Publications of NIPGR Scientists

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Author: search.filters.author.Chakraborty, SubhraStart date: 2020

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Now showing 1 - 10 of 27
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    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, Niranjan
    Global 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.
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    Cross-kingdom global proteomics reveals specific modulation of disease signaling in multi-host fungal pathogen infection in chickpea and worm
    (American Chemical Society, 2026) Narula, Kanika; Ghosh, Shobha; Khan, Iqra Nafees; Sengupta, Atreyee; Chakraborty, Niranjan; Chakraborty, Subhra
    An interconnected loop of messages and counter-messages determine the outcome of host-pathogen interactions. Multihost pathogenicity across plants and animals, particularly nematode, is a major source of new infectious diseases. Fusarium oxysporum, a multihost pathogen, causes vascular wilt in chickpea and fusariosis in worm and humans. To comprehend Fusarium-responsive multihost pathogenicity, we temporally profiled cross-kingdom species, chickpea and worm using SWATH-mass spectrometry. Morphological analyses revealed that increased wilting and intestinal disintegration elicits a disease response in chickpea and worm. Peptide-spectrum library consisted of 5629 and 3138 proteins from Fusarium infected chickpea and worm, respectively. SWATH analysis identified 1573 and 2249 disease-responsive chickpea (CaDRPs) and worm proteins (CeDRPs) linked to diverse organs, organelles, and functionality. Pairwise comparisons; over-representation analysis between time, treatment, and organism; wilt, and fusariosis diseasome revealed common and unique modules. CaDRPs involved in preformed defense, biomolecule synthesis, phytohormone regulation, ser/thr kinase, and ATP signaling have perturbed interactions and functions, majorly in chloroplast. CeDRPs linked to the cuticular support, muscle organization, neuronal information, intestinal metabolism, G-protein, and notch signaling showed a deregulated function, especially in the cytoplasm. Common biological processes, included primary metabolism, ribosome biogenesis, calcium signaling, and proteostasis. Our data provide first evidence of translational plasticity in the Fusarium diseasome providing novel insights into multihost pathogenesis.
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    Isolation of cytoskeleton and cytoskeleton-bound polysome, and identification of cytoskeletal proteins from a grain legume
    (Springer Nature Publishing AG, 2026) Kumar, Sunil; Chakraborty, Sohela; Chakraborty, Subhra; Chakraborty, Niranjan
    The plant cytoskeleton is an essential component of cellular architecture, enabling various critical metabolic processes, including cell division, differentiation, expansion and intracellular transport. It consists primarily of three distinct filamentous structures: microtubules, microfilaments and intermediate filaments. These structures are not static; they undergo continuous remodeling in response to environmental signals and developmental cues, which allow plants to adapt to changing conditions. The microtubules and actin filaments have previously been successfully isolated from various plant tissues, contributing to our understanding of their functions. Among the diverse plant families, legumes (Fabaceae) stand out as the third largest, encompassing approximately 20,000 species. They hold significant agricultural importance, ranking second to cereals in global crop production. To fully grasp the developmental and adaptive processes in legumes, it is essential to identify and understand their regulatory components. This chapter focuses on the isolation of cytoskeletal proteins from chickpea, a prominent grain legume, facilitating biochemical and proteomic analyses that may uncover new insights into the functioning of the cytoskeleton in legumes.
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    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, Niranjan
    Stress-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.
