Advances in Bioscience and Biotechnology, 2011, 2, 364-379
ABB
doi:10.4236/abb.2011.25054 Published Online October 2011 (http://www.SciRP.org/journal/abb/).
Doubling of crop yield through permutation of metabolic
pathways
Godson O. Osuji*, Tassin K. Brown, Sanique M. South, Justin C. Duncan, Dwiesha Johnson
CARC, Prairie View A & M University, Prairie View, USA.
E-mail: *goosuji@pvamu.edu; cropyielddoublingbiotechnology@yahoo.com
Received 27 July 2011; revised 25 August 2011; accepted 13 September 2011.
ABSTRACT
Hunger and food insecurity can be minimized by
doubling crop yield without increasing cultivated land
area and fertilizer applied. Since plant breeding has
not genetically doubled photosynthesis per unit leaf
area, an approach for doubling crop yield would be
through a biotechnology that reprograms metabolic
pathways in favor of photosynthesis. The anchor of
this biotechnology is glutamate dehydrogenase (GDH)
including the RNAs it synthesizes. Peanut was treated
with stoichiometric combinations of mineral salt solutions to synchronize the GDH subunit polypeptides.
Matured seeds were analyzed for fats by HPLC; the
RNA biosynthetic activity of GDH, and mRNAs encoding yield-specific enzymes by Northern hybridization. In the PK-treated peanut, the GDH-synthesized
RNAs silenced the mRNAs encoding granule-bound
starch synthase, phosphoglucomutase (glycolysis), glucosyltransferase (cellulose biosynthesis), and nitrate
reductase leaving unaffected the mRNAs encoding
acetylcoenzyme A carboxylase (fatty acid biosynthesis), phosphate translocator, and NADH-glutamate
synthase resulting to double seed (4342 kg/ha), cellulose (1829 kg/ha), and fat (1381 kg/ha) yields compared with the controls. Down-regulation of phosphate translocator and acetylcoenzyme A carboxylase
caused decreased pod yields. GDH-synthesized RNAs
that were homologous to yield-specific mRNAs shared
extensive plus/plus and plus/minus sequence similarities, and they reprogrammed metabolism by permuting the partially down-regulated, not down-regulated,
and down-regulated yield-specific pathways. Control
peanut produced 70, NPKS-treated produced 420,
NS-treated produced 1680, and PK-treated produced
280 probable rearrangements of the pathways. Therefore, down-regulation of metabolic reactions followed
by permutation of yield-related pathways, and redistribution of metabolite load to molecularly connected
pathways controls crop yield. Operating as efficient
bioreactor, peanut can be maximized to 10,000 kg
pod/ha, more than enough vegetable oil for nine billion people.
Keywords: Peanut; Fatty Acid Bioreactor; Glutamate
Dehydrogenase; Yield-Specific mRNAs
1. INTRODUCTION
Feeding a hungry humanity that will soon exceed nine
billion people is a major challenge to governments and
farmers, but an opportunity to the scientific community
[1]. More than 850 million people worldwide lack the
food they need [2] for normal growth, development and
an active life. Prospects for a continuation of the food
productivity growth seen between 1940 and 1980 [3,4]
are hindered by climate change, land degradation, and
strained water resources. Low crop yields lead to hunger
and to high cost of food [5]. The short cut to minimize
hunger, food insecurity, and cost of agricultural production is to double crop yield without increasing the cultivated land area, man hour input, fertilizer, pesticides, and
water applied.
The metabolic pathways elegantly show that crop
yield is controlled by many enzymes, but do not show
pathway discrimination and integration for the doubling
of crop yield. The biotechnological opportunity is to enhance those pathways that increase and to knock down
those that hinder storage product accumulation. Much of
such monogenic trait and polygenic control biotechnologies have been addressed with success through plant
breeding, crop protection and plant genetic engineering
approaches [6-11]. The biotechnological logic adopted
hereunder was different being based on permutation of
the metabolic pathways. Since plant breeding has not resulted in a genetic doubling of photosynthesis per unit
leaf area [4], a direct approach for doubling crop yield
would be through the manipulation of mineral ion-regulation of carbon and nitrogen intermediary metabolism
[12], and photosynthesis. The advantage of this approach
Published Online October 2011 in SciRes. http://www.scirp.org/journal/ABB
G. O. Osuji et al. / Advances in Bioscience and Biotechnology 2 (2011) 364-379
is that since there is complicated plethora of enzyme
steps in carbon and nitrogen metabolism, the permutations of the variable enzyme activities leading to maximized storage product accumulation are virtually unlimited. The basis of the yield-maximizing biotechnology
is that mineral ions [12-14] acting as electromagnets, will
alter the oxidative state in the plant cells [15-17] thereby
reprogramming the activities of those enzyme steps that
regulate and/or coordinate metabolite load redistribution
throughout intermediary metabolism with consequent
doubling of respective metabolic end-products. The anchor of the biotechnology is glutamate dehydrogenase
(GDH) including the RNAs it synthesizes which constitute the new gateway into biology. GDH charge isomers
constitute a special electric field in the cell [18]. They are
induced to isomerize and to synthesize some RNAs when
they interface with electromagnets [19]. The RNAs so
synthesized interfere with the translation of their homologous mRNAs [20]. GDH isomerization and the resultant RNAs have been applied to increase yields in soybeans, corn, alfalfa, peanut etc. [21,22]. But the ability of
the GDH-synthesized RNAs to permute metabolic pathways in order to maximize and double crop yield was not
described.
Peanut was chosen for this study because it is a universal food, fiber and oil crop grown on about 42 million
acres worldwide, with India, China, USA, and Nigeria
producing about 80% of the world crop [23]. The oil is
being favorably evaluated for the manufacture of biodiesel. Peanut is ideal for this study because the responses of its yield to applied sulfate, potash, nitrogen,
and phosphate fertilizers [23-27] are so complicated and
conflicting that they have defied biochemical explanation.
Metabolic pathway permutation may illuminate the bioscience of mineral ion reactivity.
In the yield-doubling biotechnology presented hereunder, peanut carbohydrate and fatty acid metabolic pathways acted in concert with the pathways for nitrogen
assimilation through their permutation sequentially and
spatially by the GDH-synthesized RNAs as influenced
by mineral ions to produce record high quantities of fat
and cellulose.
2. EXPERIMENTAL PROCEDURES
Treatment of peanuts with mineral ion solutions: Peanut
(Arachis hypogaea L. Cv. Virginia) seeds were planted in
243.84 × 243.84 × 30.48 cm (width × length × depth)
boxes, each filled with 18 bags of Metro mix 700 peat
moss. Each box was set up on level ground in the field
on Dewitt earth mat, a permeable weed-blocking fabric.
About 100 - 110 seeds were planted per box. There was
replanting to make up for ungerminated seeds. The applied
mineral ion compositions were based on the model com-binations in Table 1 to mimick the binomial subunit poly
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365
Table 1. Some mineral salt combinations mimicking peanut
GDH subunit compositions.
