Proteomics is one of the most explored areas of research based on global-scale analysis of proteins. It leads to direct understanding of function and regulation of genes. Significant advances in the comprehensive profiling, functional analysis, and regulation of plant proteins have not advanced much as compared to model organisms such as yeast, humans etc. The application of proteomic approaches to plants implicates; comprehensive identification of proteins, their isoforms, as well as their prevalence in each tissue, characterizing the biochemical and cellular functions of each protein and the analysis of protein regulation and its relation to other regulatory networks . Genes of higher eukaryotes (including plants) contain introns which are large and numerous. Therefore, combinational exon usage originating from complex gene structures results in a multitude of splice variants leading to generation of different protein products from a given gene. Thus, the determination of the comprehensive pattern of expression of each protein isoform is a challenging task, most importantly for poorly expressed proteins .
The two-dimensional gel electrophoresis (2-DE) is used for profiling protein expression involving separation of complex protein mixtures by molecular charge in the first dimension and by mass in the second dimension. Recent advancement in 2-DE has improved resolution and reproducibility but still automation in high-throughput setting is lagging. The alternative approaches like multi-dimensional protein identification technology involving large-scale proteomics are able to generate a large catalog of proteins present in complex cell extracts. Further, detection of low abundance proteins using sub-cellular fractionation reduces the complexity of protein extracts. These efforts have successfully characterized nuclear, chloroplast, amyloplast, plasma membrane, peroxisome, endoplasmic reticulum, cell wall, and mitochondrial proteomes of a model plant,
Food allergy can be a serious nutritional problem in children and adults. Any protein-containing food has the potential to elicit an allergic reaction in the human population. Antibody IgE-mediated reactions are the most prevalent allergic reactions to food. These responses occur after the release of chemical mediators from mast cells and basophils as a result of interactions between food proteins and specific IgE molecules on the surface of these receptor cells. Eight foods or food groups have been identified as the most frequent sources of human food allergens and account for over 90% of the documented food allergies worldwide. These foods are milk, eggs, fish, crustaceans, wheat, peanuts, tree nuts and soy . Despite their well-documented allergenicity, soy derivatives continue to be increasingly used in a variety of food products due to their well-documented health benefits. Soybean has also been one of the selected target crops for genetic modification (GM). For example, the artificial introduction of 5-enolpyruvylshikimate-3-phosphate synthase in soybean crop creates an alternative pathway which is insensitive to glyphosate (most potent herbicide), thus increasing overall crop yield. One of the major concerns regarding the safety of GM foods is the potential allergenicity of the resulting products, namely the possible occurrence of either altered or
Soybean is an important source of protein for human and animal nutrition, as well as a major source of vegetable oil. Although soybean is adapted to grow in a range of climatic conditions including adverse environmental and biological factors, still it has been affected with respect to growth, development, and global production For instance, drought reduces the yield of soybean by about 40%, affecting all stages of plant development from germination to flowering thus reducing the quality of the seeds. . Several other abiotic stresses, such as flooding, high temperature, irradiation, or the presence of pollutants in the air and soil have detrimental effects on the growth and productivity of soybean. Along with morphological and physiological studies on the responses of plants to stress conditions, several molecular mechanisms from gene transcription to translation as well as metabolites were investigated. Recent advances in the field of proteomics have created an opportunity for dissecting quantitative traits in a more meaningful way. Proteomics can investigate the molecular mechanisms of plants’ responses to stresses and provides a path toward increasing the efficiency of indirect selection for inherited traits. In soybean a comprehensive functional genomics is yet to be performed; therefore, proteomics approaches form a powerful tool for analyzing the functions of complete set of proteins including those involved in stress protection.