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    Comprehensive multi-layered analyses of genotype-dependent proteo-metabolic networks reveal organellar crosstalk and biochemical pathways regulating aroma formation in rice
    (Elsevier B.V., 2024) Narula, Kanika; Choudhary, Pooja; Sengupta, Atreyee; Chakraborty, Niranjan; Chakraborty, Subhra
    Molecular basis of rice aroma formation is sparsely known and developmental programs driving biochemical pathways towards aroma is in infancy. Here, discovery and targeted proteo-metabolome of non-aromatic and aromatic rice seeds across developmental stages identified a total of 442 aroma-responsive proteins (ARPs) and 824 aroma-responsive metabolites (ARMs) involved in metabolism, calcium and G-protein signaling. Biochemical examination revealed ARM/Ps were linked to 2-acetylpyrrolidine, γ-aminobutyrate, anthocyanin, tannins, flavonoids and related enzymes. Pairwise correlation and clustering showed positive correlation among ARM/Ps. Consistent with aroma-related QTLs, ARPs were mapped on chromosomes 3,4,5,8 and were mainly compartmentalized in cytoplasm and mitochondria. ARM/P-correlation network identified associations related to metabolism and signaling. Multiple reaction monitoring (MRM) confirmed role of catechins, quinic acid and quercetin in aroma formation. Pathway enrichment, multivariate analysis and qRT-PCR validated that calcium and G-protein signaling, aromatic/branched-chain aminoacid, 2-acetylpyrrolidine, oxylipin, melvonate and prenylpyrophosphate pathways, indole, phenylacetate, flavonoid, cinnamoic ester govern aroma formation in rice.
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    Wheat TaNACα18 functions as a positive regulator of high-temperature adaptive responses and improves cell defense machinery
    (John Wiley & Sons, 2024) Mishra, Divya; Shekhar, Shubhendu; Subba, Pratigya; Prasad, T S Keshava; Chakraborty, Subhra; Chakraborty, Niranjan
    Global wheat production amounted to >780 MMT during 2022-2023 whose market size are valued at >$128 billion. Wheat is highly susceptible to high-temperature stress (HTS) throughout the life cycle and its yield declines 5-7% with the rise in each degree of temperature. Previously, we reported an array of HTS-response markers from a resilient wheat cv. Unnat Halna and described their putative role in heat acclimation. To complement our previous results and identify the key determinants of thermotolerance, here we examined the cytoplasmic proteome of a sensitive cv. PBW343. The HTS-triggered metabolite reprograming highlighted how proteostasis defects influence the formation of an integrated stress-adaptive response. The proteomic analysis identified several promising HTS-responsive proteins, including a NACα18 protein, designated TaNACα18, whose role in thermotolerance remains unknown. Dual localization of TaNACα18 suggests its crucial functions in the cytoplasm and nucleus. The homodimerization of TaNACα18 anticipated its function as a transcriptional coactivator. The complementation of TaNACα18 in yeast and overexpression in wheat demonstrated its role in thermotolerance across the kingdom. Altogether, our results suggest that TaNACα18 imparts tolerance through tight regulation of gene expression, cell wall remodeling and activation of cell defense responses.
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    Proteomic signatures uncover phenotypic plasticity of susceptible and resistant genotypes by wall remodelers in rice blast
    (John Wiley & Sons, 2024) Sinha, Arunima; Narula, Kanika; Bhola, Latika; Sengupta, Atreyee; Choudhary, Pooja; Nalwa, Pragya; Kumar, Mohit; Elagamey, Eman; Chakraborty, Niranjan; Chakraborty, Subhra
    Molecular communication between macromolecules dictates extracellular matrix (ECM) dynamics during pathogen recognition and disease development. Extensive research has shed light on how plant immune components are activated, regulated and function in response to pathogen attack. However, two key questions remain largely unresolved: (i) how does ECM dynamics govern susceptibility and disease resistance, (ii) what are the components that underpin these phenomena? Rice blast, caused by Magnaporthe oryzae adversely affects rice productivity. To understand ECM regulated genotype-phenotype plasticity in blast disease, we temporally profiled two contrasting rice genotypes in disease and immune state. Morpho-histological, biochemical and electron microscopy analyses revealed that increased necrotic lesions accompanied by electrolyte leakage governs disease state. Wall carbohydrate quantification showed changes in pectin level was more significant in blast susceptible compared to blast resistant cultivar. Temporally resolved quantitative disease- and immune-responsive ECM proteomes identified 308 and 334 proteins, respectively involved in wall remodelling and integrity, signalling and disease/immune response. Pairwise comparisons between time and treatment, messenger ribonucleic acid expression, diseasome and immunome networks revealed novel blast-related functional modules. Data demonstrated accumulation of α-galactosidase and phosphatase were associated with disease state, while reactive oxygen species, induction of Lysin motif proteins, CAZymes and extracellular Ca-receptor protein govern immune state.
