Publications of NIPGR Scientists
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Item Nuclear proteome reprogramming and acquired thermotolerance in chickpea exposed to escalating high-temperature stress(Elsevier B.V., 2026) Pareek, Akanksha; Wardhan, Vijay; Mishra, Divya; Rathi, Divya; Khan, Iqra Nafees; Subba, Pratigya; Saxena, Harshita; Jeevaraj, Theboral; Chakraborty, Subhra; Chakraborty, NiranjanGlobal chickpea (Cicer arietinum L.) production amounted to ∼17.55 MMT during 2024-2025, whose market size is valued at ∼$16.83 billion. Chickpea is highly susceptible to high-temperature stress (HTS), and its yield declines 10-15% with the rise in each degree of temperature. In this study, the HTS-responsive nuclear proteome of a thermotolerant chickpea cultivar ICC 1205 was investigated, leading to the identification of 2705 proteins, including 424 differentially regulated proteins designated as HTS-responsive (HRPs). Of these, 212 were shared between immediate (day-1) and later (day-4) stages of HTS, with 117 proteins specific to day-1 and 95 to day-4. Functional network analysis revealed a complex network of nuclear proteins involved in regulatory and stress-related functions. Detailed analysis of the proteome revealed several non-canonical proteins, suggesting HTS-responsive reprograming of the nuclear proteome landscape. The cross-species multiple abiotic stress responses recognized unique HRPs, reflecting genetic foundation that leads to crop adaptation. Comparison of protein and mRNA expression shed light on the intricate regulatory mechanisms of thermotolerance response in chickpea. The characterization of root-phototropism 2 protein (CaRPT2), a member of the NPH3 gene-family, showed significant regulations, particularly under dehydration stress and ABA treatments. Subcellular localization of CaRPT2 demonstrated its dual localization in both plasma membrane and nucleus. Analysis of physiological indices in atrpt2 loss-of function mutants in Arabidopsis demonstrated better germination rate, resilience and growth under progressive HTS, suggesting the putative role of RPT2 in regulating multiple stress-responsive genes.Item Dissection of grasspea (Lathyrus sativus L.) root exoproteome reveals critical insights and novel proteins(Elsevier B.V., 2022) Rathi, Divya; Verma, Jitendra Kumar; Pareek, Akanksha; Chakraborty, Subhra; Chakraborty, NiranjanThe plant exoproteome is crucial because its constituents greatly influence plant phenotype by regulating physiological characteristics to adapt to environmental stresses. The root exudates constitute a dynamic aspect of plant exoproteome, as its molecular composition ensures a beneficial rhizosphere in a species-specific manner. We investigated the root exoproteome of grasspea, a stress-resilient pulse and identified 2861 non-redundant proteins, belonging to a myriad of functional classes, including root development, rhizosphere augmentation as well as defense functions against soil-borne pathogens. Significantly, we identified 1986 novel exoproteome constituents of grasspea, potentially involved in cell-to-cell communication and root meristem maintenance, among other critical roles. Sequence-based comparison revealed that grasspea shares less than 30 % of its exoproteome with the reports so far from model plants as well as crop species. Further, the exoproteome revealed 65 % proteins to be extracellular in nature and of these, 37 % constituents were predicted to follow unconventional protein secretion (UPS) mode. We validated the UPS for four stress-responsive proteins, which were otherwise predicted to follow classical protein secretion (CPS). Conclusively, we recognized not only the highest number of root exudate proteins, but also pinpointed novel signatures of dicot root exoproteome.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 The small heat shock proteins, chaperonin 10, in plants: An evolutionary view and emerging functional diversity(Elsevier B.V., 2021) Pareek, Akanksha; Mishra, Divya; Rathi, Divya; Verma, Jitendra Kumar; Chakraborty, Subhra; Chakraborty, NiranjanSmall heat shock proteins (sHSPs) constitute a class of molecular chaperones, which are evolutionarily conserved yet diverse group of molecules, rapidly produced in response to stress. In this study, we sought to identify plant sHSPs, especially chaperonin 10 (Cpn10) family members in major evolutionary lineages, and determine their biological significance. Multiple sequence alignment of Cpn10 domains revealed divergent amino acids as well as conserved sites. Phylogenetic tree depicted the diversification and expansion of Cpn10 gene family. During the process of evolution, the Ka/Ks ratio of orthologous and paralogous pairs was <1, suggesting their evolutionary convergence and biological relevance. Functional annotations demonstrated that Cpn10 are involved in protein folding, regulation of metabolic processes and abiotic stress responses. Furthermore, subcellular localization prediction revealed that Cpn10 proteins are localized in multiple compartments, indicating a critical cell-coordinated defense. In-silico gene expression analysis exhibited their expression in most tissues examined, implying functional redundancy. Interactome analysis illustrated their interaction with chloroplast and mitochondrial genes, which are majorly involved in protein folding and assembly. The transcriptional regulation revealed their stress-responsive and distinct physiological roles. Our findings would contribute to new insights on the evolutionary history of Cpn10 gene family and the distinct biological roles.