2. Proteomics: isolation, identification and classification
In plant proteomics, the type of the plant species, tissues, organs, cell organelles, and the nature of desired proteins affect the techniques that can be used for protein extraction. Furthermore, the extraction process becomes more tedious when the protein is present inside vacuoles, rigid cell walls, or membrane plastids. A perfect protein extraction method involves complete solubilization of total proteins from a given sample and minimizing post-extraction artifact formation, proteolytic degradation as well as removal of non-proteinaceous contaminants. To date, only the proteome of
In classical proteome analyses, proteins are initially separated by a 2-DE technique with isoelectric focusing (IEF) as the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) as the second dimension. A greater resolution in protein separation has been achieved by introducing immobilized pH gradients (IPGs) for the first dimension. Methodological advances in 2-DE have led to the introduction of two-dimensional fluorescence difference gel electrophoresis (2D-DIGE), which has been used for the comparative analysis of the proteome of soybean subjected to abiotic and biotic stresses . The separated proteins can be subsequently identified by sequencing or by mass spectrometry. By introduction of mass spectrometry into protein chemistry, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography/tandem mass spectrometry (LC-MS/MS) have become the methods of choice for high-throughput identification of proteins. An alternative technique known variously as ‘gel-free proteomics’, ‘shotgun proteomics’, or ‘LC-MS/MS-based proteomics’ can also be used in high-throughput protein analysis. This approach is based on LC separation of complex peptide mixtures coupled with tandem mass spectrometric analysis. A multidimensional protein identification technology (MudPIT) that usually incorporates separation on a strong cation exchange, reverse-phase column and MS/MS analysis helps the efficient separation of complex peptide mixtures. The gel-free technique have the advantage of being capable of identifying low-abundance proteins, proteins with extreme molecular weights or p
Soybean has an estimated genome size of 1115 Mbp, which is significantly larger than those of other crops, such as rice (490 Mbp) or sorghum (818 Mbp). Sequencing of the 1100 Mbp of total soybean genome predicts the presence of 46,430 protein-encoding genes, 70% more than in
Trichloroacetic acid (TCA)/acetone-based and phenol-based buffers are most frequently used in protein extraction from plants. A comprehensive proteomic study was performed on nine organs from soybean plants in various developmental stages by using three different methods for protein extraction and solubilization. The results showed that the use of an alkaline phosphatase buffer followed by TCA/acetone precipitation caused horizontal streaking in 2-DE while use of a Mg/NP-40 buffer followed by extraction with alkaline phenol and methanol/ammonium acetate produced high-quality proteome maps with well-separated spots, high spot intensities, and high numbers of separate protein spots in 2-DE gels [10, 11]. In the case of organelle proteomics particularly that of membrane proteomics, a different extraction procedure is required that involves modifications to dissolve hydrophobic proteins and additional purification steps. Furthermore, when studying protein–protein interactions, it is necessary to extract protein complexes by using buffers with less or no detergent to get the proteins in their native states. Despite the importance of seed filling in the synthesis of storage reserves for germination, systematic proteomic analysis of this phase in legumes is yet to be carried out.
Total seed proteins of soybean (cv. Maverick) at different stages of flowering (14, 21, 28, 35 and 42 days) were isolated and subsequently 2D-PAGE was done. Initially IPG strips of pH 3 to 10 were taken then narrowed down to pH range to 4 to 7 for high-resolution proteome maps. A total of 488 and 679 proteins were identified from 2D-PAGE gels of pH range 4 to 7 and 3 to 10 gels, respectively. Each of the 679 proteins was excised from reference gels for identification by MALDI-TOF MS and a total of 422 proteins (62%) were identified. One unique protein was often represented by more than one spot on the 2D-PAGE gel, most likely due to post-translational modifications or genetic isoforms. Taking into account this redundancy, 216 unique proteins out of 422 were identified. A total of 82 proteins were associated with metabolism (the largest functional class) and the second largest functional class were comprised of 52 spots assigned to the seed storage proteins
3. Implication of proteomics in understanding soybean stress
Soybean is grown worldwide with an average protein content of 40% (highest protein content with respect to other food crops) and oil content of 20% (which is second only to that of groundnut among the leguminous foods). Furthermore, soybean improves soil fertility by fixing nitrogen from the atmosphere in symbiosis with nitrogen fixing bacteria. It is, however, susceptible to various types of stresses (abiotic and biotic). Tolerance and susceptibility to stresses are complex phenomena because they are quantitatively inherited and can occur during different stages of plant growth and development. Extrinsic stress is regarded as the most important stress agent, which results from changes in abiotic factors such as temperature, climatic factors and chemical components, either naturally occurring or manmade. Further, biotic stresses (occurs as a result of damage done to plants by other living organisms, such as bacteria, viruses, fungi, parasites, beneficial and harmful insects, weeds, bacterial, fungal, algal and viral diseases) can also cause huge deterioration in plant growth and yield. Plants have developed adaptive features against these stresses. The genome remains unchanged to a large extent in any particular cell while proteins change dramatically as genes are turned on or off in response to stress. The proteome determines the cellular phenotype and its plasticity in response to external signals. It is proteins that are directly involved in both normal and stress-associated biochemical processes. Therefore, a more complete understanding of stress in soybean may be gained by looking directly into the proteins within a stressed cell or tissue. Proteomic based techniques that allow large-scale protein profiling are powerful tools for the identification of proteins involved in stress-responses in plants. Extensive studies have evaluated changes in protein levels in plant tissues in response to stresses. Unfortunately, these studies have been mainly focused on non-legume species such as
Considerable amount of research has been carried out during the last decade to find the effect of stress under extreme . These include chloroplast membrane, cell wall and nuclear envelope, while some researchers have focused on individual tissues
Following are the different categories of proteins with important properties, which have been shown to play a crucial role against abiotic environmental stress as well as biotic stress. The data so collected from various plants including soybean is based on 2-DE, mass spectrometry and bioinformatics tools.