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    Proteo-metabolomic dissection of extracellular matrix reveals alterations in cell wall integrity and calcium signaling governs wall-associated susceptibility during stem rot disease in jute
    (American Chemical Society, 2024) Arafat, Md Yasir; Narula, Kanika; Kumar, Mohit; Chakraborty, Niranjan; Chakraborty, Subhra
    The plant surveillance system confers specificity to disease and immune states by activating distinct molecular pathways linked to cellular functionality. The extracellular matrix (ECM), a preformed passive barrier, is dynamically remodeled at sites of interaction with pathogenic microbes. Stem rot, caused by Macrophomina phaseolina, adversely affects fiber production in jute. However, how wall related susceptibility affects the ECM proteome and metabolome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome and metabolome were developed in jute upon M. phaseolina infection. Morpho-histological examination revealed that leaf shredding was accompanied by reactive oxygen species production in patho-stressed jute. Electron microscopy showed disease progression and ECM architecture remodeling due to necrosis in the later phase of fungal attack. Using isobaric tags for relative and absolute quantitative proteomics and liquid chromatography-tandem mass spectrometry, we identified 415 disease-responsive proteins involved in wall integrity, acidification, proteostasis, hydration, and redox homeostasis. The disease-related correlation network identified functional hubs centered on α-galactosidase, pectinesterase, and thaumatin. Gas chromatography–mass spectrometry analysis pointed toward enrichment of disease-responsive metabolites associated with the glutathione pathway, TCA cycle, and cutin, suberin, and wax metabolism. Data demonstrated that wall-degrading enzymes, structural carbohydrates, and calcium signaling govern rot responsive wall-susceptibility. Proteomics data were deposited in Pride (PXD046937; PXD046939).
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    Combining extracellular matrix proteome and phosphoproteome of chickpea and meta-analysis reveal novel proteoforms and evolutionary significance of clade-specific wall-associated events in plant
    (John Wiley & Sons, 2024) Narula, Kanika; Sinha, Arunima; Choudhary, Pooja; Ghosh, Sudip; Elagamey, Eman; Sharma, Archana; Sengupta, Atreyee; Chakraborty, Niranjan; Chakraborty, Subhra
    Extracellular matrix (ECM) plays central roles in cell architecture, innate defense andcell wall integrity (CWI) signaling. During transition to multicellularity, modulardomain structures of ECM proteins and proteoforms have evolved due to continuousadaptation across taxonomic clades under different ecological niche. Although thisincredible diversity has to some extent been investigated at protein level, extracellu-lar phosphorylation events and molecular evolution of ECM proteoform familiesremains unexplored. We developed matrisome proteoform atlas in a grain legume,chickpea and performed meta-analyses of 74 plant matrisomes. MS/MS analysisidentified 1,424 proteins and 315 phosphoproteins involved in diverse functions.Cross-species ECM protein network identified proteoforms associated with CWImaintenance system. Phylogenetic characterization of eighteen matrix protein fami-lies highlighted the role of taxon-specific paralogs and orthologs. Novel informationwas acquired on gene expansion and loss, co-divergence, sub functionalization andneofunctionalization during evolution. Modular networks of matrix protein familiesand hub proteins showed higher diversity across taxonomic clades than amongorgans. Furthermore, protein families differ in nonsynonymous to synonymous sub-stitution rates. Our study pointed towards the matrix proteoform functionality,sequence divergence variation, interactions between wall remodelers and molecularevolution using a phylogenetic framework. This is the first report on comprehensivematrisome proteoform network illustrating presence of CWI signaling proteins inland plants.
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    Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival
    (Elsevier B.V., 2024) Kumar, Sunil; Chakraborty, Subhra; Chakraborty, Niranjan
    The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.