Fpls 04 00035

REVIEW ARTICLE
published: 28 February 2013

doi: 10.3389/fpls.2013.00035
Proteomics: a biotechnology tool for crop improvement

Moustafa Eldakak1,2 , Sanaa I. M. Milad 3 , Ali I. Nawar 3 and Jai S. Rohila1 *
1
Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
2
Department of Genetics, Faculty of Agriculture, El Shatby, Alexandria University, Alexandria, Egypt
3
Biotechnology Lab, Department of Crop Science, Faculty of Agriculture, El Shatby, Alexandria University, Alexandria, Egypt
Edited by: A sharp decline in the availability of arable land and sufficient supply of irrigation water along
Dominique Job, Centre National de la with a continuous steep increase in food demands have exerted a pressure on farmers
Recherche Scientifique, France
to produce more with fewer resources. A viable solution to release this pressure is to
Reviewed by:
Martin Hajduch, Slovak Academy of
speed up the plant breeding process by employing biotechnology in breeding programs.The
Sciences, Slovakia majority of biotechnological applications rely on information generated from various -omic
Romina P. Pedreschi, Food & technologies. The latest outstanding improvements in proteomic platforms and many
Biobased Research – Wageningen other but related advances in plant biotechnology techniques offer various new ways
University, Netherlands
to encourage the usage of these technologies by plant scientists for crop improvement
*Correspondence:
Jai S. Rohila, Department of Biology
programs. A combinatorial approach of accelerated gene discovery through genomics,
and Microbiology, South Dakota State proteomics, and other associated -omic branches of biotechnology, as an applied approach,
University, 244B Biostress Building, is proving to be an effective way to speed up the crop improvement programs worldwide.
Brookings, SD 57007, USA. In the near future, swift improvements in -omic databases are becoming critical and
e-mail: jai.rohila@sdstate.edu
demand immediate attention for the effective utilization of these techniques to produce
next-generation crops for the progressive farmers. Here, we have reviewed the recent
advances in proteomics, as tools of biotechnology, which are offering great promise and
leading the path toward crop improvement for sustainable agriculture.
Keywords: biotechnology, crop improvement, proteomics, sustainable agriculture
INTRODUCTION of the several cutting edge approaches for understanding global

According to an estimate, there are approximately 925 million peo- genes expression and their functional mechanisms is to study the
ple on the globe who live in a state of hunger (Karimizadeh et al., proteins translated from those genes and that scientific branch
2011). Moreover, an additional two billion people are expected to is known as proteomics. The word “proteome” is derived from
be added by the year 2050 (UN, 2012). In an effort to eradicate that PROTEins expressed by a genOME. Analogous to genomics, the
ugly spot of hunger from the beautiful face of the humanity, we term “proteomics” describes the study and characterization of
need to significantly increase the production and supply of food by the complete set of proteins present at a given time in the cell
integrating different elements and strengthening the plant breed- (Wilkins et al., 1995). Although genomic studies are helpful to
ing tools (Beddington et al., 2012) for crop improvements. A major scientists in knowing what is possible theoretically, proteomic
hurdle for crop improvement programs faced by the plant breeders studies reveal the functional players for mediating specific cellular
is a limited gene pool of domesticated crop species. The identifica- processes. The proteome, unlike the genome, which is static in
tion of potential useful genes across the animal and plant kingdom nature, has dynamic capabilities. The study of proteins introduces
that could play key roles toward the improvement of important post-translational modifications (PTMs) and provides the knowl-
crop traits, generally derived from research in molecular biology edge that is important for understanding the biological functions
including genomics and proteomics, is a crucial step. Such newly (Nat et al., 2007). The PTMs that play important roles during the
discovered genes, when placed into a desired crop species and then growth and development of a plant and/or in response to var-
utilized for breeding programs, could be a boon to human society ious stress conditions cannot be understood from the genome
(Figure 1 and Table 1). sequence projects and/or transcript abundance alone. Proteomics
Various completed and several ongoing plant sequencing knowledge provides functional genomics with a completeness
projects, e.g., Arabidopsis thaliana (Arabidopsis Genome Initia- toward understanding the process (Gygi et al., 2000; Dubey and
tive, 2000), rice (Goff et al., 2002; Yu et al., 2002), and soybean Grover, 2001; Park, 2004; Thurston et al., 2005). Furthermore,
(Schmutz et al., 2010) are reaching the phase where they can the development of various advanced tools for bioinformatics
provide the blueprints to modern breeders to access a great num- and computational science are connecting proteomics to other “-
ber of genes, but the benefits derived from these blueprints can omics,” and the physiological data are further opening up new
only be harvested when the spatial and temporal expressions, methods for crop improvement studies via the signaling, reg-
functions and interactions of the gene products become well- ulatory, and metabolic networks underlying plant phenotypes
characterized (Salekdeh and Komatsu, 2007). In simple words, (Kitano, 2002; Langridge and Fleury, 2011).
the genetic (DNA) information of a plant is translated via the Similar to proteomics, the biotechnology field has seen
intermediary step of transcription (mRNA) into a protein. One advancements in the past several decades (Varshney et al., 2011).
