Browsing by Author "Chakraborty, Subhra"

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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.
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.
Birth of plant proteomics in India: A new horizon
(Elsevier B.V., 2015) Narula, Kanika; Pandey, Aarti; Gayali, Saurabh; Chakraborty, Niranjan; Chakraborty, Subhra
In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. BIOLOGICAL SIGNIFICANCE: The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India.
Carboxylate clamp tetratricopeptide repeat (TPR) domain containing Hsp90 cochaperones in Triticeace: an insight into structural and functional diversification
(Elsevier B.V., 2018) Mishra, Divya; Shekhar, Shubhendu; Chakraborty, Subhra; Chakraborty, Niranjan
The molecular chaperones serve as surveillance molecules that mediates regulatory crosstalk between protein folding and degradation pathways under natural and stress conditions. In present study, we focused on the diversification and role of tetratricopeptide repeat (TPR) domain containing Hsp90 cochaperones. These cochaperone were recognized by the presence of three motifs of TPR with the basic conserved residues often referred to as carboxylate clamp (CC). A total of 213 putative CC-TPRs were found in Triticeace, clustered into 16 groups, amongst which few CC-TPR families such as TPR-RPAP3 and TPR-SMYD were documented. Domain architecture and genomic organization revealed that CC-TPRs are very diverse in nature. Evolutionary analyses showed that CC-TPRs are conserved, stable and ubiquitous in nature. Analysis of available RNA-seq data revealed a high degree of tissue-specific expression of 1-TPR and TaTPR-FKBP family members at various developmental stages. The transcripts of TaCC-TPRs displayed differential expression in two contrasting wheat cultivars under abiotic stress conditions. Complementation and heterologous expression of TaTPR-FKBP5 in yeast conferred abiotic stress tolerance. Together, these results provide a glimpse into the genetic diversity and evolution of CC-TPRs in Triticeace, which would help to better understand of how TPR-domain cochaperones function in plants.
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.
Chickpea ferritin CaFer1 participates in oxidative stress response, and promotes growth and development
(Nature Publishing Group, 2016) Parveen, Shaista; Gupta, Deepti Bhushan; Dass, Suchismita; Kumar, Amit; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, Niranjan
Ferritins store and sequester iron, and regulate iron homeostasis. The cDNA for a stress-responsive phytoferritin, previously identified in the extracellular matrix (ECM) of chickpea (Cicer arietinum), was cloned and designated CaFer1. The CaFer1 transcript was strongly induced in chickpea exposed to dehydration, hypersalinity and ABA treatment. Additionally, it has role in the defense against Fusarium oxysporum infection. Functional complementation of the yeast frataxin-deficient mutant, Δyfh1, indicates that CaFer1 functions in oxidative stress. The presence of CaFer1 in the extracellular space besides chloroplast establishes its inimitable nature from that of other phytoferritins. Furthermore, CaFer1 expression in response to iron suggests its differential mechanism of accumulation at two different iron conditions. CaFer1-overexpressing transgenic plants conferred improved growth and development, accompanied by altered expression of iron-responsive genes. Together, these results suggest that the phytoferritin, CaFer1, might play a key role in maintenance of iron buffering and adaptation to environmental challenges.
Chickpea transcription factor CaTLP1 interacts with protein kinases, modulates ROS accumulation and promotes ABA-mediated stomatal closure
(Nature Publishing Group, 2016) Wardhan, Vijay; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, Niranjan
Tubby and Tubby-like proteins (TLPs), in mammals, play critical roles in neural development, while its function in plants is largely unknown. We previously demonstrated that the chickpea TLP, CaTLP1, participates in osmotic stress response and might be associated with ABA-dependent network. However, how CaTLP1 is connected to ABA signaling remains unclear. The CaTLP1 was found to be engaged in ABA-mediated gene expression and stomatal closure. Complementation of the yeast yap1 mutant with CaTLP1 revealed its role in ROS scavenging. Furthermore, complementation of Arabidopsis attlp2 mutant displayed enhanced stress tolerance, indicating the functional conservation of TLPs across the species. The presence of ABA-responsive element along with other motifs in the proximal promoter regions of TLPs firmly established their involvement in stress signalling pathways. The CaTLP1 promoter driven GUS expression was restricted to the vegetative organs, especially stem and rosette leaves. Global protein expression profiling of wild-type, attlp2 and complemented Arabidopsis plants revealed 95 differentially expressed proteins, presumably involved in maintaining physiological and biological processes under dehydration. Immunoprecipitation assay revealed that protein kinases are most likely to interact with CaTLP1. This study provides the first demonstration that the TLPs act as module for ABA-mediated stomatal closure possibly via interaction with protein kinase.
