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Adaptation and Immunity

Eddie C. Holmes

T
he ongoing battle between change; dN) often greatly exceed because the luxury of adaptive
hosts and pathogens has long those of synonymous substitution per immunity is not available to most
been of interest to evolutionary site (silent change; dS), as expected if organisms, having probably evolved
biologists. Because hosts and pathogens most mutations are fixed because they along with the vertebrates (Bartl et al.
act as environments for each other, increase fitness (Figure 1). 1994), whereas the more widespread
their intertwined struggle for At the host level, most studies of the innate immune system is often depicted
existence is both continual and rapid. selection pressures acting on immune as a primitive characteristic.
At the molecular level, this cycle of system genes have concentrated on
environmental change and evolutionary genes implicated in the adaptive Molecular Evolution of the Innate
response means that mutations are immune response against microbial Immune System
continually being tried out by natural pathogens, particularly those producing The genes involved in innate
selection. It is therefore little wonder antibodies (Sitnikova and Nei 1998; immunity have recently come under
that the host and pathogen genes Sumiyama et al. 2002), or genes the molecular evolutionists’ gaze. One
that control infection and immunity encoding reconnaissance molecules important group are the defensins,
frequently show high levels of genetic known as the major histocompatibility a large class of short antimicrobial
diversity and present some of the best complex (MHC), which control the peptides that constitute an effective
examples of positive selection (adaptive action of T-cells (Hughes and Nei immune response team in organisms as
evolution) reported to date (Yang 1988; Yeager and Hughes 1999) (Box diverse as plants and primates (Boman
and Bielawski 2000). In particular, 1). As its name suggests, the role of 1995). Because defensins are cationic
rates of nonsynonymous substitution the adaptive immune response is to (positively charged), they are able
per site (resulting in an amino acid stimulate and ‘memorise’ immunity to to interact with negatively charged
specific pathogens. molecules on the surface of microbes
As microbial and permeate their membranes.
pathogens such as Sequence analyses of defensins and
viruses are both similar antimicrobial peptides have
abundant and revealed the telltale signatures of
rapidly evolving, positive selection, with dN greater than
positive selection dS in many comparisons (Hughes
on components 1999; Duda et al. 2002; Maxwell et
of the adaptive al. 2003). Other genes of the innate
immune response immune system also seem to be subject
is often very strong to powerful positive selection. One
(Yeager and dramatic example described in this
Hughes 1999). issue of PLoS Biology is the APOBEC3G
Far less attention gene of primates (Sawyer et al. 2004).
DOI: 10.1371/journal.pbio.0020307.g001 has been directed This case is especially striking because
Figure 1. Measuring Selection Pressures by Comparing the Ratio of toward the less rather than killing pathogens through
Nonsynonymous to Synonymous Substitutions Per Site specific innate protein or cellular interactions, like
(A) Classification of substitutions. Nonsynonymous substitutions (‘nonadaptive’) most immune genes, APOBEC3G works
(red) are those that change the amino acid sequence of the immune response,
protein encoded by the gene, while the degeneracy of the genetic
code ensures that synonymous substitutions (yellow) result in the even though this Citation: Holmes EC (2004) Adaptation and immunity.
same amino acid sequence. response requires PLoS Biol 2(9): e307.
(B) Calculation of dN/dS. By assuming that synonymous a wide array of
mutations are neutral and fixed by random genetic drift, genes and acts as Copyright: © 2004 Eddie C. Holmes. This is an
it is possible to determine the mode of selection acting on open-access article distributed under the terms of
nonsynonymous mutations. If all nonsynonymous substitutions the front line of the Creative Commons Attribution License, which
immune defence permits unrestricted use, distribution, and reproduc-
were neutral, then their rate of occurrence per site (dN) would tion in any medium, provided the original work is
be the same as that of synonymous substitutions per site (dS), (Box 1). Would properly cited.
so that dN/dS equals one. A lower ratio of nonsynonymous to we expect the
synonymous substitutions per site (dN/dS < 1) means that some same strength of Abbreviations: C, cytosine; dN, rate of nonsynonymous
proportion of the nonsynonymous mutations are deleterious and substitution per site; dS, rate of synonymous substitu-
removed by purifying selection. Conversely, positive selection positive selection tion per site; GA, guanine-to-adenine; HIV, human
fixes advantageous nonsynonymous mutations faster than genetic on a generalized immunodeficiency virus; MHC, major histocompat-
drift fixes synonymous mutations (dN/dS > 1), although this is ibility complex; U, uracil
pathogen control
usually restricted to a small proportion of amino acid sites within system? This is Eddie C. Holmes is in the Department of Zoology at
any gene. In the hypothetical example of five gene sequences the University of Oxford, Oxford, United Kingdom.
shown here, with dS given above the diagonal and dN below the a question of
E-mail: edward.holmes@zoo.ox.ac.uk
diagonal, there is no evidence for positive selection because the fundamental
mean dN/dS (0.577) is less than one. importance DOI: 10.1371/journal.pbio.0020307