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Eldakak et al. Proteomics for sustainable agriculture
the biotechnological improvement of crop plants. These pro-

teins maintain cellular homeostasis under a given environment by
controlling physiological and biochemical pathways. A search of
the published research literature revealed that genomics and pro-
teomics are the two major wheels that keep the discovery of novel
genes rolling, which can eventually be placed into the pipeline
for crop improvement programs. Two-dimensional electrophore-
sis (2-DE) and mass spectroscopy (MS), two of the most widely
used proteomics methods, are used to catalog and identify pro-
teins in different proteome states or environments. Advances in
2-DE have been extremely helpful in bringing proteomics close to
biotechnological programs; however, due to some drawbacks and
disadvantages associated with gel-based proteomics, e.g., labor
intensiveness, insensitiveness to low-copy number proteins, low
reproducibility and the inability to characterize complete pro-
teomes, many gel-free proteomic techniques have also become a
valuable tool for scientists (Baggerman et al., 2005; Lambert et al.,
2005; Scherp et al., 2011; Jayaraman et al., 2012).
POTENTIAL OF PROTEOMICS AS A BIOTECHNOLOGY TOOL

IN CROP IMPROVEMENT PROGRAMS
MOLECULAR MARKERS ARE TO ASSIST PLANT BREEDERS
Proteomics offers novel gene (DNA) identifications to plant biol-
ogists and breeders. Marker-assisted selection (MAS), which is the
employment of DNA markers in a plant breeding program, has
FIGURE 1 | An illustration showing that the -omics and the
extensively been used to select desired genes/quantitative trait loci
conventional plant breeding techniques are the pillars of bio-economy,
and a strong bio-economy is the foundation of sustainable (QTLs) in the development of a comparatively superior breeding
development of a society. By the incorporation of these technologies for line (Collard and Mackill, 2008). Damerval et al. (1994) used an
crop improvements, the bio-economy is uplifted and thus, we should be approach that brought proteomic and MAS components together;
able to reach our strategic goals set for the agricultural productions by the
year 2050.
they identified protein quantity loci (PQL) that explained some of
the spot intensity variation. Of the 72 proteins analyzed, 70 PQLs
were identified for 42 proteins, 20 of which had more than one
Comparatively, it is now a fully mature science and is proud PQL. This type of approach is especially useful in breeding pro-
to be on the list of most quickly adopted crop technologies in grams because, through intensive breeding selection, lines could
world. Biotechnology provides the capabilities to breeders to be available with differing phenotypic degrees that help in draw-
achieve certain goals that would otherwise be impossible through ing correlations between responsive genes and observed stress
conventional plant breeding approaches. Globally, today genet- tolerance phenotypes. This correlation can further be verified
ically modified crops are grown in fields at a commercial scale. by analyzing advanced mapping populations such as recombi-
Thus, the biotech crop area has increased from 1.7 million ha in nant inbred lines (RILs), near isogenic lines (NILs), and double
1996 to 160 million ha in 2011 (Khush, 2012). This trend was haploid lines (Salekdeh and Komatsu, 2007). Furthermore, the co-
well-expected by Dixon (2005) when he stated that “Genomics segregation of a protein and the QTL (or the trait) can be studied
(originally DNA- and transcript-based, but recently extended to in the two parental lines from which the mapping populations
integrate the proteome and metabolome) would play a major role were developed. Finally, the plant breeders should be able to inte-
in driving plant biotechnology.” This review corroborates his long grate the selected genes in marker-assisted breeding programs to
vision and focuses on the use of proteomics for genetic improve- improve the trait under study (Salekdeh and Komatsu, 2007). The
ments in food and biofuel crops including food quality, safety, and major limitation of this technique is that it works only with-in the
nutritional values, tolerance to abiotic and biotic stresses, manu- same species because the parents need to be cross-compatible to
facturing plant-based vaccines and proteomics-based fungicides. transfer the superior genes/alleles through this molecular breed-
Apart from these, proteomics is being used for several other crop ing approach. Under such limitations, embryo rescue or genetic
improvement programs such as, pre- and post-harvest losses, and engineering, which has no boundaries for gene transfer, could be
crop quality characteristics but that is not a part of this review very useful (Varshney et al., 2011).
because of space constraints.
CHARTING THE PROTEOME AND ITS INTERACTION MAP IS
PROTEOMIC TECHNIQUES OFFER NEW TOOLS FOR PLANT IMPORTANT FOR CREATING A KNOWLEDGE BASE
BIOTECHNOLOGY As a general statement, almost all cultivated lands fall under sub-
The knowledge of key proteins that play crucial roles in the optimal conditions for commercial agriculture (Komatsu, 2008).
proper growth and development of a plant are critical to propel Due to these sub-optimal conditions, up to 70% of the crop yields
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Table 1 | A short overview of recent gel-based and gel-free proteomics methods as biotechnological tools that could provide knowledge for crop
improvement programs.
