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Item Dehydration-reponsive nuclear proteome of rice (Oryza sativa L.) illustrates protein network, novel regulators of cellular adaptation and evolutionary perspect(The American Society for Biochemistry and Molecular Biology, Inc., 2009) Choudhary, Mani Kant; Basu, Debarati; Datta, Asis; Chakraborty, Niranjan; Chakraborty, SubhraWater deficit or dehydration is the most crucial environmental constraint on plant growth and development and crop productivity. It has been postulated that plants respond and adapt to dehydration by altering their cellular metabolism and by activating various defense machineries. The nucleus, the regulatory hub of the eukaryotic cell, is a dynamic system and a repository of various macromolecules that serve as modulators of cell signaling dictating the cell fate decision. To better understand the molecular mechanisms of dehydration-responsive adaptation in plants, we developed a comprehensive nuclear proteome of rice. The proteome was determined using a sequential method of organellar enrichment followed by two-dimensional electrophoresis-based protein identification by LC-ESI-MS/MS. We initially screened several commercial rice varieties and parental lines and established their relative dehydration tolerance. The differential display of nuclear proteins in the tolerant variety under study revealed 150 spots that showed changes in their intensities by more than 2.5-fold. The proteomics analysis led to the identification of 109 differentially regulated proteins presumably involved in a variety of functions, including transcriptional regulation and chromatin remodeling, signaling and gene regulation, cell defense and rescue, and protein degradation. The dehydration-responsive nuclear proteome revealed a coordinated response involving both regulatory and functional proteins, impinging upon the molecular mechanism of dehydration adaptation. Furthermore a comparison between the dehydration-responsive nuclear proteome of rice and that of a legume, the chickpea, showed an evolutionary divergence in dehydration response comprising a few conserved proteins, whereas most of the proteins may be involved in crop-specific adaptation. These results might help in understanding the spectrum of nuclear proteins and the biological processes they control under dehydration as well as having implications for strategies to improve dehydration tolerance in plants.Item Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity(BioMed Central, 2009) Ashraf, Nasheeman; Ghai, Deepali; Barman, Pranjan; Basu, Swaraj; Gangisetty, Nagaraju; Mandal, Mihir K; Chakraborty, Niranjan; Datta, Asis; Chakraborty, SubhraBackground: The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. Present study focuses on Fusarium wilt responsive gene expression in chickpea. Results: We report 6272 gene sequences of immune-response pathway that would provide genotype- dependent spatial information on the presence and relative abundance of each gene. The sequence assembly led to the identification of a CaUnigene set of 2013 transcripts comprising of 973 contigs and 1040 singletons, two-third of which represent new chickpea genes hitherto undiscovered. We identified 209 gene families and 262 genotype-specific SNPs. Further, several novel transcription regulators were identified indicating their possible role in immune response. The transcriptomic analysis revealed 649 non- cannonical genes besides many unexpected candidates with known biochemical functions, which have never been associated with pathostress-responsive transcriptome. Conclusion: Our study establishes a comprehensive catalogue of the immune-responsive root transcriptome with insight into their identity and function. The development, detailed analysis of CaEST datasets and global gene expression by microarray provide new insight into the commonality and diversity of organ-specific immune-responsive transcript signatures and their regulated expression shaping the species specificity at genotype level. This is the first report on differential transcriptome of an unsequenced genome during vascular wilt.Item Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.)(The American Society for Biochemistry and Molecular Biology, Inc., 2008) Pandey, Aarti; Chakraborty, Subhra; Datta, Asis; Chakraborty, NiranjanDehydration or water-deficit is one of the most important environmental stress factors that greatly influences plant growth and development and limits crop productivity. Plants respond and adapt to such stress by altering their cellular metabolism and activating various defense machineries. Mechanisms that operate signal perception, transduction, and downstream regulatory events provide valuable information about the underlying pathways involved in environmental stress responses. The nuclear proteins constitute a highly organized, complex network that plays diverse roles during cellular development and other physiological processes. To gain a better understanding of dehydration response in plants, we have developed a comparative nuclear proteome 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 nuclear proteome were examined using two-dimensional gel electrophoresis. Approximately 205 protein spots were found to be differentially regulated under dehydration. Mass spectrometry analysis allowed the identification of 147 differentially expressed proteins, presumably involved in a variety of functions including gene transcription and replication, molecular chaperones, cell signaling, and chromatin remodeling. The dehydration responsive nuclear proteome of chickpea revealed a coordinated response, which involves both the regulatory as well as the functional proteins. This study, for the first time, provides an insight into the complex metabolic network operating in the nucleus during dehydration.Item Nucleus(Wiley-Blackwell, 2008) Chakraborty, Subhra; Pandey, Aarti; Datta, Asis; Chakraborty, NiranjanThe nucleus is common to all eukaryotic cells and houses nearly all the genetic information for the expression of cellular proteins. It contains the components and enzymes necessary to maintain, transcribe, and replicate genetic material in a selective manner. Furthermore, it is responsible for the synthesis and/or assembly of components used to translate genetic material, although translation of the code contained in mRNA is performed in the cytoplasm. The nucleus consists of a complex envelope—an outer and inner membrane that surrounds a relatively amorphous internal structure and an internal structure consisting of chromatin, nuclear matrix, nuclear lamina, nucleolus, and aqueous nucleoplasm.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 Environmental sensing and signal transduction pathways regulating morphopathogenic detrminants of Candida albicans(American Society for Microbiology, 2007) Biswas, Subhrajit; Van Dijck, Patrick; Datta, AsisOpportunistic fungal pathogens, such as Candida albicans, are found in the normal gastrointestinal flora and the oral mucosa of most healthy humans. However, in immunocompromised patients, bloodstream infections often cause death, despite the use of antifungal therapies (152). The underlying molecular mechanisms for survival inside the human body and adaptation to various environments are probably distinct but overlapping. Dietary factors, such as an excess of or deficiency in certain nutrients, may alter the endogenous microbial flora. Mechanical factors, such as trauma or occlusive injury, can also alter the microenvironment, deplete the system of “friendly bacteria,” and enable the pathogenic fungus to take over. Immunocompromised or immunosuppressed persons, including AIDS patients, neonates, and transplant recipients, are also particularly susceptible to fungal infections.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.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.Item Plant pre-mRNA splicing in fission yeast, Schizosaccharomyces pombe(Academic Press, 2002) Sarmah, Bhaskarjyoti; Chakraborty, Niranjan; Chakraborty, Subhra; Datta, AsisPre-mRNA splicing or the removal of introns from precursor messenger RNAs depends on the accurate recognition of intron sequences by the splicing machinery. We have analyzed various aspects of intron sequence and structure in relation to splice site selection and splicing efficiency of a plant gene AmA1 in Schizosaccharomyces pombe. Earlier, we reported the cloning of AmA1, a seed albumin gene from Amaranthus hypochondriacus [A. Raina, A. Datta, Proc. Natl. Acad. Sci. USA 89 (1992) 11774]. In the absence of an in vitro splicing system for plants, the expression of AmA1 genomic clone in S. pombe has been used to analyze splicing of intron constructs. We aim to focus on S. pombe as a possible alternative and examined its effectiveness as a host for plant gene splicing. The results show here that pre-mRNA transcripts of AmA1 gene underwent splicing in S. pombe. Ó 2002 Elsevier Science (USA). All rights reserved.