Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.)

Advancing Chickpea Breeding: Omics Insights for Targeted Abiotic Stress Mitigation and Genetic Enhancement

Chickpea is a major source of proteins and is considered the most economically vital food legume. Chickpea production is threatened by several abiotic and biotic factors worldwide. The main constraints limiting worldwide chickpea production are abiotic conditions such as drought, heat, salinity, and cold. It is clear that chickpea is treasured for its nutritive value, in particular its high protein content, and hence study of problems like drought, cold and salinity stresses are very important concerning chickpeas. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. The most crippling economic losses in agriculture occur due to these abiotic stressors, which affect plants in many ways. All these abiotic stresses affect the water relations of the plant, both at the cellular level as well as the whole-plant level, causing both specific and non-specific reactions, damage and adaptation reactions. These stresses share common features. Breeding programs use a huge collection of over 100,000 chickpea accessions as their foundation. Significant advancements in conventional breeding, including mutagenesis, gene/allele introgression, and germplasm introduction, have been made through this method. Abiotic tolerance and yield component selection are made easier by creating unique DNA markers for the genus Cicer, which has been made possible by developments in high-throughput sequencing and molecular biology. Transcriptomics, proteomics, and metabolomics have also made it possible to identify particular genes, proteins, and metabolites linked to chickpea tolerance to abiotic stress. Chickpea abiotic stress tolerance has been directly and potentially improved by biotechnological applications, which are covered by all 'Omics' approaches. It requires information on the abiotic stress response at the different molecular levels, which comprises gene expression analysis for metabolites or proteins and its impact on phenotype. Studies on chickpea genome-wide expression profiling have been conducted to determine important candidate genes and their regulatory networks for abiotic stress response. This study aimed to offer a detailed overview of the diverse 'Omics' approaches for resilience's to abiotic stresses on chickpea plants.

Chickpea Proteome Analysis Reveals Genotype-Dependent Variations Associated with Seed Traits

Chickpea (Cicer arietinum L.) is the second most widely grown legume crop after soybean. Here, we measured the macronutrients and performed proteome profiling of eight chickpea cultivars using two complementary protein extraction solvents. The total protein, starch, and soluble sugar contents significantly differ between cultivars, and we quantified 2434 and 1809 proteins, respectively, from urea- and water-based extraction solvents using a data-independent acquisition approach. The proteome-level differences can vary from 9-25% for the urea-extracted proteins, and the storage protein abundances significantly differed between the cultivars, where legumin content was detected as the highest, followed by vicilin and albumin. Fifty common allergens were detected from two extraction solvents, primarily overrepresented in chromosomes 3, 4, and 5. Integrated analysis revealed distinct subclusters of proteins and their associated pathways for total protein, lipids, and starch content. Overall, we established chickpea pan-proteome resources and provided insights into the key pathways that define the genotypes.

Impact of Terminal Heat and Combined Heat-Drought Stress on Plant Growth, Yield, Grain Size, and Nutritional Quality in Chickpea (Cicer arietinum L.)

Chickpea is the third most consumed pulse and provides a kit of essential nutrients for an exponential population. High temperatures and drought stress are two major abiotic stresses that cause serious effects on chickpea growth and development. The comprehension of abiotic stresses' impact on chickpea productivity and nutritional quality will permit the selection of promising genotypes. The current study aimed to assess the impact of heat and drought stresses on plant growth, grain yield and its components, grain size, and nutritional quality in chickpea. For this purpose, 43 international chickpea genotypes were evaluated under normal, heat, and combined heat-drought stress conditions. The findings revealed a significant decrease of over 50% in plant height, biological yield, and seed yield under both stress conditions. Grain size and hundred-seed weight were the most heritable traits under normal, heat, and combined heat-drought stress. Proteins were accumulated under both stresses, evolving from 20.26% for normal conditions to 22.19% for heat stress and to 21.94% for combined heat-drought stress. For minerals, significant variation between treatments was observed for Mn, Mg, and Na. Our results also showed a significant impact of genotype and genotype-environment interaction factors only on K content. Using selection indices, 22 genotypes were identified as highly tolerant to the combined heat-drought stress, while eleven genotypes were heat-tolerant. Mineral profile analysis according to the contrasting tolerance clusters revealed decreased potassium content in susceptible genotypes, indicating genetic potential in the studied chickpea collection, ensuring tolerance to both stresses while maintaining good grain quality.

Proteomics for abiotic stresses in legumes: present status and future directions

Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics provides an important molecular approach to investigate proteins involved in stress response. Both the gel-based and gel-free-based techniques have significantly contributed to understanding the proteome regulatory network in leguminous plants. In the present review, we have discussed the role of different proteomic approaches (2-DE, 2 D-DIGE, ICAT, iTRAQ, etc.) in the identification of various stress-responsive proteins in important leguminous crops, including soybean, chickpea, cowpea, pigeon pea, groundnut, and common bean under variable abiotic stresses including heat, drought, salinity, waterlogging, frost, chilling and metal toxicity. The proteomic analysis has revealed that most of the identified differentially expressed proteins in legumes are involved in photosynthesis, carbohydrate metabolism, signal transduction, protein metabolism, defense, and stress adaptation. The proteomic approaches provide insights in understanding the molecular mechanism of stress tolerance in legumes and have resulted in the identification of candidate genes used for the genetic improvement of plants against various environmental stresses. Identifying novel proteins and determining their expression under different stress conditions provide the basis for effective engineering strategies to improve stress tolerance in crop plants through marker-assisted breeding.

