Browsing by Author "Sinha, Arunima"

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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.
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 proteomics of oxalate downregulated tomatoes points toward cross talk of signal components and metabolic consequences during post-harvest storage
(Frontiers Media S.A., 2016) Narula, Kanika; Ghosh, Sudip; Aggarwal, Pooja R.; Sinha, Arunima; Chakraborty, Niranjan; Chakraborty, Subhra
Fruits of angiosperms evolved intricate regulatory machinery for sensorial attributes and storage quality after harvesting. Organic acid composition of storage organs forms the molecular and biochemical basis of organoleptic and nutritional qualities with metabolic specialization. Of these, oxalic acid (OA), determines the post-harvest quality in fruits. Tomato (Solanum lycopersicum) fruit has distinctive feature to undergo a shift from heterotrophic metabolism to carbon assimilation partitioning during storage. We have earlier shown that decarboxylative degradation of OA by FvOXDC leads to acid homeostasis besides increased fungal tolerance in E8.2-OXDC tomato. Here, we elucidate the metabolic consequences of oxalate down-regulation and molecular mechanisms that determine organoleptic features, signaling and hormonal regulation in E8.2-OXDC fruit during post-harvest storage. A comparative proteomics approach has been applied between wild-type and E8.2-OXDC tomato in temporal manner. The MS/MS analyses led to the identification of 32 and 39 differentially abundant proteins associated with primary and secondary metabolism, assimilation, biogenesis, and development in wild-type and E8.2-OXDC tomatoes, respectively. Next, we interrogated the proteome data using correlation network analysis that identified significant functional hubs pointing toward storage related coinciding processes through a common mechanism of function and modulation. Furthermore, physiochemical analyses exhibited reduced oxalic acid content with concomitant increase in citric acid, lycopene and marginal decrease in malic acid in E8.2-OXDC fruit. Nevertheless, E8.2-OXDC fruit maintained an optimal pH and a steady state acid pool. These might contribute to reorganization of pectin constituent, reduced membrane leakage and improved fruit firmness in E8.2-OXDC fruit with that of wild-type tomato during storage. Collectively, our study provides insights into kinetically controlled protein network, identified regulatory module for pathway formulation and provide basis toward understanding the context of storage quality maintenance as a consequence of oxalate downregulation in the sink organ.
Extracellular matrix proteome and phosphoproteome of potato reveals functionally distinct and diverse canonical and non-canonical proteoforms
(MDPI AG, 2016) Elagamey, Eman; Narula, Kanika; Sinha, Arunima; Aggarwal, Pooja Rani; Ghosh, Sudip; Chakraborty, Niranjan; Chakraborty, Subhra
The extracellular matrix (ECM) has a molecular machinery composed of diverse proteins and proteoforms that combine properties of tensile strength with extensibility exhibiting growth-regulatory functions and self- and non-self-recognition. The identification of ECM proteoforms is the prerequisite towards a comprehensive understanding of biological functions accomplished by the outermost layer of the cell. Regulatory mechanisms of protein functions rely on post-translational modifications, phosphorylation in particular, affecting enzymatic activity, interaction, localization and stability. To investigate the ECM proteoforms, we have isolated the cell wall proteome and phosphoproteome of a tuberous crop, potato (Solanum tuberosum). LC-MS/MS analysis led to the identification of 38 proteins and 35 phosphoproteins of known and unknown functions. The findings may provide a better understanding of biochemical machinery and the integrated protein and phosphoprotein network of ECM for future functional studies of different developmental pathways and guidance cues in mechanosensing and integrity signaling.
Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea
(John Wiley & Sons, 2020) Sinha, Arunima; Haider, Toshiba; Narula, Kanika; Ghosh, Sudip; Chakraborty, Niranjan; Chakraborty, Subhra
Nutrient dynamics in storage organs is a complex developmental process that requires coordinated interactions of environmental, biochemical, and genetic factors. Although sink organ developmental events have been identified, our understanding of translational and post‐translational regulation of reserve synthesis, accumulation and utilization in legume crops is limited. To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, an integrated proteomics and phosphoproteomics study in six sequential seed developmental stages in chickpea was performed. MS/MS analyses identified 109 unique nutrient‐associated proteins (NAPs) involved in metabolism, storage and biogenesis, and protein turnover. Differences and similarities in 60 nutrient‐associated phosphoproteins (NAPPs) containing 93 phosphosites were compared with NAPs. Data revealed accumulation of carbon‐nitrogen metabolic and photosynthetic proteoforms during seed filling. Furthermore, enrichment of storage proteoforms and protease inhibitors was associated with cell expansion and seed maturation. Finally, combined proteoforms network analysis identified three significant modules, centered around malate dehydrogenase, HSP70, triose phosphate isomerase and vicilin. Novel clues suggest that ubiquitin‐proteasome pathway regulates nutrient reallocation. Second, increased abundance of NAPs/NAPPs related to oxidative and serine/threonine signalling indicate direct interface between redox sensing and signaling during seed development. Taken together, nutrient signals act as metabolic and differentiation determinant governing storage organ reprogramming.
