Publications of NIPGR Scientists
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Item Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response(American Chemical Society, 2013) Subba, Pratigya; Barua, Pragya; Kumar, Rajiv; Datta, Asis; Soni, Kamlesh Kumar; Chakraborty, Subhra; Chakraborty, NiranjanReversible protein phosphorylation is a ubiquitous regulatory mechanism that plays critical roles in transducing stress signals to bring about coordinated intracellular responses. To gain better understanding of dehydration response in plants, we have developed a differential phosphoproteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water, and the changes in the phosphorylation status of a large repertoire of proteins were monitored. The proteins were resolved by 2-DE and stained with phosphospecific fluorescent Pro-Q Diamond dye. Mass spectrometric analysis led to the identification of 91 putative phosphoproteins, presumably involved in a variety of functions including cell defense and rescue, photosynthesis and photorespiration, molecular chaperones, and ion transport, among others. Multiple sites of phosphorylation were predicted on several key elements, which include both the regulatory as well as the functional proteins. A critical survey of the phosphorylome revealed a DREPP (developmentally regulated plasma membrane protein) plasma membrane polypeptide family protein, henceforth designated CaDREPP1. The transcripts of CaDREPP1 were found to be differentially regulated under dehydration stress, further corroborating the proteomic results. This work provides new insights into the possible phosphorylation events triggered by the conditions of progressive water-deficit in plants.Item 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, SubhraSeed 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.Item Identification of extracellular matrix proteins of rice (Oryza sativa L.) involved in dehydration-responsive network : a proteomic approach(American Chemical Society, 2010) Pandey, Aarti; Rajamani, Uma; Verma, Jitendra; Subba, Pratigya; Chakraborty, Navjyoti; Datta, Asis; Chakraborty, Subhra; Chakraborty, NiranjanWater-deficit or dehydration impairs almost all physiological processes and greatly influences the geographical distribution of many crop species. It has been postulated that higher plants rely mostly on induction mechanisms to maintain cellular integrity during stress conditions. Plant cell wall or extracellular matrix (ECM) forms an important conduit for signal transduction between the apoplast and symplast and acts as front-line defense, thereby playing a key role in cell fate decision under various stress conditions. To better understand the molecular mechanism of dehydration response in plants, four-week-old rice seedlings were subjected to progressive dehydration by withdrawing water and the changes in the ECM proteome were examined using two-dimensional gel electrophoresis. Dehydration-responsive temporal changes revealed 192 proteins that change their intensities by more than 2.5-fold, at one or more time points during dehydration. The proteomic analysis led to the identification of about 100 differentially regulated proteins presumably involved in a variety of functions, including carbohydrate metabolism, cell defense and rescue, cell wall modification, cell signaling and molecular chaperones, among others. The differential rice proteome was compared with the dehydration-responsive proteome data of chickpea and maize. The results revealed an evolutionary divergence in the dehydration response as well as organ specificity, with few conserved proteins. The differential expression of the candidate proteins, in conjunction with previously reported results, may provide new insight into the underlying mechanisms of the dehydration response in plants. This may also facilitate the targeted alteration of metabolic routes in the cell wall for agricultural and industrial exploitation.Item Comparative proteomics of tuber induction, development and maturation reveal the complexity of tuberization process in potato (Solanum tuberosum L.)(American Chemical Society, 2008) Agrawal, Lalit; Chakraborty, Subhra; Jaiswal, Dinesh Kumar; Gupta, Sonika; Datta, Asis; Chakraborty, NiranjanTuberization in potato ( Solanum tuberosum L.) is a developmental process that serves a double function, as a storage organ and as a vegetative propagation system. It is a multistep, complex process and the underlying mechanisms governing these overlapping steps are not fully understood. To understand the molecular basis of tuberization in potato, a comparative proteomic approach has been applied to monitor differentially expressed proteins at different development stages using two-dimensional gel electrophoresis (2-DE). The differentially displayed proteomes revealed 219 protein spots that change their intensities more than 2.5-fold. The LC-ES-MS/MS analyses led to the identification of 97 differentially regulated proteins that include predicted and novel tuber-specific proteins. Nonhierarchical clustering revealed coexpression patterns of functionally similar proteins. The expression of reactive oxygen species catabolizing enzymes, viz., superoxide dismutase, ascorbate peroxidase and catalase, were induced by more than 2-fold indicating their possible role during the developmental transition from stolons into tubers. We demonstrate that nearly 100 proteins, some presumably associated with tuber cell differentiation, regulate diverse functions like protein biogenesis and storage, bioenergy and metabolism, and cell defense and rescue impinge on the complexity of tuber development in potato.Item The nuclear proteome of chickpea (Cicer arietinum L.) reveals predicted and unexpected proteins(American Chemical Society, 2006) Pandey, Aarti; Choudhary, Mani Kant; Bhushan, Deepti; Chattopadhyay, Arnab; Chakraborty, Subhra; Datta, Asis; Chakraborty, NiranjanNuclear proteins constitute a highly organized, complex network that plays diverse roles during cellular development and other physiological processes. The yeast nuclear proteome corresponds to about one-fourth of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. In an attempt to understand the complexity of plant nuclear proteins, we have developed a proteome reference map of a legume, chickpea, using two-dimensional gel electrophoresis (2-DE). Approximately, 600 protein spots were detected, and LC-ESI-MS/MS analyses led to the identification of 150 proteins that have been implicated in a variety of cellular functions. The largest percentage of the identified proteins was involved in signaling and gene regulation (36%), while 17% were involved in DNA replication and transcription. The chickpea nuclear proteome indicates the presence of few new nuclear proteins of unknown functions vis-a-vis many known resident proteins. To the best of our knowledge, this is the first report of a nuclear proteome of an unsequenced genome.Item Extracellular matrix proteome of chickpea (Cicer arietinum) illustrates pathway abundance, novel protein functions and evolutionary perspect(American Chemical Society, 2006) Bhushan, Deepti; Pandey, Aarti; Chattopadhyay, Arnab; Choudhary, Mani Kant; Chakraborty, Subhra; Datta, Asis; Chakraborty, NiranjanThe extracellular matrix (ECM) or cell wall is a dynamic system and serves as the first line mediator in cell signaling to perceive and transmit extra- and intercellular signals in many pathways. Although ECM is a conserved compartment ubiquitously present throughout evolution, a compositional variation does exist among different organisms. ECM proteins account for 10% of the ECM mass, however, comprise several hundreds of different molecules with diverse functions. To understand the function of ECM proteins, we have developed the cell wall proteome of a crop legume, chickpea (Cicer arietinum). This comprehensive overview of the proteome would provide a basis for future comparative proteomic efforts for this important crop. Proteomic analyses revealed new ECM proteins of unknown functions vis-a-vis the presence of many known cell wall proteins. In addition, we report here evidence for the presence of unexpected proteins with known biochemical activities, which have never been associated with ECM.