Chitosan-triggered immunity to Fusarium in chickpea is associated with changes in the plant extracellular matrix architecture, stomatal closure and remodelling of the plant metabolome and proteome
(John Wiley & Sons, 2020) Narula, Kanika; Elagamey, Eman; Abdellatef, Magdi A.E.; Sinha, Arunima; Ghosh, Sudip; Chakraborty, Niranjan; Chakraborty, Subhra
Pathogen/microbe associated molecular patterns (PAMPs/MAMPs) initiate complex defense responses by reorganizing the biomolecular dynamics of the host cellular machinery. The extracellular matrix (ECM) acts as a physical scaffold that prevents recognition and entry of phyto‐pathogens, while guard cells perceive and integrate signals metabolically. Although chitosan is known MAMP implicated in plant defense, the precise mechanism of chitosan‐triggered immunity (CTI) remains unknown. Here, we show how chitosan imparts immunity against fungal disease. Morpho‐histological examination revealed stomatal closure accompanied by reductions in stomatal conductance and transpiration rate as early responses in chitosan‐treated seedlings upon vascular fusariosis. Electron microscopy and Raman spectroscopy showed ECM fortification leading to oligosaccharide signaling, as documented by increased galactose, pectin and associated secondary metabolites. Multiomics approach using quantitative ECM proteomics and metabolomics identified 325 chitosan‐triggered immune‐responsive proteins (CTIRPs) notably novel ECM structural proteins, LYM2 and receptor‐like kinases, and 65 chitosan‐triggered immune‐responsive metabolites (CTIRMs), including sugars, sugar alcohols, fatty alcohols, organic and amino acids. Identified proteins and metabolites are linked to ROS production, stomatal movement, root nodule development and root architecture coupled with oligosaccharide signaling that leads to Fusarium resistance. The cumulative data demonstrate that ROS, NO and eATP govern CTI, in addition to induction of PR proteins, CAZymes and PAL activities, besides accumulation of phenolic compounds downstream of CTI. The immune‐related correlation network identified functional hubs in the CTI pathway. Altogether, these shifts led to the discovery of chitosan‐responsive networks that cause significant ECM and guard cell remodeling and translate ECM cues into cell fate decisions during fusariosis.
CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors
(BioMed Central Ltd, 2016) Gayali, Saurabh; Acharya, Shankar; Lande, Nilesh Vikram; Pandey, Aarti; Chakraborty, Subhra; Chakraborty, Niranjan
Background: Transcription factor (TF) databases are major resource for systematic studies of TFs in specific species as well as related family members. Even though there are several publicly available multi-species databases, the information on the amount and diversity of TFs within individual species is fragmented, especially for newly sequenced genomes of non-model species of agricultural significance. Description: We constructed CicerTransDB (Cicer Transcription Factor Database), the first database of its kind, which would provide a centralized putatively complete list of TFs in a food legume, chickpea. CicerTransDB, available at www.cicertransdb.esy.es, is based on chickpea (Cicer arietinum L.) annotation v 1.0. The database is an outcome of genome-wide domain study and manual classification of TF families. This database not only provides information of the gene, but also gene ontology, domain and motif architecture. Conclusion: CicerTransDB v 1.0 comprises information of 1124 genes of chickpea and enables the user to not only search, browse and download sequences but also retrieve sequence features. CicerTransDB also provides several single click interfaces, transconnecting to various other databases to ease further analysis. Several webAPI(s) integrated in the database allow end-users direct access of data. A critical comparison of CicerTransDB with PlantTFDB (Plant Transcription Factor Database) revealed 68 novel TFs in the chickpea genome, hitherto unexplored. Database URL: http://www.cicertransdb.esy.es
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.
