia-Lobo JM. 1987. Structure
and mobilization of an ampicillin and gentamicin resistance determi-
nant. Antimicrob. Agents Chemother. 31:12661270. http://dx.doi.org
/10.1128/AAC.31.8.1266.
604. Franke AE, Clewell DB. 1981. Evidence for a chromosome-borne resis-
tance transposon(Tn916) inStreptococcus faecalis that is capable of con-
jugal transfer in the absence of a conjugative plasmid. J. Bacteriol. 145:
494502.
605. Ulycznyj PI, Salmon KA, Douillard H, DuBow MS. 1995. Character-
ization of the Pseudomonas aeruginosa transposable bacteriophage
D3112 A and B genes. Biochim. Biophys. Acta 1264:249253. http://dx
.doi.org/10.1016/0167-4781(95)00186-7.
606. Pattee PA. 1981. Distribution of Tn551 insertion sites responsible for
auxotrophy on the Staphylococcus aureus chromosome. J. Bacteriol. 145:
479488.
607. Reddy SP, Rasmussen WG, Baseman JB. 1996. Isolation and charac-
terization of transposon Tn4001-generated, cytadherence-decient
transformants of Mycoplasma pneumoniae and Mycoplasma genitalium.
Darmon and Leach

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

FEMS Immunol. Med. Microbiol. 15:199211. http://dx.doi.org/10
.1111/j.1574-695X.1996.tb00086.x.
608. Briolat V, Reysset G. 2002. Identication of the Clostridium perfringens
genes involved in the adaptive response to oxidative stress. J. Bacteriol.
184:23332343. http://dx.doi.org/10.1128/JB.184.9.2333-2343.2002.
609. Roberts AP, Mullany P. 2009. Amodular master on the move: the Tn916
family of mobile genetic elements. Trends Microbiol. 17:251258. http:
//dx.doi.org/10.1016/j.tim.2009.03.002.
610. Nurk A, Tamm A, Horak R, Kivisaar M. 1993. In-vivo-generated fusion
promoters in Pseudomonas putida. Gene 127:2329. http://dx.doi.org/10
.1016/0378-1119(93)90612-7.
611. Lers A, Bitoun R, Zamir A. 1989. Outreading promoters are located at
both ends of the gamma-delta transposon. Mol. Gen. Genet. 216:138
143. http://dx.doi.org/10.1007/BF00332242.
612. Ciampi MS, Schmid MB, Roth JR. 1982. Transposon Tn10 provides a
promoter for transcription of adjacent sequences. Proc. Natl. Acad. Sci.
U. S. A. 79:50165020. http://dx.doi.org/10.1073/pnas.79.16.5016.
613. Lin TP, Lai EM, To KY, Chang YS, Liu ST. 1994. Transcriptional
activation of anking sequences by Tn1000 insertion. Mol. Gen. Genet.
245:417423. http://dx.doi.org/10.1007/BF00302253.
614. Ou X, Zhang B, Zhang L, Zhao G, Ding X. 2009. Characterization of
rrdA, a TetR family protein gene involved in the regulation of secondary
metabolism in Streptomyces coelicolor. Appl. Environ. Microbiol. 75:
21582165. http://dx.doi.org/10.1128/AEM.02209-08.
615. Rakin A, Noelting C, Schubert S, Heesemann J. 1999. Common and
specic characteristics of the high-pathogenicity island of Yersinia en-
terocolitica. Infect. Immun. 67:52655274.
616. Rouquette-Loughlin CE, Balthazar JT, Hill SA, Shafer WM. 2004. Mod-
ulation of the mtrCDE-encoded efux pump gene complex of Neisseria
meningitidis due to a Correia element insertion sequence. Mol. Micro-
biol. 54:731741. http://dx.doi.org/10.1111/j.1365-2958.2004.04299.x.
617. Teras R, Hrak R, Kivisaar M. 2000. Transcription from fusion pro-
