Institutional Publications
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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 Regulation of photosynthesis by mitogen-activated protein kinase in rice: antagonistic adjustment by OsMPK3 and OsMPK6(Springer Nature Publishing AG, 2023) Jonwal, Sarvesh; Rengasamy, Balakrishnan; Sinha, Alok KrishnaPhotosynthesis is the basis of almost all life on earth and is the main component of crop yield that contributes to the carbohydrate partitioning to the grains. Maintaining the photosynthetic efficiency of plants in challenging environmental conditions by regulating the associated factors is a potential research arena which will help in the improvement of crop yield. Phosphorylation is known to play a pivotal role in the regulation of photosynthesis. Mitogen Activated Protein Kinases (MAPKs) cascade although known to regulate a diverse range of processes does not have any exact reported function in the regulation of photosynthesis. To elucidate the regulatory role of MAPKs in photosynthesis we investigated the changes in net photosynthesis rate and related parameters in DEX inducible over-expressing (OE) lines of two members of MAPK gene family namely, OsMPK3 and OsMPK6 in rice. Interestingly, significant changes were found in net photosynthesis rate and related physiological parameters in OsMPK3 and OsMPK6-OE lines compared to its wild-type relatives. OsMPK3 and OsMPK6 have regulatory effects on nuclear-encoded photosynthetic genes. Untargeted metabolite profiling reveals a higher accumulation of sugars and their derivatives in MPK6 overexpressing plants and a lower accumulation of sugars and organic acids in MPK3 overexpressing plants. The accumulation of amino acids was found in abundance in both MPK3 and MPK6 overexpressing plants. Understanding the effects of MPK3 and MPK6 on the CO2 assimilation of rice plants under normal growth conditions, will help in devising strategies that can be extended for crop improvement.Item Post translational modifications at the verge of plant-geminivirus interaction(Elsevier B.V., 2023) Prasad, Ashish; Sharma, Shambhavi; Prasad, ManojPlant-virus interaction is a complex phenomenon and involves the communication between plant and viral factors. Viruses have very limited coding ability yet, they are able to cause infection which results in huge agro-economic losses throughout the globe each year. Post-translational modifications (PTMs) are covalent modifications of proteins that have a drastic effect on their conformation, stability and function. Like the host proteins, geminiviral proteins are also subject to PTMs and these modifications greatly expand the diversity of their functions. Additionally, these viral proteins can also interact with the components of PTM pathways and modulate them. Several studies have highlighted the importance of PTMs such as phosphorylation, ubiquitination, SUMOylation, myristoylation, S-acylation, acetylation and methylation in plant-geminivirus interaction. PTMs also regulate epigenetic modifications during geminivirus infection which determines viral gene expression. In this review, we have summarized the role of PTMs in regulating geminiviral protein function, influence of PTMs on viral gene expression and how geminiviral proteins interact with the components of PTM pathways to modulate their function.Item Arabidopsis MPK3 and MPK6 regulates D-Glucose signaling and interacts with G-Protein, RGS1(Elsevier B.V., 2022) Bhagat, Prakash Kumar; Sharma, Deepika; Verma, Deepanjali; Singh, Kirti; Sinha, Alok KrishnaSugar as a signaling molecule has attracted lots of attention. Even though several kinases have been shown to play a crucial role in the sugar signaling and response to exogenous D-glucose (Glc), the information on the involvement of MAP kinase cascade in sugar signaling has remain largely unexplored. In this report we demonstrate that MAP kinase signaling is essential for sensitivity to higher concentrations of D-Glc in Arabidopsis. We found that D-Glc activates MAP kinases, MPK3 and MPK6 in a concentration and time-dependent manner. The mutants of mpk3 and mpk6 display hyposensitivity to 6% D-Glc during seed germination, cotyledon greening and root growth. Interestingly, the altered sensitivity to increased D-Glc is severely enhanced by addition of 1% Sucrose in the media. Our study also deciphered the role of one of the Glc sensor proteins, RGS1 that interacts and gets phosphorylated at its C-terminal domain by MPK3 and MPK6. Overall our study provides a new insight on the involvement of MAP kinases in association with G-proteins that might regulate sugar signaling and sugar responsive growth and development in Arabidopsis.Item Regulation of photosynthetic light reaction proteins via reversible phosphorylation(Elsevier B.V., 2022) Jonwal, Sarvesh; Verma, Neetu; Sinha, Alok KrishnaThe regulation of photosynthesis occurs at different levels including the control of nuclear and plastid genes