Publications of NIPGR Scientists
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Item Lipid-mediated responses to nutrient and other stresses: Roles in plant adaptation and signaling(Oxford University Press, 2026) Pandey, Mandavi; Ganotra, Jahanvi; Singh, Astha; Parchuri, Prasad; Giri, JitenderLipids are essential components of biological membranes; however, their roles in plants go far beyond providing structural support. They are actively involved in signaling and metabolic regulation during abiotic and biotic stress. Plants use lipid-based strategies to adapt to nutrient shortages, toxic conditions, and changing environments. Signaling lipids such as phosphatidic acid (PA), phosphoinositides, sphingolipids, and oxylipins serve as molecular messengers that transmit stress signals to regulate ion transport, hormone interactions, and developmental flexibility. During nutrient deprivation, especially of phosphorus (P), nitrogen (N), and potassium (K), plants adjust membrane composition by replacing phospholipids with P-free glycolipids like galactolipids and sulfolipids, conserving critical nutrients while keeping membrane structure intact. Lipid intermediates, including PA, glycerol-3-phosphate, and negatively charged phospholipids, also act as secondary messengers in stress signaling networks. Lipid droplets and lipophagy help maintain carbon and redox balance, while enzymes like phospholipases and glycerophosphodiesterases recycle nutrients and alter lipid profiles. Under K deficiency and toxic metal exposure (e.g., aluminum (Al), cadmium (Cd)), lipid turnover influences membrane stability, reactive oxygen species (ROS) production, and transporter function. Lipid modifications also reduce toxic ion binding and cellular damage, and molecules derived from lipids, such as jasmonates, play roles in secondary metabolism and hormonal defense pathways. Although lipid-based stress responses are conserved throughout plant lineages, the regulatory mechanisms controlling lipid fluxes are not yet fully understood. New tools, like genetically coded lipid biosensors and lipidomics platforms, are uncovering the spatial and temporal dynamics of lipid signaling with unprecedented detail. Improving our understanding of lipid-mediated stress responses may enable the development of crops with better nutrient efficiency and resilience to climatic and edaphic stresses, contributing to sustainable agriculture.Item Genome-wide identification and molecular characterization of core ABA signaling components under abiotic stresses and during development in chickpea(Springer Nature Publishing AG, 2025) Kamali, Saravanappriyan; Sonkar, Kamankshi; Ankit, Ankit; Deepika, Deepika; Sharma, Ankita; Singh, AmarjeetAbscisic acid (ABA) signaling is vital for plant's response to abiotic stresses and development. Core components of ABA signaling include ABA receptors PYR/PYL/RCAR, group-A PP2Cs (PP2C-As) and SnRK2 serine/threonine kinases. These have been well studied in Arabidopsis, but their knowledge in the legume crop chickpea is missing. Here, we identified 8 PYLs, 11 PP2C-As and 13 SnRK2s genes in the chickpea genome. Gene duplication events have been found to drive their evolution and expansion in chickpea. Protein homology modeling revealed three-dimensional structure, and arrangements of α-helix, β-sheets and p-loops in respective families. In-planta subcellular localization analysis revealed that CaPYL3 and CaPYL5 proteins were localized at the plasma membrane, and CaPP2CA-1 and CaSnRK2.7 were localized in the cytoplasm and the nucleus. RNA sequencing data analysis indicated the regulatory role of CaPYLs, CaPP2C-As and CaSnRK2s in developmental stages particularly, stages of early embryogenesis to seed maturity. Through RT-qPCR analysis drought, salt and ABA responsive CaPYL, CaPP2C-A and CaSnRK2 genes, which might regulate abiotic stress response in chickpea were identified. Importantly, key genes like CaPYL4, CaPP2C-A4, CaPP2C-A11 and CaSnRK2.9 with overlapping expression in drought, ABA and seed development were identified, which might determine chickpea crop yield. In-silico interaction analysis revealed specific and overlapping interaction among ABA signaling proteins indicating their functional relevance. Overall, core ABA signaling components are crucial for abiotic stress tolerance and development in chickpea. These genes will be functionally validated in the future and will be utilized to generate abiotic stress resilience and high-yielding chickpea varieties.Item A glucose-target of rapamycin signaling axis integrates environmental history of heat stress through maintenance of transcription-associated epigenetic memory in Arabidopsis(Oxford University Press, 2022) Sharma, Mohan; Sharma, Manvi; Jamsheer, Muhammed K; Laxmi, AshveryaIn nature, plants cope with adversity and have established strategies that recall past episodes and enable them to better cope with stress recurrences by establishing a 'stress memory'. Emerging evidence suggests that Glucose (Glc) and Target of Rapamycin (TOR), central regulators of plant growth have remarkable functions in stress adaptation. However, whether TOR modulates a stress memory response is so far unknown. Global transcriptome profiling identified that Glc through TOR regulates the expression of numerous genes involved in thermomemory. Priming of TOR overexpressors with mild heat showed better stress endurance, whereas TOR RNAi showed reduced thermomemory. This thermomemory is linked with histone methylation at specific sites of heat stress (HS) genes. TOR promotes long-term accumulation of H3K4me3 on thermomemory-associated gene promoters, even when transcription of those genes reverts to their basal level. Our results suggest that ARABIDOPSIS TRITHORAX 1 (ATX1), an H3K4 methyltransferase