Publications of NIPGR Scientists
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Item Transcriptomic and OsWAK24-MPK3 crosstalk reveal resistance mechanism of primed rice seedlings against Arsenic-Iron(Oxford University Press, 2026) Bhatia, Priyanka; Mittal, Lavanya; Pandey, Shubhangi; Khatoon, Narjis Saba; Sinha, Alok Krishna; Gupta, MeetuPriming, elucidated as "memory," refers to the preconditioning of plant's stress responses to enhance resilience toward future stressors, including arsenic (As) contamination. This adaptive preparedness becomes further complex under As-Fe(iron) interplay, which remains scarcely delineated within priming background. Here, we employed Illumina sequencing to acquire global transcriptome alterations and heterologous interaction approach to chart the molecular reprogramming associated with As and As-Fe-dynamics in primed rice. The transcriptome revealed 3005 and 3650 genes to be differentially regulated in As and As-Fe-exposed primed seedlings. Comprehensive elucidation of expression profiling revealed that key genes were involved in transportation (OsNramp, OsFCR, OsNAS), signalling (OsWRKY, OsMYB, OsAP2, OsZF-TF), and defence (OsHSP, OsPRX, OsCyt P450). The antioxidant (OsGST, OsAPX) expression correlated well with their respective physiological enzyme activity. The entire WAK module, transducing extracellular signals to intercellular pathways, was differentially regulated under As and As-Fe influence. Notably, OsWAK24 revealed higher expression under As-Fe, reflecting its association with seedlings' tolerance behaviour. The computational protein network and docking unfolded OsMPK3 as an interactor of OsWAK24. The split-ubiquitin-based yeast-hybrid assay and immunoblot revealed OsWAK24-OsMPK3 association, suggesting OsMPK3 phosphorylates OsWAK24 at serine residue. Overall, the results decoded the seedling's resilience mechanism and aid in developing rice varieties with desired traits.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 Mitogen-activated protein kinase 3/6 regulates the stability of AtIAA3 and AtIAA7 during auxin signaling in Arabidopsis(Elsevier B.V., 2026) Noryang, Stanzin; Manna, Mrinalini; Verma, Neetu; Singh, Kirti; Tayyeba, Sumaira; Sinha, Alok KrishnaAuxin mediated Aux/IAA degradation is required to release the ARFs from the control of IAAs, and ARFs in the free forms perform their role of transcription activation or suppression in response to developmental ques. Auxin is known to tag IAAs for proteasomal degradation, but how this tagging is regulated has not been widely explored. Here we report that, in Arabidopsis, exogenous application of auxin activates MPK3/6 which in turn phosphorylate IAA3 and IAA7 at Ser-58 and Ser-26, respectively. Further, incubation of IAA3 and IAA7 with the protein extracts from auxin treated mpk3 or mpk6 single mutants increase the rate of degradation of IAAs. Consequently, the phospho-null mutants, IAA3S58A and IAA7S26A were observed to be comparatively more stable. Thus, MAP kinase-mediated phosphorylation destabilised IAA3 and IAA7 leading to their degradation. Additionally, over-expression of the phospho-dead mutant of IAA3 (35S:IAA3S58A) and complementation of iaa3 mutant with this phospho-dead mutant resulted in reduced primary root length because of increased stability and accumulation of IAA3. Interestingly, we found that a member of ARF, ARF7 regulated the expression of MPKs by binding to their respective promoters.Item Dispersed components drive temperature sensing and response in plants(American Association for the Advancement of Science, 2025) Yadav, Avilash Singh; Sureshkumar, Sridevi; Sinha, Alok Krishna; Balasubramanian, SureshkumarPlants are highly sensitive to temperature, and climate change is predicted to have negative impacts on agricultural productivity. Warming temperatures, coupled with a growing population, present a substantial challenge for food security and motivate research to understand how plants sense and respond to changes in temperature. Here, we synthesize our current understanding of temperature sensing and response in plants. We outline how temperature cues are integrated into preexisting signaling cascades using inherently temperature-sensitive proteins or processes. This dispersed nature of thermo-sensitive proteins and processes makes distinct signaling cascades sensitive to temperature. This