Institutional Publications
Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11
Browse
53 results
Search Results
Item OsNUOR enhances disease susceptibility by interfering with reactive oxygen species homeostasis and ferroptosis-like cell death(Oxford University Press, 2026)Necrotrophic fungal pathogens such as Rhizoctonia solani, the causal agent of rice (Oryza sativa) sheath blight disease, enhance reactive oxygen species (ROS) production to induce necrosis in infected tissues. Here, we present evidence that the host alternative NADH:ubiquinone oxidoreductase (OsNUOR) facilitates R. solani infection by promoting an oxidative-stress-enriched environment and inducing iron-dependent ferroptosis-like cell death. OsNUOR overexpression (OE) lines exhibit enhanced disease susceptibility, whereas knock-out (KO) lines developed through genome editing demonstrate increased resistance. Infected OE lines have enhanced accumulation of ROS, lipid peroxides, and ferric ions (Fe3+); a significant reduction in antioxidative enzyme (including glutathione peroxidase) activity; and depletion of glutathione levels. In KO lines, the redox status of infected tissues is maintained, and the antioxidative defense is activated. Our data suggest that upregulation of OsNUOR induces mitochondrial ROS accumulation and modulates redox signalling, leading to Fe3+ accumulation and lipid peroxidation that promote necrosis in rice. KO lines are compromised in these processes and therefore exhibit disease resistance. We demonstrate that treatment with ferroptosis inhibitors prevents necrotic lesions, whereas ferroptosis inducers enhance disease severity. Overall, our study reveals the importance of ferroptosis-like cell death in promoting necrosis during R. solani infection in rice.Item Genome-wide DNA methylation dynamics at "heading" stage of panicle and flag leaf in contrasting rice cultivars under field drought conditions(Frontiers Media S.A., 2025) Jajo, Ringyao; Kansal, Shivani; Mathur, Saloni; Raghuvanshi, SaurabhAbstract Introduction: Drought stress induces widespread genome-wide alterations in DNA methylation of rice. These changes work to alter gene expression and are relatively unexplored in reproductive tissues like flag leaf and panicle under field drought conditions. This study aims to explore the same in the panicle and flag leaf tissue of IR64 (drought-sensitive) and N22 (drought-tolerant) rice cultivars under field-drought conditions during the 'heading' stage of development. Methods: For the same, we generated whole-genome bisulfite sequencing libraries from the corresponding tissues and analysed them in detail. Results and discussion: The DNA methylation dynamics in adult tissue (flowering stage) was found to be clearly distinct from that of the seedling stage. Further, the contrasting rice genotypes also exhibited cultivar-specific and drought-induced dynamism in the methylation signatures. Notably, the two cultivars demonstrate inherent distinctions in sequence preferences of hyper- and hypo-methylation even prior to experiencing drought stress, and these preferences persist under the influence of the stress. Approximately 90% of the drought-induced differentially methylated region (DMR) are cultivar-specific, and about 70% of the cultivar differences (cultivar-DMR) under stress are unique compared to control condition. There is higher prevalence of hyper-methylated DMR that co-localized with differentially expressed genes in panicle. DMR of CHH sequence exhibit stronger negative correlation with expression compared to CpG and CHG sequence. Examination of differentially expressed genes with DMR highlights their functional relevance under drought stress, especially with DMR found in gene bodies and promoter regions. Notably, in panicle, methylation divergence of the two cultivars influences flowering regulation genes. Additionally, the findings also suggest a regulatory role for DNA methylation in drought induced response of miRNA genes, particularly in the panicle of N22 cultivars.Item KRP3 stability controls rice plant architecture and productivity via MPK3-mediated phosphorylation(John Wiley & Sons, 2026) Banerjee, Gopal; Jonwal, Sarvesh; Rengasamy, Balakrishnan; Pal, Uttam; Singh, Dhanraj; Mohit, Mohit; Sinha, Alok KrishnaYield is a critical agronomic trait in cereal crops, shaped by factors like tiller and seed number, and seed weight. Understanding the factors governing these traits will help in improving the yield of plants. In this study, we identified an orphan gene, KRP3, belonging to cereal crops as a key regulator of rice plant architecture. Altered KRP3 protein homeostasis affected plant height, tiller number, and seed production, highlighting its role in maintaining rice plant vigor and productivity. The stability of the KRP3 protein is positively regulated by MPK3-mediated phosphorylation, as unphosphorylated KRP3 is targeted for degradation via the ubiquitin-proteasome pathway. Our findings reveal that the identified MPK3-KRP3 module operates as an S-phase checkpoint, modulating the pace of cell division in the actively