N (25 mM)
NH4Cl
(25 mM)
Na2HPO4
(20 mM)
KCl (4 mM)
Na2SO4
(50 mM)
NN
PN
KN
NS
PP
PK
PS
KK
KS
P (20 mM)
K (4 mM)
S (50 mM)
SS
NN
NNN
PNN
NP
NNP
NPP
NNS
NPK
NPS
KN
KKN
KNS
PK
PKK
PKS
KKS
KSS
PP
PPP
KS
NS
PPS
NNS
NSS
PS
PSS
KK
KKK
SS
NPK
SSS
NNPK
NPPK
NPKK
NPKS
peptide compositions of the GDH isoenzymes [22]. The
first box was left as the untreated control; the second box
(N) was treated with 1 L of NH4Cl solution (25 mM), the
third box (Pi) was treated with 1 L of Na3PO4 solution
(20 mM); the fourth box (S) was treated with 1 L of
Na2SO4 solution (50 mM); the fifth box (K) was treated
with 1 L KCl solution (4 mM); the sixth box (NPKS) was
treated with 1 L of combined NH4Cl (25 mM), Na3PO4
(20 mM), Na2SO4 (50 mM), and KCl (4 mM) solution;
the seventh box (PK) was treated with 1 L of combined
Na3PO4 (20 mM) and KCl (4 mM) solution; the eighth
box (NS) was treated with 1 L of combined NH4Cl (25
mM) and Na2SO4 (50 mM) solution; the ninth box (PN)
was treated with 1 L of combined Na3PO4 (20 mM) and
NH4Cl (25 mM) solution; the tenth box (PS) was treated
with 1 L of combined Na3PO4 (20 mM) and Na2SO4
(50 mM) solution. The boxes were watered every other
day. Mineral nutrient solutions were applied sequentially,
first at pre-flowering stage (2 weeks after seed germination), second at flowering, and third at post-flowering.
When the leaves turned yellow (peanut maturity), pods
were harvested, allowed to dry on the greenhouse floor
for about 2 weeks, weighed, shelled by hand, and the
kernels (seeds) and shells weighed separately. Seeds
were stored at –30˚C.
Analyses for peanut yield: Dry and milled (composited)
seeds (100 g) per experimental treatment, sent to SGS
North America Inc., St. Rose, Louisiana, USA were custom analyzed by HPLC for percent oil weight. Milled
shells (250 g) per experimental treatment, sent to UniABB
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versal Testing, Quincy, IL, USA were custom analyzed
for dry matter, and cellulose (neutral detergent fiber, and
acid detergent fiber) using standard gravimetric method.
Purification and assay of GDH: GDH charge isomers
were purified by electrophoresis as described before [17]
from peanut seeds harvested from the control or mineral
ion-treated boxes. RNA synthetic activity of GDH isoenzymes [22] was assayed in combined deamination and
amination substrate solutions of 0.1 M Tris-HCl buffer
(pH 8.0) containing the four NTPs (0.6 mM each), CaCl2
(3.5 mM), L-glu (3.23 µM), NAD+ (0.375 µM), NH4Cl
(0.875 mM), α-ketoglutarate (10.0 mM), NADH (0.225
mM), 5 Units RNase inhibitor, 1 Unit DNase 1, and 5 µg
of actinomycin D. Reaction was started by adding 0.2
mL of whole gel-eluted GDH charge isomers containing
3 - 9 µg protein per mL. Final volume of the reaction
was brought to 0.4 mL with 0.1M Tris-HCl buffer pH 8.0.
Reactions were incubated at 16˚C overnight and stopped
by phenol-chloroform (pH 5.5) extraction of the enzyme.
RNA was precipitated with ethanol, and dissolved in minimum volume of molecular biology quality water. RNA
yield and quality were determined by photometry and by
agarose gel electrophoresis. Assays were carried out in
duplicate to verify the reproducibility of the results.
Total RNA: Total RNA was extracted from peanut
seeds harvested from the control or mineral-treated boxes
using the acidic phenol/chloroform (pH 4.5) method
[28].
cDNA synthesis, cloning, characterization, and probe
selection: cDNAs were synthesized with 2 µg of each
product RNA synthesized by the whole gel-eluted GDH
charge isomers using random hexamer primer. Restriction fragment PCR amplification; adapter ligation; sequencing gel fractionation; and purification of cDNA
fragments [22] were conducted according to the methods
of Display Systems Biotech, Vista, CA, USA. Selected
cDNA fragments were subcloned into pCR4-TOPO vector and transformed into TOP10 One Shot Chemically
Competent Escherichia coli (Invitrogen, Carlsbad, CA),
followed by overnight growth on selective plates. Up to
ten positive transformant colonies were picked per plate
and cultured overnight in LB medium containing 50
µg/mL of kanamycin. Plasmid DNA was purified with a
plasmid kit (Novagen, Madison, WI). The insert cDNA
was sequenced with T3 and T7 primers by Genemed
Synthesis, Inc. (South San Francisco, CA, USA), and
Functional Biosciences, Inc. (Madison, WI, USA). To
identify the GDH-synthesized RNAs that were homologous to mRNAs encoding the crop yield-related enzymes,
the cDNA sequences were used as queries to search the
NCBI nucleotide-nucleotide (excluding ESTs) BLAST
(blastn), and non-redundant protein translation (blastx)
databases. cDNAs that displayed the highest alignment
Copyright © 2011 SciRes.
scores with mRNAs encoding the enzymes of photosynthesis, nitrogen assimilation, glycolysis, cellulose, fatty
acid, and nucleotide biosyntheses [20,29,30] were selected as the probes.
Northern blot analysis: Equal amounts (10 µg) of total
RNA, and RNAs synthesized by GDH charge isomers
from the control and mineral nutrients-treated peanuts
were loaded, briefly electrophoresed on 2% agarose gels,
stained with ethidium bromide, and photographed to verify RNA quality. RNA was electro-transferred from the
electrophoresed gel onto Brightstar-Plus nylon membrane (Applied Biosystems, Foster City, CA, USA) as
described before [30].
The cDNAs that were used as Northern probes were
those homologous to mRNAs encoding phosphate translocator, granule-bound starch synthase (GBSS), phosphoglucomutase (PGM), glucosyltransferase, acetyl CoA
carboxylase (ACCase), NADH-glutamate synthase (GOGAT), nitrate reductase (NR), glycinamide ribonucleotide (GAR) synthetase/GAR transformylase. For the labeling of the cDNA probes, cDNA inserts were amplified by PCR from the corresponding plasmids (15 ng)
using M13 forward and M13 reverse primers (2 µM
each), [32P]-dATP (6000 Ci/mmol, 20 mCi/mL), dCTP/
dGTP/TTP mix 50 mM, (2 µL), and Taq polymerase
(1U), in a final volume of 50 µL. Amplification was according to Display Systems Biotech (Vista, CA, USA)
“touch-down” PCR procedure (denature: 94˚C, 1 min for
the first 10 cycles: 94˚C, 30 sec; anneal: 60˚C, 30 sec for
the first cycle, then reduced the temperature 0.5˚C each
cycle until an annealing temperature of 55˚C was
reached after 10 cycles; extension: 72˚C, 1 min. Continued another 25 cycles with 94˚C, 30 sec; 55˚C, 30 sec;
72˚C, 1 min; final extension 72˚C, 5 min). Nylon membranes with immobilized RNA were prehybridized with
ULTRAhyb buffer and hybridized with 32P-labeled
cDNA inserts as probes overnight at 68˚C as described
before [30]. Solutions of labeled cDNA were first heated
in boiling water bath for 10 min before adding to the
prehybridized membrane. After hybridization, the membranes were washed (30 min, 68˚C) with NorthernMax
(Applied Biosystems, Foster City, CA, USA) low stringency wash solution followed by NorthernMax high
stringency wash solution (30 min, 68˚C). The membrane
was autoradiographed by exposure to X-ray film within
intensifying screens at –80˚C. Northern band intensities
were digitalized using UN-SCAN-IT gel digitalizing
software (Silk Scientific, Inc., Orem, Utah, USA).
3. RESULTS
1) Mineral ion treatments: as was done previously [15,
18,22], mineral ion compositions were formulated to
mimic the stoichiometric ratios of, and to synchronize
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the subunit polypeptide compositions of GDH (Table 1).
This comprehensive rainbow of minerals made for internal repeats in the mineral ion compositions thus limiting
stochastic variability in peanut plot treatments, imposed
a firm control on the number of experimental repeats,
and consolidated the biochemical comprehensiveness of
the project design [30]. These conditions assured the
most efficient production metabolism of the peanuts as
natural bioreactor through synchronization in the isomerization of GDH, synthesis of RNA by GDH, silencing of
mRNAs by homologous RNAs synthesized by GDH,
structural and spatial integration of the yield-related
metabolic pathways leading at crop maturity to the doubling of pod yield.
