Publications of NIPGR Scientists
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Item OsDUF2488 acts synergistically with OsPrx1.1, regulates ROS metabolism and promotes dehydration tolerance in rice(John Wiley & Sons, 2025) Gayen, Dipak; Kumar, Sunil; Barua, Pragya; Lande, Nilesh Vikram; Karmakar, Subhasis; Dey, Amit K.; Gayali, Saurabh; Maiti, Tushar Kanti; Molla, Kutubuddin Ali; Murumkar, Snehal; Chakraborty, Subhra; Chakraborty, NiranjanStress-mediated regulation of energy metabolism and its relation to plant adaptation remain largely unknown. Mitochondrial redox potential is greatly influenced by stress-induced reactive oxygen species (ROS); therefore, we mapped the dehydration-induced alterations in the mitochondrial proteome of a resilient rice cultivar, Rasi, generating a proteome map representing the largest inventory of dehydration-responsive mitochondrial proteins from any plant species. Quantitative proteomic analysis led to the identification of an array of dehydration-responsive proteins (DRPs), associated with various cellular functions, conceivably impinging on the molecular mechanism of adaptation. One DRP identified in the mitochondrial proteome was yeast cadmium factor 54 (YCF54-like), also known as DUF (domain of unknown function) and hereafter referred to as OsDUF2488. We demonstrated that OsDUF2488 localises to mitochondria and preferentially interacts with peroxiredoxin, OsPrx1.1. Overexpression of OsDUF2488 in rice caused enhanced tolerance to dehydration and oxidative stress, while CRISPR/Cas9 knockout mutants of OsDUF2488 showed hypersensitivity to dehydration. Upon exposure to dehydration, OsDUF2488 could rescue mitochondrial dysfunction, contributing to increased ATP production in OsDUF2488-overexpressing rice. Coexpression of OsDUF2488 and OsPrx1.1 in yeast demonstrated a mutual effect on enhanced ROS catabolism, suggesting a cross-kingdom adaptive response of OsDUF2488. Our findings suggest that OsDUF2488 acts synergistically with OsPrx1.1 to regulate redox homeostasis and promote stress tolerance in rice.Item Dehydration-responsive chickpea chloroplast protein, CaPDZ1, confers dehydration tolerance by improving photosynthesis(John Wiley & Sons, 2022) Lande, Nilesh Vikram; Barua, Pragya; Gayen, Dipak; Wardhan, Vijay; Jeevaraj, Theboral; Kumar, Sunil; Chakraborty, Subhra; Chakraborty, NiranjanThe screening of a dehydration-responsive chloroplast proteome of chickpea led us to identify and investigate the functional importance of an uncharacterized protein, designated CaPDZ1. In all, we identified 14 CaPDZs, and phylogenetic analysis revealed that these belong to photosynthetic eukaryotes. Sequence analyses of CaPDZs indicated that CaPDZ1 is a unique member, which harbours a TPR domain besides a PDZ domain. The global expression analysis showed that CaPDZs are intimately associated with various stresses such as dehydration and oxidative stress along with certain phytohormone responses. The CaPDZ1-overexpressing chickpea seedlings exhibited distinct phenotypic and molecular responses, particularly increased photosystem (PS) efficiency, ETR and qP that validated its participation in PSII complex assembly and/or repair. The investigation of CaPDZ1 interacting proteins through Y2H library screening and co-IP analysis revealed the interacting partners to be PSII associated CP43, CP47, D1, D2 and STN8. These findings supported the earlier hypothesis regarding the role of direct or indirect involvement of PDZ proteins in PS assembly or repair. Moreover, the GUS-promoter analysis demonstrated the preferential expression of CaPDZ1 specifically in photosynthetic tissues. We classified CaPDZ1 as a dehydration-responsive chloroplast intrinsic protein with multi-fold abundance under dehydration stress, which may participate synergistically with other chloroplast proteins in the maintenance of the photosystem.Item Proteomic dissection of rice cytoskeleton reveals the dominance of microtubule and microfilament proteins, and novel components in the cytoskeleton-bound polysome(Elsevier B.V., 2022) Kumar, Sunil; Lande, Nilesh Vikram; Barua, Pragya; Pareek, Akanksha; Chakraborty, Subhra; Chakraborty, NiranjanThe plant cytoskeleton persistently undergoes remodeling to achieve its roles in supporting cell division, differentiation, cell expansion and organelle transport. However, the links between cell metabolism and cytoskeletal networks, particularly how the proteinaceous components execute such processes remain poorly understood. We investigated the cytoskeletal proteome landscape of rice to gain better understanding of such events. Proteins were extracted from highly enriched cytoskeletal fraction of four-week-old rice seedlings, and the purity of the fraction was stringently monitored. A total of 2577 non-redundant proteins were identified using both gel-based and gel-free approaches, which constitutes the most comprehensive dataset, thus far, for plant cytoskeleton. The data set includes both microtubule and microfilament-associated proteins and their binding proteins comprising hypothetical as well as novel cytoskeletal