Prospects of microgreens as budding living functional food: Breeding and biofortification through OMICS and other approaches for nutritional security

Nutrient deficiency has resulted in impaired growth and development of the population globally. Microgreens are considered immature greens (required light for photosynthesis and growing medium) and developed from the seeds of vegetables, legumes, herbs, and cereals. These are considered "living superfood/functional food" due to the presence of chlorophyll, beta carotene, lutein, and minerals like magnesium (Mg), Potassium (K), Phosphorus (P), and Calcium (Ca). Microgreens are rich at the nutritional level and contain several phytoactive compounds (carotenoids, phenols, glucosinolates, polysterols) that are helpful for human health on Earth and in space due to their anti-microbial, anti-inflammatory, antioxidant, and anti-carcinogenic properties. Microgreens can be used as plant-based nutritive vegetarian foods that will be fruitful as a nourishing constituent in the food industryfor garnish purposes, complement flavor, texture, and color to salads, soups, flat-breads, pizzas, and sandwiches (substitute to lettuce in tacos, sandwich, burger). Good handling practices may enhance microgreens'stability, storage, and shelf-life under appropriate conditions, including light, temperature, nutrients, humidity, and substrate. Moreover, the substrate may be a nutritive liquid solution (hydroponic system) or solid medium (coco peat, coconut fiber, coir dust and husks, sand, vermicompost, sugarcane filter cake, etc.) based on a variety of microgreens. However integrated multiomics approaches alongwith nutriomics and foodomics may be explored and utilized to identify and breed most potential microgreen genotypes, biofortify including increasing the nutritional content (macro-elements:K, Ca and Mg; oligo-elements: Fe and Zn and antioxidant activity) and microgreens related other traits viz., fast growth, good nutritional values, high germination percentage, and appropriate shelf-life through the implementation of integrated approaches includes genomics, transcriptomics, sequencing-based approaches, molecular breeding, machine learning, nanoparticles, and seed priming strategiesetc.

Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes

The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.

Current perspectives of ubiquitination and SUMOylation in abiotic stress tolerance in plants

Post-translational modification (PTM) is a critical and rapid mechanism to regulate all the major cellular processes through the modification of diverse protein substrates. Substrate-specific covalent attachment of ubiquitin and Small Ubiquitin-Like Modifier (SUMO) with the target proteins, known as ubiquitination and SUMOylation, respectively, are crucial PTMs that regulate almost every process in the cell by modulating the stability and fidelity of the proteins. Ubiquitination and SUMOylation play a very significant role to provide tolerance to the plants in adverse environmental conditions by activating/deactivating the pre-existing proteins to a great extent. We reviewed the importance of ubiquitination and SUMOylation in plants, implicating its prospects in various abiotic stress regulations. An exhaustive study of molecular mechanisms of ubiquitination and SUMOylation of plant proteins and their role will contribute to the understanding of physiology underlying mitigation of the abiotic stresses and survival in plants. It will be helpful to strategize the improvement of crops for abiotic stress tolerance.

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.

A Comprehensive Review on Chickpea (Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience

Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change.

Physiological, Proteomic Analysis, and Calcium-Related Gene Expression Reveal Taxus wallichiana var. mairei Adaptability to Acid Rain Stress Under Various Calcium Levels

As one of the serious environmental problems worldwide, acid rain (AR) has always caused continuous damage to the forestry ecosystem. Studies have shown that AR can leach calcium ions from plants and soil. Calcium (Ca) is also a crucial regulator of the plant stress response, whereas there are few reports on how Ca regulates the response of AR-resistant woody plants to AR stress. In this study, by setting different exogenous Ca levels, we study the physiological and molecular mechanism of Ca in regulating the Taxus wallichiana var. mairei response to AR stress. Our results showed that low Ca level leads to photosynthesis, and antioxidant defense system decreases in T. wallichiana var. mairei leaves; however, these negative effects could be reversed at high Ca level. In addition, proteomic analyses identified 44 differentially expressed proteins in different Ca level treatments of T. wallichiana var. mairei under AR stress. These proteins were classified into seven groups, which include metabolic process, photosynthesis and energy pathway, cell rescue and defense, transcription and translation, protein modification and degradation, signal transduction, etc. Furthermore, the study found that low Ca level leads to an obvious increase of Ca-related gene expression under AR stress in T. wallichiana var. mairei using qRT-PCR analyses and however can be reversed at high Ca level. These findings would enrich and extend the Ca signaling pathways of AR stress in AR-resistant woody plants and are expected to have important theoretical and practical significance in revealing the mechanism of woody plants tolerating AR stress and protecting forestry ecosystem in soil environment under different Ca levels.

Drought Stress Induces Morpho-Physiological and Proteome Changes of Pandanus amaryllifolius

Drought is one of the significant threats to the agricultural sector. However, there is limited knowledge on plant response to drought stress and post-drought recovery. Pandanus amaryllifolius, a moderate drought-tolerant plant, is well-known for its ability to survive in low-level soil moisture conditions. Understanding the molecular regulation of drought stress signaling in this plant could help guide the rational design of crop plants to counter this environmental challenge. This study aimed to determine the morpho-physiological, biochemical, and protein changes of P. amaryllifolius in response to drought stress and during recovery. Drought significantly reduced the leaf relative water content and chlorophyll content of P. amaryllifolius. In contrast, relative electrolyte leakage, proline and malondialdehyde contents, and the activities of antioxidant enzymes in the drought-treated and recovered samples were relatively higher than the well-watered sample. The protein changes between drought-stressed, well-watered, and recovered plants were evaluated using tandem mass tags (TMT)-based quantitative proteomics. Of the 1415 differentially abundant proteins, 74 were significantly altered. The majority of proteins differing between them were related to carbon metabolism, photosynthesis, stress response, and antioxidant activity. This is the first study that reports the protein changes in response to drought stress in Pandanus. The data generated provide an insight into the drought-responsive mechanisms in P. amaryllifolius.