Major crops Technique used Trait studied Plant part Reference
Wheat 2-DE Desiccation Embryo Irar et al. (2010)

iTRAQ and 2D-DIGE Drought Leaves Ford et al. (2011)
2D-DIGE Salinity Leaves Gao et al. (2011)
2-DE Senescence and oxidative Stem Bazargani et al. (2011)
stress
2-DE Flooding stress Root Kong et al. (2010)
2-DE Metabolism post anthesis Endosperm amyloplast Dupont (2008)
2-DE Fusarium head blight Kernels Foroud et al. (2008)
2-DE Heat Kernels Laino et al. (2010)
Maize 2-DE Unintended effects of GM GM vs. non-GM leaves Barros et al. (2010)
nanoLC-LTQ-Orbitrap C4 leaf development Leaves Majeran et al. (2010)
2-DE Desiccation Embryo Huang et al. (2012)
Shotgun proteomics Photosynthesis Chloroplast thylakoid membrane Liu et al. (2011)
Shotgun proteomics Desiccation Embryo Amara et al. (2012)
2-DE Drought Xylem sap in root and stem Alvarez et al. (2008)
iTRAQ Ear rot infection Ears Mohammadi et al. (2011)
LC-MS Greening of etiolated leaves Leaves Shen et al. (2009)
Soybean 2-DE Tolerance to Phytophthora Hypocotyls Zhang et al. (2011b)
2-DE and blue native PAGE Flooding stress Roots and hypocotyl Komatsu et al. (2011)
2-DE Oxidative stress Leaves Galant et al. (2012)
2-DE Heat stress Leaves Wang et al. (2012)
2-DE Flooding stress Roots, Hypocotyl, and leaves Khatoon et al. (2012)
2-DE Osmotic stress Roots Toorchi et al. (2009)
iTRAQ Enhancing water and nutrient Root Nguyen et al. (2012)
uptake after inoculation with
Bradyrhizobium
Rice 2-DE Response to selenium Leaves Gong et al. (2012)
2-DE Embryogenesis Embryo Zi et al. (2012)
Shotgun proteomics Grains development Grains Lee and Koh (2011)
2-DE Heat stress Spikelet Jagadish et al. (2010)
2-DE Drought stress Rice peduncles Muthurajan et al. (2011)
iTRAQ Cold stress Leaves Neilson et al. (2011)
2-DE Bacterial blight defense Leaves Mahmood et al. (2009)
signaling
could be lost (Boyer, 1982). To increase crop productivity, genes and are thus a cornerstone of systems biology (Cox and Mann,
and proteins that are responsible for stress tolerance and disease 2007). None-the-less, the knowledge about the interacting protein
resistance have to be identified continuously. In this direction, a partners, essential for the success of the function of a particular
snapshot of the cellular proteome map at a given time and under protein, might be a good target for gene pyramiding in species
given conditions facilitates the identification of changes in protein that lack the interacting protein(s). In the recent past, several suc-
expression (Hashiguchi et al., 2010). Advancements in MS-based cessful projects have been completed to create proteome maps
proteomics platforms have been considered to be “New Genomics” of various crops using 2-DE and/or other proteomic approaches.
because MS has become an indispensable tool for the investiga- For example, in wheat a reference map has been created for
tion of the PTMs to proteins, and protein interactions. These data leaves (Donnelly et al., 2005), roots (Song et al., 2007), endosperm
provide an unprecedented insight into how cells make decisions (Vensel et al., 2005), and amyloplasts (Balmer et al., 2006). This
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knowledge is helping us to understand the biological processes marker for screening heat-tolerant germplasms. Even with this
that occur in these plant organs. Rice, a staple food for more than information, knowledge on the systemic response of plants during
half of the world’s population (Narciso and Hossain, 2002), wit- heat stress remains limited because plant perception and response
nessed a boom in proteomics studies soon after its genome was to a single stress is different than to a combination of multiple
sequenced (Agrawal and Rakwal, 2006; Rohila et al., 2009; Roy stresses.
et al., 2011). A significant knowledge database has already been There is another major constraint to world agriculture in the
made in rice toward identifying and cataloging the proteins from form of limited water availability for crop irrigation. Recent cli-
various tissues and organelles. This knowledge is in the pipeline mate variability from year to year predicts a worsening situation in
and waiting to be used by biotechnologists and molecular plant the future. World climatologists predict that global warming will
breeders. result in more frequent and severe droughts in the coming years.
Drought stress causes a decrease in carbon usage by the photo-
PROTEOMICS HELP THE INVESTIGATIONS OF ABIOTIC AND BIOTIC synthetic machinery that result in net yield losses on the farm.