model integrates current knowledge and distinguishes thermosensing from other conventional sensing and signaling mechanisms in plants.Item Unveiling the molecular mechanism underlying PSKR-mediated amplification of the ABA signaling in Arabidopsis thaliana(Springer Nature Publishing AG, 2025) Yadav, Nikita; Nagar, Preeti ; Rawat, Abhilasha ; Rakhi, R. ; Singh, Dhanraj; Habibzai, Hedayaturahman ; Sinha, Alok Krishna; Mustafiz, AnandaAbscisic acid (ABA) serves as a vital signaling molecule that help plants respond to various environmental stresses, ensuring their survival and adaptability. The ABA signaling pathway begins when ABA is recognized by receptors known as PYR/PYL/RCAR. Upon ABA binding, these receptors undergo structural changes, but the precise modifications occurring during post-translational stages and their impact on ABA signaling are not fully understood. In this study, we have identified and characterized the ABA receptor family as target of PSKRs in both Arabidopsis and rice. In addition, we pinpointed the critical active sites in AtPSKR1 (N865) and OsPSKR15 (N892) that are responsible for kinase activity of the respective receptors and also important for direct interaction with ABA receptors. In vitro kinase experiments demonstrated phosphorylation of ABA receptors at S99 in AtPYL4, and S79 in AtPYL9. In addition, our genetic analysis demonstrated that PSKR plays a positive role in regulating ABA-mediated physiological responses, and promotes ABA-dependent leaf senescence in Arabidopsis. Phenotypic studies and expression analysis of ABA-related genes in complementation lines (AtPSKR1:pyl9 and OsPSKR15:pyl9) suggested that the overexpression of PSKR can partially restore the insensitivity of pyl9 mutant plants to ABA. These findings underscore the critical role of PSKR in enhancing ABA signaling via phosphorylation of PYL4/PYL9 in Arabidopsis.Item MPK3 mediated phosphorylation inhibits the dimerization of ABI5 to fine-tune the ABA signaling in Arabidopsis(Elsevier B.V., 2025) Bhagat, Prakash Kumar; Verma, Neetu; Pandey, Shubhangi; Verma, Deepanjali; Sinha, Alok KrishnaSeed germination is, a critical physiological process, is tightly regulated by the phytohormone abscisic acid (ABA). However, the cross talk between multiple regulatory pathways involved in seed germination remains poorly understood. Here, we show that ABA activates two MAP kinases, AtMPK3/AtMPK6, which interact with and phosphorylate AtABI5, a master regulator of ABA signaling. MAP kinase-mediated AtABI5 phosphorylation at the serine-314 position regulates its nuclear localization and dimerization. Interestingly, AtABI5 provides feedback regulation by directly binding to the promoter of AtMPK3 to modulate its transcription. Further, functional analyses revealed that overexpression of a phospho-null AtABI5S314A variant in the abi5-8 mutant background conferred increased ABA sensitivity during seed germination, heightened drought sensitivity, and delayed flowering compared to wild-type plants. Conversely, overexpression of phospho-mimic AtABI5S314D in abi5-8 mutant showed ABA insensitivity during seed germination, drought tolerance, and early floral transition similar to abi5-8 mutant. Collectively, our findings highlight that MAP kinase-mediated phosphorylation of AtABI5 fine-tunes ABA signaling by regulating its dimerization, providing new insights into the dynamic regulation of plant responses to environmental and developmental cues.Item Nutrient and water availability influence rice physiology, root architecture and ionomic balance via auxin signalling(John Wiley & Sons, 2025) Manna, Mrinalini; Rengasamy, Balakrishnan; Sinha, Alok KrishnaWater and soil nutrients are the vital ingredients of crop production, and their efficient uptake is essentially dependent on root development, majorly regulated by auxin. For a water-loving crop like rice, how water availability regulates nutrient acquisition, additionally, how ambient nutrient level modulates water uptake, and the role of auxin therein is not well studied. While investigating the cross-talks among these components, we found water to be essential for auxin re-distribution in roots and shaping the root architecture. We also found that supplementing rice seedlings with moderate concentrations of mineral nutrients facilitated faster water uptake and greater nutrient enrichment in leaves compared