Proteome changes and associated physiological roles in chickpea (Cicer arietinum) tolerance to heat stress under field conditions

Interrogative proteome analyses are used to identify and quantify the expression of proteins involved in heat tolerance and to identify associated physiological processes in heat-stressed plants. The objectives of the study were to identify and quantify the expression of proteins involved in heat tolerance and to identify associated physiological processes in chickpea (Cicer arietinum L.) heat-tolerant (Acc#7) and sensitive genotype (Acc#8) from a field study. Proteomic and gene ontological analyses showed an upregulation in proteins related to protein synthesis, intracellular traffic, defence and transport in the heat-tolerant genotype compared to the susceptible one at the warmer site. Results from KEGG analyses indicate the involvement of probable sucrose-phosphate synthase (EC 2.4.1.14) and sucrose-phosphate phosphatase (EC 3.1.3.24) proteins, that were upregulated in the heat-tolerant genotype at the warmer site, in the starch and sucrose pathway. The presence of these differentially regulated proteins including HSP70, ribulose bisphosphate carboxylase/oxygenase activase, plastocyanin and protoporphyrinogen oxidase suggests their potential role in heat tolerance, at flowering growth stage, in field-grown chickpea. This observation supports unaltered physiological and biochemical performance of the heat-tolerant genotypes (Acc#7) relative to the susceptible genotype (Acc#8) in related studies (Makonya et al. 2019). Characterisation of the candidate proteins identified in the current study as well as their specific roles in the tolerance to heat stress in chickpea are integral to further crop improvement initiatives.

Label-Free Quantitative Proteome Analysis Reveals the Underlying Mechanisms of Grain Nuclear Proteins Involved in Wheat Water-Deficit Response

In this study, we performed the first nuclear proteome analysis of wheat developing grains under water deficit by using a label-free based quantitative proteomic approach. In total, we identified 625 unique proteins as differentially accumulated proteins (DAPs), of which 398 DAPs were predicted to be localized in nucleus. Under water deficit, 146 DAPs were up-regulated and mainly involved in the stress response and oxidation-reduction process, while 252 were down-regulated and mainly participated in translation, the cellular amino metabolic process, and the oxidation-reduction process. The cis-acting elements analysis of the key nuclear DAPs encoding genes demonstrated that most of these genes contained the same cis-acting elements in the promoter region, mainly including ABRE involved in abscisic acid response, antioxidant response element, MYB responsive to drought regulation and MYC responsive to early drought. The cis-acting elements related to environmental stress and hormones response were relatively abundant. The transcription expression profiling of the nuclear up-regulated DAPs encoding genes under different organs, developmental stages and abiotic stresses was further detected by RNA-seq and Real-time quantitative polymerase chain reaction, and more than 50% of these genes showed consistency between transcription and translation expression. Finally, we proposed a putative synergistic responsive network of wheat nuclear proteome to water deficit, revealing the underlying mechanisms of wheat grain nuclear proteome in response to water deficit.

Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence

Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.

Drought stress-induced physiological mechanisms, signaling pathways and molecular response of chloroplasts in common vegetable crops

Drought stress is one of the most adverse abiotic stresses that hinder plants' growth and productivity, threatening sustainable crop production. It impairs normal growth, disturbs water relations and reduces water-use efficiency in plants. However, plants have evolved many physiological and biochemical responses at the cellular and organism levels, in order to cope with drought stress. Photosynthesis, which is considered one of the most crucial biological processes for survival of plants, is greatly affected by drought stress. A gradual decrease in CO₂ assimilation rates, reduced leaf size, stem extension and root proliferation under drought stress, disturbs plant water relations, reducing water-use efficiency, disrupts photosynthetic pigments and reduces the gas exchange affecting the plants adversely. In such conditions, the chloroplast, organelle responsible for photosynthesis, is found to counteract the ill effects of drought stress by its critical involvement as a sensor of changes occurring in the environment, as the first process that drought stress affects is photosynthesis. Beside photosynthesis, chloroplasts carry out primary metabolic functions such as the biosynthesis of starch, amino acids, lipids, and tetrapyroles, and play a central role in the assimilation of nitrogen and sulfur. Because the chloroplasts are central organelles where the photosynthetic reactions take place, modifications in their physiology and protein pools are expected in response to the drought stress-induced variations in leaf gas exchanges and the accumulation of ROS. Higher expression levels of various transcription factors and other proteins including heat shock-related protein, LEA proteins seem to be regulating the heat tolerance mechanisms. However, several aspects of plastid alterations, following a water deficit environment are still poorly characterized. Since plants adapt to various stress tolerance mechanisms to respond to drought stress, understanding mechanisms of drought stress tolerance in plants will lead toward the development of drought tolerance in crop plants. This review throws light on major droughts stress-induced molecular/physiological mechanisms in response to severe and prolonged drought stress and addresses the molecular response of chloroplasts in common vegetable crops. It further highlights research gaps, identifying unexplored domains and suggesting recommendations for future investigations.

Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress

Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.

Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses

Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.

Proteomic responses to progressive dehydration stress in leaves of chickpea seedlings

Background

Chickpea is an important food legume crop with high protein levels that is widely grown in rainfed areas prone to drought stress. Using an integrated approach, we describe the relative changes in some physiological parameters and the proteome of a drought-tolerant (MCC537, T) and drought-sensitive (MCC806, S) chickpea genotype.

Results

Under progressive dehydration stress, the T genotype relied on a higher relative leaf water content after 3 and 5 d (69.7 and 49.3%) than the S genotype (59.7 and 40.3%) to maintain photosynthetic activities and improve endurance under stress. This may have been facilitated by greater proline accumulation in the T genotype than the S genotype (14.3 and 11.1 μmol g^− 1 FW at 5 d, respectively). Moreover, the T genotype had less electrolyte leakage and lower malondialdehyde contents than the S genotype under dehydration stress, indicating greater membrane stability and thus greater dehydration tolerance. The proteomic analysis further confirmed that, in response to dehydration, the T genotype activated more proteins related to photosynthesis, stress response, protein synthesis and degradation, and gene transcription and signaling than the S genotype. Of the time-point dependent proteins, the largest difference in protein abundance occurred at 5 d, with 29 spots increasing in the T genotype and 30 spots decreasing in the S genotype. Some of the identified proteins—including RuBisCo, ATP synthase, carbonic anhydrase, psbP domain-containing protein, L-ascorbate peroxidase, 6-phosphogluconate dehydrogenase, elongation factor Tu, zinc metalloprotease FTSH 2, ribonucleoproteins and auxin-binding protein—may play a functional role in drought tolerance in chickpea.