Combining extracellular matrix proteome and phosphoproteome of chickpea and meta-analysis reveal novel proteoforms and evolutionary significance of clade-specific wall-associated events in plant
(John Wiley & Sons, 2024) Narula, Kanika; Sinha, Arunima; Choudhary, Pooja; Ghosh, Sudip; Elagamey, Eman; Sharma, Archana; Sengupta, Atreyee; Chakraborty, Niranjan; Chakraborty, Subhra
Extracellular matrix (ECM) plays central roles in cell architecture, innate defense andcell wall integrity (CWI) signaling. During transition to multicellularity, modulardomain structures of ECM proteins and proteoforms have evolved due to continuousadaptation across taxonomic clades under different ecological niche. Although thisincredible diversity has to some extent been investigated at protein level, extracellu-lar phosphorylation events and molecular evolution of ECM proteoform familiesremains unexplored. We developed matrisome proteoform atlas in a grain legume,chickpea and performed meta-analyses of 74 plant matrisomes. MS/MS analysisidentified 1,424 proteins and 315 phosphoproteins involved in diverse functions.Cross-species ECM protein network identified proteoforms associated with CWImaintenance system. Phylogenetic characterization of eighteen matrix protein fami-lies highlighted the role of taxon-specific paralogs and orthologs. Novel informationwas acquired on gene expansion and loss, co-divergence, sub functionalization andneofunctionalization during evolution. Modular networks of matrix protein familiesand hub proteins showed higher diversity across taxonomic clades than amongorgans. Furthermore, protein families differ in nonsynonymous to synonymous sub-stitution rates. Our study pointed towards the matrix proteoform functionality,sequence divergence variation, interactions between wall remodelers and molecularevolution using a phylogenetic framework. This is the first report on comprehensivematrisome proteoform network illustrating presence of CWI signaling proteins inland plants.
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 analysis of phytochemicals and nutrient availability in two contrasting cultivars of sweet potato (Ipomoea batatas L.)
(Elsevier B.V., 2014) Shekhar, Shubhendu; Mishra, Divya; Buragohain, Alak Kumar; Chakraborty, Subhra; Chakraborty, Niranjan
Sweet potato ranks as the world's seventh most important food crop, and has major contribution to energy and phytochemical source of nutrition. To unravel the molecular basis for differential nutrient availability, and to exploit the natural genetic variation(s) of sweet potato, a series of physiochemical and proteomics experiment was conducted using two contrasting cultivars, an orange-fleshed sweet potato (OFSP) and a white-fleshed sweet potato (WFSP). Phytochemical screening revealed high percentage of carbohydrate, reducing sugar and phenolics in WFSP, whereas OFSP showed increased levels of total protein, flavonoids, anthocyanins, and carotenoids. The rate of starch and cellulose degradation was found to be less in OFSP during storage, indicating tight regulation of gene(s) responsible for starch-degradation. Comparative proteomics displayed a cultivar-dependent expression of proteins along with evolutionarily conserved proteins. These results suggest that cultivar-specific expression of proteins and/or their interacting partners might play a crucial role for nutrient acquisition in sweet potato.
