Browsing by Author "Datta, Asis"

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Abiotic stress tolerance in plants: Brassinosteroids navigate competently
(MDPI AG, 2022) Chaudhuri, Abira; Halder, Koushik; Abdin, Malik Z; Majee, Manoj; Datta, Asis
Brassinosteroid hormones (BRs) multitask to smoothly regulate a broad spectrum of vital physiological processes in plants, such as cell division, cell expansion, differentiation, seed germination, xylem differentiation, reproductive development and light responses (photomorphogenesis and skotomorphogenesis). Their importance is inferred when visible abnormalities arise in plant phenotypes due to suboptimal or supraoptimal hormone levels. This group of steroidal hormones are major growth regulators, having pleiotropic effects and conferring abiotic stress resistance to plants. Numerous abiotic stresses are the cause of significant loss in agricultural yield globally. However, plants are well equipped with efficient stress combat machinery. Scavenging reactive oxygen species (ROS) is a unique mechanism to combat the deleterious effects of abiotic stresses. In light of numerous reports in the past two decades, the complex BR signaling under different stress conditions (drought, salinity, extreme temperatures and heavy metals/metalloids) that drastically hinders the normal metabolism of plants is gradually being untangled and revealed. Thus, crop improvement has substantial potential by tailoring either the brassinosteroid signaling, biosynthesis pathway or perception. This review aims to explore and dissect the actual mission of BRs in signaling cascades and summarize their positive role with respect to abiotic stress tolerance.
Active site geometry of oxalate decarboxylase from Flammulina velutipes: Role of histidine coordinated manganese in substrate recognition
(Cold Spring Harbor Laboratory Press, 2002) Chakraborty, Subhra; Chakraborty, Niranjan; Jain, Deepti; Salunke, Dinakara M; Datta, Asis
Oxalate decarboxylase (OXDC) from the wood-rotting fungus Flammulina velutipes, which catalyzes the conversion of oxalate to formic acid and CO2 in a single-step reaction, is a duplicated double-domain germin family enzyme. It has agricultural as well as therapeutic importance. We reported earlier the purification and molecular cloning of OXDC. Knowledge-based modeling of the enzyme reveals a ␤-barrel core in each of the two domains organized in the hexameric state. A cluster of three histidines suitably juxtaposed to coordinate a divalent metal ion exists in both the domains. Involvement of the two histidine clusters in the catalytic mechanism of the enzyme, possibly through coordination of a metal cofactor, has been hypoth- esized because all histidine knockout mutants showed total loss of decarboxylase activity. The atomic absorption spectroscopy analysis showed that OXDC contains Mn2+ at up to 2.5 atoms per subunit. Docking of the oxalate in the active site indicates a similar electrostatic environment around the substrate-binding site in the two domains. We suggest that the histidine coordinated manganese is critical for substrate recognition and is directly involved in the catalysis of the enzyme.
Agricultural biotechnology for food sufficiency and benefit to human health
(Prentice Hall of India, 2015) Ghosh, Sumit; Datta, Asis
Analysis of the grasspea proteome and identification of stress-responsive proteins upon exposure to high salinity, low temperature, and abscisic acid treatment
(Elsevier, 2011) Chattopadhyay, Arnab; Subba, Pratigya; Pandey, Aarti; Bhushan, Deepti; Kumar, Rajiv; Datta, Asis; Chakraborty, Subhra; Chakraborty, Niranjan
Abiotic stress causes diverse biochemical and physiological changes in plants and limits crop productivity. Plants respond and adapt to such stress by altering their cellular metabolism and activating various defense machineries. To understand the molecular basis of stress tolerance in plants, we have developed differential proteomes in a hardy legume, grasspea (Lathyrus sativus L.). Five-week-old grasspea seedlings were subjected independently to high salinity, low temperature and abscisic acid treatment for duration of 36h. The physiological changes of stressed seedlings were monitored, and correlated with the temporal changes of proteome using two-dimensional gel electrophoresis. Approximately, 400 protein spots were detected in each of the stress proteome with one-fourth showing more than 2-fold differences in expression values. Eighty such proteins were subjected to LC-tandem MS/MS analyses that led to the identification of 48 stress-responsive proteins (SRPs) presumably involved in a variety of functions, including metabolism, signal transduction, protein biogenesis and degradation, and cell defense and rescue. While 33 proteins were responsive to all three treatments, 15 proteins were expressed in stress-specific manner. Further, we explored the possible role of ROS in triggering the stress-induced degradation of large subunit (LSU) of ribulose-1,5-bisphosphate carboxylase (Rubisco). These results might help in understanding the spectrum of stress-regulated proteins and the biological processes they control as well as having implications for strategies to improve stress adaptation in plants.
