Publications of NIPGR Scientists

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Subject: search.filters.subject.Stress response

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    AraNSdb: a dedicated database of stress-responsive non-coding RNAs in Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Vivek, A.T.; Bhatia, Manika; Sahu, Namrata; Kalakoti, Garima; Kaushik, Love; Mukherjee, Kanka; Kumar, Shailesh
    Plants, as sessile organisms, are constantly exposed to biotic and abiotic stresses, making their ability to respond crucial for survival. Non-coding RNAs (ncRNAs) have emerged as key regulators in these stress responses, with several studies identifying numerous stress-responsive ncRNAs (SRNs). However, a comprehensive collection of SRNs derived from sequencing data in Arabidopsis thaliana has been lacking. To address this, we utilized high-throughput experimental data and mined published studies to construct AraNSdb (Arabidopsis ncRNA Stress Database), a systematic resource for storing and querying SRNs. AraNSdb documents over 1,000 expression profiles from diverse stress datasets, encompassing 6,616 SRNs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). The database features an intuitive web interface for exploring SRNs associated with specific stress types and provides detailed ncRNA annotations to support functional and regulatory studies. AraNSdb offers a valuable platform for advancing our understanding of ncRNA-mediated stress responses and is freely accessible at http://www.nipgr.ac.in/AraNSdb.
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    Comprehensive study of tRNA-derived fragments in plants for biotic stress responses
    (Springer Nature Publishing AG, 2025) Swain, Supriya P. ; Bisht, Niyati ;  Kumar, Shailesh
    Plant growth and development are often disrupted by biological stressors as they interfere with the regulatory pathways. Among the key regulators, transfer-RNA-derived fragments (tRFs) have emerged as key players in plant defense mechanisms. While tRF-mediated responses to abiotic stress have been well studied, their role in biotic stress remains less understood, as various stressors may elicit different regulatory systems. In this study, tRF-mediated biotic responses in three species, viz. Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum are investigated using in-silico approaches. Analysis of predicted tRFs across various biotic stress conditions reveals specific interactions with mRNA targets, microRNAs (miRNAs), and transposable elements (TEs), highlighting their regulatory significance in plant adaptation mechanisms. These findings provide new insights into tRF-mediated stress responses and establish a computational framework for further functional studies. The study’s database is publicly available at http://www.nipgr.ac.in/PbtRFdb.
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    Comparative transcriptome profiling of two contrasting foxtail millet cultivars provides insights into molecular mechanisms underlying dehydration stress response
    (Springer Nature Publishing AG, 2023) Muthamilarasan, Mehanathan; Suresh, Bonthala Venkata; Singh, Roshan Kumar; Choudhary, Pooja; Aggarwal, Pooja Rani; Prasad, Manoj
    Foxtail millet (Setaria italica L.) has emerged as a model system to understand its adaptation to environmental stresses in the past decade. However, studies on understanding the molecular mechanism underlying the adaptation to dehydration stress and the regulatory network involved in the process remain elusive. In the present study, RNA-seq was performed during dehydration stress in the tolerant (IC4) and sensitive (IC41) cultivars at different time points (0, 6, and 12 h). A total of 2467 and 3318 differentially expressed genes (DEGs) were identified in IC4, and 2535 and 5572 in IC41 at 6 h and 12 h compared to control (0 h), respectively. Gene ontology (GO) analysis revealed that the DEGs were enriched in water transport, response to water deprivation, oxidative stress, amino acid and sugar transport, lipid biosynthesis, and regulation of stomatal opening. Pathway analysis suggested a significant modulation of genes involved in the metabolism of glutathione and tryptophan and biosynthesis of flavonoid, ascorbate, arginine, and proline in IC4 compared to IC41. Genes encoding for DIVARICATA, SBP family protein (teosinte glume architecture 1), and SRS family proteins (LATERAL ROOT PRIMORDIUM 1 and SHI-RELATED SEQUENCE 1) were found to be exclusively upregulated in IC4 during dehydration stress. Gene co-expression networks constructed based on the expression data showed the key modules and hubs that play critical roles during dehydration stress. Altogether, the present study has identified key genes, pathways, and regulatory modules that would serve as a base for further studies to gain insights into the dehydration-responsive molecular circuitry in foxtail millet.