STRESS TOLERANCE MECHANISMS Physiological experiments have shown that drought conditions
As with any living organism, crop plants also have to cope with inhibit plant photosynthesis within a short time of a limited water
various biotic and abiotic stress conditions. Contrary to green- supply resulting in a drop in the CO2 assimilation rates (Ribas-
house nurseries, plants in the field experiences a combination of Carbo et al., 2005). To minimize water loss, plants need to close
various biotic and abiotic stresses either concurrently or at differ- their stomata under water deficient conditions. The guard cells
ent developmental stages throughout the growing season (Tester help the plant in the process of controlling the opening and closing
and Bacic, 2005; Mittler, 2006). of the stomata. The closure/opening of the stomata is controlled
A recent estimate suggested that the increased temperatures of by the plant hormone, abscisic acid (ABA). In a plant cell, ABA
the past two decades have caused a loss of approximately $5 bil- flux concentrations are controlled in response to the availability of
lion by impacting the yields of major food crops such as wheat, water to the plant. ABA has been found to play an indispensable
rice, maize, and soybeans (Peng et al., 2004). Temperatures reach- role in the plant response to drought conditions by inducing many
ing 35◦ C in the field cause rice and maize to show sterility. Such transcription factors. In this direction, the guard cell proteome
high heat conditions in the field also lead to flowering and fruiting profiling by Zhao et al. (2008) revealed 336 proteins responsive
failure in other crops. Molecular plant physiologists know very to water stress conditions, with a further 52 proteins considered
well that heat stress increases membrane damage and impairs to be signaling proteins. Abiotic stresses in general cause a water
metabolic functions (Taiz and Zeiger, 2010). A plant breeder deficit condition in cells that results in a myriad of complex cellular
needs to activate the proper protection systems in a crop plant and physiological responses at the plant cellular and organismal
to enable the survival of the plant’s cells under such heat stress levels. In general, the net photosynthesis rate is reduced either
conditions. Heat stress tolerance is a complex mechanism and because of stomatal closure or via metabolic impairment (Reddy
is controlled by multiple genes and proteins involving a num- et al., 2004). The changes in mitochondrial respiration and the
ber of physiological and biochemical changes in the cell, e.g., photosynthetic electron transport chain lead to the generation of
adjustments in the membrane structure and function, tissue water highly toxic reactive oxygen species (ROS), such as superoxides and
content, protein composition, lipids, and primary and secondary peroxides, and cause chemical damage to the DNA and proteins.
metabolites (Huang and Xu, 2008). Global proteomic profiling This damage has serious effects on cellular metabolism (Mittler,
projects are useful techniques for increasing the knowledge base 2002). During evolution, plants have developed several strate-
of plant breeders. For example, a study comparing various wheat gies to address ROS, e.g., avoidance by anatomical adaptation,
cultivars with different heat tolerance capabilities revealed low photosynthesis suppression and photosystem and antenna protein
molecular weight (16–17 kDa) heat shock protein (HSPs) and complex modulations. Several metabolites, such as ascorbate and
other metabolic proteins crucial for the heat tolerance phenotype glutathione, and enzymes, such as peroxidases and superoxide dis-
(Majoul et al., 2004). Proteins from the HSP family and the tran- mutases, help to scavenge the ROS (Mittler, 2006). Another plant
scription factors upstream of these HSPs have been found to have strategy to address drought conditions is to maintain the turgor
crucial roles in providing thermotolerance to the crop. Disarm- pressure of plant cells by the overproduction of osmolytes, such as
ing the function of HSP100 by introducing an antisense construct proline, glycine betaine, and trehalose. These metabolites provide
in tomato plants resulted in their poor survival under heat stress secondary protective effects to proteins against misfolding (Hare
conditions (Yang et al., 2006). However, in another study, trans- et al., 1998). Moreover, dehydration responsive proteins, such as
genic lines overexpressing a different HSP protein (HSP70) showed dehydrins and HSPs, are over produced to protect the intracellular
superior thermotolerance in soybean plants (Zhu et al., 2006). Fur- metabolic machinery (Wang et al., 2003). In short, with such a
thermore, protein–protein interaction studies have proved that wealth of knowledge, drought-tolerant plants can be generated by
HSP90 interacts with calmodulin-binding protein (CBP) (Virdi the modification of these mechanisms, e.g., ABA signaling can be
et al., 2009). Thus, the studies by Zhang et al. (2009) showed that adjusted for the better survival of a crop plant under such stress
the knockdown of calmodulin resulted in reduced thermotoler- conditions. The level of sphingosine-1-phosphate, a messenger
ance. Proteins other than HSPs, e.g., CBP in the above study, molecule, is controlled by ABA through the sphingosine kinase
have been identified in other proteomic studies as differentially protein. In another study using a sphingosine-1-phosphate lyase
expressed proteins during heat stress conditions. Süle et al. mutant, the accumulation of sphingosine-1-phosphate decreased
(2004) proposed S-adenosylmethionine synthetase as a molecular the fresh weight loss of plants under drought stress conditions by
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controlling water loss from the stomata (Nishikawa et al., 2008). Proteins from the rice plasma membrane were studied by Chen
Hajheidari et al. (2005) report the predominance of proteins that et al. (2007), who analyzed the early defense responses involved in
are related to ROS management and protein stability after investi- Xa21-mediated disease resistance. Xa21 is a receptor kinase in rice,