Conclusions

This study highlights the significance of genotype- and time-specific proteins associated with dehydration stress and identifies potential resources for molecular drought tolerance improvement in chickpea.

Defense Response in Chickpea Pod Wall due to Simulated Herbivory Unfolds Differential Proteome Profile

The pod wall of legumes is known to protect the developing seeds from pests and pathogens. However, the mechanism of conferring defense against insects has not yet been deciphered. Here, we have utilized 2-dimensional gel electrophoresis (2D-GE) coupled with mass spectrometry (MS/MS) to identify over expressed proteins in the pod wall of two different cultivars (commercial cultivar: JG 11 and tolerant cultivar: ICC 506-EB) of chickpea after 12 h of application of Helicoverpa armigera oral secretions (simulated herbivory). The assays were performed with a view that larvae are a voracious feeder and cause substantial damage to the pod within 12 h. A total of 600 reproducible protein spots were detected on gels, and the comparative analysis helped identify 35 (12 up-regulated, 23 down-regulated) and 20 (10 up-regulated, 10 down-regulated) differentially expressed proteins in JG 11 and ICC 506-EB, respectively. Functional classification of protein spots of each cultivar after MS/MS indicated that the differentially expressed proteins were associated with various metabolic activities. Also, stress-related proteins such as mannitol dehydrogenase (MADH), disease resistance-like protein-CSA1, serine/threonine kinase (D6PKL2), endoglucanase-19 etc. were up-regulated due to simulated herbivory. The proteins identified with a possible role in defense were further analyzed using the STRING database to advance our knowledge on their interacting partners. It decoded the involvement of several reactive oxygen species (ROS) scavengers and other proteins involved in cell wall reinforcement. The biochemical analysis also confirmed the active role of ROS scavengers during simulated herbivory. Thus, our study provides valuable new insights on chickpea-H.armigera interactions at the protein level.

Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses

Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.

Comparative proteomics and gene expression analyses revealed responsive proteins and mechanisms for salt tolerance in chickpea genotypes

BACKGROUND

Salinity is a major abiotic stress that limits the growth, productivity, and geographical distribution of plants. A comparative proteomics and gene expression analysis was performed to better understand salinity tolerance mechanisms in chickpea.

RESULTS

Ten days of NaCl treatments resulted in the differential expression of 364 reproducible spots in seedlings of two contrasting chickpea genotypes, Flip 97-43c (salt tolerant, T1) and Flip 97-196c (salt susceptible, S1). Notably, after 3 days of salinity, 80% of the identified proteins in T1 were upregulated, while only 41% in S2 had higher expression than the controls. The proteins were classified into eight functional categories, and three groups of co-expression profile. The second co-expressed group of proteins had higher and/or stable expression in T1, relative to S2, suggesting coordinated regulation and the importance of some processes involved in salinity acclimation. This group was mainly enriched in proteins associated with photosynthesis (39%; viz. chlorophyll a-b binding protein, oxygen-evolving enhancer protein, ATP synthase, RuBisCO subunits, carbonic anhydrase, and fructose-bisphosphate aldolase), stress responsiveness (21%; viz. heat shock 70 kDa protein, 20 kDa chaperonin, LEA-2 and ascorbate peroxidase), and protein synthesis and degradation (14%; viz. zinc metalloprotease FTSH 2 and elongation factor Tu). Thus, the levels and/or early and late responses in the activation of targeted proteins explained the variation in salinity tolerance between genotypes. Furthermore, T1 recorded more correlations between the targeted transcripts and their corresponding protein expression profiles than S2.

CONCLUSIONS

This study provides insight into the proteomic basis of a salt-tolerance mechanism in chickpea, and offers unexpected and poorly understood molecular resources as reliable starting points for further dissection.

Research Progress and Perspective on Drought Stress in Legumes: A Review

Climate change, food shortage, water scarcity, and population growth are some of the threatening challenges being faced in today's world. Drought stress (DS) poses a constant challenge for agricultural crops and has been considered a severe constraint for global agricultural productivity; its intensity and severity are predicted to increase in the near future. Legumes demonstrate high sensitivity to DS, especially at vegetative and reproductive stages. They are mostly grown in the dry areas and are moderately drought tolerant, but severe DS leads to remarkable production losses. The most prominent effects of DS are reduced germination, stunted growth, serious damage to the photosynthetic apparatus, decrease in net photosynthesis, and a reduction in nutrient uptake. To curb the catastrophic effect of DS in legumes, it is imperative to understand its effects, mechanisms, and the agronomic and genetic basis of drought for sustainable management. This review highlights the impact of DS on legumes, mechanisms, and proposes appropriate management approaches to alleviate the severity of water stress. In our discussion, we outline the influence of water stress on physiological aspects (such as germination, photosynthesis, water and nutrient uptake), growth parameters and yield. Additionally, mechanisms, various management strategies, for instance, agronomic practices (planting time and geometry, nutrient management), plant growth-promoting Rhizobacteria and arbuscular mycorrhizal fungal inoculation, quantitative trait loci (QTLs), functional genomics and advanced strategies (CRISPR-Cas9) are also critically discussed. We propose that the integration of several approaches such as agronomic and biotechnological strategies as well as advanced genome editing tools is needed to develop drought-tolerant legume cultivars.