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    Sequestering miR165/166 enhances seed germination in Arabidopsis thaliana under normal condition and ABA treatment
    (Springer Nature Publishing AG, 2020) Sarkar Das, Shabari; Majee, Manoj; Nandi, Asis K.; Karmakar, Prakash
    Seed germination is a dynamic process involving imbibition, increased metabolic activity and protrusion of a tiny plantlet rupturing the seed coat. Many genes, phytohormones like ABA and GA have been implicated in germination of Arabidopsis thaliana seeds. Although many microRNAs (miRNAs) have been shown to be differentially expressed during seed germination process, their role remains mostly unaddressed. Here we address the role of developmentally important miR165/166 in the process of seed germination. We demonstrate that the seeds of transgenic A. thaliana having target mimic-miR165/166 (eTM-miR165/166), where miR165/166 is sponged, show better germination efficiency. The seeds of this line also maintain better germination even under ABA treatment, which is a negative regulator of seed germination. Thus, our results suggest that, sequestering miR165/166 activity enhances seed germination efficiency under normal and ABA-stress condition.
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    Versatile roles of aquaporin in physiological processes and stress tolerance in plants
    (Elsevier B.V., 2020) Singh, Roshan Kumar; Deshmukh, Rupesh; Muthamilarasan, Mehanathan; Rani, Rekha; Prasad, Manoj
    Aquaporins are pore-forming transmembrane proteins that facilitate the movement of water and many other small neutral solutes across the cells and intracellular compartments. Plants exhibits high diversity in aquaporin isoforms and broadly classified into five different subfamilies on the basis of phylogenetic distribution and subcellular occurrence: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like proteins (NIPs), small basic intrinsic proteins (SIPs) and uncharacterized intrinsic proteins (XIPs). The gating mechanism of aquaporin channels is tightly regulated by post-translational modifications such as phosphorylation, methylation, acetylation, glycosylation, and deamination. Aquaporin expression and transport functions are also modulated by the various phytohormones-mediated signalling in plants. Combined physiology and transcriptome analysis revealed the role of aquaporins in regulating hydraulic conductance in roots and leaves. The present review mainly focused on aquaporin functional activity during solute transport, plant development, abiotic stress response, and plant-microbe symbiosis. Genetically modified plants overexpressing aquaporin-encoding genes display improved agronomic and abiotic stress tolerance.
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    Transcript profiling reveals potential regulators for oxidative stress response of a necrotrophic chickpea pathogen Ascochyta rabiei
    (Springer Nature Publishing AG, 2020) Maurya, Ranjeet; Singh, Yeshveer; Sinha, Manisha; Singh, Kunal; Mishra, Pallavi; Singh, Shreenivas Kumar; Verma, Sandhya; Prabha, Kanchan; Kumar, Kamal; Verma, Praveen K.
    Necrotrophic pathogens experience host-generated oxidative stress during pathogenesis. They overcome such hostile environment by intricate mechanisms which are largely understudied. In this article, reference-based transcriptome analysis of a devastating Ascochyta Blight (AB) disease causing chickpea pathogen Ascochyta rabiei was explored to get insights into survival mechanisms under oxidative stress. Here, expression profling of mock-treated and menadione-treated fungus was carried out by RNA-Seq approach. A signifcant number of genes in response to oxidative stress were overrepresented, suggestive of a robust and coordinated defense system of A. rabiei. A total 73 diferentially expressed genes were fltered out from both the transcriptomes, among them 64 were up-regulated and 9 were found down-regulated. The gene ontology and KEGG mapping were conducted to comprehend the possible regulatory roles of diferentially expressed genes in metabolic networks and biosynthetic pathways. Transcript profling, KEGG pathway and gene ontology-based enrichment analysis revealed 12 (16.43%) stress responsive factors, 25 (34.24%) virulence associated genes, 10 (13.69%) putative efectors and 28 (38.35%) important interacting proteins associated with various metabolic pathways. In addition, genes with diferential expression were further explored for underlying putative pathogenicity factors. We identifed fve genes ST47_g10291, ST47_g9396, ST47_g10294, ST47_g4395, and ST47_g7191 that were common to stress and fungal pathogenicity. The factors recognized in this work can be used to establish molecular tools to explain the regulatory gene networks engaged in stress response of fungal pathogens and disease management.
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    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, Niranjan
    Phosphorylation 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.