gating the proteomic profiling of field-grown plants under drought and is predicted to detect the pathogen (Xanthomonas) signal on
stress conditions. the cell surface. In this investigation, 20 proteins were found dif-
Proteomic approaches are useful in the study of the molecu- ferentially expressed by Xanthomonas infection after 12 and 24 h
lar mechanism involved in the interaction between a plant and its of inoculation. Eight of these proteins were plasma membrane-
pathogens (Zhou et al., 2006). This group inoculated the wheat associated proteins and had potential functions in rice defense,
spikelet with the fungal spores of Fusarium graminearum and sub- whereas two proteins were not associated with the plasma mem-
jected the total proteins from the infected spikelet to 2-DE for brane. By comparing two partially resistant lines with a susceptible
proteome profiling under normal and infected conditions. They control tomato line over time (72 and 144 h post-inoculation),
discovered that 41 proteins were differentially regulated due to plant proteins were found to be regulated in response to Clav-
Fusarium infection. The gene ontology (GO) annotation revealed ibacter michiganensis ssp. Michiganensis infection. Using a 2-DE
that the up-regulated proteins were from the antioxidant and JA approach, 26 differentially regulated plant proteins were discov-
signaling pathways, pathogenesis-related response, amino acid ered, with 12 being stress response proteins and related to defense
synthesis and nitrogen metabolism, whereas the down-regulated protein families (PR3 and PR9; Coaker et al., 2004). The resistant
proteins were from the photosynthesis pathway. A DNA-damage tomato line showed the up-regulation of PR3, SOD, thioredoxin,
inducible protein was found to be up-regulated and glycosylated and S-adenosylhomocysteine hydrolase genes. In Medicago truncat-
(a type of PTM) in a Fusarium-infected spikelet. Furthermore, ula, a global proteomic analysis was used to characterize the plant
utilizing the TargetP software, several identified plant proteins response to the pathogenic bacterium Pseudomonas aeruginosa
were predicted to localize to the chloroplast. This knowledge fur- (Mathesius et al., 2003). The study established that 154 proteins
ther strengthened the previous finding that the chloroplast is the were accumulated upon exposure to P. aeruginosa, with 21 of
organelle most affected by Fusarium infections. Several fungal pro- those proteins reported to be related to the defense and stress
teins were also identified and found to possess antioxidant and response mechanisms. Afroz et al. (2009) reported the differential
carbon-acquiring functions from the plant through the glycoly- expression of proteins in bacterial wilt-sensitive and wilt-resistant
sis reaction during a compatible interaction between Fusarium tomato cultivars using 2-DE and Edman sequencing. Molecular
and the plant. Studying the proteome response of the resis- chaperones and proteins related to defense storage were highly
tant wheat cultivar Wangshuibai, Wang et al. (2005) found that expressed in the resistant cultivars compared with the susceptible
expression of the carbon metabolism and photosynthesis genes cultivars.
decreased significantly after 6, 12, and 24 h of spike inoculation All of the studies described above, and many that are not
with the fungus Fusarium. In a separate study, the global pro- included here because of space limitations, are decent examples
teomic analysis of germinating maize embryos after infection with that prove that proteomics is highly capable of discovering novel
Fusarium verticillioides highlighted the contribution of protein genes/proteins that could be potential candidates for further stud-
synthesis, protein folding, and stabilization, and oxidative stress ies via biotechnological approaches. We hope that, with time, the
tolerance proteins (Campo et al., 2004). Chivasa et al. (2005) stud- data sets for crop proteomics will strengthen further and that we
ied a maize cell suspension culture with pathogen elicitors and will be able to see examples in which such proteomic-based knowl-
showed that the responses to the pathogen attacks were localized edge is used directly for the improvement of the stress tolerance
to the extracellular matrix. The elicitor treatment of the cell cul- of a crop plant (Agrawal et al., 2012).
tures induced a rapid change in the phosphorylation status of
extracellular peroxidases, the disappearance of the putative extra- MANUFACTURING PLANT-BASED VACCINES IS A POSSIBILITY IN NEAR
cellular b-N -acetylglucosaminidase, and the accumulation of the FUTURE
putative secreted xylanase inhibitor protein. The accumulation of An antigen of interest, when overexpressed in plant tissues by
glyceraldehyde-3-phosphate dehydrogenase and a fragment of a a biotechnological approach, is considered to be a plant-based
putative HSP were observed at the start of the defense response vaccine (Chargelegue et al., 2001). In situations dealing with a
time. Konishi et al. (2001) identified protein expression changes poorly characterized pathogen, a genomic or proteomic approach
in rice leaves infected with the blast fungus Magnaporthe grisea. is specifically useful to identify the candidate antigens that possess
They found a correlation between quantitative expression changes favorable characteristics (Scarselli et al., 2005; Streatfield, 2005). A
in blast responsive proteins and the amount of applied nitrogen major advantage of plant-based vaccines is “no safety concerns”
fertilizer. The large and small RuBisCO subunits were among the (Tacket et al., 1998a, 2000; Kapusta et al., 1999). The production
proteins that were increased by the nitrogen applications, whereas of vaccine antigens in plants can be achieved through, either sta-
the small RuBisCO subunit was reduced after a nitrogen applica- ble expression or transient expression systems. The stable genetic
tion and Magnaporthe infection. After the Magnaporthe infection, transformation produces a genetically engineered plant produc-