2) Mineral ions, GDH isomerization and RNA synthesis: isoelectric focusing of GDH followed by native
polyacrylamide gel electrophoresis fractionated the charge
isomers to their isoenzymes. The isoenzymes focused in
almost the same 8 - 9 Rotofor chambers (Figures 1(a)-(k))
irrespective of mineral treatments thus confirming process reproducibility and the firm control imposed on random variability in treatments and experiments. The GDH
isoenzyme population patterns were also generally in
agreement with the expected binomial distribution of the
three subunits in the hexameric isoenzymes, on the basis
of the twin nonallelic GDH1 and GDH2 gene structure,
with the gene (GDH1) encoding the more acidic subunits
(a and α) being heterozygous and codominant, whereas
the other gene (GDH2) encoding the less acidic subunit
(β) is homozygous [31]. Although the isoenzyme distribution patterns appeared to be identical, the RNAs that
the isoenzyme population synthesized were dramatically
different. The abundant RNA bands in the arrays of
GDH-synthesized RNAs were the 4.5 kb, 2 kb, and 0.1
kb bands [22]. There was a fourth one of very high molecular weight (>10 kb). The proportions of the four
bands differed for each mineral-treated peanut (Figures
1(i)-(x)). The differences in the GDH isoenzyme populations and in the RNAs that the isoenzymes synthesized
constituted the molecular basis for the yield doubling
biotechnology. The GDH isoenzyme population taken together with the array of RNA synthesized per mineral
regiment (Figure 1) described the biochemical comprehensiveness of the research approach.
3) Northern hybridization: the Northern hybridization
results described the molecular mechanism of metabolic
pathway permutation. The Northern blots determined the
population distribution of probe per array of GDH-synthesized RNA, the threshold quantities of the probes per
GDH-synthesized RNA, the mRNAs that were homologous to the probes, GDH-synthesized RNA present in
total RNA; and confirmed absence of total RNA from
GDH-synthesized RNA preparations. The control peanut
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367
without mineral ion treatment was the negative control;
the NPKS-treated peanut with the full mineral ion composition and concentration was the positive control for
verification of the bioscience of silencing by GDH-synthesized RNA [29]. The probes (Table 2) were cDNAs
of the GDH-synthesized RNAs that were homologous to
mRNAs. Some of the cDNA probes (for the mRNAs encoding Pi translocator, glucosyltransferase, and nitrate
reductase) have been reported before [15,22]. Two probes (3E, and 48Q) were used for detection/quantitation of
the GDH-synthesized RNA and mRNAs encoding glycinamide ribonucleotide (GAR) synthetase/(GAR) transformylase (Table 2). The two probes targeted different
sequences in the mRNAs encoding GARS/GART.
In many respects, each Northern blot population of
bands was a reflection of the distribution of the GDHsynthesized RNA bands on the agarose gel landscape
(Figures 1(i)-(x)). The tenacious binding of the complimentary strands of the probes to their targets in mRNAs,
and GDH-synthesized RNAs showed that the GDHsynthesized RNAs were very specific in their silencing
of mRNAs. The Northern band population (Figure 2) for
the GDH-synthesized RNAs of the control peanut,
showed that the probes for the mRNAs encoding Pi
translocator, NR, PGM, and GARS/GART hybridized to
the 4.5 kb, and 2 kb RNA bands, without hybridizing to
the >10 kb, and the 0.1 kb RNA bands (Figure 1(i)).
Residual quantities of GDH-synthesized RNAs, as well
as of the mRNAs encoding Pi translocator, GARS/
GART, NR, or PGM were not detected in the respective
total RNA lanes. This suggested that the GDH-synthesized RNAs knocked out their homologous mRNAs.
Northern assays for the mRNAs encoding GBSS, glucosyltransferase, ACCase, and NADH-GOGAT gave no
bands meaning that the GDH of the control peanut
discriminated by not synthesizing RNAs that were homologous to the four mRNAs.
The Northern band population for the GDH-synthesized RNAs of the NPKS-treated peanut, showed that the
probes for the mRNAs encoding Pi translocator, PGM,
glucosyltransferase, GARS/GART, and NR hybridized to
the high molecular weight (>10 kb) RNA bands (Figure
1(ii)), whereas the probe for the mRNA encoding GBSS
hybridized to the 4.5 kb and 2 kb GDH-synthesized RNA
bands. Residual quantities of GDH-synthesized high
molecular weight (>10 kb) RNAs, as well as the mRNAs
encoding Pi translocator, and GARS/GART were detected in the Northern blots in the corresponding total
RNA lanes. This suggested that in those cases, the GDHsynthesized RNAs only knocked down the homologous
mRNAs. But the probes for the mRNAs encoding GBSS,
PGM, and glucosyltransferase did not detect residual
mRNA in the total RNA lanes. Northern assays for the
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Figure 1. Responses of GDH isoenzyme (a)-(k), and RNA arrays (i)-(x) synthesized by the isoenzymes to
mineral treatments of peanut. M is RNA molecular weight marker; t is total RNA.
Copyright © 2011 SciRes.
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G. O. Osuji et al. / Advances in Bioscience and Biotechnology 2 (2011) 364-379
369
Table 2. cDNA sequences of peanut GDH-synthesized RNAs used as probes. Bold and underlined sequences indicate internally
repeated sequences.
Granule-bound Starch Synthase (GBSS) gb|ACL98483.1| starch synthase IIa
GTTACGATTCGCCCTTATGAGTCCTGACCGAGAACCGCGTTGATGGGGATGAGTCCGGACCGCCAACGGCATGATAACGATGAGT
CTGGACGGAGCTTACTCTTTATAATGATGAGTCCTGACCGACAACGGGTTTGATAGCTATGATTCCTGACCGACTGCGGCATTGA
TAGCGATGAGTCTGGATGGGATATGCAGACTACCAGAACCTGATTGGCGACT
Phosphoglucomutase (PGM) emb|AJ250770.1|
TGGNGGCGGCGGGNAACGCACTTGACGAGATCTGAANGAANNGANNGCAANTANNCAGCCNTATGAGACATANCTNGGNNTNAAA
NCAGGTTNCGCATAACCGCGTAAGAAGATNACCACCGCTTACCAGTGNNCGTTGTCNAGTNGAGGTAGAGCCGTTGATTACCTAAGT
CAGTGTTGAGTATCCTTCGGTTAATGATGCGGTAAGTGAAGTACTTGGGAAGCATCCCATCCGCGGTTAGCAAANGCGGTGCTTTGG
TTTCCCGGGTTTCGTACGTGAAGGGTGACTTGTACGCTTGGACCGGATCCAGAGACANGTACAGGTGCGGGTTGTCCGCTACGATCA
AGAAAGTCGGGTACGCAGTCTACGAGACCAA
GARS/GART AY189138.1 Plasmid 48Q
TTTTGGCCGACTCGTCGGCGAATTCCCCCTTAAGTGCCTCAACAAAGCCCACGCCCGAGCAAGAAAGCGGGGACAACACTCGTAAT
TGTCCTCCACCCACGGCGGCGAGTGGATGCCCAGCTTTATGAGGTGCACCCCCCATGGAGATCATCTGCGGGGTGTGTTTTCCCCCC
GACACACTGAGGGGGGTATTTTTGGAGAGACATTTTCTCACAAACATCCCCCAAAAAAACCCCCCCCCCCACTTTATGAAAGATGTT
GGAGCGCTATCTTAGCAAAACACTTAAGACGGAATCTTTTTAAACCCGAGCGACACTCCTCTTTAGAGAGGGTTACTTCTAACCTGG
CCCAGTCATGTGCATAGCGCTTTCTGCTGTGAAAATGTGATCGCCCCCCACTCCCCAACAACATAGACCCGTGAACCAT
GARS/GART: U30896.1 Plasmid 3E
CCGATTTTNNTTGACGAACGCGCGAATCCCCTTCCGTGACTGCGTACCCGGTCAGGACTCATCGCTGATTCGGTCAAGACTCATACT
GGTCTCGTAGACTGCGCACTGGTCTCGAGACTGCGTAATCGGTCAGGACTCATCACTACTGGTCTCGTAGACTGCGTACTGGTCTCGT
AGACTGCGTACTGGTCTCGTAGACTGCGTACTGGTCTCGTAGACTGCGGATTCGGTCAGGACTCATCGCTGATTCGGTCAGGACTCAT
AGCTGATTCGGTCAGGACTCATAGCTACTGGTCTCGTAGACTGCGTACTGGTCTCGTAGACTGCGTACTGGTCTCGTAGACTGCGCAC
TGGTCTCGTAGACTGCGATTCGGTCAGGACAA
NADH-GOGAT gb|L01660.1
CCCATATTNGNNNAACGTCCGCGCGAATCCCCTTACTGGTCTCGAGACTGCGTACCCGATGCAGAAGGCGGGAAAACATGAAATGA
GCGTCAAGCAGGCCGTGAAGGTTGCCGAGCTTTTGAAGTGCAACCCGATGGAGGTTATCTGCGGGGTGATGTTTCACCAGGACGT
AATGGAGCGGGATTTCTGGACGGACATTTTCCAGCAGACAGTCACCGAAAACGACCGCCGCCACTACTTCAAGAAGGTTTAGGC
AGGCTATCGGTCAGGACTCATAA
Figure 2. Population distribution of Northern bands
for the RNAs synthesized by the GDH charge isomers
of control peanut. Total RNA from control peanut was
the marker. Probes were cDNAs of the GDH-synthesized
RNAs that were homologous to the mRNAs encoding
the indicated yield-specific enzymes (Figure 2(i)-(iii)).