Application of RNA silencing in improving plant traits for industrial use
(CABI, 2017) Ghosh, Sumit; Irfan, Mohammad; Datta, Asis
The discovery of RNA silencing mechanisms has transformed research into gene function and has also allowed novel traits to be developed in plants, including some for industrial applications. To silence the expression of an undesirable gene, RNA silencing may be preferable over direct gene mutation as it leads to a dominant trait. This helps in straightforward screening of the desirable phenotypes. Moreover, RNA silencing is useful in tissue, organ and time-specific silencing of the genes that may play essential roles in plant life and, therefore, direct gene mutation may not be effective. This chapter summarizes the implication of RNA silencing in improving plant traits for industrial applications. Plants developed after RNA silencing of genes that act on cellular organization or metabolism are emerging as convenient and renewable raw materials for industries producing fuels, oils, pharmaceuticals, fibres, papers, seeds and processed foods. Several genetically modified plants, which may not have use in human consumption, have nevertheless been developed for specific industrial applications and await commercial-scale cultivation. Many more industrial crops are under different stages of development by industry and research organizations.
Attenuation of virulence and changes in morphology in Candida albicans by disruption of the N-acetylglucosamine catabolic pathway
(American Society for Microbiology, 2001) Singh, Praveen; Ghosh, Sharmistha; Datta, Asis
A Candida albicans mutant with mutations in the N-acetylglucosamine (GlcNAc) catabolic pathway gene cluster, including the GlcNAc-6-phosphate deacetylase (DAC1), glucosamine-6-phosphate deaminase (NAG1), and GlcNAc kinase (HXK1) genes, was not able to grow on amino sugars, exhibited highly attenuated virulence in a murine systemic candidiasis model, and was less adherent to human buccal epithelial cells in vitro. No germ tubes were formed by the mutant after induction with GlcNAc, but the mutant exhibited hyperfilamen- tation under stress-induced filamentation conditions. In addition, the GlcNAc catabolic pathway played a vital role in determining the colony phenotype. Our results imply that this pathway is very important because of its diverse links with pathways involved in virulence and morphogenesis of the organism.
Biotechnology for drug discovery and crop improvement
(Springer, 2017) Kamthan, Ayushi; Kamthan, Mohan; Datta, Asis
Genomics has emerged as the single most powerful discipline for detailed analysis of organization expression, and interaction of an organism at the genome level. Pathogens like Candida albicans, Vibrio cholerae etc. are responsible for causing morbidity and mortality in human beings. Besides, phytopathogens like Magnaporthe oryzae can lead to potential loss of yield in staple crop of rice. Genes of N-Acetyl-d-glucosamine metabolic pathway has been found to be universal in the diverse pathogens like C. albicans, V. cholerae and M. oryzae, playing an important role in their virulence. Lack of optimal treatment and emergence of multi-drug resistance necessitate the designing of better/new drugs against these pathogens. Research on these pathogens has increased the understanding of virulence and pathogenicity factors which can serve as potential drug targets that can be efficiently utilized to design a successful therapy to combat various diseases. Agricultural biotechnology has provided new tools for effectively ensuring food and nutritional security that can overcome many of the technical roadblocks that limit the application of conventional biological techniques in agricultural research. Limitations of water resources, decreased fertility of arable land skyrocketing cost of energy and galloping increases in the population make it imperative that food supplies of the 21st century will depend on a new form of agriculture in which custom-made food plants will dominate the world market. The ultimate goal is to create crops that are tailored to provide better nutrition for humans, improved fruit shelf life and enhanced tolerance to various stresses.
