Biotechnology, Applied Microbiology and Biotechnology, Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology
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Scopus Publications
Scopus Publications
Dissecting plant-virus interactions through proteomics Nidhi Choudhary, Sampat Nehra, Raj Kumar Gothwal Plant Proteomics Implications in Growth Quality Improvement and Stress Resilience, 2024 Plant viruses propagate themselves by first penetrating a particular healthy cellular environment and then by releasing certain proteins that interact with the host protein molecules, membrane and metabolism and take over the control mechanism of the cell by host protein alterations as well as systemic infections. To prevent such plant–virus interactions, it was necessary to understand the whole pathways and alterations that such viruses are able to create and this gave rise to the field of proteomics. Now, new advanced and specialized proteomics methods are emerging as useful approaches for the identification and quantification of all the host proteins that end up being part of a virus infection. Many different proteomics techniques have been developed with the aim of identifying and subduing plant–virus interactions. These methods work by measuring and comparing differential protein expression in virus-infected cells against the uninfected cells, by analyzing viral and host protein components or molecular structures in the protein–virus complexes, as well as proteome-wide screens to separate host protein – viral protein interactions. In this study, we will try to highlight the progress made in plant virology using various proteomics methods and observe the functions of some of the identified host proteins during viral infections. Since mere proteomics approaches do not usually identify the molecular mechanism of the identified host factors during host protein–viral interactions during the infection stage, additional experiments become necessary using genetics, biochemistry, cell biology, etc., to characterize, record and define the functions of host factors. In spite of its challenges and certain weaknesses, the field of proteomics-based technologies can play a very critical role in our further understanding of plant–virus interactions which will help us a lot in protecting crop damages and move toward more efficient yields.
Proteomic-driven approaches for unravelling plant-microbe interactions Raj Kumar Gothwal, Sampat Nehra, Parul Sinha, Aruna N. C. Shekhar, Purnendu Ghosh Plant Proteomics Implications in Growth Quality Improvement and Stress Resilience, 2024 The life cycle of a plant includes interaction with microorganisms in a very intricate and complex manner. While certain microorganisms inhabit the plant only for their own gain, certain others interact with plants in a mutually beneficial way. A highly effective defence mechanism that can withstand possible attacks by microbial pathogens has been created as a result of the evolution of the plant immune response. The basic immune response has developed to recognise typical characteristics of microbial infections and is known as the pathogen-associated molecular pattern (PAMP)-induced immunity. In order to gain an understanding of pathogen infection or symbiosis, studies are being focused on identifying the molecular elements involved in plant–microbe interaction. For this, researchers have been employing a wide range of high-throughput “omics” methodologies, such as transcriptomics, that quantify messenger RNA (mRNA) transcripts; proteomics, which examines protein composition; metabolomics, to detect and quantify cellular metabolites; and genomics, to analyse the structural and functional characteristics of genes as well as evaluate the degree of gene expression in dissimilar genotypes. Such platforms are being widely employed to interpret and choose effective endophytic or beneficial strains with a variety of improved features like nutrition uptake and the ability to withstand biotic and abiotic stress while interacting with the host. In this chapter, an attempt has been made to discuss the role of “omics” platforms, in exploring the interactions between plants and microorganisms.
Deciphering plant-microbe crosstalk through proteomics tools Sampat Nehra, Aarushi Sachdeva, Jinal Paresh Bhavsar, Erica Zinnia Nehra, Raj Kumar Gothwal, Purnendu Ghosh Plant Proteomics Implications in Growth Quality Improvement and Stress Resilience, 2024 In order to better understand the molecular interactions that take place between the host, pathogen, and helpful microbes, proteomic methods are being applied. Using proteomic approaches, it has been possible to identify antioxidant, stress-related, and pathogenic proteins that are expressed during interactions between plants and microbes. For successful pathogen identification, generation of resistance, and the maintenance of host integrity, it is believed that precise control of protein expression occurs. However, our understanding of the molecular interactions between plants and microbes is still limited and unimportant. This study seeks to provide light on various approaches utilised for proteomic research, such as peptide/protein separation, quantification and identification during host defensive response. The emphasis of this chapter will be placed on the most recent developments in the proteomics of plant defence responses to viral, bacterial and fungal pathogens in plants. The proteome level modifications brought on by beneficial microbes are also reviewed.