Copyright © 2011 SciRes.
mRNAs encoding ACCase, and NADH-GOGAT gave
no bands meaning that the GDH of NPKS-treated peanut
discriminated by not synthesizing RNAs that were homologous to the two mRNAs.
The Northern band populations for the GDH-synthesized RNAs of the NS-treated peanut showed that the
probes for the mRNAs encoding PGM, ACCase, and
glucosyltransferase hybridized to the >10 kb RNA bands,
whereas the probe for the mRNA encoding NR hybridized to the 4.5 kb and 2 kb GDH-synthesized RNA
bands in agreement with the population pattern of the
GDH-synthesized RNA (Figure 1(iii)). Residual quantities of GDH-synthesized 4.5 kb, and 2 kb RNAs, as well
as 0.1 kb mRNA fragments were detected in the Northern blots in the respective total RNA lanes. Northern
assays for the mRNAs encoding Pi translocator, GBSS,
GARS/GART, and NADH-GOGAT gave no bands
meaning that the GDH of the NS-treated peanut exercised discrimination by not synthesizing RNAs that were
homologous to the four mRNAs.
The Northern band population patterns (Figure 3) for
the GDH-synthesized RNAs of the Pi-treated peanut,
showed that the probes for the mRNAs encoding PGM,
glucosyltransferase, ACCase, GARS/GART, and NADHGOGAT hybridized to the >10 kb RNA bands. There
were no 4.5 kb and 2 kb Northern bands in agreement
with the RNA population of the GDH-synthesized RNA
(Figure 1(iv)). Residual quantities of GDH-synthesized
high molecular weight (>10 kb) RNAs, as well as the
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mRNAs encoding PGM, glucosyltransferase, and ACCase were detected in the Northern blots in the respective
total RNA lanes. This suggested that in those cases, the
GDH-synthesized RNAs only knocked down the homo-
logous mRNAs. The probes for the mRNAs encoding
GARS/GART, and NADH-GOGAT did not detect residual mRNA in the total RNA lanes (Figure 3). Northern
assays for the mRNAs encoding Pi translocator, GBSS,
Figure 3. Population distribution of Northern bands for the RNAs synthesized
by the GDH charge isomers of phosphate-treated peanut. Total RNA from phosphate-treated peanut was the marker. Probes were cDNAs of the GDH-synthesized
RNAs that were homologous to the mRNAs encoding the indicated yield-specific
enzymes (Figures 3(i)-(v)).
Copyright © 2011 SciRes.
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G. O. Osuji et al. / Advances in Bioscience and Biotechnology 2 (2011) 364-379
and NR gave no bands meaning that the GDH of the Pitreated peanut discriminated by not synthesizing RNAs
that were homologous to the three mRNAs.
Visually, the ten treated peanuts grew excellently and
the leaves were green to the same extent. There were no
symptoms of mineral nutrient deficiency. However, comparison of the Northern blots for the control and Pitreated peanuts (Figures 2 and 3) give a clearer molecular differentiation. Whereas Figure 2 depicts the control
peanut as a miserable low quality crop whose metabolism was uncoordinated, Figure 3 depicts the Pi-treated
peanut as a robust crop whose primary metabolic pathways were under efficient coordination. These differences at the molecular level were confirmed by the different vegetable oil and cellulose yields. Therefore, Northern assays using GDH-synthesized RNAs as probes are
good pictorial demonstrations of the efficiency of metabolic processes of crops.
The Northern band populations for the GDH-synthesized RNAs of the KCl-treated peanut showed that the
probes for the mRNAs encoding glucosyltransferase, NR,
and Pi translocator hybridized to the >10 kb, 4.5 kb, and
2 kb RNA bands (Figure 1(v)). Residual quantities of
GDH-synthesized high molecular weight RNA bands
were detected in the Northern blots in the corresponding
total RNA lanes. Northern assays for the mRNAs encoding GBSS, PGM, ACCase, GARS/GART, and NADHGOGAT gave no bands meaning that the GDH of the
KCl-treated peanut did not synthesize RNAs that were
homologous to the five mRNAs.
The Northern band populations for the GDH-synthesized RNAs of the sulfate-treated peanut showed that the
probe for the mRNA encoding Pi translocator hybridized
to the >10 kb RNA bands (Figure 1(vi)), whereas the
probe for the mRNA encoding NR hybridized to the 4.5
kb and >10 kb GDH-synthesized RNA bands. Residual
quantities of GDH-synthesized high molecular weight
RNA bands, as well as the mRNAs encoding Pi translocator, and NR were detected in the Northern blots in the
respective total RNA lanes. The probe for the mRNA
encoding GARS/GART hybridized to the >10 kb, and
low molecular weight (0.1 kb) RNA bands to give a
population of Northern bands that was identical to the
pattern of GDH-synthesized RNA bands (Figure 1(vi)).
Northern assays for the mRNAs encoding GBSS, PGM,
glucosyltransferase, ACCase, and NADH-GOGAT gave
no bands meaning that the GDH of the sulfate-treated
peanut did not synthesize RNAs that were homologous
to the five mRNAs.
The Northern bands for the GDH-synthesized RNAs
of the PS-treated peanut showed that the probes for the
mRNAs encoding Pi translocator, PGM, GBSS, glucosyltransferase, and GARS/GART hybridized to the >10
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371
kb RNA bands (Figure 1(vii)); and in addition the probe
for the mRNA encoding GARS/GART hybridized to the
0.1 kb GDH-synthesized RNA bands. Northern assays
for the mRNA encoding ACCase gave no bands meaning
that the GDH of the PS-treated peanut exercised discrimination by not synthesizing RNA that was homologous to the mRNA. Residual quantities of GDH-synthesized >10 kb RNA bands, as well as of mRNAs were
detected in the Northern blots in the respective total
RNA lanes. There were no 4.5 kb Northern bands just as
there were no 4.5 kb RNA bands in the array of the
RNAs that were synthesized by the GDH of PS-treated
peanut (Figure 1(vii)).