A calmodulin like EF hand protein positively regulates oxalate decarboxylase expression by interacting with E-box elements of the promoter
(Nature Publishing Group, 2015) Kamthan, Ayushi; Kamthan, Mohan; Kumar, Avinash; Sharma, Pratima; Ansari, Sekhu; Thakur, Sarjeet Singh; Chaudhuri, Abira; Datta, Asis
Oxalate decarboxylase (OXDC) enzyme has immense biotechnological applications due to its ability to decompose anti-nutrient oxalic acid. Flammulina velutipes, an edible wood rotting fungus responds to oxalic acid by induction of OXDC to maintain steady levels of pH and oxalate anions outside the fungal hyphae. Here, we report that upon oxalic acid induction, a calmodulin (CaM) like protein-FvCaMLP, interacts with the OXDC promoter to regulate its expression. Electrophoretic mobility shift assay showed that FvCamlp specifically binds to two non-canonical E-box elements (AACGTG) in the OXDC promoter. Moreover, substitutions of amino acids in the EF hand motifs resulted in loss of DNA binding ability of FvCamlp. F. velutipes mycelia treated with synthetic siRNAs designed against FvCaMLP showed significant reduction in FvCaMLP as well as OXDC transcript pointing towards positive nature of the regulation. FvCaMLP is different from other known EF hand proteins. It shows sequence similarity to both CaMs and myosin regulatory light chain (Cdc4), but has properties typical of a calmodulin, like binding of 45Ca2+, heat stability and Ca2+ dependent electrophoretic shift. Hence, FvCaMLP can be considered a new addition to the category of unconventional Ca2+ binding transcriptional regulators.
Candidiasis: A yeast infection caused by Candia albicans
(The National Academy of Sciences, India & Capital Publishing Co., New Delhi, 2016) Kamthan, M; Datta, Asis
Candidiasis, or candidosis, is the fourth leading cause of nosocomial blood infection (BSI) with an estimated annual cost of US$2 billion and mortality that exceeds 40%. The causative agent of this disease is Candida which is a common human fungal pathogen. More than 95% of Candida-associated BSIs are caused by five major species: C. albicans, C. glabrata, C. Parapsilasis, C. tropicalis and C. krusei, C. albicans is the most common causative species of candidaemia.
Characterization of a putative spindle assembly checkpoint kinase Mps1, suggests its involvement in cell division, morphogenesis and oxidative stress tolerance in Candida albicans
(PLOS, 2014) Kamthan, Mohan; Nalla, Vijaya Kumar; Ruhela, Deepa; Kamthan, Ayushi; Maiti, Protiti; Datta, Asis
In Saccharomyces cerevisiae MPS1 is one of the major protein kinase that governs the spindle checkpoint pathway. The S. cerevisiae structural homolog of opportunistic pathogen Candida albicans CaMPS1, is indispensable for the cell viability. The essentiality of Mps1 was confirmed by Homozygote Trisome test. To determine its biological function in this pathogen conditional mutant was generated through regulatable MET3 promoter. Examination of heterozygous and conditional (+Met/Cys) mps1 mutants revealed a mitosis specific arrest phenotype, where mutants showed large buds with undivided nuclei. Flowcytometry analysis revealed abnormal ploidy levels in mps1 mutant. In presence of anti-microtubule drug Nocodazole, mps1 mutant showed a dramatic loss of viability suggesting a role of Mps1 in Spindle Assembly Checkpoint (SAC) activation. These mutants were also defective in microtubule organization. Moreover, heterozygous mutant showed defective in-vitro yeast to hyphae morphological transition. Growth defect in heterozygous mutant suggest haploinsufficiency of this gene. qRT PCR analysis showed around 3 fold upregulation of MPS1 in presence of serum. This expression of MPS1 is dependent on Efg1 and is independent of other hyphal regulators like Ras1 and Tpk2. Furthermore, mps1 mutants were also sensitive to oxidative stress. Heterozygous mps1 mutant did not undergo morphological transition and showed 5-Fold reduction in colony forming units in response to macrophage. Thus, the vital checkpoint kinase, Mps1 besides cell division also has a role in morphogenesis and oxidative stress tolerance, in this pathogenic fungus.
