Browsing by Author "Sengupta, Shantanu"

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Dehydration-induced alterations in chloroplast proteome and reprogramming of cellular metabolism in developing chickpea delineate interrelated adaptive responses
(Elsevier B.V., 2020) Lande, Nilesh Vikam; Barua, Pragya; Gayen, Dipak; Kumar, Sunil; Varshney, Swati; Sengupta, Shantanu; Chakraborty, Subhra; Chakraborty, Niranjan
Chloroplast, the energy organelle unique to photosynthetic eukaryotes, executes several crucial functions including photosynthesis. While chloroplast development and function are controlled by the nucleus, environmental stress modulated alterations perceived by the chloroplasts are communicated to the nucleus via retrograde signaling. Notably, coordination of chloroplast and nuclear gene expression is synchronized by anterograde and retrograde signaling. The chloroplast proteome holds significance for stress responses and adaptation. We unraveled dehydration-induced alterations in the chloroplast proteome of a grain legume, chickpea and identified an array of dehydration-responsive proteins (DRPs) primarily involved in photosynthesis, carbohydrate metabolism and stress response. Notably, 12 DRPs were encoded by chloroplast genome, while the rest were nuclear-encoded. We observed a coordinated expression of different multi-subunit protein complexes viz., RuBisCo, photosystem II and cytochrome b6f, encoded by both chloroplast and nuclear genome. Comparison with previously reported stress-responsive chloroplast proteomes showed unique and overlapping components. Transcript abundance of several previously reported markers of retrograde signaling revealed relay of dehydration-elicited signaling events between chloroplasts and nucleus. Additionally, dehydration-triggered metabolic adjustments demonstrated alterations in carbohydrate and amino acid metabolism. This study offers a panoramic catalogue of dehydration-responsive signatures of chloroplast proteome and associated retrograde signaling events, and cellular metabolic reprograming.
Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes
(Elsevier B.V, 2019) Gayen, Dipak; Gayali, Saurabh; Barua, Pragya; Lande, Nilesh Vikram; Varshney, Swati; Sengupta, Shantanu; Chakraborty, Subhra; Chakraborty, Niranjan
Mitochondria play crucial roles in regulating multiple biological processes particularly electron transfer and energy metabolism in eukaryotic cells. Exposure to water-deficit or dehydration may affect mitochondrial function, and dehydration response may dictate cell fate decisions. iTRAQ-based quantitative proteome of a winter legume, chickpea, demonstrated the central metabolic alterations in mitochondria, presumably involved in dehydration adaptation. Three-week-old chickpea seedlings were subjected to progressive dehydration and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical characteristics and mitochondrial architecture. The proteomics analysis led to the identification of 40 dehydration-responsive proteins whose expressions were significantly modulated by dehydration. The differentially expressed proteins were implicated in different metabolic processes, with obvious functional tendencies toward purine-thiamine metabolic network, pathways of carbon fixation and oxidative phosphorylation. The linearity of dehydration-induced proteome alteration was examined with transcript abundance of randomly selected candidates under multivariate stress conditions. The differentially regulated proteins were validated through sequence analysis. An extensive sequence based localization prediction revealed >62.5% proteins to be mitochondrial resident by, at least, one prediction algorithm. The results altogether provide intriguing insights into the dehydration-responsive metabolic pathways and useful clues to identify crucial proteins linked to stress tolerance. BIOLOGICAL SIGNIFICANCE: Investigation on plant mitochondrial proteome is of significance because it would allow a better understanding of mitochondrial function in plant adaptation to stress. Mitochondria are the unique organelles, which play a crucial role in energy metabolism and cellular homeostasis, particularly when exposed to stress conditions. Chickpea is one of the cultivated winter legumes, which enriches soil nitrogen and has very low water footprint and thus contributes to fortification of sustainable agriculture. We therefore examined the dehydration-responsive mitochondrial proteome landscape of chickpea and queried whether molecular interplay of mitochondrial proteins modulate dehydration tolerance. A total of 40 dehydration-induced mitochondrial proteins were identified, predicted to be involved in key metabolic processes. Our future efforts would focus on understanding both posttranslational modification and processing for comprehensive characterization of mitochondrial protein function. This approach will facilitate mining of more biomarkers linked to the tolerance trait and contribute to crop adaptation to climate change.
Dehydration-responsive alterations in the chloroplast proteome and cell metabolomic profile of rice reveals key stress adaptation responses
(Elsevier B.V., 2019) Gayen, Dipak; Barua, Pragya; Lande, Nilesh Vikram; Varshney, Swati; Sengupta, Shantanu; Chakraborty, Subhra; Chakraborty, Niranjan
Chloroplast is a semi-autonomous organelle in plants and other photosynthetic eukaryotes, playing a fundamental role of regulating photosynthesis. It is also responsible for sustaining essential biosynthetic reactions including synthesis of amino acids, fatty acids and terpenes. Photosynthesis, the conversion of light energy into chemical energy, serves as the sensor of environmental changes and augments different cellular functions to initiate adaptive responses. However, the molecular processes and regulatory mechanisms of dehydration tolerance adopted by chloroplast remain largely unknown. To gain a better understanding of dehydration response, a chloroplast proteome map of rice was developed. Four-week-old rice seedlings were subjected to dehydration by withholding water for 9 d, and the magnitude of dehydration-induced damage to the chloroplast was monitored. The iTRAQ-based quantitative proteome analysis led to the identification of 40 differentially regulated proteins (DRPs). The DRPs were presumably involved in a wide array of metabolic processes including chloroplast energy metabolism, photosynthesis and defense response. Furthermore, dehydration-induced changes in the metabolite profile and network analysis revealed a high abundance of branched chain amino acids and sugar that might reduce osmotic potential, thereby protecting cellular integrity. The proteomics approach revealed altered status of major photosynthesis related proteins, while cell metabolite profile demonstrated alteration of tricarboxylic acid cycle intermediates, indicating dehydration-triggered alterations in ATP production and energy metabolism. Altogether, these results demonstrated that the global regulation of chloroplast proteome is intimately linked to cellular metabolic rewiring of adaptive responses, which may favor genetic manipulation of crop species for better adaptation.