The Northern band populations for the GDH-synthesized RNAs of the NH4Cl-treated peanut showed that the
probes for the mRNAs encoding Pi translocator, GBSS,
PGM, and glucosyltransferase hybridized to the >10 kb
RNA bands (Figure 1(viii)), and there were Northern
smears similar to the RNA smears observed in the array
of RNAs synthesized by the GDH of NH4Cl-treated
peanut (Figure 1(viii)). Residual quantities of GDHsynthesized high molecular weight RNA bands, as well
as the mRNAs encoding Pi translocator, and GBSS were
detected in the Northern blots in the corresponding total
RNA lanes. Northern assays for the mRNAs encoding
ACCase, GARS/GART, NR, and NADH-GOGAT gave
no bands meaning that the GDH of the NH4Cl-treated
peanut did not synthesize RNAs that were homologous
to the four mRNAs.
The Northern bands for the GDH-synthesized RNAs
of the PN-treated peanut showed that the probes for the
mRNAs encoding Pi translocator, GBSS, PGM, and glucosyltransferase hybridized to the >10 kb RNA bands
(Figure 1(ix)). In contrast to the RNA band pattern
(Figure 1(ix)), there were no 4.5 kb, 2 kb, and 0.1 kb
Northern bands. Residual quantities of GDH-synthesized
high molecular weight RNA bands, as well as the
mRNAs encoding Pi translocator, GBSS, and PGM were
detected in the Northern blots in the corresponding total
RNA lanes. Northern assays for the mRNAs encoding
GARS/GART, NR, and NADH-GOGAT gave no bands
meaning that the GDH of the PN-treated peanut exercised discrimination by not synthesizing RNAs that were
homologous to the three mRNAs.
The Northern band populations for the GDH-synthesized RNAs of the PK-treated peanut showed that the
probes for the mRNAs encoding GBSS, PGM, glucosyltransferase, and GARS/GART hybridized to the >10 kb
RNA bands (Figure 1(x)), whereas the probe for the
mRNA encoding NR hybridized to all the GDH-synthesized RNA bands. The Northern result for the nitrate
reductase-encoded probe was remarkable in that all the
GDH-synthesized RNA had sequences that were homoABB
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logous to the probe. Residual quantities of GDH-synthesized high molecular weight RNA bands were present
only in the total RNA lane of the GARS/GART Northern
result. Northern assays for the mRNAs encoding Pi
translocator, and NADH-GOGAT gave no bands meaning that the GDH of the PK-treated peanut did not synthesize RNA that was homologous to the four mRNAs.
Digital (UN-SCAN-IT) quantitation of the Northern
bands showed that GDH synthesized the required RNA
sequences in sufficient quantities to meet the thresholds
for silencing the target homologous mRNAs. A minimum 2:1 ratio between the GDH-synthesized RNA to the
target mRNA was the requisite threshold for the silencing reaction. The ratio was the baseline control platform
applied for unbiased judgment of the Northern bands
across experimental repeats and mineral ion treatments.
The Northern analyses in which total RNAs were loaded
side-by-side to the GDH synthesized RNAs (Figures
1(i)-(x)) made for easier interpretation of the efficiency
of transcript silencing by the GDH-synthesized RNAs.
The definitive detection of the high molecular weight
(>10 kb) RNAs synthesized by GDH in the total RNA
lanes in the Northern hybridizations was an evidence that
GDH synthesizes RNAs in vivo. The Northern results
further highlighted the importance of the preponderant
>10 kb GDH-synthesized RNA in the efficiency of
mRNA silencing. The >10 kb GDH-synthesized RNA
assured a maximum structural interaction with the homologous mRNAs, a crucial tertiary stabilization for the
initiation of silencing [32].
4) Sequential permutation by GDH-synthesized RNA:
the Northern blot results demonstrated a spider web-like
molecular connectivity between photosynthesis, glycolysis, cellulose biosynthesis, nitrogen assimilation, and fatty acid biosynthesis in the peanut. This connectivity described metabolic pathway integration at the molecular
level. The GDH-synthesized RNA that is homologous to
the mRNA encoding GBSS shared two-fold plus/plus
sequence similarity with that homologous to the mRNA
encoding ACCase. The plus/plus sequence similarities
between GDH-synthesized RNAs ensured an ordered
variation of the abundances of homologous mRNAs. The
GDH-synthesized RNA that is homologous to the mRNA
encoding GBSS also shared six-fold plus/minus sequence similarities with the GDH-synthesized RNA
(plasmid 3E) that is homologous to the mRNAs encoding
GARS/GART; two-fold plus/plus sequence similarities
with that homologous to the mRNA encoding NR; and
two-fold plus/minus sequence similarities with that homologous to the mRNA encoding NADH-GOGAT. This
is a reciprocal regulation of the mRNAs which are homologous to the same GDH-synthesized RNA so that at
least one in the group of mRNAs could not be knocked
Copyright © 2011 SciRes.
out with the other three. Reciprocal regulation of glycolysis and nitrogen assimilation was further enforced by
the GDH-synthesized RNA that is homologous to the
mRNA encoding PGM. The probe shared ten-fold plus/
minus sequence similarities with the GDH-synthesized
RNA (plasmid 3E) that is homologous to the mRNAs
encoding GARS/GART; and two-fold plus/minus sequence similarities with that homologous to the mRNA
encoding NADH-GOGAT. This sequential permutation
meant that at least one of the mRNAs could not suffer
demise with the other two. The GDH-synthesized RNA
that is homologous to the mRNA encoding ACCase
shared 22-fold plus/plus sequence similarity with the
probe (plasmid 3E) that is homologous to the mRNAs
encoding GARS/GART, but 7-fold plus/minus sequence
similarities with those homologous to the mRNAs encoding NR and NADH-GOGAT. This spider web-like
coordination by the GDH-synthesized RNAs that are
homologous to the mRNAs encoding NADH-GOGAT,
GARS/GART, and NR provided all-round metabolic
pathway integration so that all three of them could not
suffer demise with the mRNA encoding ACCase under
any applied mineral ion regimen. This explains the robust capability of peanut to produce oil even on acid
sandy, infertile, droughty soil [33]. The GDH-synthesized RNA that is homologous to the mRNAs encoding
the GARS/GART shared 6-fold plus/plus sequence similarities with that homologous to the mRNAs encoding
NR; and 16-fold plus/plus similarity with that homologous to the mRNA encoding NADH-GOGAT. This
structural integration meant that all the three mRNAs
could not be knocked out simultaneously. These were
important structural provisions that prevented the total
shut-down of the pathways for nitrogen assimilation
while metabolites were preferentially channeled towards
saccharide and fatty acid metabolism. The cob web-like
cross connections between metabolic pathways at the
molecular level introduce the concept of probability or
likelihood for metabolites to flow in one or alternative
directions in peanuts treated with mineral ions.