PR1 was among the proteins that were induced by the nitrogen ing the antigen, and this plant can be propagated either asexually
application. Based on the results of this study, these proteins were through stem cuttings or sexually through seeds (Tacket et al.,
proposed to potentially be involved in the incompatible interac- 1998b, 2000). On the other hand, transient expression uses recom-
tions between the plants and the fungus and thus might be good binant plant virus that carries the vaccine gene and directs the
candidates for approaching through plant biotechnology. plant to produce the antigen via systematic infection (Koprowski
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and Yusibov, 2001). Tomato is good alternative for edible vaccines for investigating the protein biomarkers for the selection of suit-
and was used to express orally immunogenic respiratory syncytial able durum wheat cultivars for pasta making (De Angelis et al.,
virus (RSV) fusion (F) protein in the fruit (Sandhu et al., 2000). 2008). Flour quality is highly correlated with protein composi-
Banana is also another good alternative for edible plant vaccines tion and functional quality, thus proteomics can be very useful
since it is widely grown and transformation has been reported to identify protein markers for suitable cultivars for flour making
(May et al., 1995). Potato is considered a good model for edible (Yahata et al., 2005). The proteomic analysis of wheat kernels for
vaccines and the first edible vaccine was tested in potatoes (Tacket amphiphilic proteins increased the knowledge of the physiolog-
et al., 1998b). However, from an economic point of view, it would ical and technological functions of wheat kernels (Amiour et al.,
be better if major crops such as soybean, alfalfa, or corn can also 2002). Salt et al. (2005) used 2-DE approach to identify the sol-
be made efficient plant systems for recombinant antigen protein uble proteins that play an important role in stabilizing the gas
production (Sanford et al., 1993). Enterotoxigenic bacteria such bubbles in dough and influencing the crumbling structure of pro-
as Escherichia and Cholera cause diarrhea due to the secretion of teins. Proteomics has also helped in the construction of proteome
toxins that specifically bind to GM1 gangliosides present on epithe- map investigating the level of protein modification during barley
lial cell surfaces of small intestine (Sixma et al., 1991). Cholera malting and detecting the proteins associated with beer quality
toxin (CT) and E. coli liable toxin (LT) are homologous multi- (Iimure et al., 2010). Proteomics also had a role in food authentic-
subunit proteins in which the non-toxic B subunit mediates GM1 ity, through using sensitive protein biomarkers (Pischetsrieder and
and thus can be candidates for vaccines that can neutralize toxin Baeuerlein, 2009). Proteomics was used to identify cheaper sub-
activity. Both LT-B (Mason et al., 1998) and CT-B (Arakawa et al., stitutes for cheaper cultivars of coffee varieties through the use of
1998) expressed in transgenic potatoes produced toxin-protective specific biomarkers (Gil-Agusti et al., 2005). Plant or fruit extracts
intestinal antibody responses after ingestion, and this shows that used in formulas can also be authenticated by the use of protein
plants produced correctly folded proteins and assembled native biomarkers to assess the genuineness of the formula or product
GM1 -binding parametric complexes. LT-B potatoes have been used (D’Amato et al., 2011; Fasoli et al., 2011).
in a clinical study to test the edible plant vaccine (Tacket et al., Food allergens are a great threat to people suffering from such
1998b). This study successfully shows that transgenic plant mate- allergies. However, DNA-based techniques have successfully been
rial expressing the antigen, are capable of simulating the antibody used but these techniques have limitations as in many instances
response in humans. Similarly, several clinical trials have also been DNA was completely absent while high quantities of allergy trig-
performed for other projects, e.g., rabies (Modelska et al., 1998), gering proteins were still present, as in the case of egg white
and E. coli O157:H7 (Judge et al., 2004). A step ahead, Wirz et al. (Popping and Godefroy, 2011). Proteomics is a crucial field for
(2012) described a fully automated “factory” that uses tobacco sensitively detecting and quantifying food allergens. A combina-
plants to produce large quantities of vaccines and other therapeutic tion of 2-DE and IgE reactive proteins using an allergic patient’s
biologics within weeks using a biotechnology approach, represent- sera has been applied as an approach to characterize the aller-
ing a perfect example and motivation for future endeavors in this genicity of food proteins (Akagawa et al., 2007; Pischetsrieder and
direction. Baeuerlein, 2009). Through a proteomics experiment, in which
extracted sesame seed proteins were separated by 2-DE followed
ANALYSES OF FOOD QUALITY, SAFETY, AND NUTRITIONAL VALUES ARE by immuno-labeling with individual patient sera from 20 patients
MORE MEANINGFUL with sesame seed allergy, four allergen including 7S vicilin-type
The field of proteomics has been used to analyze the differences globulin, 2S albumin seed maturation protein, and embryogenic
between the nutritional values of food crops through the analysis abundant protein were identified in this study (Beyer et al., 2002).
of their proteomes. Iwahashi and Hosoda (2000) reported that Petersen et al. (2006) compared the allergenic potency of maize
heat stress increased the expression of invertases in tomato fruits, pollen and the native grass Phleum pratense using 2-DE followed
thus increasing their sucrose content and producing sweeter toma- by immuno-blotting, and found that maize pollen showed less
toes. As physiological disorders appears in crop if they are not allergic response in comparison to the native grass due to lower
harvested at right stage and may result in huge economic losses allergen content and lower allergic groups found in maize pollen.
