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Online Journal of Bioinformatics ©
Volume 12(1):175-197, 2011
In silico identification of residues for anoxia tolerance across species.
Tanmaya Kumar Sahu (M.Sc.)1, A.R. Rao (PhD)1*, Alka Singh (M.Sc.), B.K. Behera (PhD)2 and T. Mohapatra (PhD)3
1Indian Agricultural Statistics Research Institute, New Delhi, 2Central Inland Fishery Research Institute, Barrackpore, Kolkata,3National Research Centre on Plant Biotechnology, New Delhi, India
Sahu TK, Rao AR, Singh A, Behera BK, Mohapatra T., In silico identification of residues for anoxia tolerance across species, Onl J Bioinform., 12(1):175-197, 2011. Anoxia is an important abiotic stress factor which negatively impacts agricultural systems. Vitellogenin (VTG), an anoxia tolerant gene, is widely reported in fish and other oviparous species. Similarly, Submergence 1, a submergence tolerance gene is reported in rice. It is expected that there must be a common mechanism during the process of evolution in which both genes exhibited tolerance to reduced oxygen across species. In silico conserved/key residues responsible for anoxia tolerance across species are described. Initially, the protein domain of vitellogenin gene of Danio rerio was extracted and subjected to similarity searches across species. Selected proteins from similarity search were compared with the submergence 1 gene products of plant species, specifically, with Oryza species to identify the conserved regions of interest by multiple sequence alignment. Residue(s) conservation was determined across species by in silico proteomic analysis. Results show that the residue arginine was conserved at a defined position in the final alignment profile of proteins of the species studied and identified as a key residue responsible for reduced oxygen tolerance across species. From an evolutionary point of view, proteins responsible for submergence tolerance in aquatic plants were found much closer to the proteins responsible for anoxia tolerance in fishes.
Keywords:Anoxia, Zebrafish, Vitellogenin, Apolipophorin, Apolipoprotein, Submergence, Oryza sativa, Oryza rufipogon, Oryza nivara, Abiotic stress.