Publications of NIPGR Scientists

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    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, Pinky
    Grain 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.
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    Comparative proteomics reveals a role for seed storage protein, AmA1 in cellular growth, development and nutrient accumulation
    (American Chemical Society, 2013) Agrawal, Lalit; Narula, Kanika; Basu, Swaraj; Shekhar, Shubhendu; Ghosh, Sudip; Datta, Asis; Chakraborty, Niranjan; Chakraborty, Subhra
    Seed storage proteins are known to be utilized as carbon and nitrogen source for growing seedlings and thus are considered as potential candidates for nutritional improvement. However, their precise function remains unknown. We have earlier shown that ectopic expression of a seed storage protein, AmA1, leads to increase in protein besides high tuber yield in potato. To elucidate the AmA1-regulated molecular mechanism affecting increased protein synthesis, reserve accumulation, and enhanced growth, a comparative proteomics approach has been applied to tuber life-cycle between wild-type and AmA1 potato. The differential display of proteomes revealed 150 AmA1-responsive protein spots (ARPs) that change their intensities more than 2.5-fold. The LC-ESI-MS/MS analyses led to the identification of 80 ARPs presumably associated with cell differentiation, regulating diverse functions, viz., protein biogenesis and storage, bioenergy and metabolism, and cell signaling. Metabolome study indicated up-regulation of amino acids paralleling the proteomics analysis. To validate this, we focused our attention on anatomical study that showed differences in cell size in the cortex, premedullary zone and pith of the tuber, coinciding with AmA1 expression and localization. Further, we interrogated the proteome data using one-way analysis of variance, cluster, and partial correlation analysis that identified two significant protein modules and six small correlation groups centered around isoforms of cysteine protease inhibitor, actin, heat shock cognate protein 83 and 14-3-3, pointing toward AmA1-regulated overlapping processes of protein enhancement and cell growth perhaps through a common mechanism of function. A model network was constructed using the protein data sets, which aim to show how target proteins might work in coordinated fashion and attribute to increased protein synthesis and storage reserve accumulation in AmA1 tubers on one hand and organ development on the other.