Publications of NIPGR Scientists

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Author: search.filters.author.Choudhary, PoojaSubject: search.filters.subject.Cicer arietinum

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    Combining extracellular matrix proteome and phosphoproteome of chickpea and meta-analysis reveal novel proteoforms and evolutionary significance of clade-specific wall-associated events in plant
    (John Wiley & Sons, 2024) Narula, Kanika; Sinha, Arunima; Choudhary, Pooja; Ghosh, Sudip; Elagamey, Eman; Sharma, Archana; Sengupta, Atreyee; Chakraborty, Niranjan; Chakraborty, Subhra
    Extracellular matrix (ECM) plays central roles in cell architecture, innate defense andcell wall integrity (CWI) signaling. During transition to multicellularity, modulardomain structures of ECM proteins and proteoforms have evolved due to continuousadaptation across taxonomic clades under different ecological niche. Although thisincredible diversity has to some extent been investigated at protein level, extracellu-lar phosphorylation events and molecular evolution of ECM proteoform familiesremains unexplored. We developed matrisome proteoform atlas in a grain legume,chickpea and performed meta-analyses of 74 plant matrisomes. MS/MS analysisidentified 1,424 proteins and 315 phosphoproteins involved in diverse functions.Cross-species ECM protein network identified proteoforms associated with CWImaintenance system. Phylogenetic characterization of eighteen matrix protein fami-lies highlighted the role of taxon-specific paralogs and orthologs. Novel informationwas acquired on gene expansion and loss, co-divergence, sub functionalization andneofunctionalization during evolution. Modular networks of matrix protein familiesand hub proteins showed higher diversity across taxonomic clades than amongorgans. Furthermore, protein families differ in nonsynonymous to synonymous sub-stitution rates. Our study pointed towards the matrix proteoform functionality,sequence divergence variation, interactions between wall remodelers and molecularevolution using a phylogenetic framework. This is the first report on comprehensivematrisome proteoform network illustrating presence of CWI signaling proteins inland plants.
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    Genotype-independent Agrobacterium rhizogenes-mediated root transformation of chickpea: a rapid and efficient method for reverse genetics studies
    (BioMed Central Ltd, 2018) Aggarwal, Pooja Rani; Nag, Papri; Choudhary, Pooja; Chakraborty, Niranjan; Chakraborty, Subhra
    Background: Chickpea (Cicer arietinum L.), an important legume crop is one of the major source of dietary protein. Developing an efcient and reproducible transformation method is imperative to expedite functional genomics studies in this crop. Here, we present an optimized and detailed procedure for Agrobacterium rhizogenes-mediated root transformation of chickpea. Results: Transformation positive roots were obtained on selection medium after two weeks of A. rhizogenes inoculation. Expression of green fuorescent protein further confrmed the success of transformation. We demonstrate that our method adequately transforms chickpea roots at early developmental stage with high efciency. In addition, root transformation was found to be genotype-independent and the efcacy of our protocol was highest in two (Annigiri and JG-62) of the seven tested chickpea genotypes. Next, we present the functional analysis of chickpea hairy roots by expressing Arabidopsis TRANSPARENT TESTA 2 (AtTT2) gene involved in proanthocyanidins biosynthesis. Overexpression of AtTT2 enhanced the level of proanthocyanidins in hairy roots that led to the decreased colonization of fungal pathogen, Fusarium oxysporum. Furthermore, the induction of transgenic roots does not afect functional studies involving infection of roots by fungal pathogen. Conclusions: Transgenic roots expressing genes of interest will be useful in downstream functional characterization using reverse genetics studies. It requires 1 day to perform the root transformation protocol described in this study and the roots expressing transgene can be maintained for 3–4 weeks, providing sufcient time for further functional studies. Overall, the current methodology will greatly facilitate the functional genomics analyses of candidate genes in root-rhizosphere interaction in this recalcitrant but economically important legume crop.