5) Spatial permutation by GDH-synthesized RNAs:
metabolic pathway integration at the molecular level was
consolidated by statistical redistribution of metabolite
load to molecularly connected pathways. GDH-synthesized RNAs are statistical in nature, their primary structure being dependent on the binomial subunit compositions of the GDH isoenzymes [30]. Therefore several
probabilities arise under a prevailing mineral nutrient
combination/concentration for the GDH-synthesized RNA
to reprogram the mRNA abundances and consequently
the rates of yield production. The reprogramming of the
sequence of metabolism in response to the prevailing
mineral ions in order to maximize crop yield can best be
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G. O. Osuji et al. / Advances in Bioscience and Biotechnology 2 (2011) 364-379
approached by permuting the yield-specific pathways
guided by the enzyme systems that were not down-regulated, partially down-regulated, and fully down-regulated
by GDH-synthesized RNAs per mineral environment,
and limited to the eight metabolic pathways affected. The
number of permutations varied widely: control peanut
produced 70; NPKS-treated peanut produced 420; NStreated peanut produced 1680; Pi-treated peanut produced 560; PN, PK, and NH4Cl-treated peanuts, each
produced 280; Na2SO4, PS, and KCl-treated peanuts,
each produced 168 permutations. Therefore, there were
many probable rearrangements of peanut metabolic pathways in response to any mineral ion regimen. This is the
explanation for the contradictions and conflicts about the
peanut yield responses to applied mineral nutrients [3437]. Frequency distribution plot of the metabolic pathways versus the number of permutations gave a positively skewed graph reminiscent of the GDH binomial
isoenzyme population distribution pattern [22]. The
mode (224) of the frequency distribution plot had a frequency of 4 suggesting that the yield of peanut could be
increased further about 50% of the yield of the PKtreated peanut to about 10,000 kg·pod·ha–1 by other mineral nutrient treatments. With a doubled peanut yield of
10,000 kg·ha–1 and assuming about 50% oil content, 70%
weight of peanut pod in the shell [33], peanut will have
the potential to yield 880 - 1100 gallons of biodiesel·ha–1,
which will be a remarkable contribution to bioenergy
supply without cultivation of more land, and without
application of more fertilizer and pesticides. There are
many stoichiometric combinations of mineral nutrients
for this purpose (Table 1).
6) Yield biochemistry of peanut: phosphate translocator: peanut photosynthetic reduction of CO2 produces
triose phosphates, the key compounds used in starch
synthesis in the chloroplast; or after leaving the chloroplasts to cytosol, in the sucrose synthesis in cytosol [12].
Pi translocator exports triose phosphates from the chloroplast to the cytosol in exchange for Pi import from the
cytosol into the chloroplast [38]. Therefore, in PKtreated peanut where the mRNA encoding Pi translocator
was not down-regulated by GDH-synthesized RNA, triose phosphates were maximally metabolized to acetyl
CoA and channeled towards fatty acid biosynthesis thus
resulting to maximum yields of seeds and pods (Figure
4). Conversely, in control peanut (Figure 2) where the
mRNA encoding Pi translocator was down-regulated by
GDH-synthesized RNA, Pi and triose phosphates were
minimally mobilized with consequent decreased biosynthesis of fatty acids, and minimum yields of seeds, and
pods (Figure 4).
Starch synthase: granule-bound starch synthase 1
(GBSS1) is responsible for the synthesis of linear glucan
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373
(amylase) in the starch granule [39], whereas another
isoform, GBSSII is important in the synthesis of the
branched (amylopectin) component [40]. In the peanut
chloroplast, the export of triose phosphates to the cytosol
by Pi translocator competed with their utilization in the
chloroplast for starch biosynthesis. Therefore, in PKtreated peanut where the mRNAs encoding the GBSS
isoforms were down-regulated and in addition the mRNA
encoding Pi translocator was not down-regulated by
GDH-synthesized RNAs, triose phosphates and Pi were
maximally mobilized and metabolized to acetyl CoA and
channeled towards fatty acid biosynthesis thus resulting
to maximum yields of seeds and pods (Figure 4). Here,
we observed at the molecular level the sequential combination of two metabolic pathways by GDH-synthesized
RNAs to double crop yield (Figure 4). Conversely, in
the Pi-treated (Figure 3), and NS-treated peanuts where
the mRNAs encoding the GBSS isoforms and phosphate
translocator were not down-regulated by GDH-synthesized RNAs, starch biosynthesis and phosphate translocation competed for the triose phosphates with consequent decreased biosynthesis of fatty acids resulting to
minimum yields of fats, seeds, and pods (Figure 4).
Phosphoglucomutase (PGM, EC 2.7.5.1) generates
glucose-1-phosphate (Glc-1-P) from glucose-6-phosphate (Glc-6-P). It is localized both in the plastids and
cytosol [41]. The plastidic PGM is essential for starch
synthesis to store photosynthates in leaves during the day,
and in the degradation of starch [42]. The cytosolic PGM
is involved in sucrose catabolism to provide intermediates for glycolysis etc [43]. Deficiency in PGM activity
resulted in “starchless” and wrinkled seed phenotypes
accompanied by significantly increased seed lipid contents [44]. Therefore, PGM plays an important role in the
distribution of Glc-6-P between glycolytic, starch, and
fatty acid pathways. In KCl-treated peanut where the
mRNA encoding PGM was not down-regulated by
GDH-synthesized RNA, the pod yield was double that of
NPKS-treated peanut where the mRNA encoding PGM
was down-regulated (Figure 4). In the control (Figure 2)
and NS-treated peanuts where the mRNA encoding
GBSS was not down-regulated but that encoding PGM
was down-regulated, pod yields (Figure 4) were the
lowest meaning that PGM activity exercised a stronger
influence than GBSS on starch synthesis and crop yield
in agreement with the role of PGM in the supply of
Glc-6-P utilized in the starch pathway [45]. Therefore,
combination of down-regulated PGM and GBSS doubled
the yields in the NH4Cl, and PK-treated peanuts (Figure
4). In PN-treated peanut where the mRNAs encoding
PGM, GBSS, and Pi translocator were only partially
down-regulated, pod, seed and fatty acid yields were
14% - 24% higher than in sulfate-treated peanut where
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Figure 4. Yield (pod, kernel, oil, and cellulose) responses of peanut to stoichiometric combinations of mineral salt solutions that synchronize GDH synthesis of RNA and GDH isomerization.
the mRNAs encoding PGM and GBSS were not downregulated and in addition that encoding Pi translocator
was partially down-regulated. Variable reprogramming
of mRNA enables fine-tuning of encoded enzyme for
efficient modulation of metabolite flow through the metabolic pathway. Variable partial down-regulation of
mRNA by metabolic non-genomic RNA (GDH-synthesized RNA) is a unique mechanism of metabolic coordination in biology.
Glucosyltransferases catalyze the formation of glucosidic linkages between monosaccharide residues from
UDP-glucose and specific acceptors [46] in the initiation
of cellulose biosynthesis [47]. Peanut shell biomass is
dense in cellulose, is an important solid biofuel with a
relatively high energy content of 16 Mj/kg [48], and
readily convertible to liquid fuel (cellulosic ethanol).
Mineral-treated peanuts yielded high percentages (71% 90%) of shell neutral detergent fiber (NDF). Shell NDF
(cellulose) yield of the control peanut was at least doubled in the PS, Na2SO4, Pi, PN, and PK-treated peanuts
(Figure 4). At the molecular level, these doubling of
shell NDF yields were accounted for by the sequential
permutation of the abundances of the mRNA encoding
glucosyltransferase, GBSS, PGM, and Pi translocator. In
the control (Figure 2) and NS-treated peanuts where the
mRNA encoding GBSS was not down-regulated, the
Copyright © 2011 SciRes.
mRNA encoding PGM was down-regulated, and the mRNA encoding glucosyltransferase was partially or not
down-regulated, the shell cellulose yields were the lowest compared with Pi (Figure 3), Na2SO4, and PK-treated
peanuts where the mRNAs encoding GBSS, and glucosyltransferase were not down-regulated, partially or fully
down-regulated, the shell cellulose yields were at least
doubled (Figure 4). The metabolic control of cellulose
by the pathways of starch synthesis, and glycolysis is
understandable based on the reaction steps catalyzed by
GBSS and PGM in the respective pathways. The influence of Pi translocator on peanut cellulose relies on the
plus/plus sequence similarity between the GDH-synthesized RNAs that are homologous to the mRNAs encoding glucosyltransferase and phosphate translocator. The
mRNAs encoding Pi translocator and glucosyltransferase
cannot be completely knocked out simultaneously under
any applied mineral nutrient environment [20]. The
GDH-synthesized RNAs make for permutation of the
mRNAs homologous to them and in that way the encoded enzymes are fine-tuned to maximize metabolite
production. This is the structural permutation of metabolic pathways for the doubling of crop yield.