PLoS Biology | www.plosbiology.org 1267 September 2004 | Volume 2 | Issue 9 | e307

 normally able to overcome this burden
Box 1. Glossary of deleterious mutation because of its
remarkable reproductive power; each
Adaptive immune system. The pathogen-specific part of the vertebrate immune system. day, on the order of 1010 virions are
It is comprised of two major arms, antibodies (the humoral response) and T-cells (the cellular produced in a single infected individual
response), both of which lay down an immunological memory for future defence. (Perelson et al. 1996), so that enough
Innate immune system. The nonspecific part of the vertebrate immune system. It has fit and able recruits will make it
a wide variety of components, ranging from lysozymes in saliva to cytokines, defensins, through to the next generation.
interferons, and natural killer cells in a variety of tissues.
Endogenous retroviruses. The (usually) dead remnants of functional retroviruses that
Treating RNA Virus Infections
are now passed on through the germ line like normal genes. It has been estimated that
Through Lethal Mutagenesis
approximately 5% of the human genome is composed of endogenous retroviruses.
The high mutation rates of RNA
viruses mean that adaptively useful
by manipulating the genome sequence scenario is that GA hypermutation genetic variation is produced
of the invading microbe. results in the generation and frequently. The rub, however, is that
The genomes of primates contain incorporation of a multitude of fitness-enhancing mutations are a small
a family of nine APOBEC genes that deleterious mutations that fatally minority, and the preponderance of
encode enzymes involved in the editing disrupt viral functions. This strategy deleterious mutations means that RNA
of RNA and/or DNA through the is likely to work well for retroviruses viruses live on the edge of survival
deamination of cytosine (C), so that like HIV because their genomes are (Domingo 2000). By increasing the
this nucleotide mutates to uracil (U). so compact that individual sequence rate at which deleterious mutations
This is essential for various aspects regions often perform multiple appear, APOBEC3G pushes viruses
of cellular function. APOBEC1, for functions. Under these cramped over this edge, causing a form of
example, is involved in the CU conditions, most mutations are likely ‘lethal mutagenesis’ that results in
editing of apolipoprotein B mRNA to severely disrupt some aspect of their destruction; the rate of mutation
(therein christening the family), viral function and thereby reduce becomes so high that no genome
while another family member, the fitness (Holmes 2003). Indeed, it has can reproduce itself faithfully, and
activation-induced deaminase, has been estimated that the deleterious the population crashes. Intriguingly,
a vital role in adaptive immunity in mutation rate in viruses that replicate researchers designing new antiviral
that it assists in the diversification using RNA polymerases (either reverse drugs have also begun to realise that
of antibodies. Two more enzymes, transcriptase in the case of retroviruses forcing viruses into this sort of ‘error
APOBEC3G and APOBEC3F, form or RNA-dependent RNA polymerase catastrophe’ might be an effective
part of the innate immune system; for other RNA viruses) is on the order way to treat them (Figure 2). There
they function as antiviral agents and of one error per replication cycle, are a growing number of studies in
are being intensively studied in the so that many of the viral progeny which mutagens, such as ribavirin
context of infection with the human produced by replication are defective and 5-fluorouracil, are applied to
immunodeficiency virus (HIV), the (Elena and Moya 1999). HIV is viral infections in vitro and in vivo,
cause of AIDS. In particular, including HIV, in the hope
APOBEC3G targets the that these will induce so
reverse transcription step of many deleterious mutations
the HIV life cycle, in which that the virus suffers an error
the viral genomic RNA is catastrophe and is cleared
converted into proviral DNA, (Loeb et al. 1999; Sierra et al.
which is then integrated into 2000; Crotty et al. 2001; Ruiz-
the host genome (Mangeat Jarabo et al. 2003). The results
et al. 2003). APOBEC3G- produced to date are highly
induced deamination at this encouraging, particularly
stage results in monotonous when these error-inducing
guanine-to-adenine (GA) drugs are combined with
nucleotide changes, a more conventional treatment
phenomenon called GA strategies that aim to reduce
DOI: 10.1371/journal.pbio.0020307.g002
hypermutation that had long the rate of viral replication
been noted by HIV researchers Figure 2. Lethal Mutagenesis As a Means of Controlling RNA Virus (Pariente et al. 2001). The
without a clear understanding Infections discovery that a natural
of its cause. We now know that (A) In a viral population prior to the application of mutagens, antiviral agent, APOBEC3G,
the mean error rate (white) is on the order of one per genome
GA hypermutation is part of per replication (mutations marked by asterisks). (B) If a mutagen probably works in much the
the innate immune response such as ribavirin is then applied to an infected patient, the mean same way should provide even
to retroviral infections. error rate of the virus (black) is increased so that the population more encouragement.
Although there is still crosses a threshold of ‘error catastrophe’; after this point fitness Sadly, however, the
declines dramatically and the population crashes. This drug-
some debate over exactly how induced lethal mutagenesis seems to work more efficiently when pathogens have fought back.
APOBEC3G leads to viral it is used in combination with drugs that reduce the rate of viral The anti-HIV properties of
eradication, the most likely replication. APOBEC3G were discovered

PLoS Biology | www.plosbiology.org 1268 September 2004 | Volume 2 | Issue 9 | e307

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PLoS Biology | www.plosbiology.org 1269 September 2004 | Volume 2 | Issue 9 | e307