dividing zones and maintaining a balance between cell division and elongation. These findings provide valuable insights for improving plant growth and grain yield in rice.Item Zinc finger transcriptional repressor ZOS5-09 regulates grain filling and development in rice(John Wiley & Sons, 2025) Jaiswal, Priya; Qasim, Falah; Mahto, Arunima; Vichitra, Ankur; Das, Upasana; Tyagi, Akhilesh K.; Agarwal, PinkyGrain size is one of the key determinants of grain yield. Our study focuses on a novel seed-preferential C2H2 zinc finger transcription factor, ZOS5-09 (LOC_Os05g38600) that plays an important role in regulating rice grain traits. Rice plants with the ZOS5-09 promoter::GUS construct showed high expression of ZOS5-09 in rice endosperm. In planta reporter effector assays and localization studies showed that ZOS5-09 is a nuclear-localized transcriptional repressor. It has two C2H2 zinc finger domains and a C-terminal NoRS (nucleolar retention signal). Ectopic and seed-preferential overexpression of ZOS5-09 resulted in lethality. Seed-preferential overexpression without NoRS was detrimental to grain filling. Rice plants with knock-down or CRISPR-based knock-out of ZOS5-09 displayed reduced grain length and weight but increased grain width. Grain size change was due to lower cell proliferation and increased cell size in the transverse direction because of downregulation of cell cycle-related genes and increased expression of expansins. Decreased expression of ZOS5-09 also resulted in reduced total starch and protein content and higher endosperm chalkiness, thus negatively affecting grain quality. ZOS5-09 directly bound to a zinc finger–binding site and regulated a seed storage protein-encoding gene, GLU6. It acted as a repressor by promoting deacetylation upon interaction with a histone deacetylase. In summary, our results indicate that an optimum expression of ZOS5-09 is essential for proper rice grain development. Our study highlights the role of a transcriptional repressor in regulating rice grain traits and improves our understanding of the transcriptional regulatory networks affecting grain size.Item Wax deposition is vital for thermotolerance in rice(Elsevier B.V., 2025) Sonkar, Kamankshi; Singh, AmarjeetRice is a staple food and source of nutrition for over half of the world’s population. Unfortunately, it is highly susceptible to heat stress both, at vegetative and reproductive developmental stages. In the current scenario of climate change and global warming, even a 1°C rise in environmental temperature could decline cereal production by 6–7% (Lesk et al., 2016). Thus, it could be a serious threat for the food security of ever-growing world population. To combat the environmental emergency there is a dire need of enhancing the thermotolerance important crop plant rice.Item Overexpression of phytoglobin1 in rice leads to enhanced nitrogen use efficiency via modulation of nitric oxide(John Wiley & Sons, 2025) Samant, Sanjib Bal; Swain, Jagannath; Yadav, Nidhi; Yadav, Reena; Singh, Pooja; Rai, Preeti; Sheri, Vijay; Sreeman, Sheshshayee; Subramanyam, Rajagopal; Pareek, Ashwani; Gupta, Kapuganti JagadisNitric oxide (NO) is one of the byproducts of nitrogen metabolism. Excess amount of NO is scavenged by phytoglobins. The role of phytoglobin mediated NO homoeostasis in modulation of nitrate transporters was investigated using NO scavenger cPTIO, phytoglobin overexpressing rice and Arabidopsis. Growing plants under low nitrate leads to generation of reduced levels of NO accompanied by elevated expression of high affinity transporters (HATs) such as NRT2.1, NRT2.3 and NRT2.4. Scavenging of NO by cPTIO under optimal nitrate caused enhanced HATs expression. Phytoglobin overexpressing Arabidopsis showed improved growth and enhanced expression of HATs under low nitrogen in comparison to WT. Pretreatment of optimal nitrate grown plants with NO scavenger cPTIO enhanced HATs expression and shifting of these primed plants from optimal to low nitrate leads to further elevation of HATs expression accompanied by enhanced nitrogen uptake and its accumulation with positive effect on growth. Phytoglobin overexpression in rice leads to enhanced HATs expression, improved growth, nitrogen accumulation under low nitrate. Pgb OE lines showed enhanced accumulation of amino acids. Taken together our results suggest an important role of phytoglobins in nitrogen uptake and assimilation.Item Stripping off the rice panicle: induced genetic variation awakens the sheathed spikelet for a better yield(Oxford University Press, 2024) Mohanty, Jitendra K.; Parida, Swarup K.The rice panicle is the reproductive structure that contains the seeds, so a productive spikelet in a panicle contributes to increased yield. A sheathed panicle covers a signifcant portion of spikelets with the fag leaf and impairs effective pollination which subsequently compromises the yield. Through induced mutagenesis and integrated molecular breeding strategies, Ballichatla et al. (2024) uncovered the intricate regulation of complete panicle exsertion (CPE) in rice. This study also delineates