Root Proteomics Reveals the Effects of Wood Vinegar on Wheat Growth and Subsequent Tolerance to Drought Stress

Wood vinegar (WV) or pyroligneous acid (PA) is a reddish-brown liquid created during the dry distillation of biomass, a process called pyrolysis. WV contains important biologically active components, which can enhance plant growth and tolerance to drought stress. However, its mechanism of action remains unknown. Our results after presoaking wheat seeds with various concentrations of WV indicate that a 1:900 WV concentration can significantly enhance growth. To investigate the response of wheat roots to drought stress, we compared quantitative proteomic profiles in the roots of wheat plants grown from seeds either presoaked (treatment) or non-presoaked (control) with WV. Our results indicated that the abscisic acid (ABA) content of wheat roots in the WV treatment was significantly increased. Reactive oxygen species (ROS) and malonaldehyde (MDA) levels roots were significantly lower than in the control treatment under drought stress, while the activity of major antioxidant enzymes was significantly increased. Two-dimensional electrophoresis (2D-PAGE) identified 138 differentially accumulated protein (DAP) spots representing 103 unique protein species responding to drought stress in wheat roots of the control and WV-treated groups. These DAPs are mostly involved in the stress response, carbohydrate metabolism, protein metabolism, and secondary metabolism. Proteome profiles showed the DAPs involved in carbohydrate metabolism, stress response, and secondary metabolism had increased accumulation in roots of the WV-treated groups. These findings suggest that the roots from wheat seeds presoaked with WV can initiate an early defense mechanism to mitigate drought stress. These results provide an explanation of how WV enhances the tolerance of wheat plants to drought stress.

Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes

Mitochondria play crucial roles in regulating multiple biological processes particularly electron transfer and energy metabolism in eukaryotic cells. Exposure to water-deficit or dehydration may affect mitochondrial function, and dehydration response may dictate cell fate decisions. iTRAQ-based quantitative proteome of a winter legume, chickpea, demonstrated the central metabolic alterations in mitochondria, presumably involved in dehydration adaptation. Three-week-old chickpea seedlings were subjected to progressive dehydration and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical characteristics and mitochondrial architecture. The proteomics analysis led to the identification of 40 dehydration-responsive proteins whose expressions were significantly modulated by dehydration. The differentially expressed proteins were implicated in different metabolic processes, with obvious functional tendencies toward purine-thiamine metabolic network, pathways of carbon fixation and oxidative phosphorylation. The linearity of dehydration-induced proteome alteration was examined with transcript abundance of randomly selected candidates under multivariate stress conditions. The differentially regulated proteins were validated through sequence analysis. An extensive sequence based localization prediction revealed >62.5% proteins to be mitochondrial resident by, at least, one prediction algorithm. The results altogether provide intriguing insights into the dehydration-responsive metabolic pathways and useful clues to identify crucial proteins linked to stress tolerance. BIOLOGICAL SIGNIFICANCE: Investigation on plant mitochondrial proteome is of significance because it would allow a better understanding of mitochondrial function in plant adaptation to stress. Mitochondria are the unique organelles, which play a crucial role in energy metabolism and cellular homeostasis, particularly when exposed to stress conditions. Chickpea is one of the cultivated winter legumes, which enriches soil nitrogen and has very low water footprint and thus contributes to fortification of sustainable agriculture. We therefore examined the dehydration-responsive mitochondrial proteome landscape of chickpea and queried whether molecular interplay of mitochondrial proteins modulate dehydration tolerance. A total of 40 dehydration-induced mitochondrial proteins were identified, predicted to be involved in key metabolic processes. Our future efforts would focus on understanding both posttranslational modification and processing for comprehensive characterization of mitochondrial protein function. This approach will facilitate mining of more biomarkers linked to the tolerance trait and contribute to crop adaptation to climate change.

Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response

Nonavailability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NPs) and phosphoproteins (NPPs) execute crucial cellular functions that form the regulatory hub for coordinated stress response. Phosphoproteins hold enormous influence over cellular signalling. Four-week-old seedlings of a grain legume, chickpea, were subjected to gradual dehydration, and NPs were extracted from unstressed control and from 72- and 144-hr stressed tissues. We identified 4,832 NPs and 478 phosphosites, corresponding to 299 unique NPPs involved in multivariate cellular processes including protein modification and gene expression regulation, among others. The identified proteins included several novel kinases, phosphatases, and transcription factors, besides 660 uncharacterized proteins. Spliceosome complex and splicing related proteins were dominant among differentially regulated NPPs, indicating their dehydration modulated regulation. Phospho-motif analysis revealed stress-induced enrichment of proline-directed serine phosphorylation. Association mapping of NPPs revealed predominance of differential phosphorylation of spliceosome and splicing associated proteins. Also, regulatory proteins of key processes viz., protein degradation, regulation of flowering time, and circadian clock were observed to undergo dehydration-induced dephosphorylation. The characterization of novel regulatory proteins would provide new insights into stress adaptation and enable directed genetic manipulations for developing climate-resilient crops.

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants.

Drought stress impact on leaf proteome variations of faba bean (Vicia faba L.) in the Qinghai-Tibet Plateau of China

Water scarcity is a major abiotic stress factor that strongly influences growth, development and yield of grain legumes in arid and semi-arid area of the world. Drought stress frequently occurs during the seedling stage and finally affects yield of faba bean (Vicia faba L.). However, the responses of plant leaf to drought have not been documented very well at the proteomic level. "Ga da dou" of the drought-tolerant faba bean cultivar was exposed to drought to examine the proteome changes of leaves. In this study, 2-week-old seedlings were subjected to water deficit by 7 days drought stress, whereas control plants were regularly irrigated. After withdrawing water, plants exposed to drought for 7 days and control plants at the same developmental stage were included in quantitative proteomic analysis using two-dimensional electrophoresis gels of proteins in combination with mass spectrometry. Over 300 proteins were detected by 2-DE, 50 differentially expressed proteins were detected by t test and 30 proteins were successfully identified by MALDI-TOF/TOF, in which 25 proteins were clearly downregulated and five proteins were upregulated. The quantified proteins were grouped into five functional groups, mainly regulatory proteins (46.7%), energy metabolism (23.3%), cell cytoskeleton (6.7%), other functions (20%) and unknown function (3.3%). Chitinase was upregulated under drought, suggesting that it was an important part of the plant defense system, playing an important role in stress resistance. 50S ribosomal protein was upregulated under drought, suggesting its role in protecting plants against stress by re-establishing normal protein conformations. The abundance of proteins involved in protein synthesis such as chitinase, Bet protein and glutamate-glyoxylate aminotransferase was upregulated under drought stress. These proteins could play important roles in drought tolerance and contribute to the relatively stronger drought tolerance of "Ga da dou".

