Institutional Publications
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Item Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea(John Wiley & Sons, 2020) Sinha, Arunima; Haider, Toshiba; Narula, Kanika; Ghosh, Sudip; Chakraborty, Niranjan; Chakraborty, SubhraNutrient dynamics in storage organs is a complex developmental process that requires coordinated interactions of environmental, biochemical, and genetic factors. Although sink organ developmental events have been identified, our understanding of translational and post‐translational regulation of reserve synthesis, accumulation and utilization in legume crops is limited. To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, an integrated proteomics and phosphoproteomics study in six sequential seed developmental stages in chickpea was performed. MS/MS analyses identified 109 unique nutrient‐associated proteins (NAPs) involved in metabolism, storage and biogenesis, and protein turnover. Differences and similarities in 60 nutrient‐associated phosphoproteins (NAPPs) containing 93 phosphosites were compared with NAPs. Data revealed accumulation of carbon‐nitrogen metabolic and photosynthetic proteoforms during seed filling. Furthermore, enrichment of storage proteoforms and protease inhibitors was associated with cell expansion and seed maturation. Finally, combined proteoforms network analysis identified three significant modules, centered around malate dehydrogenase, HSP70, triose phosphate isomerase and vicilin. Novel clues suggest that ubiquitin‐proteasome pathway regulates nutrient reallocation. Second, increased abundance of NAPs/NAPPs related to oxidative and serine/threonine signalling indicate direct interface between redox sensing and signaling during seed development. Taken together, nutrient signals act as metabolic and differentiation determinant governing storage organ reprogramming.Item Quantitative extracellular matrix proteomics suggests cell wall reprogramming in host-specific immunity during vascular wilt caused by Fusarium oxysporum in chickpea(John Wiley & Sons, 2017) Elagamey, Eman; Narula, Kanika; Sinha, Arunima; Ghosh, Sudip; Abdellatef, Magdi A.E.; Chakraborty, Niranjan; Chakraborty, SubhraExtracellular matrix (ECM) is the unique organelle that perceives stress signals and reprograms molecular events of host cell during patho-stress. However, our understanding of how ECM dictates plant immunity is largely unknown. Vascular wilt caused by the soil borne filamentous fungus Fusarium oxysporum is a major impediment for global crop productivity. To elucidate the role of ECM proteins and molecular mechanism associated with cell wall mediated immunity, the temporal changes of ECM proteome was studied in vascular wilt resistant chickpea cultivar upon F. oxysporum infection. The 2-DE protein profiling coupled with mass spectrometric analysis identified 166 immune responsive proteins (IRPs) involved in variety of functions. Our data suggest that wall remodeling; protein translocation, stabilization and chitin triggered immunity; extracellular ATP signaling are major players in early, middle and later phases of ECM signaling during fungal attack. Furthermore, we interrogated the proteome data using network analysis that identified modules enriched in known and novel immunity-related prognostic proteins centered around nascent aminopolypeptide complex (NAC), amine oxidase, thioredoxin and chaperonin. This study for the first time provides an insight into the complex network operating in the ECM and impinges on the surveillance mechanism of innate immunity during patho-stress in crop plant.Item Chickpea transcription factor CaTLP1 interacts with protein kinases, modulates ROS accumulation and promotes ABA-mediated stomatal closure(Nature Publishing Group, 2016) Wardhan, Vijay; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, NiranjanTubby and Tubby-like proteins (TLPs), in mammals, play critical roles in neural development, while its function in plants is largely unknown. We previously demonstrated that the chickpea TLP, CaTLP1, participates in osmotic stress response and might be associated with ABA-dependent network. However, how CaTLP1 is connected to ABA signaling remains unclear. The CaTLP1 was found to be engaged in ABA-mediated gene expression and stomatal closure. Complementation of the yeast yap1 mutant with CaTLP1 revealed its role in ROS scavenging. Furthermore, complementation of Arabidopsis attlp2 mutant displayed enhanced stress tolerance, indicating the functional conservation of TLPs across the species. The presence of ABA-responsive element along with other motifs in the proximal promoter regions of TLPs firmly established their involvement in stress signalling pathways. The CaTLP1 promoter driven GUS expression was restricted to the vegetative organs, especially stem and rosette leaves. Global protein expression profiling of wild-type, attlp2 and complemented Arabidopsis plants revealed 95 differentially expressed proteins, presumably involved in maintaining physiological and biological processes under dehydration. Immunoprecipitation assay revealed that protein kinases are most likely to interact with CaTLP1. This study provides the first demonstration that the TLPs act as module for ABA-mediated stomatal closure possibly via interaction with protein kinase.Item RNA-seq analysis identifies key genes involved in chickpea (Cicer arietinum L.) shoot development(Botanical Society of Bengal, 2016) Biswas, S; Aggarwal, PR; Tayal, R; Sarkar, MP; Chakraborty, Niranjan; Chakraborty, SubhraUnderstanding the mechanism of plant development is particularly important for studying the regulatory genes and their specific functions. Here, we used paired end RNA sequencing to understand the complexity of legume shoot development in a non-model crop chickpea (Cicer arietinum L.). A total of 149.5 million paired end reads were obtained from two developmental stages of chickpea shoot. Differential gene expression analysis revealed the enrichment of transcripts associated with shoot development. Validation of few genes showed the reproducibility of our RNA-seq data. Collectively, the present study will not only help to generate a comprehensive organ specific transcriptome map but will also serve as a resource for gene discovery and future crop improvement program.Item CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors(BioMed Central Ltd, 2016) Gayali, Saurabh; Acharya, Shankar; Lande, Nilesh Vikram; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, NiranjanBackground: Transcription factor (TF) databases are major resource for systematic studies of TFs in specific species as well as related family members. Even though there are several publicly available multi-species databases, the information on the amount and diversity of TFs within individual species is fragmented, especially for newly sequenced genomes of non-model species of agricultural significance. Description: We constructed CicerTransDB (Cicer Transcription Factor Database), the first database of its kind, which would provide a centralized putatively complete list of TFs in a food legume, chickpea. CicerTransDB, available at www.cicertransdb.esy.es, is based on chickpea (Cicer arietinum L.) annotation v 1.0. The database is an outcome of genome-wide domain study and manual classification of TF families. This database not only provides information of the gene, but also gene ontology, domain and motif architecture. Conclusion: CicerTransDB v 1.0 comprises information of 1124 genes of chickpea and enables the user to not only search, browse and download sequences but also retrieve sequence features. CicerTransDB also provides several single click interfaces, transconnecting to various other databases to ease further analysis. Several webAPI(s) integrated in the database allow end-users direct access of data. A critical comparison of CicerTransDB with PlantTFDB (Plant Transcription Factor Database) revealed 68 novel TFs in the chickpea genome, hitherto unexplored. Database URL: http://www.cicertransdb.esy.esItem Characterization of the secretome of chickpea suspension culture reveals pathway abundance and the expected and unexpected secreted proteins(Am. Chemical Society, 2011) Gupta, Sonika; Wardhan, Vijay; Verma, Shikha; Gayali, Saurabh; Rajamani, Uma; Datta, Asis; Chakraborty, Subhra; Chakraborty, NiranjanThe secretome of an organism is defined as a set of secreted proteins that encompasses all proteins exported to the extracellular space. To better understand the chickpea secretome, we used callus culture to isolate and identify secreted proteins as a step toward determining their functions. Proteins in the extracellular media of the suspension culture were examined using SDS-PAGE and mass spectrometry (LC-MS/MS). Proteomic analysis led to the identification of 773 proteins, presumably involved in a variety of functions including metabolism, signal transduction, transport, and cell defense, in addition to maintaining redox status of extracellular space. Bioinformatic analysis confirmed 724 proteins, accounting for 94% of the identified proteins, as constituents of the secretome. Analysis of the secretome revealed the presence of several proteins of unknown function and a large number of classical and nonclassical secreted proteins. This represents the first comprehensive secretome of a legume genome, which is yet to be sequenced. Comparative analysis of the chickpea secretome with those of Medicago, Arabidopsis, and rice revealed that the majority of identified proteins are seemingly species-specific. This study demonstrates that characterization of the chickpea secretome in vitro can be used to identify secreted proteins, which has implications for systems biology research.Item Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress(The American Society for Biochemistry and Molecular Biology, Inc., 2007) Bhushan, Deepti; Pandey, Aarti; Choudhary, Mani Kant; Datta, Asis; Chakraborty, Subhra; Chakraborty, NiranjanWater deficit or dehydration is the most crucial environmental factor that limits crop productivity and influences geographical distribution of many crop plants. It is suggested that dehydration-responsive changes in expression of proteins may lead to cellular adaptation against water deficit conditions. Most of the earlier understanding of dehydration-responsive cellular adaptation has evolved from transcriptome analyses. By contrast, comparative analysis of dehydration-responsive proteins, particularly proteins in the subcellular fraction, is limiting. In plants, cell wall or extracellular matrix (ECM) serves as the repository for most of the components of the cell signaling process and acts as a frontline defense. Thus, we have initiated a proteomics approach to identify dehydration- responsive ECM proteins in a food legume, chickpea. Several commercial chickpea varieties were screened for the status of dehydration tolerance using different physiological and biochemical indexes. Dehydration-responsive temporal changes of ECM proteins in JG-62, a relatively tolerant variety, revealed 186 proteins with variance at a 95% significance level statistically. The comparative proteomics analysis led to the identification of 134 differentially expressed proteins that include predicted and novel dehydration-responsive proteins. This study, for the first time, demonstrates that over a hundred ECM proteins, presumably involved in a variety of cellular functions, viz. cell wall modification, signal transduction, metabolism, and cell defense and rescue, impinge on the molecular mechanism of dehydration tolerance in plants.