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Author: search.filters.author.Chakraborty, SubhraSubject: search.filters.subject.Comparative proteomics

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    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.
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    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.
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    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.