Reactive oxygen species (ROS) in plant cellulars are produced as a consequence of myriad stimuli ranging from abiotic and biotic stress, production of hormonal regulators, as well as cell processes such as polar growth and programmed cell death . These reactive molecules are generated at a number of cellular sites, including mitochondria, chloroplasts, peroxisomes, and at the extracellular side of the plasma membrane. ROS trigger signal transduction events, such as mitogen-activated protein kinase cascades eliciting specific cellular response.s. The influence of these molecules on cellular processes is mediated by both the perpetuation of their production and their amelioration by scavenging enzymes such as superoxide dismutase, ascorbate peroxidase, and catalase. The location, amplitude, and duration of production of these molecules are determined by the specificity of the responses . Accumulation of ROS as a result of various environmental stresses is a major cause of loss of crop productivity worldwide. ROS affect many cellular functions by damaging nucleic acids, oxidizing proteins, and causing lipid peroxidation. It is important to note that whether ROS will act as damaging, protective or signaling factors depends on the delicate equilibrium between ROS production and scavenging at the proper site and time. ROS can damage cells as well as initiate responses such as new gene expression. The cell response evoked is strongly dependent on several factors. The subcellular location for formation of ROS may be especially important for a highly reactive ROS, because it diffuses only a very short distance before reacting with a cellular molecule. Stress-induced ROS accumulation is counteracted by enzymatic antioxidant systems that include a variety of scavengers, such as superoxide dismutase, ascorbate peroxidase, glutathione peroxidase, glutathione S-transferase, catalase and non-enzymatic low molecular metabolites, such as ascorbate, glutathione (red.), α-tocopherol, carotenoids and flavonoids. In addition, proline can now be added to an elite list of non-enzymatic antioxidants that microbes, animals, and plants need to counteract the inhibitory effects of ROS . Plant stress tolerance may therefore be improved by the enhancement of
Abscissic acid (ABA) has been implicated in plant response to environmental stress by interfering at different levels with signaling. Its level increases under stress conditions to trigger metabolic and physiological changes . It has become increasingly clear that the isolated abiotic signaling network is controlled by ABA and the biotic network is controlled by salicylic acid, jasmonic acid and ethylene are interconnected at various levels . The concept of marker genes whose expression is believed to be regulated by individual hormones does not do justice to the nature of the network. The apparent cross-talk in stress-hormone signaling makes it difficult to assign a marker gene or a mutant phenotype to a specific hormone-controlled pathway. The signaling network into which the four stress hormones and other signals feed is apparently designed to allow plants to adapt optimally to specific situations by integrating possibly conflicting information from environmental conditions, biotic stress, and developmental as well as nutritional status. Promoter analyses of ABA/stress-responsive genes revealed that a DNA sequence element consisting of ACGTGGC is important for ABA regulation. For the past several years, researchers have been trying to identify transcription factors that regulate the expression of ABA/stress-responsive genes
Like other eukaryotes, plants use mitogen-activated protein kinase (MAPK) cascades to regulate various cellular processes in response to a broad range of biotic and abiotic stress. These cascades promote the transient activation of MAPKs by a dual phosphorylation of Thr and Tyr within the activation loop of the MAPK. Recent studies indicate that MAPKs are not only regulated through phosphorylation by upstream kinases, but also by direct binding of different protein factors . The constitutive activation of MAPKs was found to result in detrimental effects, underlining the importance of a negative regulation of MAPK signaling. MAPK phosphatases (MKPs) are negative regulators of MAPKs. Recent progress in analyzing plant MKP mutants has revealed their important role in fine-tuning MAPK signaling. In particular, the dual-specificity phosphatase MKP1 and the protein tyrosine phosphatase (PTP1) negatively regulate defense responses and resistance to a bacterial pathogen by counter balancing the activation of two MAPKs (MPK3 and MPK6). Interestingly, MKP1 and PTP1 bind CaM, and the phosphatase activity of MKP1 is increased by CaM in a Ca2+-dependent manner. Thus, Ca2+ and MAPK signaling pathways appear to be connected through the regulation of plant MAPKs and MKPs by CaM .