already shown to regulate H3K4me3 levels at the promoters of HS recovery genes, is a direct target of TOR signaling. The TOR activating E2Fa binds to the promoter of ATX1, regulates its expression which ultimately regulates thermomemory. Collectively, our findings reveal a mechanistic framework in which Glc-TOR signaling determines the integration of stress and energy signaling to regulate thermomemory.Item Molecular components associated with the regulation of flavonoid biosynthesis(Elsevier B.V., 2022) Naik, Jogindra; Misra, Prashant; Trivedi, Prabodh Kumar; Pandey, AshutoshFlavonoids exhibit amazing structural diversity and play different roles in plants. Besides, these compounds have been associated with several health benefits in humans. Several exogenous and endogenous cues, for example, light, temperature, nutrient status, and phytohormones have been reported as modulators of biosynthesis and accumulation of flavonoids. Thus, multiple hormones and stress-related signaling pathways are involved in the regulation of gene expression associated with this pathway. The transcriptional regulators belonging to the MYB and bHLH family transcription factors are well documented as the direct regulators of the structural genes associated with flavonoid biosynthesis. Recent studies also suggest that some of these factors are regulated by molecular components involved in stress and hormone signaling pathways. Adapter proteins for transcriptional activation or repression via recruitment of co-activators and co-repressors, respectively, E2 ubiquitin ligases, miRNA processing complex, and DNA methylation/demethylation factors have been recently discovered in various plants to play key roles in fine-tuning flavonoids synthesis. In the present review, we aim to provide comprehensive information about the role of different factors in the regulation of flavonoid biosynthesis. Besides, we describe the potential upstream regulators involved in the regulation of flavonoid biosynthesis within the context of available information. To sum up, the present review furnishes an updated account of signal transduction pathways modulating the biosynthesis of flavonoids.Item Heavy metal stress in rice: uptake, transport, signaling and tolerance mechanisms(John Wiley & Sons, 2021) Kaur, Ravneet; Das, Susmita; Bansal, Sakshi; Singh, Gurbir; Sardar, Shaswati; Dhar, Hena; Ram, HasthiHeavy metal contamination of agricultural fields has become a global concern as it causes a direct impact on human health. Rice is the major food crop for almost half of the world population and is grown under diverse environmental conditions, including heavy metal-contaminated soil. In recent years, the impact of heavy metal contamination on rice yield and grain quality has been shown through multiple approaches. In this review article, different aspects of heavy metal stress, i.e. uptake, transport, signalling and tolerance mechanisms, are comprehensively discussed with special emphasis on rice. For uptake, some of the transporters have specificity to one or two metal ions, whereas many other transporters are able to transport many different ions. After uptake, the intercellular signalling is mediated through different signaling pathways involving the regulation of various hormones, alteration of calcium levels and the activation of Mitogen-Activated Protein kinases. Heavy metal stress signals from various intermediate molecules activate various transcription factors, which triggers the expression of various antioxidant enzymes. Activated antioxidant enzymes then scavenge various reactive oxygen species, which eventually leads to stress tolerance in plants. Non-enzymatic antioxidants, such as ascorbate, metalloids and even metal-binding peptides (metallothionein and phytochelatin) can also help to reduce metal toxicity in plants. Genetic engineering has been successfully used in rice and many other crops to increase metal tolerance and reduce heavy metals accumulation. A comprehensive understanding of uptake, transport, signalling and tolerance mechanisms will help to grow rice plants in agricultural fields with less heavy metal accumulation in grains.Item Emerging role of phospholipase C mediated lipid signaling in abiotic stress tolerance and development in plants(Springer Nature Publishing AG, 2021) Sagar, Sushma; Singh, AmarjeetEnvironmental stimuli are primarily perceived at the plasma membrane. Stimuli perception leads to membrane disintegration and generation of molecules which trigger lipid signaling. In plants, lipid signaling regulates important biological functions however, the molecular mechanism involved is unclear. Phospholipases C (PLCs) are important lipid-modifying enzymes in eukaryotes. In animals, PLCs by hydrolyzing phospholipids, such as phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] generate diacylglycerol (DAG) and inositol- 1,4,5-trisphosphate (IP3). However, in plants their phosphorylated variants i.e., phosphatidic acid (PA) and inositol hexakisphosphate (IP6) are proposed to mediate lipid signaling. Specifc substrate preferences divide PLCs into phosphatidylinositol–PLC (PI–PLC) and non-specifc PLCs (NPC). PLC activity is regulated by various cellular factors including, calcium (Ca2+) concentration, phospholipid substrate, and post-translational modifcations. Both PI–PLCs and NPCs are implicated in plants’ response to stresses and development. Emerging evidences show that PLCs regulate structural and developmental features, like stomata movement, microtubule organization, membrane remodelling and root development under abiotic stresses. Thus, crucial insights are provided into PLC mediated regulatory mechanism of abiotic stress responses in plants. In this review, we describe the structure and regulation of plant PLCs. In addition, cellular