Comparative analysis of sequence-structure function relationship of the SUN-domain protein CaSUN1
(OMICS International, 2017) Mishra, Poonam; Wardhan, Vijay; Pandey, Aarti; Chakraborty, Subhra; Garg, Gunjan; Chakraborty, Niranjan
Sad1/UNC-84 (SUN)-domain proteins are residents of inner nuclear membrane (INM), and share structural features across species. We previously reported a highly conserved C-terminal SUN-domain family protein, designated CaSUN1, in the stress-responsive proteomic landscape of a grain legume, chickpea. In this study, we identified two other chickpea SUN proteins, CaSUN2 and CaSUN3, and performed a comparative analysis of the sequence-structure-function relationship to better understand the diversification of SUN-domain superfamily proteins. Sequence similarity across the species was investigated using multiple sequence alignment, which showed conserved patterns between CaSUN1 and the homologs. Phylogenetic analysis showed that plant SUN-domain proteins are clustered in a unique and distinct group. Using ab-initio approach, a 3D protein structure was generated and further validated using various tools including the Ramachandran plot. The results displayed 90.1% of the Ã Â and Ã Â± residues angles in the most favoured regions, suggesting a high-quality structural model for CaSUN1. Model deviation and fluctuation analysis were performed using molecular dynamics (MD) simulation of CaSUN1. The secondary structure analysis of CaSUN revealed a similarity between the structural components shared among them. CaSUN1 revealed two functional domains viz., SUN and muskelin, and the presence of kelch-repeat domain pointed out its putative role in oligomerization, while its binding affinity with different ligands indicates diverse functions. These results would not only give deeper insights into the structure-function relationships within the SUNsuperfamily proteins, but also their putative physiological roles.
Comparative nuclear proteomics analysis provides insight into the mechanism of signaling and immune response to blast disease caused by Magnoporthe oryzae in rice
(John Wiley & Sons, 2019) Narula, Kanika; Choudhary, Pooja; Ghosh, Sudip; Elagamey, Eman; Chakraborty, Niranjan; Chakraborty, Subhra
Modulation of plant immune system by extrinsic/intrinsic factors and host-specific determinants fine-tunes cellular components involving multiple organelles, particularly nucleus to mount resistance against pathogen attack. Rice blast, caused by hemibiotrophic fungus Magnaporthe oryzae, is one of the most devastating diseases that adversely affect rice productivity. However, the role of nuclear proteins and their regulation in response to M. oryzae remains unknown. Here, we elucidate the nucleus-associated immune pathways in blast resistant rice genotype. Temporal analysis of nuclear proteome was carried out using 2-DE coupled MS/MS analysis. A total of 140 immune responsive proteins (IRPs) were identified associated with nuclear reorganization, cell division, energy production/deprivation, signaling and gene regulation. We interrogated the proteome data using correlation network analysis that identified significant functional modules pointing towards immune related coinciding processes through a common mechanism of remodelling and homeostasis. Novel clues regarding blast resistance include nucleus associated redox homeostasis and glycolytic enzyme mediated chromatin organization which manipulates cell division and immunity. Taken together, our study provides evidence that coordination of nuclear function and reprogramming of host translational machinery regulate resistance mechanism against blast disease.
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.
Comparative proteomics of dehydration response in the rice nucleus: new insights into the molecular basis of genotype-specific adaptation
(John Wiley & Sons, 2013) Jaiswal, Dinesh Kumar; Ray, Doel; Choudhary, Mani Kant; Subba, Pratigya; Kumar, Amit; Verma, Jitendra; Kumar, Rajiv; Datta, Asis; Chakraborty, Subhra; Chakraborty, Niranjan
Dehydration is the most crucial environmental factor that considerably reduces the crop harvest index, and thus has become a concern for global agriculture. To better understand the role of nuclear proteins in water-deficit condition, a nuclear proteome was developed from a dehydration-sensitive rice cultivar IR-64 followed by its comparison with that of a dehydration-tolerant c.v. Rasi. The 2DE protein profiling of c.v. IR-64 coupled with MS/MS analysis led to the identification of 93 dehydration-responsive proteins (DRPs). Among those identified proteins, 78 were predicted to be destined to the nucleus, accounting for more than 80% of the dataset. While the detected number of protein spots in c.v. IR-64 was higher when compared with that of Rasi, the number of DRPs was found to be less. Fifty-seven percent of the DRPs were found to be common to both sensitive and tolerant cultivars, indicating significant differences between the two nuclear proteomes. Further, we constructed a functional association network of the DRPs of c.v. IR-64, which suggests that a significant number of the proteins are capable of interacting with each other. The combination of nuclear proteome and interactome analyses would elucidate stress-responsive signaling and the molecular basis of dehydration tolerance in plants.