(Lliso et al., 2007; Pedreschi et al., 2007, 2008, 2009), proteomic- Herndl et al. (2007) also studied apple allergen using 2-DE with IgE
based approaches have become useful to detect biomarkers for immune-blotting and identified four new apple allergens known
optimal harvest maturity (Abdi et al., 2002). Analysis of post- as Mal d 1, Mal d 2, Mal d 3, and Mal d 4. Proteomic analysis of rice
harvest withering process in grapes is very critical to produce high leaf, root, and seed showed the presence of many allergenic pro-
quality wines, and thus gel-based proteomics analysis of this proteins in the seeds, which implicate the uses of proteomic analysis
cess has been employed for improving grape quality (Di Carli of foods for the presence of allergens (Koller et al., 2002). Shotgun
et al., 2011). Also understanding the ripening and post-harvest proteomics was also used to characterize the allergenicity of certain
physiology during storage will not only have impact on food qual- foods (Chassaigne et al., 2007; Heick et al., 2011b). The generated
ity but also on the optimization of the technological processes information is key for targeted approaches, such as selective reac-
involved. Proteomics have investigated the reason that heat treat- tion monitoring (SRM), which not only detect the allergen but
ment for peach fruits will improve the peach fruit quality and also quantify it (Heick et al., 2011a; Lutter et al., 2011). Recently,
shelf-life, and the reason was the differentially expressed proteins multi-allergen detection based on an SRM approach was used in
that were involved in fruit development and ripening (Zhang et al., the detection of seven allergic foods in bread, five of which are
2011a). On the other hand, in cereal industry, proteomics was used plant origin (Heick et al., 2011a). None-the-less, once a protein of
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a specific gene or gene families of allergen is confirmed, its expres- proteins (and genes) to improve energy crops for their growing on
sion can be silenced through biotechnological approaches for a marginal lands, cheaper breakdown of cellulose and increased total
safer human consumption of that food (Thelen, 2009). biomass will be reflected in the yield and quantity of their biofuel
Recently, proteomics has been used to investigate “plant-based production capabilities. Chlamydomonas reinhardtii is considered
bioactives” to improve the nutritional value of food crops. Bioac- as a model system for photoautotrophic growth and lipid and
tives are the peptides that are released either during digestion by the hydrogen production. As these unicellular green algae has been
host enzymes or during food processing and ripening by microbial studied and sequenced in many laboratories, now it serves as a
enzymes (Brambilla et al., 2009). Bioactives were reported from model of choice for physiological, ecophysiological, and econom-
different plant sources, such as wheat, rice, maize, soybean, mush- ical study for the production of biofuels (Huang, 1986; Merchant
rooms, pumpkins, and sorghum (Möller et al., 2008). Soybean et al., 2007). The remarkable metabolism of Chlamydomonas for
bioactive peptides, such as lunasin, Bowman–Birk inhibitor, lectin, energy productions was observed based on its proteomic inves-
and beta-conglycinin, have attracted the attention of researchers tigations (Wienkoop et al., 2010). During the investigation, the
who study their antioxidant activities (de Lumen, 2005) to treat metabolism showed pronounced effects of carbon concentrat-
oxidative stress in the future (Kussmann et al., 2010). Lupin also ing mechanism, which makes the CO2 more available for Calvin
contains alpha and beta-conglutins as storage proteins and appears cycle using carbonic anhydrases. Nearly, 12 isoforms of carbonic
to have bioactive effects (Brambilla et al., 2009). anhydrases (CAH4) were found in Chlamydomonas, and five iso-
forms were measured with targeted proteomics and revealed the
BIOFUEL CROP SCIENCE IS ON RIGHT TRACK TO GET BENEFITTED BY differences of theses isoforms in respect of concentration pat-
PROTEOMICS terns (attomole/1000 cells). The mitochondrial isoform of CAH4
Biofuels are obtained primarily from plant biomass, and are showed a very high dynamic range and high activity under the
believed to have the capacity in the future for substituting fos- limiting conditions of CO2 (Wienkoop et al., 2010). This indi-
sil fuels for sustainable bioenergy needs (Yuan et al., 2008). Uses cates to the significant role of carbonic anhydrases in CO2 -sensing
of biofuels make a balance between the consumption and release pathways in higher plants as well as microalgae, and this novel
of CO2 in the atmosphere. Biofuels, unlike fossil fuels, are made information improves our understanding and can be used to
from clean renewable resources such as plants, algae, or photoau- enhance CO2 fixation mechanisms for better biomass production
totrophic microbes (Schnoor, 2010; Somerville et al., 2010). As the and for increasing the efficiency of biofuel productions irrespec-
transition from the use of prevalent fossil fuels to the renewable tive of plants or microalgae (Hu et al., 2009; Moroney et al., 2011;
energy resources is a complicated procedure comprising scientific Xue et al., 2011).
