Publications of NIPGR Scientists

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Author: search.filters.author.Sinha, Alok KrishnaSubject: search.filters.subject.rice

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Now showing 1 - 9 of 9
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    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 Krishna
    Yield 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.
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    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 Krishna
    CDKs 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.
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    Root-expressed rice PAP3b enhances secreted APase activity and helps utilize organic phosphate
    (Oxford University Press, 2023) Bhadouria, Jyoti; Mehra, Poonam; Verma, Lokesh; Pazhamala, Lekha T; Rumi, Rumi; Panchal, Poonam; Sinha, Alok Krishna; Giri, Jitender
    Phosphate (Pi) deficiency leads to the induction of purple acid phosphatases (PAPs) in plants, which dephosphorylates organic phosphorus complexes in the rhizosphere and intracellular compartments to release Pi. In this study, we demonstrate that OsPAP3b belongs to group III low molecular weight PAP, and is low Pi responsive, preferentially in roots. The expression of OsPAP3b is negatively regulated with Pi re-supply. Interestingly, OsPAP3b was found to be dual localized to the nucleus and secretome. Furthermore, OsPAP3b is transcriptionally regulated by OsPHR2 as substantiated by DNA-protein binding assay. Through in-vitro biochemical assays, we further demonstrate that OsPAP3b is a functional acid phosphatase with broad substrate specificity. Overexpression of OsPAP3b in rice led to increased secreted APase activity and improved mineralization of organic P sources, reflected in better growth of transgenics compared to wild type when grown on organic P as exogenous P substrate. Under Pi deprivation, OsPAP3b knockdown and knockout lines showed no significant changes in total P content and dry biomass. However, the expression of other phosphate starvation-induced (PSI) genes and the levels of metabolites were found to be altered in the overexpression and knockdown lines. In addition, in-vitro pull-down assay revealed multiple putative interacting proteins of OsPAP3b. Our data collectively suggest that OsPAP3b can aid in organic P utilization in rice. The APase isoforms behavior and nuclear localization indicate its additional role, possibly in stress signaling. Considering its important roles, OsPAP3b could be a potential target for improving low Pi adaptation in rice.
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    Transcriptional regulation of rice HSP101 promoter: Mitogen-activated protein kinase-mediated HSFA6a phosphorylation affects its stability and transactivation
    (John Wiley & Sons, 2022) Singh, Garima; Banerjee, Gopal; Sarkar, Neelam K.; Sinha, Alok Krishna; Grover, Anil
    Heat shock proteins (HSPs) and heat stress factors (HSFs) control the plant heat stress response to a large extent. HSP101 plays a decisive role in development of plant heat tolerance. We have previously shown that rice (Oryza sativa) cells contain 25 HSFs and among these, HSFA6a most predominantly binds to the HSP101 promoter and controls its transcript expression. This study shows that mitogen-activated protein kinases (MAPKs), specifically MPK3, MPK4, and MPK6 phosphorylate HSFA6a. HSFA6a showed physical interaction with MPK3/MPK4, specifically in the nucleus and this interaction involved the C-terminal end of HSFA6a. Four serine residues at positions Ser136, Ser141, Ser264, and Ser356 of HSFA6a are the putative sites of MAPK phosphorylation: we generated phospho-mutant of HSFA6a by changing the serine residues to alanine either individually or all four together. The Hsp101 promoter binding potential of Ser136 mutant was enhanced while it declined for the other three phospho-mutant HSFA6a forms. HSFA6a mutant lacking all the above four Ser residues exhibited reduced DNA binding and transactivation potential. We implicate the role of phosphorylation in the regulation of HSFA6a activity.
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    MicroRNA biogenesis factor DRB1 is a phosphorylation target of mitogen activated protein kinase, MPK3 in both rice and Arabidopsis
    (John Wiley & Sons, 2015) Raghuram, Badmi; Sheikh, Arsheed H.; Rustagi, Yashika; Sinha, Alok Krishna
    MicroRNA (miRNA) biogenesis requires AtDRB1 (double-stranded RNA binding protein)/HYL1 (Hyponastic Leaves1) protein for processing and maturation of miRNA precursors. The AtDRB1/HYL1 protein associates with AtDCL1 (Dicer-Like1) and accurately processes primary-miRNAs (pri-mRNAs) first to precursor-miRNAs (pre-miRNAs) and finally to mature miRNAs. The dephosphorylation of AtDRB1/HYL1 protein is very important for the precise processing of miRNA precursors. The monocot model crop plant Oryza sativa encodes four orthologues of AtDRB1/HYL1 protein, the only one encoded by Arabidopsis thaliana. The present study focuses on the functionality of the O. sativa DRBs as the orthologues of AtDRB1/HYL1 by using RNA binding assays and in planta protein–protein interaction analysis. Further, mitogen-activated protein kinase MPK3 is established as the kinase phosphorylating DRB1 protein in both the model plants, O. sativa and Arabidopsis. MicroRNA microarray analysis in atmpk3 and atmpk6 mutants indicate the importance of AtMPK3 in maintaining the level of miRNAs in the plant.