Characterization of the nuclear proteome of a dehydration-sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar
(John Wiley & Sons Ltd, 2013) Subba, Pratigya; Kumar, Rajiv; Gayali, Saurabh; Shekhar, Shubhendu; Parveen, Shaista; Pandey, Aarti; Datta, Asis; Chakraborty, Subhra; Chakraborty, Niranjan
Water deficit or dehydration hampers plant growth and development, and shrinks harvest size of major crop species worldwide. Therefore, a better understanding of dehydration response is the key to decipher the regulatory mechanism of better adaptation. In recent years, nuclear proteomics has become an attractive area of research, particularly to study the role of nucleus in stress response. In this study, a proteome of dehydration-sensitive chickpea cultivar (ICCV-2) was generated from nuclei-enriched fractions. The LC-MS/MS analysis led to the identification of 75 differentially expressed proteins presumably associated with different metabolic and regulatory pathways. Nuclear localisation of three candidate proteins was validated by transient expression assay. The ICCV-2 proteome was then compared with that of JG-62, a tolerant cultivar. The differential proteomics and in silico analysis revealed cultivar-specific differential expression of many proteins involved in various cellular functions. The differential tolerance could be attributed to altered expression of many structural proteins and the proteins involved in stress adaptation, notably the ROS catabolising enzymes. Further, a comprehensive comparison on the abiotic stress-responsive nuclear proteome was performed using the datasets published thus far. These findings might expedite the functional determination of the dehydration-responsive proteins and their prioritisation as potential molecular targets for better adaptation.
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.
Chromatin-based transcriptional reprogramming in plants under abiotic stresses
(MDPI AG, 2022) Halder, Koushik; Chaudhuri, Abira; Abdin, Malik Z.; Majee, Manoj; Datta, Asis
Plants’ stress response machinery is characterized by an intricate network of signaling cascades that receive and transmit environmental cues and ultimately trigger transcriptional reprogramming. The family of epigenetic regulators that are the key players in the stress-induced signaling cascade comprise of chromatin remodelers, histone modifiers, DNA modifiers and regulatory noncoding RNAs. Changes in the histone modification and DNA methylation lead to major alterations in the expression level and pattern of stress-responsive genes to adjust with abiotic stress conditions namely heat, cold, drought and salinity. The spotlight of this review falls primarily on the chromatin restructuring under severe abiotic stresses, crosstalk between epigenetic regulators along with a brief discussion on stress priming in plants.
Classification of CRISPR/Cas system and its application in tomato breeding
(Springer Nature Publishing AG, 2022) Chaudhuri, Abira; Halder, Koushik; Datta, Asis
Remarkable diversity in the domain of genome loci architecture, structure of effector complex, array of protein composition, mechanisms of adaptation along with difference in pre-crRNA processing and interference have led to a vast scope of detailed classification in bacterial and archaeal CRISPR/Cas systems, their intrinsic weapon of adaptive immunity. Two classes: Class 1 and Class 2, several types and subtypes have been identified so far. While the evolution of the effector complexes of Class 2 is assigned solely to mobile genetic elements, the origin of Class 1 effector molecules is still in a haze. Majority of the types target DNA except type VI, which have been found to target RNA exclusively. Cas9, the single effector protein, has been the primary focus of CRISPR-mediated genome editing revolution and is an integral part of Class 2 (type II) system. The present review focuses on the different CRISPR types in depth and the application of CRISPR/Cas9 for epigenome modification, targeted base editing and improving traits such as abiotic and biotic stress tolerance, yield and nutritional aspects of tomato breeding.