Molecular dissection of extracellular matrix proteome reveals discrete mechanism regulating Verticillium dahliae triggered vascular wilt disease in potato
(John Wiley & Sons, 2017) Elagamey, Eman; Sinha, Arunima; Narula, Kanika; Abdellatef, Magdi A.E.; Chakraborty, Niranjan; Chakraborty, Subhra
Plants exposed to patho-stress mostly succumb due to disease by disruption of cellular integrity and changes in the composition of the extracellular matrix (ECM). Vascular wilt, caused by the soil borne hemibiotrophic filamentous fungus Verticillium dahliae, is one of the most significant diseases that adversely affects plant growth and productivity. The virulence of the pathogen associated with the ECM-related susceptibility of the host plant is far from being understood. To better understand ECM-associated disease responses that allow the pathogen to supress plant immunity, a temporal analysis of ECM proteome was carried out in vascular wilt susceptible potato cultivar upon V. dahliae infection. The proteome profiling led to the identification of 75 patho-stress responsive proteins (PSRPs), predominantly involved in wall hydration, architecture, and redox homeostasis. Two novel clues regarding wilt disease of potato were gained from this study. First, wall crosslinking and salicylic acid signaling significantly altered during patho-stress. Second, generation of reactive oxygen species and scavenging proteins increased in abundance leading to cell death and necrosis of the host. We provide evidence for the first time that how fungal invasion affects the integrity of ECM components and host reprogramming for susceptibility may function at the cell surface by protein plasticity. This article is protected by copyright. All rights reserved.
Proteometabolomic analysis of transgenic tomato overexpressing oxalate decarboxylase uncovers novel proteins potentially involved in defense mechanism against Sclerotinia
(Elsevier B.V., 2016) Ghosh, Sudip; Narula, Kanika; Sinha, Arunima; Ghosh, Rajgourab; Jawa, Priyanka; Chakraborty, Niranjan; Chakraborty, Subhra
Oxalic acid (OA) plays dual role in fungal pathogenicity in a concentration dependent manner. While at higher concentration it induces programmed cell death leading to fungal invasion, low oxalate build resistance in plant. Although OA has been identified as a virulence determinant for rot disease caused by Sclerotinia sp., our understanding of how oxalate downregulation impart host immunity is limited. We have earlier shown that ectopic expression of oxalate decarboxylase (FvOXDC) specifically degrades OA in tomato (Solanum lycopersicum). To elucidate low oxalate regulated molecular mechanism imparting immunity, a comparative proteomics approach has been applied to E8.2-OXDC tomato fruit displaying fungal resistance. Mass spectrometric analyses identified 92 OXDC-responsive immunity related protein spots (ORIRPs) presumably associated with acid metabolism, defense signaling and endoplasmic reticulum stress. Metabolome study indicated increased abundance of some of the organic acids paralleling the proteomic analysis. Further, we interrogated the proteome data using network analysis that identified modules enriched in known and novel immunity-related prognostic proteins centered around 14-3-3, translationally controlled tumor protein, annexin and chaperonin. Taken together, our data demonstrate that low oxalate may act as metabolic and immunity determinant through translational reprogramming.
Proteometabolomic study of compatible interaction in tomato fruit challenged with Sclerotinia rolfsii illustrates novel protein network during disease progression
(Frontiers Media S.A., 2016) Ghosh, Sudip; Narula, Kanika; Sinha, Arunima; Ghosh, Rajgourab; Jawa, Priyanka; Chakraborty, Niranjan; Chakraborty, Subhra
Fruit is an assimilator of metabolites, nutrients, and signaling molecules, thus considered as potential target for pathogen attack. In response to patho-stress, such as fungal invasion, plants reorganize their proteome, and reconfigure their physiology in the infected organ. This remodeling is coordinated by a poorly understood signal transduction network, hormonal cascades, and metabolite reallocation. The aim of the study was to explore organ-based proteomic alterations in the susceptibility of heterotrophic fruit to necrotrophic fungal attack. We conducted time-series protein profiling of Sclerotinia rolfsii invaded tomato (Solanum lycopersicum) fruit. The differential display of proteome revealed 216 patho-stress responsive proteins (PSRPs) that change their abundance by more than 2.5-fold. Mass spectrometric analyses led to the identification of 56 PSRPs presumably involved in disease progression; regulating diverse functions viz. metabolism, signaling, redox homeostasis, transport, stress-response, protein folding, modification and degradation, development. Metabolome study indicated differential regulation of organic acid, amino acids, and carbohydrates paralleling with the proteomics analysis. Further, we interrogated the proteome data using network analysis that identified two significant functional protein hubs centered around malate dehydrogenase, T-complex protein 1 subunit gamma, and ATP synthase beta. This study reports, for the first-time, kinetically controlled patho-stress responsive protein network during post-harvest storage in a sink tissue, particularly fruit and constitute the basis toward understanding the onset and context of disease signaling and metabolic pathway alterations. The network representation may facilitate the prioritization of candidate proteins for quality improvement in storage organ.