moters generated during transposition of transposon Tn4652 is posi-
tively affected by integration host factor in Pseudomonas putida. J. Bac-
teriol. 182:589598. http://dx.doi.org/10.1128/JB.182.3.589-598.2000.
618. De Gregorio E, Silvestro G, Petrillo M, Carlomagno MS, Di Nocera PP.
2005. Enterobacterial repetitive intergenic consensus sequence repeats in
yersiniae: genomic organization and functional properties. J. Bacteriol. 187:
79457954. http://dx.doi.org/10.1128/JB.187.23.7945-7954.2005.
619. Shimoji Y, Mori Y, Sekizaki T, Shibahara T, Yokomizo Y. 1998.
Construction and vaccine potential of acapsular mutants of Erysipelo-
thrix rhusiopathiae: use of excision of Tn916 to inactivate a target gene.
Infect. Immun. 66:32503254.
620. Foster TJ, Lundblad V, Hanley-Way S, Halling SM, Kleckner N. 1981.
Three Tn10-associated excision events: relationship to transposition and
role of direct and inverted repeats. Cell 23:215227. http://dx.doi.org/10
.1016/0092-8674(81)90286-5.
621. Swartley JS, McAllister CF, Hajjeh RA, Heinrich DW, Stephens DS.
1993. Deletions of Tn916-like transposons are implicated in tetM-
mediated resistance in pathogenic Neisseria. Mol. Microbiol. 10:299
622. Merrick M, Filser M, Dixon R, Elmerich C, Sibold L, Houmard J. 1980.
The use of translocatable genetic elements to construct a ne-structure
map of the Klebsiella pneumoniae nitrogen xation (nif) gene cluster. J.
Gen. Microbiol. 117:509520.
623. Nisen PD, Kopecko DJ, Chou J, Cohen SN. 1977. Site-specic DNA
deletions occurring adjacent to the termini of a transposable ampicillin
resistance element (Tn3). J. Mol. Biol. 117:975978. http://dx.doi.org/10
.1016/S0022-2836(77)80008-9.
624. Csonka LN, Clark AJ. 1979. Deletions generated by the transposon Tn10
in the srl recA region of the Escherichia coli K-12 chromosome. Genetics
93:321343.
625. Faelen M, Toussaint A. 1978. Stimulation of deletions in the Escherichia
coli chromosome by partially induced Mucts62 prophages. J. Bacteriol.
136:477483.
626. Song H, Hwang J, Yi H, Ulrich RL, Yu Y, Nierman WC, Kim HS. 2010.
The early stage of bacterial genome-reductive evolution in the host. PLoS
Pathog. 6:e1000922. http://dx.doi.org/10.1371/journal.ppat.1000922.
627. Claus H, Elias J, Meinhardt C, Frosch M, Vogel U. 2007. Deletion of the
meningococcal fetA gene used for antigen sequence typing of invasive and
commensal isolates from Germany: frequencies and mechanisms. J. Clin.
Microbiol. 45:29602964. http://dx.doi.org/10.1128/JCM.00696-07.
628. Weber PC, Levine M, Glorioso JC. 1988. Simple assay for quantitation
of Tn5 inversion events in Escherichia coli and use of the assay in deter-
mination of plasmid copy number. J. Bacteriol. 170:49724975.
629. Rice LB, Carias LL, Marshall S, Rudin SD, Hutton-Thomas R. 2005.
Tn5386, a novel Tn916-like mobile element inEnterococcus faeciumD344R
that interacts with Tn916 to yield a large genomic deletion. J. Bacteriol.
187:66686677. http://dx.doi.org/10.1128/JB.187.19.6668-6677.2005.
630. Cabezn T, Faelen M, De Wilde M, Bollen A, Thomas R. 1975.
Expression of ribosomal protein genes in Escherichia coli. Mol. Gen.