and socio-economic problems (Kullander, 2010), it is very impor-
tant to shift from using the first generation biofuel crops, such as DEVELOPMENT OF PROTEOMICS-BASED FUNGICIDES IS A POSSIBILITY
sugar cane or corn, to the second generation biofuel crops, such as This possibility relies on the hypothesis that the majority of drug
Miscanthus, and Cordgrass for the production of bioethanol from targets are proteins and the proteomics can provide the candi-
lignocellulosic materials found in plants to make a swift change date proteins involved in a specific biological mechanism. Several
to the most recent and third generation biofuel organisms such as changes in the design of chemical fungicides are being undertaken
photoautotroph microbes and microalgae. Currently, maize, sug- by the scientific research community by summarizing the available
arcane, and rapeseed are among major the crops that are being genomic and proteomic information. Moreover, bioinformatics
used for biofuels. One good example of including a new bio- may come to help in predicting a protein as a fungicide. Biosyn-
fuel crop to the list that is under investigation is African grain thetic fungicide design that is disease-associated target oriented
sorghum. It has been used as food and feed and is now gaining has been established as a new focus in fungicide development (Col-
much attention as energy crop (Calviño and Messing, 2012). The in lado et al., 2007; Acero et al., 2011). However, this field is mostly at
vitro suspension culture of sorghum and the characterization of its its beginning stage but the fungicide design and selection based on
cell secretome using 2-DE and MS/MS have been studied (Ngara target identification information utilizing proteomics experiments
et al., 2008; Ngara and Ndimba, 2011). Another important crop is is going to change the market in the next 10 years (Garrido et al.,
a non-domesticated oil crop, Jatropha curcas L.; has been getting 2010; Acero et al., 2011). In depth proteomic and genomic studies
much attention for its oil, which can be converted to bio-diesel, of fungal infection biology are a pre-requisite of such projects. The
and for its ability to be easily cultivated in arid and semi-arid use of modified natural compounds provides a potential species-
regions, including wastelands (Johnson et al., 2011). Proteomics specific method of controlling plant pathogens by the specific
has been used to explore the oil body and identify the proteins inhibition of those proteins involved in the infection cycle (Pinedo
for oil biogenesis (Liu et al., 2009; Yang et al., 2009). These pro- et al., 2008). The use of these compounds minimizes their environ-
teins can be used to employ phylogenetic and molecular breeding mental impact if they are biodegradable, possesses high specificity,
strategies in the improvement of this crop (Johnson et al., 2011). and have the further advantage of poor penetration into the food
Populus trichocarpa is a tree model system for energy crops (Singh chain. In short, such an application of chemo-genomics to protein
et al., 2011). Kalluri et al. (2009) used a proteomic, a LC-MS/MS- targets is named “chemo-proteomics,” although a more explicit
based approach, and discovered new potential candidate genes in definition is target related affinity profiling (TRAP), defined as
xylem tissue that play an important role in cell wall biosynthesis the use of biology to inform chemistry (Beroza et al., 2002).
in addition to cellulose synthase, sucrose synthase, and polygalac- The accumulation of proteomic information about fungal plant
turonase. In this way, the use of proteomics to identify candidate pathogens may be an incentive to the development of new and
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environmentally friendly fungicides. One of the most promising which have played a key role during the green revolution in the
biotechnologies downstream of proteomics is the use of specific 20th century, feel handicapped in the 21st century because mod-
peptide sequences that are able to modify protein activities in the ern plant breeders require precise gene modifications with a gene
pathogen. One encouraging strategy to combat fungal diseases tracking system for the modified trait. In this post-genomic era,
in the field is the use of a novel chemical proteomics tool called the integration of proteomics into the field of crop science will
activity-based protein profiling (ABPP; Richau and van der Hoorn, certainly enrich genome annotation efforts and accelerate the
2010). This technology reveals the activities of proteomes, and that development of crop models for the elucidation of gene func-
is why understanding the involved biological processes is so cru- tions influencing phenotypes for the success of field crops. The
cial. A small-molecule fluorescent probe is used in ABPP; the probe only caveat to the application of proteomics in biotechnology
irreversibly reacts with the catalytic sites of catalytic subunits in programs is that the genetic modification should be expressed
an activity-dependent manner. By using fluorescent protein gels, at protein level. Progress made with the help of various -omics
the protein activities can be quantified to study these activities in approaches along with the creation of a wider gene pool by
vitro and in vivo (Gu et al., 2010). utilizing modern biotechnological tools is the best approach to
improve crop productivity for meeting food production goals
CONCLUSION by 2050.
During the recent past, world agriculture has come under more
climatic variability along with less arable land availability per per- ACKNOWLEDGMENTS
son, which compounds the stress situation on producer groups. The authors acknowledge the funding from USAID/USDA in Jai
In the present scenario, pressure is building upon the plant breed- S. Rohila and Sanaa I. M. Milad and Ali I. Nawar labs. Jai S. Rohila
ers and plant biologists to come up with “smart crop varieties” also acknowledge financial support from, SD Agriculture Experi-
that are better suited genotypes with the ability to withstand ment Station, SD Wheat Commission and SD Soybean Research
a wider range of climatic variability to tackle the food inse- and Promotion Council. Sara Glisczinski, Mai A. El-Shabasy, and
curities of future generations along with maintaining/exceeding Manali Shirke help in critical reading of the manuscript and in
quality parameters. Conventional plant breeding approaches, figure preparation is especially appreciated.
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embryogenesis: discovery of the that could be construed as a potential a biotechnology tool for crop improve- article distributed under the terms of the
embryogenesis-dependent globulins. conflict of interest. ment. Front. Plant Sci. 4:35. doi: Creative Commons Attribution License,
Electrophoresis 33, 1129–1138. 10.3389/fpls.2013.00035 which permits use, distribution and
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Proteomics: a biotechnology tool for crop improvement

INTRODUCTION of the several cutting edge approaches for understanding global

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the biotechnological improvement of crop plants. These pro-

POTENTIAL OF PROTEOMICS AS A BIOTECHNOLOGY TOOL

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Major crops Technique used Trait studied Plant part Reference

Wheat 2-DE Desiccation Embryo Irar et al. (2010)

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