Proteomic signatures uncover phenotypic plasticity of susceptible and resistant genotypes by wall remodelers in rice blast
(John Wiley & Sons, 2024) Sinha, Arunima; Narula, Kanika; Bhola, Latika; Sengupta, Atreyee; Choudhary, Pooja; Nalwa, Pragya; Kumar, Mohit; Elagamey, Eman; Chakraborty, Niranjan; Chakraborty, Subhra
Molecular communication between macromolecules dictates extracellular matrix (ECM) dynamics during pathogen recognition and disease development. Extensive research has shed light on how plant immune components are activated, regulated and function in response to pathogen attack. However, two key questions remain largely unresolved: (i) how does ECM dynamics govern susceptibility and disease resistance, (ii) what are the components that underpin these phenomena? Rice blast, caused by Magnaporthe oryzae adversely affects rice productivity. To understand ECM regulated genotype-phenotype plasticity in blast disease, we temporally profiled two contrasting rice genotypes in disease and immune state. Morpho-histological, biochemical and electron microscopy analyses revealed that increased necrotic lesions accompanied by electrolyte leakage governs disease state. Wall carbohydrate quantification showed changes in pectin level was more significant in blast susceptible compared to blast resistant cultivar. Temporally resolved quantitative disease- and immune-responsive ECM proteomes identified 308 and 334 proteins, respectively involved in wall remodelling and integrity, signalling and disease/immune response. Pairwise comparisons between time and treatment, messenger ribonucleic acid expression, diseasome and immunome networks revealed novel blast-related functional modules. Data demonstrated accumulation of α-galactosidase and phosphatase were associated with disease state, while reactive oxygen species, induction of Lysin motif proteins, CAZymes and extracellular Ca-receptor protein govern immune state.
Quantitative extracellular matrix proteomics suggests cell wall reprogramming in host-specific immunity during vascular wilt caused by Fusarium oxysporum in chickpea
(John Wiley & Sons, 2017) Elagamey, Eman; Narula, Kanika; Sinha, Arunima; Ghosh, Sudip; Abdellatef, Magdi A.E.; Chakraborty, Niranjan; Chakraborty, Subhra
Extracellular matrix (ECM) is the unique organelle that perceives stress signals and reprograms molecular events of host cell during patho-stress. However, our understanding of how ECM dictates plant immunity is largely unknown. Vascular wilt caused by the soil borne filamentous fungus Fusarium oxysporum is a major impediment for global crop productivity. To elucidate the role of ECM proteins and molecular mechanism associated with cell wall mediated immunity, the temporal changes of ECM proteome was studied in vascular wilt resistant chickpea cultivar upon F. oxysporum infection. The 2-DE protein profiling coupled with mass spectrometric analysis identified 166 immune responsive proteins (IRPs) involved in variety of functions. Our data suggest that wall remodeling; protein translocation, stabilization and chitin triggered immunity; extracellular ATP signaling are major players in early, middle and later phases of ECM signaling during fungal attack. Furthermore, we interrogated the proteome data using network analysis that identified modules enriched in known and novel immunity-related prognostic proteins centered around nascent aminopolypeptide complex (NAC), amine oxidase, thioredoxin and chaperonin. This study for the first time provides an insight into the complex network operating in the ECM and impinges on the surveillance mechanism of innate immunity during patho-stress in crop plant.
Seed proteomics: An overview
(Springer, 2016) Narula, Kanika; Sinha, Arunima; Haider, Toshiba; Chakraborty, Niranjan; Chakraborty, Subhra
Seed is vital for propagation of spermatophytes in biome and as food source for inhabitants of the earth. Studies on seed proteins provide platform for new avenues to explore molecular networks and pathways governing seed filling, maturation, germination, and seedling formation. Protein expression changes of three genetically different sub-regions of angiosperm seeds are reflected in ordered chain of biological events represented from family differences in different taxas. Different families of angiosperm show divergence of seed protein evolution and thus provide insights into seed structure and function. A gamut of information is available on seed proteomic datasets from approximately 3500 proteins that impinge on protein function in diverse plant families. The functional modularity of seed proteins were compared amongst species that span from dicot to moncot and diploid to polyploid. Transitions of protein complement revealed difference between dormancy and germination towards understanding biological check point at translational level. Goal of this chapter is to critically review data available till date on seed proteomic studies and identify family and cross genera knowledge gaps. The information thus obtained would unravel new components and an unparallel understanding of the molecular processes underlying translational and post-translational variations under different conditions that involves histodifferentiation and organogenesis of the seed.