Browsing by Author "Gupta, Sonika"

Now showing 1 - 4 of 4

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, Niranjan
The 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.
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, Niranjan
Tuberization 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.
Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicer arietinum L.), promotes stress tolerance
(Springer, 2012) Wardhan, Vijay; Jahan, Kishwer; Gupta, Sonika; Chennareddy, Srinivasarao; Datta, Asis; Chakraborty, Subhra; Chakraborty, Niranjan
Dehydration is the most crucial environmental constraint on plant growth and development, and agricultural productivity. To understand the underlying mechanism of stress tolerance, and to identify proteins for improving such important trait, we screened the dehydration-responsive proteome of chickpea and identified a tubby-like protein, referred to as CaTLP1. The CaTLP1 was found to predominantly bind to double-stranded DNA but incapable of transcriptional activation. We investigated the gene structure and organization and demonstrated, for the first time, that CaTLP1 may be involved in osmotic stress response in plants. The transcripts are strongly expressed in vegetative tissues but weakly in reproductive tissues. CaTLP1 is upregulated by dehydration and high salinity, and by treatment with abscisic acid (ABA), suggesting that its stress-responsive function might be associated with ABA-dependent network. Overexpression of CaTLP1 in transgenic tobacco plants conferred dehydration, salinity and oxidative stress tolerance along with improved shoot and root architecture. Molecular genetic analysis showed differential expression of CaTLP1 under normal and stress condition, and its preferential expression in the nucleus might be associated with enhanced stress tolerance. Our work suggests important roles of CaTLP1 in stress response as well as in the regulation of plant development.
Secretome analysis of chickpea reveals dynamic extracellular remodeling and identifies a Bet v1- like protein, CaRRP1 that participates in stress response
(Nature Publishing Group, 2015) Gupta, Sonika; Wardhan, Vijay; Kumar, Amit; Rathi, Divya; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, Niranjan
Secreted proteins maintain cell structure and biogenesis besides acting in signaling events crucial for cellular homeostasis during stress adaptation. To understand the underlying mechanism of stress-responsive secretion, the dehydration-responsive secretome was developed from suspension-cultured cells of chickpea. Cell viability of the suspension culture remained unaltered until 96 h, which gradually declined at later stages of dehydration. Proteomic analysis led to the identification of 215 differentially regulated proteins, involved in a variety of cellular functions that include metabolism, cell defence, and signal transduction suggesting their concerted role in stress adaptation. One-third of the secreted proteins were devoid of N-terminal secretion signals suggesting a non-classical secretory route. Screening of the secretome identified a leaderless Bet v 1-like protein, designated CaRRP1, the export of which was inhibited by brefeldin A. We investigated the gene structure and genomic organization and demonstrated that CaRRP1 may be involved in stress response. Its expression was positively associated with abiotic and biotic stresses. CaRRP1 could complement the aberrant growth phenotype of yeast mutant, deficient in vesicular transport, indicating a partial overlap of protein secretion and stress response. Our study provides the most comprehensive analysis of dehydration-responsive secretome and the complex metabolic network operating in plant extracellular space.