Nuclear Proteome: Isolation of Intact Nuclei, Extraction of Nuclear Proteins, and 2-DE Analysis

Proteome profiling aims to unravel the mystery of biological complexity encoded by the genome. The successful proteome profiling largely depends upon analytical approaches because single-step proteome characterization of eukaryotic cells is difficult due to the large number of proteins expressed and their complex physiochemical properties. Organellar proteomics helps in identifying a refined set of proteins by pinpointing certain activities to specific organelles, thereby increasing our knowledge of cellular processes. The reliability of a plant organelle proteome is intimately dependent on the purity of the organelle preparation. Methodological improvements in sample handling, organelle fractionation, and protein extraction are therefore crucial to plant subcellular proteomics. The nuclear proteins are organized into complex regulatory networks and perform varied cellular functions. Therefore, characterization of the nuclear proteome is an important step toward accumulating knowledge about regulation of gene expression and function. In this chapter, we present methods for the isolation of nuclei, purification of nuclear proteins, and proteome profiling that have been adapted for proteomic characterization of economically important crop species, such as chickpea.

UNcleProt (Universal Nuclear Protein database of barley): The first nuclear protein database that distinguishes proteins from different phases of the cell cycle

Proteins are the most abundant component of the cell nucleus, where they perform a plethora of functions, including the assembly of long DNA molecules into condensed chromatin, DNA replication and repair, regulation of gene expression, synthesis of RNA molecules and their modification. Proteins are important components of nuclear bodies and are involved in the maintenance of the nuclear architecture, transport across the nuclear envelope and cell division. Given their importance, the current poor knowledge of plant nuclear proteins and their dynamics during the cell's life and division is striking. Several factors hamper the analysis of the plant nuclear proteome, but the most critical seems to be the contamination of nuclei by cytosolic material during their isolation. With the availability of an efficient protocol for the purification of plant nuclei, based on flow cytometric sorting, contamination by cytoplasmic remnants can be minimized. Moreover, flow cytometry allows the separation of nuclei in different stages of the cell cycle (G1, S, and G2). This strategy has led to the identification of large number of nuclear proteins from barley (Hordeum vulgare), thus triggering the creation of a dedicated database called UNcleProt, http://barley.gambrinus.ueb.cas.cz/.

Plant nuclear proteomics for unraveling physiological function

The nucleus is the subcellular organelle that functions as the regulatory hub of the cell and is responsible for regulating several critical cellular functions, including cell proliferation, gene expression, and cell survival. Nuclear proteomics is a useful approach for investigating the mechanisms underlying plant responses to abiotic stresses, including protein-protein interactions, enzyme activities, and post-translational modifications. Among abiotic stresses, flooding is a major limiting factor for plant growth and yields, particularly for soybean. In this review, plant nuclei purification methods, modifications of plant nuclear proteins, and recent contributions to the field of plant nuclear proteomics are summarized. In addition, to reveal the upstream regulating mechanisms controlling soybean responses to flooding stress, the functions of flooding-responsive nuclear proteins are reviewed based on the results of nuclear proteomic analysis of soybean in the early stages of flooding stress.

Carbon assimilation in Eucalyptus urophylla grown under high atmospheric CO2 concentrations: A proteomics perspective

Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO₂ concentrations. Growth under a high concentration of CO₂ could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO₂. Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species. Among the 816 isolated proteins, those involved in carbon fixation were found to be the most abundant ones. An increase in the abundance of six key enzymes out of the eleven core enzymes involved in carbon fixation was detected in plants grown at a high CO₂ concentration. Proteome changes were corroborated by the detection of a decrease in the stomatal aperture and in the vascular bundle area in Eucalyptus urophylla plantlets grown in an environment of high atmospheric CO₂. Our proteomics approach indicates a positive metabolic response regarding carbon fixation in a CO₂-enriched atmosphere. The slight but significant increase in the abundance of the Calvin enzymes suggests that stomatal closure did not prevent an increase in the carbon assimilation rates.

BIOLOGICAL SIGNIFICANCE

The sample enrichment strategy and data analysis used here enabled the identification of all enzymes and most protein isoforms involved in the Calvin-Benson-Bessham cycle in Eucalyptus urophylla. Upon growth in CO₂-enriched chambers, Eucalyptus urophylla plantlets responded by reducing the vascular bundle area and stomatal aperture size and by increasing the abundance of six of the eleven core enzymes involved in carbon fixation. Our proteome approach provides an estimate on how a commercially important C3-type plant would respond to an increase in CO₂ concentrations. Additionally, confirmation at the protein level of the predicted genes involved in carbon assimilation may be used in plant transformation strategies aiming to increase plant adaptability to climate changes or to increase plant productivity.

Comparative proteomics illustrates the complexity of drought resistance mechanisms in two wheat (Triticum aestivum L.) cultivars under dehydration and rehydration

BACKGROUND

Drought stress is one of the most adverse environmental constraints to plant growth and productivity. Comparative proteomics of drought-tolerant and sensitive wheat genotypes is a strategy to understand the complexity of molecular mechanism of wheat in response to drought. This study attempted to extend findings regarding the potential proteomic dynamics in wheat under drought stress and to enrich the research content of drought tolerance mechanism.

RESULTS

A comparative proteomics approach was applied to analyze proteome change of Xihan No. 2 (a drought-tolerant cultivar) and Longchun 23 (a drought-sensitive cultivar) subjected to a range of dehydration treatments (18 h, 24 h and 48 h) and rehydration treatment (R24 h) using 2-DE, respectively. Quantitative image analysis showed a total of 172 protein spots in Xihan No. 2 and 215 spots from Longchun 23 with their abundance significantly altered (p < 0.05) more than 2.5-fold. Out of these spots, a total of 84 and 64 differentially abundant proteins were identified by MALDI-TOF/TOF MS in Xihan No. 2 and Longchun 23, respectively. Most of these identified proteins were involved in metabolism, photosynthesis, defence and protein translation/processing/degradation in both two cultivars. In addition, the proteins involved in redox homeostasis, energy, transcription, cellular structure, signalling and transport were also identified. Furthermore, the comparative analysis of drought-responsive proteome allowed for the general elucidation of the major mechanisms associated with differential responses to drought of both two cultivars. These cellular processes work more cooperatively to re-establish homeostasis in Xihan No. 2 than Longchun 23. The resistance mechanisms of Xihan No. 2 mainly included changes in the metabolism of carbohydrates and amino acids as well as in the activation of more antioxidation and defense systems and in the levels of proteins involved in ATP synthesis and protein degradation/refolding.