to adequate nutrient supplementation. Additionally, moderate nutrient availability favoured greater stomatal density, stomatal conductance, photosynthesis, transpiration rate and water use efficiency when water was not limiting. Further, auxin supplementation enhanced root formation in rice, while affecting their water uptake ability, photosynthesis and transpiration causing differential mineral-specific uptake trends. The present study uncovers the existence of an intricate crosstalk among water, nutrients and auxin signalling the knowledge of which will enable optimizing the growth conditions for speed breeding of rice and harnessing the components of auxin signalling to improve water and nutrient use efficiency of rice.Item Revisiting rice transformation for a fail-safe protocol and its application for various gene functional and molecular studies(Springer Nature Publishing AG, 2025) Manna, Mrinalini; Rengasamy, Balakrishnan; Reddy, Malireddy K.; Sinha, Alok KrishnaAn efcient transformation and regeneration system is prerequisite for gene functional studies in rice, the staple food crop of the Asian subcontinent. Despite the availability of a large number of rice transformation protocols, it is hard to fnd a simple and minimum input based, but fail-safe protocol that ensures zero number of escapes (or the non-transformants). The fear of obtaining an unpredictable percentage of escapes at the end of rice tissue culture prompts carrying out multiple batches of transformation which not only consumes costly resources and time but also burdens one with screening of a large number of tissue culture derived plants. In the present study, we have described a simple but fail-safe rice transformation protocol for functional validation of the genes by overexpression and CRISPR-Cas9 mediated gene knockout systems. By taking the advantage of high transformability of japonica rice tissues, we have also revealed that the present rice transformation protocol can be efectively employed to visualize protein localization in various subcellular compartments of rice root and callus tissues, an alternative to conventional tobacco/onion peel infltration or protoplast transformation which are either time consuming or tricky. Additionally, the paper also discusses the importance of Southern blotting in gene overexpression studies, utility of non-conventional antibiotic selection approaches and signifcance of sgRNA designing for gene knockout studies in rice. Various troubleshooting advice are also being presented. Overall, the present protocol might serve as an excellent guide for functional validation of several genes present in the rice genome waiting to be explored.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 MPK4-mediated phosphorylation of PHYTOCHROME INTERACTING FACTOR4 controls thermosensing by regulating histone variant H2A.Z deposition(Oxford University Press, 2024) Verma, Neetu; Singh, Dhanraj; Mittal, Lavanya; Banerjee, Gopal; Noryang, Stanzin; Sinha, Alok KrishnaPlants can perceive a slight upsurge in ambient temperature and respond by undergoing morphological changes, such as elongated hypocotyls and early flowering. The dynamic functioning of PHYTOCHROME INTERACTING FACTOR4 (PIF4) in thermomorphogenesis is well established, although the complete regulatory pathway involved in thermosensing remains elusive. We establish that an increase in temperature from 22˚C to 28˚C induces upregulation and activation of MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) in Arabidopsis (Arabidopsis thaliana), subsequently leading to the phosphorylation of PIF4. Phosphorylated PIF4 represses the expression of ACTIN-RELATED PROTEIN 6 (ARP6), which is required for mediating the deposition of histone variant H2A.Z at its target loci. Furthermore, we demonstrate that variations in ARP6 expression in PIF4 phosphor-null and phosphor-mimetic seedlings affect hypocotyl growth at 22˚C and 28˚C by modulating the regulation of ARP6-mediated H2A.Z deposition at the loci of genes involved in elongating hypocotyl cells. Interestingly, the expression of MPK4 is also controlled by H2A.Z deposition in a temperature-dependent manner. Taken together, these findings highlight the regulatory mechanism of thermosensing by which MPK4-mediated phosphorylation of PIF4 affects ARP6-mediated H2A.Z deposition at the genes involved in hypocotyl cell elongation.