Acetyl-coenzyme A carboxylase (ACCase EC 6.4.1.2)
catalyzes the first committed reaction in lipid biosynthesis with production of malonyl-CoA. The regulation of
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the enzyme is an important control point in lipid biosynthesis [49]. ACCase controls the production of fats in
peanut [22] similar to soybean [50]. In PK-treated peanut
where the mRNA encoding ACCase was not downregulated by GDH-synthesized RNAs, the kernel yield
was double that (Figure 4) where the mRNA was downregulated as in NS-treated peanut. Because triose phosphates, starch, Glc-6-P, and acetyl coenzyme A are involved in fatty acid metabolism, it is necessary to understand the effects of the permutation of the activities of
phosphate translocator, GBSS, PGM, and ACCase on
peanut yield. In the NPKS-treated peanut where the
mRNA encoding Pi translocator was partially downregulated, the mRNAs encoding PGM, and GBSS were
down-regulated but the mRNA encoding ACCase was
not down-regulated, the kernel and fatty acid yields were
the lowest (Figure 4) compared with the PK-treated
peanut with doubled kernel, pod, and fatty acid yields
where the mRNAs encoding Pi translocator and ACCase
were not down-regulated, and the mRNAs encoding
PGM and GBSS were down-regulated, by the GDH-synthesized RNAs. In the PK-treated peanut, because the
mRNA encoding Pi translocator was not down-regulated,
there was maximum phosphate translocator activity to
import Pi into the chloroplast for maximum synthesis of
triose phosphates; the mRNA encoding GBSS was
down-regulated, the triose phosphates were not expended
in starch synthesis; the mRNA encoding PGM was
down-regulated, Glc-6-P was sufficiently channeled to
glycolysis; and finally the mRNA encoding the ACCase
was not down-regulated thereby ensuring maximum
utilization of acetyl-Co A from citric acid cycle to synthesize maximum quantity of fatty acids. This is an aspect of the process by which GDH-synthesized RNA
sequentially coordinates and permutes metabolic pathways at the molecular level to maximize end product
formation and doubling of crop yield.
Nitrogen assimilation: three metabolic pathways cooperated to assimilate nitrogen in peanut. They are purine biosynthesis, nitrate reduction, and glutamine synthetase-glutamate synthase (GS-GOGAT) cycle. The purine metabolic pathway is employed in tropical legumes
to assimilate and detoxify ammonia [39]. GAR synthase
catalyzes the second step, and GAR transformylase catalyzes the third step in purine biosynthetic pathway.
GDH-synthesized RNA, probes 3E and 48Q (Table 2)
were found to be homologous to the mRNAs encoding
GARS and GART [22]. NR catalyzes the reduction of
nitrate to nitrite which is then reduced by nitrite reductase to NH 4 ion [51], followed by incorporation into
amino acids by GS-GOGAT cycle [52]. NADH-GOGAT
is an important enzyme in the salvage of NH 4 ion [53].
The role was confirmed in the peanut because most of
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375
the mineral treatments (except Pi, and PS treatments)
failed to induce the GDH synthesis of the RNA homologous to the mRNA encoding NADH-GOGAT, the induction of which in the Pi (Figure 3), and PS-treated peanuts caused up to 38% decrease in crop yield compared
with the PK-treated peanut where NADH-GOGAT was
not down-regulated. In control peanut (Figure 2) where
the GDH-synthesized RNA down-regulated the mRNAs
encoding GARS, GART, and NR but the mRNA encoding NADH-GOGAT was not, pod yield was the lowest
as compared with the PK-treated peanut where the
mRNAs encoding GARS/GART was only partially downregulated, the mRNA encoding NR was down-regulated,
and the mRNA encoding NADH-GOGAT was not downregulated, the pod yield was increased by 2.4 folds (Figure 4). Therefore purine biosynthesis is important in
salvaging nitrogen and doubling peanut yield.
7) Bioscience of GDH-synthesized RNA: as a new
gateway into biology, procedures for analyzing transcript
silencing by GDH-synthesized RNAs are slightly different from classical siRNA approaches in that there are no
transfection and reverse transcription steps, and the GDHsynthesized RNAs are endogenously elicited. Transcript
silencing by GDH-synthesized RNA takes place as a
biochemical reaction at the molecular level; and it is inducible at-will in crops. Experimentation on GHD-synthesized RNA embodies many layers of technical repeats,
normalization, and standardization that assure result reproducibility across experiments. GDH purification by
whole gel electro-elution into the 14 chambers of BioRad’s mini whole gel eluter give 14 instead of one preparation of the enzyme, an infinite opportunity for verifying the RNA synthetic activity 14 times (Figure 1)
instead of once per treated-peanut. The binomial assembly of the subunit polypeptides in the hexameric isoenzymes did not permit the combination of the 14 fractions
to make a single preparation. Equal weights (10 µg) of
RNA synthesized per the 14 GDH samples were agarose
gel-electrophoresed, trans-blotted after electrophoresis,
followed by Northern hybridization (Figures 2 and 3).
Therefore, in these protocols, there were 14 repeats of
the purified GDH, 14 repeats of RNA synthesis, and 14
repeats of RNA loading into gel. More than 90% of the
GDH and RNA lanes (Figure 1) showed that protein and
RNA repetitive loadings onto gels were consistent, efficient and reproducible across mineral-treated peanuts.
Northern blots were performed in duplicate using each
cDNA of GDH-synthesized probe, thereby making a
total of 28-repeat RNA tracks per treated peanut. There
were several evidence for internal control reactions in the
transcript silencing including the plus/plus and/or plus/
minus sequence similarities among the GDH-synthesized
RNAs, partial silencing of mRNAs encoding distinct
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enzymes, GDH-synthesized RNA present in total RNA,
absence of total RNA from GDH-synthesized RNA etc.
Residual quantities of mRNAs encoding PGM and ACCase in the Northern blots (Figure 3) of Pi-treated peanut confirmed the sequence similarities between the
GDH-synthesized RNAs homologous to the mRNAs
encoding PGM, NADH-GOGAT, ACCase, and GARS/
GART. Absence of total RNA from GDH-synthesized
RNA (Figure 1(i)-(x)) assured that Northern bands were
not false positives. Messenger RNAs encoding several
housekeeping enzymes were not useful references in the
Northern assays because Northern results [29] in which
GDH-synthesized RNAs were used as probes suggested
the housekeeping mRNAs were also reprogrammed under the experimental regimen. Therefore, a ratio of 2:1
between the GDH-synthesized RNA and the target
mRNA was adopted as the minimum normalization and
standardization factor for silencing. Although the ideal
reference internal mRNA is one that does not vary as a
function of experimental treatment [54], it has been difficult to identify a single mRNA that meets the criterion.
Where the mRNAs were fully silenced and there were no
residual mRNAs as in the Northern blots for GARS/
GART (Figure 3(iv)), and NADH-GOGAT (Figure 3(v))
it was assumed that the 2:1 ratio was upheld. Where the
mRNAs were partially silenced as in the Northern blots
for PGM (Figure 3(i)), glucosyltransferase (Figure 3(ii)),
and ACCase (Figure 3(iii)) it was assumed that the residual mRNA constituted 50% of the total mRNA. The
full amount of mRNA was determined when the GDH of
the peanut did not synthesize the homologous RNA and
the mRNA was the lone band in the Northern assay. The
limits of the bioscience of the GDH-synthesized RNA
experimentation were defined by the peanut without any
mineral ion treatment representing the negative control;
and the peanut with the full mineral ion concentration
and composition (NPKS) representing the positive control (Figure 1). The positive control is important to provide the line of verification for the molecular mechanism
of GDH action, and for result verification, confirmation
and validation.