transcription, RNA processing and translation, protein translocation, assemblies and their post translational modifications. Out of all these, post translational modification enables rapid response of plants towards changing environmental conditions. Among all post-translational modifications, reversible phosphorylation is known to play a crucial role in the regulation of light reaction of photosynthesis. Although, phosphorylation of PS II subunits has been extensively studied but not much attention is given to other photosynthetic complexes such as PS I, Cytochrome b6f complex and ATP synthase. Phosphorylation reaction is known to protect photosynthetic apparatus in challenging environment conditions such as high light, elevated temperature, high salinity and drought. Recent studies have explored the role of photosynthetic protein phosphorylation in conferring plant immunity against the rice blast disease. The evolution of phosphorylation of different subunits of photosynthetic proteins occurred along with the evolution of plant lineage for their better adaptation to the changing environment conditions. In this review, we summarize the progress made in the research field of phosphorylation of photosynthetic proteins and highlights the missing links that need immediate attention.Item A dual-specificity phosphatase, MAP kinase phosphatase 1, positively regulates blue light-mediated seedling development in Arabidopsis(Springer Nature Publishing AG, 2021) Verma, Deepanjali; Bhagat, Prakash Kumar; Sinha, Alok KrishnaReversible phosphorylation of proteins is one of the major post-translational modifications in nearly all signaling pathways in plants. MAP kinase phosphatases are very crucial in the regulation of MAPKs as they dephosphorylate both threonine (Thr) and tyrosine (Tyr) residues within the T-X-Y motif of active MAPKs. Therefore, to gain insight of involvement of MAP kinase phosphatases in the regulation of light signaling, we searched for the potential phosphatase which may regulate the function of MPK6, a negative regulator of blue light (BL)-mediated photomorphogenic development. We report here the identification of a dual-specificity phosphatase, MAP kinase phosphatase 1 (MKP1) as a positive regulator of BL-mediated seedling development. Overexpression of MKP1 enhances the BL-induced inhibition of hypocotyl elongation and displays more opened cotyledons. We also show that MKP1OE accumulates more pigments and positively affects the expression of downstream light-related genes in response to BL. In vitro and in vivo evidences also demonstrate that MKP1 not only interacts with but also dephosphorylates MPK6 in BL. In addition, MKP1 regulates stability as well as activity of MPK6 upon BL. Taken together our study highlights the important role of phosphatases in the regulation of a signaling pathway and identifies the role of MKP1 in the negative regulation of MPK6 activity leading to a change in BL-induced photomorphogenic responses.Item Structure and regulation of SWEET transporters in plants: An update(Elsevier B.V., 2020) Anjali, Anjali; Fatima, Urooj; Manu, M.S.; Ramasamy, Sureshkumar; Senthil-Kumar, MuthappaSugar will eventually be exported transporters (SWEETs), a novel family of sugar transporters found in both eukaryotes and prokaryotes, facilitate sugar flux across the cell membrane. Although these transporters were first discovered in plants, their homologs have been reported in different organisms. SWEETs have critical roles in various developmental processes, including phloem loading, nectar secretion, and pathogen nutrition. The structure of bacterial homologs, called SemiSWEETs, has been well studied thus far. Here, we provide an overview of SWEET protein structure and dynamic function by analyzing the solved crystal structures and predicted models that are available for a few SWEETs in a monocot plant (rice) and dicot plant (Arabidopsis thaliana). Despite the advancement in structure-related studies, the regulation of SWEETs remains unknown. In light of reported regulatory mechanisms of a few other sugar transporters, we propose the regulation of SWEETs at the post-translational level. We then enumerate the potential post-translational modification sites in SWEETs using computational tools. Overall, in this review, we critically analyze SWEET protein structure in plants to predict the post-translational regulation of SWEETs. Such findings have a direct bearing on plant nutrition and defense and targeting the regulation at these levels will be important in crop improvement.Item A protein phosphatase 2C, AP2C1 interacts with and negatively regulates the function of CIPK9 under potassium deficient conditions in Arabidopsis(Oxford University Press, 2018) Singh, Amarjeet; Yadav, Akhilesh K.; Kaur, Kanwaljeet; Sanyal, Sibaji K.; Jha, Saroj K.; Fernandes, Joel L.; Sharma, Pankhuri; Tokas, Indu; Pandey, Amita; Luan, Sheng; Pandey, Girdhar K.Potassium (K+) is a major macronutrient required for plant