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    Transcriptome profiling illustrates expression signatures of dehydration tolerance in developing grasspea seedlings
    (Springer Nature, 2019) Rathi, Divya; Gayali, Saurabh; Pareek, Akanksha; Chakraborty, Subhra; Chakraborty, Niranjan
    Main conclusion This study highlights dehydration-mediated temporal changes in physicochemical, transcriptome and metabolome profles indicating altered gene expression and metabolic shifts, underlying endurance and adaptation to stress tolerance in the marginalized crop, grasspea. Grasspea, often regarded as an orphan legume, is recognized to be fairly tolerant to water-defcit stress. In the present study, 3-week-old grasspea seedlings were subjected to dehydration by withholding water over a period of 144 h. While there were no detectable phenotypic changes in the seedlings till 48 h, the symptoms appeared during 72 h and aggravated upon prolonged dehydration. The physiological responses to water-defcit stress during 72–96 h displayed a decrease in pigments, disruption in membrane integrity and osmotic imbalance. We evaluated the temporal efects of dehydration at the transcriptome and metabolome levels. In total, 5201 genes of various functional classes including transcription factors, cytoplasmic enzymes and structural cell wall proteins, among others, were found to be dehydration-responsive. Further, metabolome profling revealed 59 dehydration-responsive metabolites including sugar alcohols and amino acids. Despite the lack of genome information of grasspea, the time course of physicochemical and molecular responses suggest a synchronized dehydration response. The cross-species comparison of the transcriptomes and metabolomes with other legumes provides evidence for marked molecular diversity. We propose a hypothetical model that highlights novel biomarkers and explain their relevance in dehydration-response, which would facilitate targeted breeding and aid in commencing crop improvement eforts.
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    The plant LIM proteins: unlocking the hidden attractions
    (Springer, 2017) Srivastava, Vikas; Verma, Praveen K.
    MAIN CONCLUSION: The plant LIMs comprise two sub-families with one (DA1/DAR) and two (2LIM) LIM domains. This review comprehensively discussed the structure and potential role of this protein family in diverse area of plant biology. The description of first eukaryote lineage-specific plant LIM domain (LIN11, ISL1, and MEC3) proteins was observed in Helianthus long back. The successive study of LIM proteins in diverse plants has shown its vital relation to development, metabolism and defence. This nascent gene family has been worked out for their role in actin dynamics, organ size determination and transcription regulation. On grounds of protein architecture, two sub-families have been delineated as DA1/DAR (one LIM domain) and 2LIMs (two LIM domains). The genomic and expression study guides to the identification of diverse sub-categories. The significance of 2LIMs in regulation of actin dynamics leading to pollen growth and development has prospects to understand the plant reproductive behaviour. Interestingly, new facet of these LIMs as a transcriptional regulator in biological pathway/biosynthesis was also reported. Recently, the cumulative contribution of these features was also recognized for obtaining good quality fibre, thus giving translational outlook to this family. The DA1/DAR proteins are orchestrated with additional domains and provide a key role in regulation of organ size and tolerance to biotic and abiotic stress. This review will focus the journey of plant LIMs till date and will cover details of its structure, type, classification and functional relevance. This will provide insight to identify the potential of this gene family in the improvement of desired crop features.
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    Legume proteomics: Progress, prospects and challenges
    (John Wiley & Sons, 2016) Rathi, Divya; Gayen, Dipak; Gayali, Saurabh; Chakraborty, Subhra; Chakraborty, Niranjan
    Legumes are the major sources of food and fodder with strong commercial relevance, and are essential components of agricultural ecosystems owing to their ability to carry out endosymbiotic nitrogen fixation. In recent years, legumes have become one of the major choices of plant research. The legume proteomics is currently represented by more than 100 reference maps and an equal number of stress-responsive proteomes. Among the 48 legumes in the protein databases, most proteomic studies have been accomplished in two model legumes, soybean, and barrel medic. This review highlights recent contributions in the field of legume proteomics to comprehend the defence and regulatory mechanisms during development and adaptation to climatic changes. Here, we attempted to provide a concise overview of the progress in legume proteomics and discuss future developments in three broad perspectives: (i) proteome of organs/tissues; (ii) subcellular compartments; and (iii) spatiotemporal changes in response to stress. Such data mining may aid in discovering potential biomarkers for plant growth, in general, apart from essential components involved in stress tolerance. The prospect of integrating proteome data with genome information from legumes will provide exciting opportunities for plant biologists to achieve long-term goals of crop improvement and sustainable agriculture.