Genet. 137:125129. http://dx.doi.org/10.1007/BF00341678.
631. Haack KR, Roth JR. 1995. Recombination between chromosomal IS200
elements supports frequent duplication formation in Salmonella typhi-
murium. Genetics 141:12451252.
632. Sinclair MI, Holloway BW. 1991. Chromosomal insertion of TOL trans-
posons in Pseudomonas aeruginosa PAO. J. Gen. Microbiol. 137:1111
1120. http://dx.doi.org/10.1099/00221287-137-5-1111.
633. Chumley FG, Roth JR. 1980. Rearrangement of the bacterial chromo-
some using Tn10 as a region of homology. Genetics 94:114.
634. Daveran-Mingot ML, Campo N, Ritzenthaler P, Le Bourgeois P. 1998.
A natural large chromosomal inversion in Lactococcus lactis is mediated
by homologous recombination between two insertion sequences. J. Bac-
teriol. 180:48344842.
635. Chiang SJ, Clowes RC. 1980. Intramolecular transposition and inver-
sion in plasmid R6K. J. Bacteriol. 142:668682.
636. Scott AE, Timms AR, Connerton PL, Loc Carrillo C, Adzfa Radzum K,
Connerton IF. 2007. Genome dynamics of Campylobacter jejuni in re-
sponse to bacteriophage predation. PLoS Pathog. 3:e119. http://dx.doi
.org/10.1371/journal.ppat.0030119.
637. Weightman AJ, Topping AW, Hill KE, Lee LL, Sakai K, Slater JH,
Thomas AW. 2002. Transposition of DEH, a broad-host-range trans-
poson anked by ISPpu12, in Pseudomonas putida is associated with
genomic rearrangements and dehalogenase gene silencing. J. Bacteriol.
184:65816591. http://dx.doi.org/10.1128/JB.184.23.6581-6591.2002.
638. Desmet L, Faelen M, Lefbvre N, Rsibois A, Toussaint A, van Gijsegem
F. 1981. Genetic study of MutranspositionandMu-mediatedchromosomal
rearrangements. Cold Spring Harb. Symp. Quant. Biol. 45(Part 1):355363.
639. Reimmann C, Haas D. 1987. Mode of replicon fusion mediated by the
duplicated insertion sequence IS21 in Escherichia coli. Genetics 115:619
625.
640. Mahillon J, Lereclus D. 1988. Structural and functional analysis of
Tn4430: identication of an integrase-like protein involved in the co-
integrate-resolution process. EMBO J. 7:15151526.
641. Robillard NJ, Tally FP, Malamy MH. 1985. Tn4400, a compound
transposonisolated fromBacteroides fragilis, functions inEscherichia coli.
J. Bacteriol. 164:12481255.
642. Shoemaker NB, Li L-Y, Salyers AA. 1994. An unusual type of cointe-
grate formation between a Bacteroides plasmid and the excised circular
form of an integrated element (NBU1). Plasmid 32:312317. http://dx
.doi.org/10.1006/plas.1994.1070.
643. Faelen M, Toussaint A. 1980. Chromosomal rearrangements induced
by temperate bacteriophage D108. J. Bacteriol. 143:10291030.

o
n

J
u
n
e

8
,

2
0
1
4

b
y

P
O
N
T
I
F
I
C
I
A

U
N
I
V

J
A
V
E
R
I
A
N
A
h
t
t
p
:
/
/
m
m
b
r
.
a
s
m
.
o
r
g
/
D
o
w
n
l
o
a
d
e
d

f
r
o
m

Microbiol. Mol. Biol. Rev.-2014-Darmon-1-39

Uploaded by

Copyright:

Available Formats

Microbiol. Mol. Biol. Rev.-2014-Darmon-1-39

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Microbiol. Mol. Biol. Rev.-2014-Darmon-1-39

Uploaded by

Copyright:

Available Formats

10.1128/MMBR.00035-13.

2014, 78(1):1. DOI: Microbiol. Mol. Biol. Rev.

Bacterial Genome Instability

You might also like