a set of high-confdence novel genomic loci and superior gene alleles which have a substantial translational signifcance in rice crop improvement towards future food security.Item The small RNA biogenesis in rice is regulated by MAP kinase-mediated OsCDKD phosphorylation(John Wiley & Sons, 2024) Singh, Dhanraj; Verma, Neetu; Rengasamy, Balakrishnan; Banerjee, Gopal; Sinha, Alok KrishnaCDKs are the master regulator of cell division and their activity is controlled by the regulatory subunit cyclins and phosphorylation by the CAKs. However, the role of MAP kinases in regulating plant cell cycle or CDKs have not been explored. Here, we report that the MAP kinases OsMPK3, OsMPK4, and OsMPK6 physically interact and phosphorylate OsCDKD and its regulatory subunit OsCYCH in rice. MAP kinases phosphorylate CDKD at Ser-168 and Thr-235 residues in OsCDKD. The MAP kinase-mediated phosphorylation of OsCDKD is required for its activation to control the small RNA biogenesis. The phosphodead version of OsCDKD fails to activate the C-terminal domain of RNA Polymerase II, thereby negatively impacting small RNA transcription. Further, the overexpression lines of wild-type (WT) OsCDKD and phosphomimic OsCDKD show increased root growth, plant height, tiller number, panicle number, and seed number in comparison to WT, phosphodead OsCDKD-OE, and kinase-dead OsCDKD-OE plants. In a nutshell, our study establishes a novel regulation of OsCDKD by MAPK-mediated phosphorylation in rice. The phosphorylation of OsCDKD by MAPKs imparts a positive effect on rice growth and development by regulating miRNAs transcription.Item PROTEIN L-ISOASPARTYL METHYLTRANSFERASE protects enolase dysfunction by repairing isoaspartyl-induced damage and is positively implicated in agronomically important seed traits(John Wiley & Sons, 2024) Kamble, Nitin Uttam; Ghosh, Shraboni; Petla, Bhanu Prakash; Achary, Rakesh Kumar; Gautam, Shikha; Rao, Venkateswara; Salvi, Prafull; Hazra, Abhijit; Varshney, Vishal; Majee, ManojThe protein-repairing enzyme (PRE) PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT) influences seed vigor by repairing isoaspartyl-mediated protein damage in seeds. However, PIMTs function in other seed traits, and the mechanisms by which PIMT affects such seed traits are still poorly understood. Herein, through molecular, biochemical, and genetic studies using overexpression and RNAi lines in Oryza sativa and Arabidopsis thaliana, we demonstrate that PIMT not only affects seed vigor but also affects seed size and weight by modulating enolase (ENO) activity. We have identified ENO2, a glycolytic enzyme, as a PIMT interacting protein through Y2H cDNA library screening, and this interaction was further validated by BiFC and co-immunoprecipitation assay. We show that mutation or suppression of ENO2 expression results in reduced seed vigor, seed size, and weight. We also proved that ENO2 undergoes isoAsp modification that affects its activity in both in vivo and in vitro conditions. Further, using MS/MS analyses, amino acid residues that undergo isoAsp modification in ENO2 were identified. We also demonstrate that PIMT repairs such isoAsp modification in ENO2 protein, protecting its vital cellular functions during seed maturation and storage, and plays a vital role in regulating seed size, weight, and seed vigor. Taken together, our study identified ENO2 as a novel substrate of PIMT, and both ENO2 and PIMT in turn implicate in agronomically important seed traits.Item Methionine biosynthetic genes and methionine sulfoxide reductase A are required for Rhizoctonia solani AG1-IA to cause sheath blight disease in rice(John Wiley & Sons, 2024) Das, Joyati; Ghosh, Srayan; Tyagi, Kriti; Sahoo, Debashis; Jha, GopaljeeRhizoctonia solani is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. It deploys effector molecules as well as carbohydrate-active enzymes and enhances the production of reactive oxygen species for killing host tissues. Understanding R. solani ability to sustain growth under an oxidative-stress-enriched environment is important for developing disease control strategies. Here, we demonstrate that R. solani upregulates methionine biosynthetic genes, including Rs_MET13 during infection in rice, and double-stranded RNA-mediated silencing of these genes impairs the pathogen's ability to cause disease. Exogenous treatment with methionine restores the disease-causing ability of Rs_MET13-silenced R. solani and facilitates its growth on 10 mM H2O2-containing minimal-media. Notably, the Rs_MsrA gene that encodes methionine sulfoxide reductase A, an antioxidant enzyme involved in the repair of oxidative damage of methionine, is upregulated upon H2O2 treatment and also during infection in rice. Rs_MsrA-silenced R. solani is unable to cause disease, suggesting that it is important for the repair of oxidative damage in methionine during host colonization. We propose that spray-induced gene silencing of Rs_MsrA and designing of antagonistic molecules that block MsrA activity can be exploited as a drug target for effective control of sheath blight disease in rice.