Browsing by Author "Lalit Agrawal"

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Comprehensive illustration of transcriptomic and proteomic dataset for mitigation of arsenic toxicity in rice (Oryza sativa L.) by microbial consortium
(Elsevier Inc., 2022) Surabhi Awasthi; Reshu Chauhan; Yuvraj Indoliya; Abhishek Singh Chauhan; Shashank Kumar Mishra; Lalit Agrawal; Sanjay Dwivedi; Shiv Naresh Singh; Suchi Srivastava; Poonam C. Singh; Puneet Singh Chauhan; Debasis Chakrabarty; Sudhakar Srivastava; Rudra Deo Tripathi
The present article represents the data for analysis of microbial consortium (P.putida+C.vulgaris) mediated amelioration of arsenic toxicity in rice plant. In the current study the transcriptome profiling of treated rice root and shoot was performed by illumina sequencing (Platform 2000). To process the reads and to analyse differential gene expression, Fastxtoolkit, NGSQCtoolkit, Bowtie 2 (version 2.1.0), Tophat program (version 2.0.8), Cufflinks and Cuffdiff programs were used. For Proteome profiling, total soluble proteins in shoot of rice plant among different treatments were extracted and separated by 2D poly acrylamide gel electrophoresis (PAGE) and then proteins were identified with the help of MALDI-TOF/TOF. In gel based method of protein identification, the isoelectric focusing machine (IPGphor system,Bio-Rad USA), gel unit (SDS-PAGE) and MALDI-TOF/TOF (4800 proteomic analyzer Applied Biosystem, USA) were used for successful separation and positive identification of proteins. To check the differential abundance of proteins among different treatments, PDQuest software was used for data analysis. For protein identification, Mascot search engine (http://www.matrixscience.com) using NCBIprot/SwissProt databases of rice was used. The analyzed data inferred comprehensive picture of key genes and their respective proteins involved in microbial consortium mediated improved plant growth and amelioration of As induced phyto-toxicity in rice. For the more comprehensive information of data, the related full-length article entitled “Microbial consortium mediated growth promotion and Arsenic reduction in Rice: An integrated transcriptome and proteome profiling” may be accessed. © 2022
Microbial consortium mediated growth promotion and Arsenic reduction in Rice: An integrated transcriptome and proteome profiling
(Academic Press, 2021) Surabhi Awasthi; Reshu Chauhan; Yuvraj Indoliya; Abhishek Singh Chauhan; ShashankKumar Mishra; Lalit Agrawal; Sanjay Dwivedi; Shiv Naresh Singh; Suchi Srivastava; Poonam C. Singh; Puneet Singh Chauhan; Debasis Chakrabarty; Sudhakar Srivastava; Rudra Deo Tripathi
The adverse effects of arsenic (As) contamination are well known. Rice is a staple food for 50% of the world population but the accumulation of As into rice hampers the food security and safety. Thus the amelioration of As stress and reduction of As levels in rice are needed. In this study, transcriptome (Illumina sequencing) and proteome (2D gel electrophoresis) explored mechanisms of consortium (P. putida+C. vulgaris) mediated growth promotion and As amelioration in rice. The rice seedlings grown hydroponically in the Hewitt nutrient medium and after acclimatization, exposed to 50 µM As alone as well as with microbial consortium to observe the impact at morphological and molecular level. The inoculation of microbial consortium significantly ameliorated the As toxicity, improved growth of root hairs and maintained cellular integrity of the epidermis, exodermis and the stele region during As exposure. Several genes showed differential expression in As and As+P. putida. Down-regulation of As transporters (OsPIP2;2 and OsPIP2;3, OsTIP2;1) and higher expression of WRKY gene (WRKY28) during As+P. putida+C.vulgaris suggested reduction of As uptake in rice. The up-regulation of nutrient elements transporters (OsZIFL9, OsZIFL5, OsZIFL12 and OsZIP2, OsYSL15 and OsCOPT6) in the presence of consortium indicated the improved nutrient status of rice. Higher expression of regulatory elements like auxin/indole 3 acetic acid (AUX/IAA), WRKY and myeloblastosis (MYB) TFs and down-regulation of defense responsive genes such Glutathione-S-transferase, Peroxidase and Glutaredoxinduring As+P. putida+C.vulgaris exposure was also observed. Proteome profiling demonstrated differential abundance of proteins involved in photosynthesis (chlorophyll a/b binding protein, photosystem I Fe-S centre), energy metabolism (ATP synthase subunit beta) transport, signaling (tubulin 1, actin 1), defense (glutathione S-transferase, phenylalanine ammonia lyase) and amino acid metabolism (cysteine synthase, glutamine synthetase), which supported the As ameliorative and growth-promoting potential of microbial consortium during As stress in rice plants. The study gives comprehensive information about gene and protein changes in rice plants in As+consortium exposure. © 2021 The Authors
Transcriptome and proteome analyses reveal selenium mediated amelioration of arsenic toxicity in rice (Oryza sativa L.)
(Elsevier B.V., 2020) Reshu Chauhan; Surabhi Awasthi; Yuvraj Indoliya; Abhishek Singh Chauhan; Shashank Mishra; Lalit Agrawal; Sudhakar Srivastava; Sanjay Dwivedi; Poonam C. Singh; Shekhar Mallick; Puneet Singh Chauhan; Veena Pande; Debasis Chakrabarty; Rudra Deo Tripathi
Arsenic (As), a chronic poison and non-threshold carcinogen, is a food chain contaminant in rice, posing yield losses as well as serious health risks. Selenium (Se), a trace element, is a known antagonist of As toxicity. In present study, RNA seq. and proteome profiling, along with morphological analyses were performed to explore molecular cross-talk involved in Se mediated As stress amelioration. The repair of As induced structural deformities involving disintegration of cell wall and membranes were observed upon Se supplementation. The expression of As transporter genes viz., NIP1;1, NIP2;1, ABCG5, NRAMP1, NRAMP5, TIP2;2 as well as sulfate transporters, SULTR3;1 and SULTR3;6, were higher in As + Se compared to As alone exposure, which resulted in reduced As accumulation and toxicity. The higher expression of regulatory elements like AUX/IAA, WRKY and MYB TFs during As + Se exposure was also observed. The up-regulation of GST, PRX and GRX during As + Se exposure confirmed the amelioration of As induced oxidative stress. The abundance of proteins involved in photosynthesis, energy metabolism, transport, signaling and ROS homeostasis were found higher in As + Se than in As alone exposure. Overall, present study identified Se responsive pathways, genes and proteins involved to cope-up with As toxicity in rice. © 2020 Elsevier B.V.