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    miRNA plays a role in the antagonistic effect of selenium on arsenic stress in rice seedlings
    (Royal Society of Chemistry, 2015) Pandey, Chandana; Raghuram, Badmi; Sinha, Alok Krishna; Gupta, Meetu
    MicroRNAs (miRNAs), the small non-coding RNAs, have been implicated in various biological processes including adaptation during environmental stress. The present work explores the involvement of miRNA during arsenic (As) and selenium (Se) treatment in rice seedlings. Arsenic is a heavy metalloid causing severe adverse effects on the growth and development of plants while Se is another metalloid and an essential micro-nutrient when present in appropriate amounts. It was observed that the presence of Se along with As mitigated the adverse effects of As on seedling germination, root-shoot growth, total chlorophyll and protein contents. The measurement of stress indicators such as proline, cysteine and MDA also indicated similar effects. Analysis of the miRNA profile using microarrays under As, Se and As + Se treatments showed differential regulation of at least 46 miRNAs in rice seedlings compared to untreated control. 18 of these miRNAs showed differential regulation among different treatments. Furthermore the microarray data were validated using real time PCR. The target genes of a few of these miRNAs showed inverse transcript accumulation. The possible role of miR395 and miR398 in the antagonistic effect on the adverse response of As in the presence of Se in rice seedlings is discussed.
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    Regulation of MAP kinase signaling cascade by microRNAs in Oryza sativa
    (Taylor & Francis Group, 2014) Raghuram, Badmi; Sheikh, Arsheed Hussain; Sinha, Alok Krishna
    Mitogen activated protein kinase (MAPK) pathway is one of the most conserved signaling cascade in plants regulating a plethora of cellular processes including normal growth and development, abiotic and biotic stress responses. The perception of external cues triggers the phosphorylation of three tier MAPKKK-MAPKK-MAPK cascade which finally modifies a downstream substrate thereby regulating the cellular processes. Whereas, the transcription regulation by MAPKs, mediated through their substrates is well studied in plants, the transcription and post-transcriptional regulation of the MAPK genes are poorly understood. Previous studies from the animals systems suggested the miRNAs regulate the post-transcriptional regulation of MAPK transcripts. Here we attempt to unravel the post-transcriptional regulation of MAPKs by miRNAs in model crop plant Oryza sativa. Using in silico tools, we predict the miRNAs for 98 out of 99 MAPK transcripts. The predicted miRNAs were validated for the biological relevance of their function. The inverse correlation between relative transcript levels between the MAPKs and their predicted miRNAs validated the in silico prediction. Taken together, this report demonstrates the significance of miRNAs in regulation of the MAPK pathway in plants with a new direction to study the plant signaling molecules.
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    In silico analysis reveals 75 members of mitogen-activated protein kinase kinase kinase gene family in rice
    (Oxford University Press, 2010) Rao, Kudupudi Prabhakara; Richa, Tambi; Kumar, Kundan; Raghuram, Badmi; Sinha, Alok Krishna
    Mitogen-Activated Protein Kinase Kinase Kinases (MAPKKKs) are important components of MAPK cascades, which are universal signal transduction modules and play important role in plant growth and development. In the sequenced Arabidopsis genome 80 MAPKKKs were identified and currently being analysed for its role in different stress. In rice, economically important monocot cereal crop only five MAPKKKs were identified so far. In this study using computational analysis of sequenced rice genome we have identified 75 MAPKKKs. EST hits and full-length cDNA sequences (from KOME or Genbank database) of 75 MAPKKKs supported their existence. Phylogenetic analyses of MAPKKKs from rice and Arabidopsis have classified them into three subgroups, which include Raf, ZIK and MEKK. Conserved motifs in the deduced amino acid sequences of rice MAPKKKs strongly supported their identity as members of Raf, ZIK and MEKK subfamilies. Further expression analysis of the MAPKKKs in MPSS database revealed that their transcripts were differentially regulated in various stress and tissue-specific libraries.
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    Rhythmic expression of mitogen activated protein kinase activity in rice
    (Springer, 2009) Rao, Kudupudi Prabhakara; Vani, Gubbala; Kumar, Kundan; Sinha, Alok Krishna
    Mitogen activated protein kinase (MAPK) are known to get activated during various stress signals and transduce the message from the cell membrane to the nucleus for appropriate cellular reorganization. Though, a certain basal activity of MAPK is often observed in the control plants. Prolonged exposure of rice plants to lowered or elevated temperature exhibited a rhythm in the activation of MAPKs. We analyzed existence of a possible endogenous rhythm in the activity of MAPKs in rice plants. The plants growing at constant temperature entrained in 16/8 h day-night cycle showed diurnal rhythm in activity. When the activation of MAPK was tested under continuous conditions by shifting plants to continuous darkness for a period of 72 h, the periodic rhythm persisted and followed a circadian pattern. Analysis of the transcripts of group A, B and C members of MAPKs under above conditions by quantitative real time PCR revealed that the members of group C exhibit periodic rhythm. Our data indicates that the MAP kinase activity in rice follows rhythmic expression in a circadian manner.