Understanding post-translational protein modification through proteomics tools Sampat Nehra, Raj Kumar Gothwal, Aruna N. C. Shekhar, Parul Sinha, Erica Zinnia Nehra, Alok Kumar Varshney, Pooran Singh Solanki, Purnendu Ghosh Plant Proteomics Implications in Growth Quality Improvement and Stress Resilience, 2024 The post-translational modification (PTM) of proteins creates a dramatic boom in protein dynamics and complexity, allowing finer control over biological processes. A PTM of proteins involves acylation, nitration, ubiquitination, phosphorylation and glycosylation as reversible modification steps. In plants, PTM is one of the earliest and quickest responses to environmental changes, highlighting the importance of understanding PTM mechanisms and dynamics in plant research. Modifications in the structure of proteins impact their function, intracellular localisation, stability and interactions with other proteins and chemicals. Despite its significant role in cellular activity, PTM research has remained a mission till recently. Detection of PTM calls for big ranges of proteins and extraordinarily sensitive detection strategies. The development of proteomics strategies has made it possible to discover global post-translational changes. There have been significant advancements in sample pre-treatment methods and mass spectrometry tools. Proteins are usually pre-fractionated by chromatographic purification and affinity enrichment to minimise complexity and increase the range of modified proteins suitable for analysis. The purpose of this chapter is to describe discoveries about PTMs of plants. There is likewise an outline of the way the samples had been organised and prepared for every study. These include affinity-based enrichment methods for studying ubiquitination and phosphorylation and phase partitioning methodologies for glycosylphosphatidylinositol modification. Additionally, by merging data-independent spectra capture with data-dependent spectra capture, it is possible to interrogate spectra for unforeseen information in addition to anticipated targets.
Mechanism of Antagonism: Hyperparasitism and Antibiosis Sampat Nehra, Raj Kumar Gothwal, Siddhant Dhingra, Alok Kumar Varshney, Pooran Singh Solanki, Poonam Meena, P. C. Trivedi, P. Ghosh Microbial Biocontrol Sustainable Agriculture and Phytopathogen Management Volume 1, 2022
Bio-management of Fusarium spp. associated with fruit crops Sampat Nehra, Raj Kumar Gothwal, Alok Kumar Varshney, Pooran Singh Solanki, Shivani Chandra, Poonam Meena, P.C. Trivedi, P. Ghosh Fungi Bio Prospects in Sustainable Agriculture Environment and Nano Technology Volume 1 Fungal Diversity of Sustainable Agriculture, 2020
Bioactivation of Jhamarkotra rock phosphate by a thermotolerant phosphate-solubilizing bacterium Bacillus sp. BISR-HY63 isolated from phosphate mines Hemendra Yadav, Raj Kumar Gothwal, Sujata Mathur, Purnendu Ghosh Archives of Agronomy and Soil Science, 2015 Rock phosphate (RP) is a natural source of phosphorus (P), but due to its poor solubility, its application has been restricted to acidic soils. We performed bioactivation of RP in order to increase its efficacy as a fertilizer in direct application to alkaline soils. Simulation of super phosphate (SP) formation was performed, where inorganic acids used in the preparation of SP were replaced by different concentrations of culture supernatant of a thermotolerant phosphate-solubilizing bacterium isolated from RP mines having Fe-P- and Al-P-solubilizing ability to make an environmentally clean SP. Increases in water soluble and citrate soluble P were observed by the treatment of RP with culture supernatant. Organic acid secretion along with decrease in pH was observed and was found to be the major cause in solubilization of RP. HPLC analysis of the culture supernatant showed the presence of citric, malic, and acetic acids. Phylogenetic analysis of the culture showed it to belong to the genus Bacillus.
Isolation and Characterization of Thermo-tolerant Phosphate-Solubilizing Bacteria From a Phosphate Mine and Their Rock Phosphate Solubilizing Abilities H. Yadav, R. K. Gothwal, P. S. Solanki, S. Nehra, S. Sinha-roy, P. Ghosh Geomicrobiology Journal, 2015 A study of rock phosphate (RP) mines, rich in R2O3 (Fe2O3 and Al2O3) contents, was done to explore the possibilities of isolating and characterizing thermo-tolerant phosphate solubilizing bacteria (PSB) having the ability to solubilize ferric phosphate (Fe-P) and aluminium phosphate (Al-P) efficiently. One hundred and ten thermo-tolerant PSB were isolated employing Pikovskaya (PVK) broth amended with RP, and six of these isolates were selected for further study. The phosphate solubilizing efficiency (PSE) was determined in PVK broth containing tri-calcium phosphate (TCP), hydroxyapatite (Hy-P), Fe-P, Al-P or RP. These isolates showed solubilization of all the phosphorus (P) sources used in this study, particularly Fe-P, Al-P and RP. The main mechanism of P-solubilization seemed to be mediated by the production of organic acids leading to medium acidification. HPLC analysis revealed production of multiple organic acids (oxalic, citric, malic, succinic, formic, acetic and gluconic acids) in the culture supernatant along with some unknown acids. Based on the partial sequence analysis of 16S rRNA genes, these thermo-tolerant isolates were found to belong to two bacterial genera, Brevibacillus and Bacillus.