CONCLUSIONS

This study revealed that the levels of a number of proteins involved in various cellular processes were affected by drought stress in two wheat cultivars with different drought tolerance. The results showed that there exist specific responses to drought in Xihan No. 2 and Longchun 23. The proposed hypothetical model would explain the interaction of these identified proteins that are associated with drought-responses in two cultivars, and help in developing strategies to improve drought tolerance in wheat.

Hop (Humulus lupulus L.) response mechanisms in drought stress: Proteomic analysis with physiology

Drought is one of the major environmental devastating stressors that impair the growth and productivity of crop plants. Despite the relevance of drought stress, changes in physiology and resistance mechanisms are not completely understood for certain crops, including hop (Humulus lupulus L.). In this research the drought response of hop was studied using a conventional physiological approach (gas exchange techniques, fluorescence, relative water content measurements) and proteomic analysis (2D-DIGE). Plants of two cultivars (Aurora and Savinjski golding) were exposed to progressive drought in a pot experiment and analysed at different stress stages (mild, moderate and severe). Measurements of relative water content revealed a hydrostable water balance of hop. Photosynthesis was decreased due to stomatal and non-stomatal limitation to the same extent in both cultivars. Of 28 identified differentially abundant proteins, the majority were down regulated and included in photosynthetic (41%) and sugar metabolism (33%). Fifteen % of identified proteins were classified into the nitrogen metabolism, 4% were related to a ROS related pathway and 7% to other functions.

Plant subcellular proteomics: Application for exploring optimal cell function in soybean

Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions.

BIOLOGICAL SIGNIFICANCE

Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of subcellular proteomics are presented, and functional proteins regulated among different subcellular are discussed. Subcellular proteomics contributes greatly to uncovering responses and interactions among subcellular compartments during development and under stressful environmental conditions in soybean.

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.

Gel-based and gel-free search for plasma membrane proteins in chickpea (Cicer arietinum L.) augments the comprehensive data sets of membrane protein repertoire

Plasma membrane (PM) encompasses total cellular contents, serving as semi-porous barrier to cell exterior. This living barrier regulates all cellular exchanges in a spatio-temporal fashion. Most of the essential tasks of PMs including molecular transport, cell-cell interaction and signal transduction are carried out by their proteinaceous components, which make the PM protein repertoire to be diverse and dynamic. Here, we report the systematic analysis of PM proteome of a food legume, chickpea and develop a PM proteome reference map. Proteins were extracted from highly enriched PM fraction of four-week-old seedlings using aqueous two-phase partitioning. To address a population of PM proteins that is as comprehensive as possible, both gel-based and gel-free approaches were employed, which led to the identification of a set of 2732 non-redundant proteins. These included both integral proteins having bilayer spanning domains as well as peripheral proteins associated with PMs through posttranslational modifications or protein-protein interactions. Further, the proteins were subjected to various in-silico analyses and functionally classified based on their gene ontology. Finally an inventory of the complete set of PM proteins, identified in several monocot and dicot species, was created for comparative study with the generated PM protein dataset of chickpea.

BIOLOGICAL SIGNIFICANCE

Chickpea, a rich source of dietary proteins, is the second most cultivated legume, which is grown over 10 million hectares of land worldwide. The annual global production of chickpea hovers around 8.5 million metric tons. Recent chickpea genome sequencing effort has provided a broad genetic basis for highlighting the important traits that may fortify other crop legumes. Improvement in chickpea varieties can further strengthen the world food security, which includes food availability, access and utilization. It is known that the phenotypic trait of a cultivar is the manifestation of the orchestrated functions of its proteins. Study of the PM proteome offers insights into the mechanism of communication between the cell and its environment by identification of receptors, signalling proteins and membrane transporters. Knowledge of the PM protein repertoire of a relatively dehydration tolerant chickpea variety, JG-62, can contribute in development of strategies for metabolic reprograming of crop species and breeding applications.

Plant Organellar Proteomics in Response to Dehydration: Turning Protein Repertoire into Insights

Stress adaptation or tolerance in plants is a complex phenomenon involving changes in physiological and metabolic processes. Plants must develop elaborate networks of defense mechanisms, and adapt to and survive for sustainable agriculture. Water-deficit or dehydration is the most critical environmental factor that plants are exposed to during their life cycle, which influences geographical distribution and productivity of many crop species. The cellular responses to dehydration are orchestrated by a series of multidirectional relays of biochemical events at organelle level. The new challenge is to dissect the underlying mechanisms controlling the perception of stress signals and their transmission to cellular machinery for activation of adaptive responses. The completeness of current descriptions of spatial distribution of proteins, the relevance of subcellular locations in diverse functional processes, and the changes of protein abundance in response to dehydration hold the key to understanding how plants cope with such stress conditions. During past decades, organellar proteomics has proved to be useful not only for deciphering reprograming of plant responses to dehydration, but also to dissect stress-responsive pathways. This review summarizes a range of organellar proteomics investigations under dehydration to gain a holistic view of plant responses to water-deficit conditions, which may facilitate future efforts to develop genetically engineered crops for better adaptation.

Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana.