and physiological roles of PLCs in abiotic stresses, phosphorus defciency, aluminium toxicity, pollen tube growth, and root development are discussed.Item Decoding and relay of calcium signals by CBL-CIPK module in plants(Indian National Science Academy, 2019) Meena, Mukesh Kumar; Sardar, Atish; Chattopadhyay, DebasisCalcium is an essential macronutrient and a second messenger for signal transduction in plants. Apart from acting as a second messenger, calcium is also required for cytoskeleton, cell division, pollen tube growth and as a co-factor. Cytoplasmic calcium ion ([Ca2+](cyt)) is maintained at a low level, however, is rapidly elevated using storages in organelles on perception of a stimulus. Ca2+-binding proteins that sense the kinetics and magnitude of elevated [Ca2+](cyt) convert the chemical signals to biological signals and define specificity of responses. These proteins are broadly classified into sensor relays and sensor responders. Sensor relay proteins require another interacting protein to transmit the signal; whereas, the sensor responders combine within one protein the relay, amplification and response functions. A significant achievement has been made in the last three decades that identified and characterized various proteins instrumental in decoding Ca2+-signals in plant cells. The latest addition in Ca2+-signaling is Calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs). It is believed that flexibility of interactions between different CBL and CIPK proteins and their sub-cellular localizations are crucial in sensing and responding to specific signals. In this review, we have laid emphasis on the recent and emerging advancements in understanding of the CBL-CIPK module.Item Neomycin: an effective inhibitor of jasmonate-induced reactions in plants(Springer Nature, 2019) Vadassery, Jyothilakshmi; Ballhorn, Daniel J.; Fleming, Steven R.; Mazars, Christian; Pandey, Shree P.; Schmidt, Axel; Schuman, Meredith C.; Yeh, Kai‑Wun; Yilamujiang, Ayufu; Mithöfer, AxelJasmonates are important phytohormones involved in both plant developmental processes as well as defense reactions. Many JA-mediated plant defense responses have been studied in model plants using mutants of the jasmonate signaling pathway. However, in plant species where JA-signaling mutants are not accessible, the availability of a tool targeting JA signaling is crucial to investigate jasmonate-dependent processes. Neomycin is a poly-cationic aminoglycoside antibiotic that blocks the release of Ca2+ from internal stores. We examined the inhibitory activities of neomycin on different jasmonate-inducible responses in eight different plant species: Intracellular calcium measurements in Nicotiana tabacum cell culture, Sporamin gene induction in Ipomoea batatas, PDF2.2 gene expression in Triticum aestivum, Nepenthesin protease activity measurement in Nepenthes alata, extrafloral nectar production in Phaseolus lunatus, nectary formation in Populus trichocarpa, terpene accumulation in Picea abies, and secondary metabolite generation in Nicotiana attenuata. We are able to show that neomycin, an easily manageable and commercially available compound, inhibits JA-mediated responses across the plant kingdom.Item Alterations in plant sugar metabolism: signatory of pathogen attack(Springer Nature, 2019) Kanwar, Poonam; Jha, GopaljeeMain conclusion This review summarizes the current understanding, future challenges and ongoing quest on sugar metabolic alterations that infuence the outcome of plant–pathogen interactions. Intricate cellular and molecular events occur during plant–pathogen interactions. They cause major metabolic perturbations in the host and alterations in sugar metabolism play a pivotal role in governing the outcome of various kinds of plant–pathogen interactions. Sugar metabolizing enzymes and transporters of both host and pathogen origin get diferentially regulated during the interactions. Both plant and pathogen compete for utilizing the host sugar metabolic machinery and in turn promote resistant or susceptible responses. However, the kind of sugar metabolism alteration that is benefcial for the host or pathogen is yet to be properly understood. Recently developed tools and methodologies are facilitating research to understand the intricate dynamics of sugar metabolism during the interactions. The present review elaborates current understanding, future challenges and ongoing quest on sugar metabolism, mobilization and regulation during various plant–pathogen interactions.Item Characterization of mediator complex and its associated proteins from rice(Springer, 2017) Samanta, Subhasis; Thakur, Jitendra K.The Mediator complex is a multi-protein complex that acts as a molecular bridge conveying transcriptional messages from the cis element-bound transcription factor to the RNA Polymerase II machinery. It is found in all eukaryotes including members of the plant kingdom. Increasing number of reports from plants regarding different Mediator subunits involved in a multitude of processes spanning from plant development to environmental interactions have firmly established it as a central hub of plant regulatory networks. Routine isolation of Mediator complex in a particular species is a necessity because of many reasons. First, composition of the Mediator complex varies from species to species. Second, the composition of the Mediator complex in a particular species is not static under all developmental and environmental conditions. Besides this, at times, Mediator complex is used in in vitro transcription systems. Rice, a staple food crop of the world, is used as a model monocot crop. Realizing the need of a reliable protocol for the isolation of Mediator complex from plants, we describe here the isolation of Mediator complex from rice.