Cloning and characterization of 5'-flanking region of oxalate decarboxylase gene from Flammulina velutipes
(Biochemical Society, 2002) Azam, Mohammad; Kesarwani, Meenu; Chakraborty, Subhra; Natarajan, Krishnamurthy; Datta, Asis
The oxalate-degrading enzyme, oxalate decarboxylase (OXDC), was purified and characterized from Flammulina elutipes, a basidiomycetous fungus [Mehta and Datta (1991) J. Biol. Chem. 266, 23548–23553]. The cDNA cloning and analyses revealed that OXDC transcription was induced by oxalic acid. However, in this report, we show that OXDC transcription is induced by low pH, not by oxalate. To understand the regulatory mechanism of OXDC expression, we have cloned and analysed a 580-bp genomic fragment from the 5h-flanking region of the OXDC gene. Sequence analysis showed the presence of several eukaryotic transcription factor binding motifs within the k580 bp of the upstream region. Electrophoretic-mobility-shift assays with partially purified cell extracts revealed specific binding of a factor in acid-induced, but not in uninduced, extracts. Furthermore, DNase I protection assays using the partially purified fraction from oxalic acid-induced extract revealed a footprint of a 13-bp sequence 5hGCGGGGTCGCCGA3h, termed low pH responsive element (LPRE), corresponding to the k287 to k275 bp region of the OXDC promoter. Our results suggest that in F. elutipes cells, activation of OXDC transcription in response to low pH is mediated by the binding of a novel transcription factor through the LPRE site in the OXDC promoter.
Cloning, expression, purification and crystallization of a novel GlcNAc metabolic protein, gig2 (duf1479) from pathogenic fungus Candida albicans
(Proteomics Society, India (PSI), 2017) Rani, Priya; Gautam, Gunjan; Rao, Kongara Hanumantha; Ghosh, Swagata; Gourinath, Samudrala; Dhar, Suman Kumar; Datta, Asis
N-acetylglucosamine (GlcNAc), an alternative sugar, is emerging as an important molecule having a multifarious role in Candida albicans including a major role in signaling. GlcNAc Inducible Gene 2, GIG2 is one of the highly upregulated genes in GlcNAc grown cells in C. albicans. Our earlier studies show the involvement of Gig2 in the formation of N-acetylneuraminic (NANA) acid from GlcNAc-6-phosphate through an understudied route. The crystal structure of Gig2 would help us in determining the exact reaction that this enzyme catalyzes. Here the cloning, expression, purification and crystallization of this protein are reported along with preliminary X-ray crystallographic analysis at 2.4Å resolution. The crystal belonged to P2 1 space group, with unit cell parameters a=59.59, b= 54.43, c= 73.29Å; α = 90°, β = 102.7° and γ = 90°. The structure was solved using PDB ID 2CSG as a template which has only 27% identity. Molecular replacement yielded a solution with LLG score of 87. The structure is currently under further refinement.
Comparative analyses of extracellular matrix proteome: an under-explored area in plant research
(intechopen.com, 2012) Narula, Kanika; Elagamey, Eman; Datta, Asis; Chakraborty, Niranjan; Chakraborty, Subhra
Within their social milieu, cells are petite and deformable, enclosed in a flimsy plasma membrane which swerves from their default spherical shape to more polar shapes due to the local deposition, complex interactions and the remodelling of the extracellular matrix (ECM). Consequently, multicellularity has evolved, albeit independently in plants and animals. Although animals are truly multicellular, plants are supracellular organisms because their immobile cells divide via phragmoplast-based incomplete cytokinesis, which results in the formation of cytoplasmic cell-to-cell channels known as plasmodesmata (Baluska et al., 2003). The ECM in plants, often referred as the cell wall, is integrated into the apoplast—a structurally coherent superstructure extending throughout the plant body. In lieu, plant cells are not fully separated and both the plasma membrane and endoplasmic reticulum traverse cellular borders through plasmodesmata (Baluska et al., 2003; Fincher, G. 2009.). The ECM is a fundamental component of the microenvironment of both animal and plant cells that has been substantially expanded during evolution. Throughout the plant kingdom, the formation and regulation of the ECM architecture has been shown to have the potential to influence many conduits of development, position-dependent differentiation, patterning and totipotent cell niches, besides environmental stress response and pathobiology (Brownlee & Berger, 1995; Degenhardt & Gimmer, 2000; Wilson, 2010). Furthermore, it has been reported that the ECM plays an important