Morpho-Physiological and Proteome Level Responses to Cadmium Stress in Sorghum

Cadmium (Cd) stress may cause serious morphological and physiological abnormalities in addition to altering the proteome in plants. The present study was performed to explore Cd-induced morpho-physiological alterations and their potential associated mechanisms in Sorghum bicolor leaves at the protein level. Ten-day-old sorghum seedlings were exposed to different concentrations (0, 100, and 150 μM) of CdCl2, and different morpho-physiological responses were recorded. The effects of Cd exposure on protein expression patterns in S. bicolor were investigated using two-dimensional gel electrophoresis (2-DE) in samples derived from the leaves of both control and Cd-treated seedlings. The observed morphological changes revealed that the plants treated with Cd displayed dramatically altered shoot lengths, fresh weights and relative water content. In addition, the concentration of Cd was markedly increased by treatment with Cd, and the amount of Cd taken up by the shoots was significantly and directly correlated with the applied concentration of Cd. Using the 2-DE method, a total of 33 differentially expressed protein spots were analyzed using MALDI-TOF/TOF MS. Of these, treatment with Cd resulted in significant increases in 15 proteins and decreases in 18 proteins. Major changes were absorbed in the levels of proteins known to be involved in carbohydrate metabolism, transcriptional regulation, translation and stress responses. Proteomic results revealed that Cd stress had an inhibitory effect on carbon fixation, ATP production and the regulation of protein synthesis. Our study provides insights into the integrated molecular mechanisms involved in responses to Cd and the effects of Cd on the growth and physiological characteristics of sorghum seedlings. We have aimed to provide a reference describing the mechanisms involved in heavy metal damage to plants.

Gel-free/label-free proteomic analysis of root tip of soybean over time under flooding and drought stresses

Growth in the early stage of soybean is markedly inhibited under flooding and drought stresses. To explore the responsive mechanisms of soybean, temporal protein profiles of root tip under flooding and drought stresses were analyzed using gel-free/label-free proteomic technique. Root tip was analyzed because it was the most sensitive organ against flooding, and it was beneficial to root penetration under drought. UDP glucose: glycoprotein glucosyltransferase was decreased and increased in soybean root under flooding and drought, respectively. Temporal protein profiles indicated that fermentation and protein synthesis/degradation were essential in root tip under flooding and drought, respectively. In silico protein-protein interaction analysis revealed that the inductive and suppressive interactions between S-adenosylmethionine synthetase family protein and B-S glucosidase 44 under flooding and drought, respectively, which are related to carbohydrate metabolism. Furthermore, biotin/lipoyl attachment domain containing protein and Class II aminoacyl tRNA/biotin synthetases superfamily protein were repressed in the root tip during time-course stresses. These results suggest that biotin and biotinylation might be involved in energy management to cope with flooding and drought in early stage of soybean-root tip.

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.

Optimized procedure of extraction, purification and proteomic analysis of nuclear proteins from mouse brain

BACKGROUND

The cell nucleus is a highly dynamic subcellular compartment performing crucial processes for functioning and administration of the cell. Proteomic analysis of isolated nuclear fraction enables in-depth insight into these processes leading to better understanding of physiological and pathological state of the brain. There is no universal method for nuclear proteome investigation and each biological material needs individual optimization. An additional difficulty is the large amount of nucleic acids, which impairs isoelectrofocusing of proteins and shotgun mass spectrometry analysis of complex peptide samples.

NEW METHOD

We performed the first comprehensive optimization of intact nuclei isolation from mouse brain in combination with nuclear protein purification prior to two-dimensional gel electrophoresis (2DE) and gel-free proteomic analysis.

RESULTS

Application of sonication, digestion with nuclease and protein precipitation with acetone allowed to obtain high quality 2DE gels. Shotgun mass spectrometry analysis of isolated proteins proved an enrichment in nuclear proteins. The 66.4% of 265 identified proteins had assigned nucleus localization in UniProt database. Gene Ontology analysis using DAVID platform revealed the highest fold enrichment in spliceosome (24.5), nuclear periphery (12.4) and nuclear matrix (11.3).

COMPARISON WITH EXISTING METHODS

The proposed procedure is tailored to mouse brain tissue nuclear subproteome investigation. The quality of isolated nuclei, the effectiveness of the protein purification, efficiency of protein recovery after precipitation and overall method reproducibility was taken into detailed consideration.

CONCLUSIONS

The elaborated procedure could be further applied for in-depth proteomic analysis of molecular processes occurring in the mouse brain nucleus.

Proteomic Techniques and Management of Flooding Tolerance in Soybean

Climate change is considered a major threat to world agriculture and food security. To improve the agricultural productivity and sustainability, the development of high-yielding stress-tolerant, and climate-resilient crops is essential. Of the abiotic stresses, flooding stress is a very serious hazard because it markedly reduces plant growth and grain yield. Proteomic analyses indicate that the effects of flooding stress are not limited to oxygen deprivation but include many other factors. Although many flooding response mechanisms have been reported, flooding tolerance mechanisms have not been fully clarified for soybean. There were limitations in soybean materials, such as mutants and varieties, while they were abundant in rice and Arabidopsis. In this review, plant proteomic technologies are introduced and flooding tolerance mechanisms of soybeans are summarized to assist in the improvement of flooding tolerance in soybeans. This work will expedite transgenic or marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Comparative Proteomic Analysis of Brassica napus in Response to Drought Stress

Drought is one of the most widespread stresses leading to retardation of plant growth and development. We examined proteome changes of an important oil seed crop, canola (Brassica napus L.), under drought stress over a 14-day period. Using iTRAQ LC-MS/MS, we identified 1976 proteins expressed during drought stress. Among them, 417 proteins showed significant changes in abundance, and 136, 244, 286, and 213 proteins were differentially expressed in the third, seventh, 10th, and 14th day of stress, respectively. Functional analysis indicated that the number of proteins associated with metabolism, protein folding and degradation, and signaling decreased, while those related to energy (photosynthesis), protein synthesis, and stress and defense increased in response to drought stress. The seventh and 10th-day profiles were similar to each other but with more post-translational modifications (PTMs) at day 10. Interestingly, 181 proteins underwent PTMs; 49 of them were differentially changed in drought-stressed plants, and 33 were observed at the 10th day. Comparison of protein expression changes with those of gene transcription showed a positive correlation in B. napus, although different patterns between transcripts and proteins were observed at each time point. Under drought stress, most protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to protein diversity and functions.