Plant cells are equipped with highly efficient mechanisms to perceive, transduce and respond to a wide variety of internal and external signals during their growth and development. Perception of signals
4. Significance of proteomics in soybean allergenicity
Soybeans have played a central role in concerns about GM introduced allergens and in using GM to remove intrinsic allergens. Soybean is a rich and inexpensive source of proteins for humans and animals. Soybean milk and dairy product replacement is growing in acceptance, not only by people sensitive to lactose and/or milk proteins, but also for health considerations. Soybean protein is widely used in thousands of processed foods throughout the industrialized world and is a staple crop in Asia. Soybean ranks among the eight most significant food allergens. Soybean sensitivity is estimated to occur in 5-8% of children and 1-2% of adults. The allergic reaction is only rarely life-threatening with the primary adverse reactions to consumption being atopic (skin) reactions and gastric distress. Symptoms of soy allergy usually appear within a few minutes to two hours of eating soy ingredients. People with soy allergies may cross-react with peanuts or other legumes, such as beans or peas. Soy is one of the most common allergens for infants who have not yet begun eating solid foods, because they may be fed soy-based infant formula. It is rare for babies to have a traditional IgE mediated food allergy to soy, but some babies may develop milk-soy protein intolerance [31-34] or food protein induced enterocolitis syndrome [http://foodallergies.about.com/od/soyallergies/a/Soy-Allergy-Overview.htm]. Infants will usually develop these sensitivities within a few months of birth, and most will outgrow them by the age of two. Most people with soy allergies can tolerate the small amount of soy protein that remains in refined soybean oil and soy lecithin. Both of these ingredients may cause allergic reactions in highly sensitized people. There are some data available that describe the natural variation in allergen proteins that occur in soybean. For a better understanding of the variation of allergen proteins that might be expected to occur in GM soybeans, it is important to determine the natural variation of protein composition both in wild and GM soybeans. “Proteomics” approach is the foremost one which allows protein identification and quantification with utmost accuracy.
Biotechnology critics have claimed that an apparent rise in the number of soybean allergic individuals in the UK is correlated with the development of GM soybeans in the American market. GM-soybeans that have been developed in the US include herbicide-resistance (glyphosate) and seeds with higher percentage of essential amino acids,
Plant biotechnology has not only tried to produce GM-soy which is herbicide resistance or with enhanced methionine content but also aimed to remove naturally occurring allergens in native soy varieties. Presently primary treatment for food allergies is avoidance, but it is unavoidable in case of soybean protein which is present in thousands of products. Therefore, it is very difficult to avoid soybean and its derived products. Research is going on to produce hypoallergenic variants of soybean which has potential to reduce the risk of adverse reactions. Soybeans possess as many as 15 proteins recognized by IgEs from soybean-sensitive people . The immunodominant soybean allergens are the
The fear of allergic reactions has produced much of the concern about the risks of GM crops. In order to broadly apply genetic modification to crops, there is an urgent need for better biochemical and molecular methods, including animal models, to test for food allergens experimentally so that the supporting data can be provided to evaluate newly proposed and actual GM products. In order to design transgenes, it would be useful to predict allergenicity but, currently, there are no models that would permit accurate assessment of allergenic potential of proteins unrelated to known allergens. Liver represents a suitable model for monitoring the effects of a diet, due to its key role in controlling the whole metabolism. Previous studies on hepatocytes from young female mice fed on GM soybean demonstrated nuclear modifications involving transcription and splicing pathways [42, 43]. The morpho-functional characteristics of the liver of 24-month-old mice, fed from weaning on control or GM soybean, were investigated by combining a proteomic approach with ultrastructural, morphometrical and immunoelectron microscopical analyses. Several proteins belonging to hepatocyte metabolism, stress response, calcium signaling and mitochondria were differentially expressed in GM-fed mice, indicating a more marked expression of senescence markers in comparison to controls. Moreover, hepatocytes of GM-fed mice showed mitochondrial and nuclear modifications indicative of reduced metabolic rate. This study demonstrates that GM soybean intake can influence some liver features, although the mechanisms remain unknown. Therefore, it is required to investigate the long-term consequences of GM-diets, further studies are required for potential synergistic effects with other factors like ageing, stress etc.