growth. In response to low- K+ condition, an adaptive mechanism entails activation of the Ca2+ signaling network consisting of calcineurin B-like proteins (CBLs) and their interacting kinases (CIPKs) in plants. The CBL-interacting protein kinase 9 (CIPK9) is previously implicated in low-K+ responses in Arabidopsis thaliana. Here, we report a protein phosphatase 2C (PP2C), AP2C1, as an interactor of CIPK9. Fluorescence resonance energy transfer (FRET), bimolecular fluorescence complementation (BiFC) and co-localization analyses revealed that CIPK9 and AP2C1 interact in the cytoplasm. AP2C1 dephosphorylates the auto-phosphorylated form of CIPK9 in vitro, presenting a regulatory mechanism for CIPK9 function. Furthermore, genetic and molecular analysis revealed that ap2c1 null mutants (ap2c1-1 and ap2c1-2) are tolerant to low-K+ conditions, retained higher K+ content and showed higher expression of K+ deficiency related genes contrary to cipk9 mutants (cipk9-1 and cipk9-2). In contrast, transgenic plants overexpressing AP2C1 were sensitive to low-K+ conditions. Thus, this study shows that AP2C1 and CIPK9 interact to regulate K+-deficiency responses in Arabidopsis. CIPK9 functions as positive regulator whereas, AP2C1 acts as a negative regulator of Arabidopsis root growth and seedling development under low-K+ conditions.Item Light-induced phosphorylation and degradation of the negative regulator PIF1 depends upon its direct physical interactions with photoactivated phytochromes(American Society of Plant Biologists, 2008) Shen, Hui; Zhu, Ling; Castillon, Alicia; Majee, Manoj; Downie, Bruce; Huq, EnamulThe phytochrome (phy) family of photoreceptors regulates changes in gene expression in response to red/far-red light signals in part by physically interacting with constitutively nucleus-localized phy-interacting basic helix-loop-helix transcription factors (PIFs). Here, we show that PIF1, the member with the highest affinity for phys, is strongly sensitive to the quality and quantity of light. phyA plays a dominant role in regulating the degradation of PIF1 following initial light exposure, while phyB and phyD and possibly other phys also influence PIF1 degradation after prolonged illumination. PIF1 is rapidly phosphorylated and ubiquitinated under red and far-red light before being degraded with a half-life of ~1 to 2 min under red light. Although PIF1 interacts with phyB through a conserved active phyB binding motif, it interacts with phyA through a novel active phyA binding motif. phy interaction is necessary but not sufficient for the light-induced phosphorylation and degradation of PIF1. Domain-mapping studies reveal that the phy interaction, light-induced degradation, and transcriptional activation domains are located at the N-terminal 150–amino acid region of PIF1. Unlike PIF3, PIF1 does not interact with the two halves of either phyA or phyB separately. Moreover, overexpression of a light-stable truncated form of PIF1 causes constitutively photomorphogenic phenotypes in the dark. Taken together, these data suggest that removal of the negative regulators (e.g., PIFs) by light-induced proteolytic degradation might be sufficient to promote photomorphogenesis.Item Cloning and characterization of a novel LpWRKY1 transcription factor in tomato(Elsevier B.V., 2008) Hofmann, Markus Georg; Sinha, Alok Krishna; Proels, Reinhard Korbinian; Roitsch, ThomasThe initiation of defence responses in plants is accompanied by fundamental changes in gene expression: the expression of pathogenesis- related genes is co-ordinately regulated with metabolic changes such as down regulation of photosynthesis and induction of sink metabolism. To identify candidate regulators of this co-ordinated regulatory mechanism, the role of WRKY transcription factors in the initiation of defence response was analysed in tomato. A WRKY-type transcription factor (LpWRKY1) from tomato was cloned by a reverse Northern approach. The corresponding mRNA is rapidly and transiently induced after challenging the cells with an elicitor-preparation derived from the wilt inducing fungus Fusarium oxysporum lycopersici (E-FOL) and the fungal elicitor chitosan, whereas the endogenous signals systemin and salicylic acid are inactive. Inhibition of protein biosynthesis by cycloheximide results in sustained induction of mRNA for LpWRKY1. In contrast, the transient induction of the gene encoding LpWRKY1 in response to elicitation by E-FOL is inhibited by the protein-kinase inhibitor staurosporine and may be mimicked by the phosphatase inhibitors endothall and cantharidine indicating the involvement of protein phosphorylation in the regulation of WRKY-type transcription factors. Direct proof of this postranslational modification of LpWRKY1 was obtained by demonstrating in-gel kinase assays using recombinant LpWRKY1 as substrate. A 44 kDa and a 67 kDa protein kinase were shown to be transiently activated to phosphorylate LpWRKY1 protein in response to elicitation with E-FOL.