Browsing by Author "Kumar, Rajiv"

Now showing 1 - 7 of 7

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.
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.
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.
Dancing to the tune of the light regime: from perception to secondary metabolite biosynthesis in plants
(Taylor & Francis Group, 2026) Punia, Ashwani; Satyakam; Saini, Vishal; Chouhan, Monika; Chakraborty, Niranjan; Kumar, Rajiv
The orchestra of ambient light intensity and wavelengths are pivotal in regulating the biosynthesis of secondary metabolites. Hence, the implications of light on plants' secondary metabolites are an active area of research, and new information is slowly being accrued. Plants have inbuilt light-sensitive molecules, such as: phytochromes, cryptochromes, phototropins, UVR8, and zeitlupe family proteins. In particular, blue light absorbed by cryptochrome has positive effects on antioxidants and other bioactive compounds. However, far-red light perceived by phytochrome reduces anthocyanin biosynthesis in plants, whereas mixed light in varying proportions is more beneficial for secondary metabolite synthesis. This article reviews the current information on plants' perception of light, their downstream signaling, and the role of different light regimes on secondary metabolite biosynthesis and accumulation. It also examines the epigenetic regulation of secondary metabolite biosynthesis under various light regimes. Additionally the review examines the economic and medicinal aspects of manipulating/controlling/optimizing secondary metabolite synthesis by light modulation. Consequently, this review is expected to benefit any researchers involved in fundamental and applied research.
Nuclear phosphoproteome of developing chickpea seedlings (Cicer arietinum L.) and protein-kinase interaction network
(Elsevier B.V., 2014) Kumar, Rajiv; Kumar, Amit; Subba, Pratigya; Gayali, Saurabh; Barua, Pragya; Chakraborty, Subhra; Chakraborty, Niranjan
Nucleus, the control centre of eukaryotic cell, houses most of the genetic machineries required for gene expression and their regulation. Post translational modifications of proteins, particularly phosphorylation control a wide variety of cellular processes but its functional connectivity, in plants, is still elusive. This study profiled the nuclear phosphoproteome of a grain legume, chickpea, to gain better understanding of such event. Intact nuclei were isolated from 3-week-old seedlings using two independent methods, and nuclear proteins were resolved by 2-DE. In a separate set of experiments, phosphoproteins were enriched using IMAC method and resolved by 1-DE. The separated proteins were stained with phosphospecific Pro-Q Diamond stain. Proteomic analyses led to the identification of 107 putative phosphoproteins, of which 86 were non-redundant. Multiple sites of phosphorylation were predicted on several key elements, which included both regulatory and functional proteins. The analysis revealed an array of phosphoproteins, presumably involved in a variety of cellular functions, viz., protein folding (24%), signalling and gene regulation (22%), DNA replication, repair and modification (16%), and metabolism (13%), among others. These results represent the first nucleus-specific phosphoproteome map of a non-model legume, which would provide insights into the possible function of protein phosphorylation in plants. BIOLOGICAL SIGNIFICANCE: Chickpea is grown over 10 million hectares of land worldwide, and global production hovers around 8.5 million metric tons annually. Despite its nutritional merits, it is often referred to as 'orphan' legume and has remained outside the realm of large-scale functional genomics studies. While current chickpea genome initiative has primarily focused on sequence information and functional annotation, proteomics analyses are limited. It is thus important to study the proteome of the cell organelle particularly the nucleus, which harbors most of the genetic information and gene expression machinery. Phosphorylation-dependent modulation of gene expression plays a vital role but the complex networks of phosphorylation are poorly understood. This inventory of nuclear phosphoproteins would provide valuable insights into the dynamic regulation of cellular phenotype through phosphorylation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response
(American Chemical Society, 2013) Subba, Pratigya; Barua, Pragya; Kumar, Rajiv; Datta, Asis; Soni, Kamlesh Kumar; Chakraborty, Subhra; Chakraborty, Niranjan
Reversible protein phosphorylation is a ubiquitous regulatory mechanism that plays critical roles in transducing stress signals to bring about coordinated intracellular responses. To gain better understanding of dehydration response in plants, we have developed a differential phosphoproteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water, and the changes in the phosphorylation status of a large repertoire of proteins were monitored. The proteins were resolved by 2-DE and stained with phosphospecific fluorescent Pro-Q Diamond dye. Mass spectrometric analysis led to the identification of 91 putative phosphoproteins, presumably involved in a variety of functions including cell defense and rescue, photosynthesis and photorespiration, molecular chaperones, and ion transport, among others. Multiple sites of phosphorylation were predicted on several key elements, which include both the regulatory as well as the functional proteins. A critical survey of the phosphorylome revealed a DREPP (developmentally regulated plasma membrane protein) plasma membrane polypeptide family protein, henceforth designated CaDREPP1. The transcripts of CaDREPP1 were found to be differentially regulated under dehydration stress, further corroborating the proteomic results. This work provides new insights into the possible phosphorylation events triggered by the conditions of progressive water-deficit in plants.
Systemic acquired resistance specifc proteome of Arabidopsis thaliana
(Springer Nature Publishing AG, 2020) Kumar, Rajiv; Barua, Pragya; Chakraborty, Niranjan; Nandi, Ashis Kumar
Key message A comparative proteomic study between WT and SAR-compromised rsi1/fd mutant reveals a set of proteins having possible roles in the SAR development. Abstract A partly infected plant shows enhanced resistance during subsequent infection through the development of systemic acquired resistance (SAR). Mobile signals generated at the site of primary infection travel across the plant for the activation of SAR. These mobile signals are likely to cause changes in the expression of a set of proteins in the distal tissue, which contributes to the SAR development. However, SAR-specifc proteome is not revealed for any plant. The reduced systemic immunity 1 (rsi1)/(allelic to fowering locus D; fd) mutant of Arabidopsis is compromised for SAR but shows normal local resistance. Here we report the SAR-specifc proteome of Arabidopsis by comparing diferentially abundant proteins (DAPs) between WT and fd mutant. Plants were either mock-treated or SAR-induced by primary pathogen inoculation. For proteomic analysis, samples were collected from the systemic tissues before and after the secondary inoculation. Protein identifcation was carried out by using two-dimensional gel electrophoresis (2-DE) followed by tandem mass spectrometry. Our work identifed a total of 94 DAPs between mock and pathogen treatment in WT and fd mutant. The DAPs were categorized into diferent functional groups along with their subcellular localization. The majority of DAPs are involved in metabolic processes and stress response. Among the subcellular compartments, plastids contained the highest number of DAPs, suggesting the importance of plastidic proteins in SAR activation. The fndings of this study would provide resources to engineer efcient SAR activation traits in Arabidopsis and other plants.