morphoregulatory role during somatic embryogenesis and organogenesis in plants, besides its pivotal role in cellular osmo- and volume-regulation (Šamaj et al., 1999; Rose et al., 2004). The plant ECM has biomechanical and morphogenetic functions with the immense ability to turn cells into hydraulic machines which establish a crucial functional difference between cell walls and other cellular surface structures. It encloses the cell hermetically and constrains the hydrostatic pressure evoked by osmotic gradients between the cell and its environment which controls cellular osmo- and volume-regulation (Peters et al., 2000; Cosgrove, D. J. 2005). Plasticity in the ECM allows the cellular uptake of massive amounts of water into a central vacuole while rigidity in the ECM determines the conductance of enormous amounts of water and dissolved solutes through vascular bundles. The secretion of an ECM by one cell can also influence the neighbouring cells, conceivably the best exemplified paracrine interaction known in the plant kingdom (for a review, see Brownlee, 2002). Beyond their paramount importance in the generation of form, cell walls are frequently considered ‘growth-controlling’ (Wolf et al., 2009). Cells devoid of the ECM inevitably lose their polar shape and the loss of cellular polarisation prevents cell-to-cell interactions and communication. The ECM/cell wall is evolutionary and inherently bestowed with information that can be both stored and relayed to cell interior via templating processes. It serves as the first line mediator in cell signalling for perceiving and transmitting extra- and intercellular signals in many cellular pathways. Communication between the cytoplasm and the cell wall is necessary and evident because of events such as cell expansion (Cosgrove, 1997, Schröder, F et al 2009), mechanical stress (Kumar et al., 2006; Telewski, 2006), environmental perturbation (Gail McLean et al., 1997; Thelen, J. and Peck, S. 2007) and pathogen infection (Hammond- Kosack & Jones, 1996) which lead to altered biosynthesis and the modification of wall components and downstream cytoplasmic events. In addition, it can act as a substrate for migration and has also been recognised as a surrogate for providing inputs into cell behaviour (Hall et al., 2002), although the available data is rather scarce for higher plants and critical linker molecules between the cytoskeleton and the ECM are still missing. Thus, the ECM/cell wall primarily serves a dual function, as a cell support system and for signalling during development and stress. The ECM/cell wall must therefore be dynamic as cells divide and elongate, modulating its composition and architecture during its synthesis and after it has been deposited. The wall function is a multi-step, complex process and the underlying mechanisms governing these steps are not fully understood.
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, Subhra
Background: 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.
Comparative analyses of nuclear proteome: extending its function
(Frontiers, 2013) Narula, Kanika; Datta, Asis; Chakraborty, Niranjan; Chakraborty, Subhra
Organeller proteomics is an emerging technology that is critical in determining the cellular signal transduction pathways. Nucleus, the regulatory hub of the eukaryotic cell is a dynamic system and a repository of various macromolecules that serve as modulators of such signaling that dictate cell fate decisions. Nuclear proteins (NPs) are predicted to comprise about 10-20% of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. Indeed, NPs constitute a highly organized but complex network that plays diverse roles during development and physiological processes. In plants, relatively little is known about the nature of the molecular components and mechanisms involved in coordinating NP synthesis, their action and function. Proteomic study hold promise to understand the molecular basis of nuclear function using an unbiased comparative and differential approach. We identified a few hundred proteins that include classical and non-canonical nuclear components presumably associated with variety of cellular functions impinging on the complexity of nuclear proteome. Here, we review the nuclear proteome based on our own findings, available literature, and databases focusing on detailed comparative analysis of NPs and their functions in order to understand how plant nucleus works. The review also shed light on the current status of plant nuclear proteome and discusses the future prospect.
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, Niranjan
Water 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.