proteins. Further, various in-silico analyses were performed, and the proteins were functionally classified on the basis of their gene ontology. The catalogued proteins were validated through their sequence analysis. Extensive comparative analysis of our dataset with the non-redundant set of cytoskeletal proteins across plant species affirms unique as well as overlapping candidates. Together, these findings unveil new insights of how cytoskeletons undergo dynamic remodeling in rice to drive seedling development processes in rapidly changing in planta environment.Item Systemic acquired resistance specifc proteome of Arabidopsis thaliana(Springer Nature Publishing AG, 2020) Kumar, Rajiv; Barua, Pragya; Chakraborty, Niranjan; Nandi, Ashis KumarKey message A comparative proteomic study between WT and SAR-compromised rsi1/fd mutant reveals a set of proteins having possible roles in the SAR development. Abstract A partly infected plant shows enhanced resistance during subsequent infection through the development of systemic acquired resistance (SAR). Mobile signals generated at the site of primary infection travel across the plant for the activation of SAR. These mobile signals are likely to cause changes in the expression of a set of proteins in the distal tissue, which contributes to the SAR development. However, SAR-specifc proteome is not revealed for any plant. The reduced systemic immunity 1 (rsi1)/(allelic to fowering locus D; fd) mutant of Arabidopsis is compromised for SAR but shows normal local resistance. Here we report the SAR-specifc proteome of Arabidopsis by comparing diferentially abundant proteins (DAPs) between WT and fd mutant. Plants were either mock-treated or SAR-induced by primary pathogen inoculation. For proteomic analysis, samples were collected from the systemic tissues before and after the secondary inoculation. Protein identifcation was carried out by using two-dimensional gel electrophoresis (2-DE) followed by tandem mass spectrometry. Our work identifed a total of 94 DAPs between mock and pathogen treatment in WT and fd mutant. The DAPs were categorized into diferent functional groups along with their subcellular localization. The majority of DAPs are involved in metabolic processes and stress response. Among the subcellular compartments, plastids contained the highest number of DAPs, suggesting the importance of plastidic proteins in SAR activation. The fndings of this study would provide resources to engineer efcient SAR activation traits in Arabidopsis and other plants.Item Quantitative phosphoproteomic analysis of legume using TiO2-based enrichment coupled with isobaric labeling(Springer Nature Publishing AG, 2020) Barua, Pragya; Lande, Nilesh Vikram; Kumar, Sunil; Chakraborty, Subhra; Chakraborty, NiranjanPhosphorylation of proteins is the most dynamic protein modification, and its analysis aids in determining the functional and regulatory principles of important cellular pathways. The legumes constitute the third largest family of higher plants, Fabaceae, comprising about 20,000 species and are second to cereals in agricultural importance on the basis of global production. Therefore, an understanding of the developmental and adaptive processes of legumes demands identification of their regulatory components. The most crucial signature of the legume family is the symbiotic nitrogen fixation, which makes this fascinating and interesting to investigate phosphorylation events. The research on protein phosphorylation in legumes has been focused primarily on two model species, Medicago truncatula and Lotus japonicus. The development of reciprocal research in other species, particularly the crops, is lagging behind which has limited its beneficial uses in agricultural productivity. In this chapter, we outline the titanium dioxide-based enrichment of phosphopeptides for nuclear proteome analysis of a grain legume, chickpea.Item Dehydration-induced alterations in chloroplast proteome and reprogramming of cellular metabolism in developing chickpea delineate interrelated adaptive responses(Elsevier B.V., 2020) Lande, Nilesh Vikam; Barua, Pragya; Gayen, Dipak; Kumar, Sunil; Varshney, Swati; Sengupta, Shantanu; Chakraborty, Subhra; Chakraborty, NiranjanChloroplast, the energy organelle unique to photosynthetic eukaryotes, executes several crucial functions including photosynthesis. While chloroplast development and function are controlled by the nucleus, environmental stress modulated alterations perceived by the chloroplasts are communicated to the nucleus via retrograde signaling. Notably, coordination of chloroplast and nuclear gene expression is synchronized by anterograde and retrograde signaling. The chloroplast proteome holds significance for stress responses and adaptation. We unraveled dehydration-induced alterations in the chloroplast proteome of a grain legume, chickpea and identified an array of dehydration-responsive proteins (DRPs) primarily involved in photosynthesis, carbohydrate metabolism and stress response. Notably, 12 DRPs were encoded by chloroplast genome, while the rest were nuclear-encoded. We observed a coordinated