5. Challenges and perspectives
Soybean is a species of great agronomic and economic interest. It is one of the most recalcitrant plant species to be used as experimental material in proteomic analysis. Furthermore, there are several difficulties in the study of proteins (irrespective of source) with respect to DNA and RNA. The foremost important thing is the maintenance of secondary and tertiary structure during their analysis. They have problems with easy denaturation on exposure to high temperature, extremes of pH, oxidation, specific chemicals etc. There are some classes of proteins which are difficult to analyze due to their poor solubility. Proteins cannot be amplified like DNA, therefore less abundant species are very difficult to detect. However, many potentially important proteins (in scarce) are lost due to non-specific binding or the co-removal of proteins/peptides intrinsically bound to the high abundant carrier proteins. Following are two methods developed recently to resolve detection of less abundant plant proteins :
The use of equalizer beads coupled with a combinational library of ligands containing diverse population of beads with equivalent binding capacity to most of the proteins present in a sample.
The ultra-microarrays have been found to have high specificity and sensitivity with detection levels in the range of attomole (10-18 mole).
The current depth of knowledge regarding the soybean proteome is significantly less than that for some other plants. The soybean proteome map which is available in the database (http://proteome.dc.affrc.go.jp/soybean/) corresponds to various types of stresses, allergenicity, and studies on natural product biosynthesis in soybean. The other challenges in plant proteomics including soybean are standardization of methodologies, dissemination of proteomics data into publicly available databases and most importantly its cost expensiveness. Furthermore, most proteomics technologies use complex instrumentation and critical computing power. Currently, there is no expertise available for functional interpretation of data obtained from integration of proteomics with genomics and metabolomics.
The significance of proteomics over genomics and transcriptomics has been debated since the field has emerged. The importance of the proteome cannot be overstated as it is the proteins within the cell that provide structure, produce energy, as well as allow communication, movement, and reproduction. Basically, proteins provide structural and functional framework for cellular life. Genetic information is static while the protein complement of a cell is dynamic. Differential proteomics is a scientific discipline that detects the proteins associated with a diseased state (either due to abiotic or biotic stress, toxicity due to allergenicity, genetic modifications etc.) by means of their altered levels of expression between the control and diseased states. Extensive research towards the development of a soybean proteome map would permit the rapid comparison of soybean cultivars, mutants, and transgenic lines. Moreover, studies of soybean physiology will also benefit from the existence of a detailed and quantitative proteome reference map of the soybean plant. The information obtained from soybean proteomics will be helpful in predicting the function of plant proteins and will aid in molecular cloning of the corresponding genes in the future. The identification of novel genes, the determination of their expression patterns in response to stress, and an understanding of their functions in stress adaptation will provide us with the basis for effective strategies for engineering improved stress tolerance in soybean. With the advancement of new technologies in proteomics combined with advanced bioinformatics, we are currently identifying molecular signatures of diseases based on protein pathways and signaling cascades. Applying these findings will improve our understanding of the roles of individual proteins or the entire cellular pathways in the initiation and development of disease. The abundance of information provided by proteomics research is entirely complementary with the genetic information being generated by genomics research. Proteomics makes a key contribution to the development of functional genomics. The combination of genomics and proteomics will play a major role in understanding molecular mechanisms in plant pathology, and it will have a significant impact on the development of high yield varieties, with better resistance towards adverse environmental factors as well as various pathogenic diseases caused by bacteria, viruses and fungi in the future.