4. DISCUSSION
Metabolic variants of peanut: ability of GDH to spontaneously isomerize and synthesize RNAs that silence homologous mRNAs constitutes one aspect of the functions
of the enzyme. The other aspect is the signal integration
and discrimination function [19] and is implemented
through the permutation of the metabolic pathways in
sequence and in space, by the GDH-synthesized RNAs.
The two functions of GDH constitute the new gateway
into biology. GDH-synthesized RNAs are metabolic and
non-genomic [29], and so they do not suffer from mutaCopyright © 2011 SciRes.
tional changes. The two functions introduce the concept
of metabolic variants as different from genetic variants.
The yield-doubling variants with respect to the control,
and NPKS-treated peanut included the Pi, NH 4 , and
PK-treated peanuts.
Pathway discrimination and integration in Control metabolic variant: the control peanut yield metabolism was
unique because GBSS, ACCase, NADH-GOGAT, and
glucosyltransferase were not down-regulated; but Pi
translocator, NR, GARS/GART, and PGM were downregulated leading to low production of pods (2637
kg·ha–1), kernel (1922 kg·ha–1), and fatty acids (855
kg·ha–1). There were no partially down-regulated yieldspecific enzyme steps. This is the kind of low yield (Figure 4) that peasant farmers achieve in the developing
countries when they cultivate peanut according to the
recommended tradition of crop rotation technology [25].
The low efficiency of the metabolism of the control peanut confirmed that the nitrogen fixing ability of the rhizobia was not sufficient for the growth and yield doubling of the crop (Figure 4) compared with mineraltreated variants.
Pathway discrimination and integration in NPKS metabolic variant: GARS/GART, and Pi translocation were
partially down-regulated. Nitrate reductase, glucosyltransferase, and GBSS were down-regulated. But ACCase and NADH-GOGAT were not down-regulated. The
consequences were decreases in fatty acids (656 kg·ha–1),
and kernel (1491 kg·ha–1) yields (Figure 4). This is the
kind of low yield that farmers obtained when peanuts
followed a heavily fertilized small grain crop in the rotation, or when peanut is planted on soils with high residual NPKS fertility [55]. The low efficiency of the metabolism of the NPKS-treated peanut confirmed that the
NPKS combination of mineral ions was not an effective
mix for the induction of the maximum production metabolism of the crop.
Pathway discrimination and integration in Phosphate
metabolic variant: Na3PO4-treated peanut had the downregulation of GARS/GART, and NADH-GOGAT; partial down-regulation of PGM, ACCase, and glucosyltransferase; leaving Pi translocator, GBSS, and NR not
down-regulated with the advantage that pod (3955 kg·ha–1),
kernel (2433 kg·ha–1), and fatty acid (1022 kg·ha–1) yields
were increased (Figure 4) compared with control peanut.
Phosphorus fertilizer is cautiously recommended for
peanuts because it did not increase fatty acid yields on
sandy soils [25,56].
Pathway discrimination and integration in NH4Cl metabolic variant: fertilizer nitrogen is generally not recommended for peanut because rhizobia assist to fix atmospheric nitrogen for the crop [36]. Comparison of the
control peanut yield with that of NH4Cl-treated peanut
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shows the overwhelming superiority and doubling of
yield by the NH4Cl variant (Figure 4).The NH4Cl treatment instantaneously relieved the demise of the purine
nucleotide biosynthesis, and NR in the untreated peanut
with dramatic increases in pod (4541 kg·ha–1), kernel
(3245 kg·ha–1), and fatty acid (1361 kg·ha–1) yields (Figure 4). PGM, and glucosyltransferase were down-regulated;
Pi translocator, and GBSS were partially down-regulated;
leaving ACCase, GS-GOGAT cycle, NR, and GARS/
GART not down-regulated. Crop yield doubling biotechnology calls for fresh recommendations for nitrogen
fertilization of leguminous crop species.
Pathway discrimination and integration in PK metabolic variant: irrespective of soil type, location, and peanut variety, the most popular mineral ion recommendation for peanut production worldwide is the PK combination [34,35], although detrimental quantities of potash
were generally applied [25]. The production metabolism
of the PK variant attests to this popularity because GBSS
suffered demise, all the triose phosphates were used for
glycolysis; PGM suffered demise, all the Glc-6-P was
used for glycolysis; glucosyltransferase suffered partial
demise, the amount of ATP utilized in UDP-Glc synthesis was minimized; GARS/GART suffered partial demise,
there was sufficient ATP to power glucose metabolism;
and NR suffered demise, the amount of NADH utilized
in intermediary metabolism was very low. But NADHGOGAT did not suffer demise thereby allowing nitrogen
assimilation to proceed in support of amino acid and
purine nucleotide biosyntheses; and Pi translocator did
not suffer demise, so all the triose phosphates were channeled to acetyl coenzyme A production. Finally, ACCase
was not down-regulated giving the peanut variant the
advantage that the maximum photosynthates were priority-channeled to fatty acid, cellulose, and amino acid
production. The PK-treated peanut was therefore the
most efficient metabolic variant, the pod (6377 kg·ha–1),
kernel (4342 kg·ha–1), oil (1381 kg·ha–1), and cellulose
(1829 kg·ha–1) yields being doubled compared with the
controls (NPKS, and untreated control) that were the
most inefficient for yield production (Figure 4).
From the foregoing, demise (full down-regulation) of
metabolic reaction steps followed by permutation of
yield-related metabolic pathways and redistribution of
metabolite load to molecularly connected metabolic
pathways controls crop yield. Because the metabolic variants are distinct bioreactors, the yields of pods, fatty
acids etc are also distinct, there being no biochemical
justification for calculating average yields (Figure 4)
between two or more variants.
5. CONCLUSIONS
Many research projects had investigated a genetic base
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377
for crop yield [10,11]. Crop yield-doubling biotechnology is different, being based on metabolic pathway demise, statistical redistribution of metabolite load to molecularly connected pathways, coordination of metabolic
pathways at the molecular level and concomitant alteration of yield by the GDH-synthesized RNAs, which constitute a new gateway into biology. Different metabolic
variants of peanut exist based on the discrimination and
integration (permutation) of metabolic pathways and
altered crop yield. Metabolic variants prove that peanut
is a natural bioreactor for the production of large quantities of fatty acids through the discrimination against
saccharide metabolism. Some of the peanut bioreactors
(PK, PN, PS, Pi, NH4Cl, and SO 24 -treated) are more
energy efficient than others (control, NS, NPKS, and
KCl-treated). The demise of pathways, statistical redistribution of metabolite load, and alteration of crop yield
are programmable by mineral ions. The yield doubling
biotechnology is a manifestation of the property of crops
as programmable bioreactors. A maximum yield of
10,000 kg·pods·ha–1 is achievable based on the bioreactor
property of peanut. This is a biotechnological approach
for doubling crop yield [57] to feed a human population
that will soon be nine billion people. Farmers’ optimal
yield of peanut was about 3400 kg·ha–1 [58], suggesting
that yields can be tripled by cultivating the crop as an
energy efficient bioreactor rather than by crop rotation,
dependence on biological nitrogen fixation, or by application of kg amounts of fertilizer [24]. The bioreactor
peanut yield-doubling biotechnology requires mM amounts
of mineral salts per hectare, a thousand-fold saving in
financial input by farmers. Crop yield doubling biotechnology has the promise to reformulate fertilizer compositions, and minimize not only the cost of agricultural
production but also food insecurity.
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