expression of different multi-subunit protein complexes viz., RuBisCo, photosystem II and cytochrome b6f, encoded by both chloroplast and nuclear genome. Comparison with previously reported stress-responsive chloroplast proteomes showed unique and overlapping components. Transcript abundance of several previously reported markers of retrograde signaling revealed relay of dehydration-elicited signaling events between chloroplasts and nucleus. Additionally, dehydration-triggered metabolic adjustments demonstrated alterations in carbohydrate and amino acid metabolism. This study offers a panoramic catalogue of dehydration-responsive signatures of chloroplast proteome and associated retrograde signaling events, and cellular metabolic reprograming.Item Proteomic dissection of the chloroplast: Moving beyond photosynthesis(Elsevier B.V., 2020) Lande, Nilesh Vikram; Barua, Pragya; Gayen, Dipak; Kumar, Sunil; Chakraborty, Subhra; Chakraborty, NiranjanChloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO2 and H2O. It also serves as a major production site of multivariate pro-defense molecules, and coordinate with other organelles for cell defense. Chloroplast harbors 30–50% of total cellular proteins, out of which 80% are membrane residents and are difficult to solubilize. While proteome profiling has illuminated vast areas of biological protein space, a great deal of effort must be invested to understand the proteomic landscape of the chloroplast, which plays central role in photosynthesis, energy metabolism and stress-adaptation. Therefore, characterization of chloroplast proteome would not only provide the foundation for future investigation of expression and function of chloroplast proteins, but would open up new avenues for modulation of plant productivity through synchronizing chloroplastic key components. In this review, we summarize the progress that has been made to build new understanding of the chloroplast proteome and implications of chloroplast dynamicsing generate metabolic energy and modulating stress adaptation.Item Dehydration-responsive alterations in the chloroplast proteome and cell metabolomic profile of rice reveals key stress adaptation responses(Elsevier B.V., 2019) Gayen, Dipak; Barua, Pragya; Lande, Nilesh Vikram; Varshney, Swati; Sengupta, Shantanu; Chakraborty, Subhra; Chakraborty, NiranjanChloroplast is a semi-autonomous organelle in plants and other photosynthetic eukaryotes, playing a fundamental role of regulating photosynthesis. It is also responsible for sustaining essential biosynthetic reactions including synthesis of amino acids, fatty acids and terpenes. Photosynthesis, the conversion of light energy into chemical energy, serves as the sensor of environmental changes and augments different cellular functions to initiate adaptive responses. However, the molecular processes and regulatory mechanisms of dehydration tolerance adopted by chloroplast remain largely unknown. To gain a better understanding of dehydration response, a chloroplast proteome map of rice was developed. Four-week-old rice seedlings were subjected to dehydration by withholding water for 9 d, and the magnitude of dehydration-induced damage to the chloroplast was monitored. The iTRAQ-based quantitative proteome analysis led to the identification of 40 differentially regulated proteins (DRPs). The DRPs were presumably involved in a wide array of metabolic processes including chloroplast energy metabolism, photosynthesis and defense response. Furthermore, dehydration-induced changes in the metabolite profile and network analysis revealed a high abundance of branched chain amino acids and sugar that might reduce osmotic potential, thereby protecting cellular integrity. The proteomics approach revealed altered status of major photosynthesis related proteins, while cell metabolite profile demonstrated alteration of tricarboxylic acid cycle intermediates, indicating dehydration-triggered alterations in ATP production and energy metabolism. Altogether, these results demonstrated that the global regulation of chloroplast proteome is intimately linked to cellular metabolic rewiring of adaptive responses, which may favor genetic manipulation of crop species for better adaptation.Item Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes(Elsevier B.V, 2019) Gayen, Dipak; Gayali, Saurabh; Barua, Pragya; Lande, Nilesh Vikram; Varshney, Swati; Sengupta, Shantanu; Chakraborty, Subhra; Chakraborty, NiranjanMitochondria 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.Item Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response(John Wiley & Sons, 2019) Barua, Pragya; Lande, Nilesh Vikram; Subba, Pratigya; Gayen, Dipak; Pinto, Sneha; Prasad, T.S. Keshav; Chakraborty, Subhra; Chakraborty, NiranjanNon-availability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NP) 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 nuclear proteins were extracted from unstressed control as well as from 72 and 144 h stressed tissues. We identified 4832 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 uncharacterised 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.