Molecular cloning and in silico analysis of elongation factor 1A in Schizothorax richardsonii

Abstract

In this manuscript, we report the cloning and in silico characterization of elongation factor 1A in a coldwater Trans-Himalayan cyprinid, Schizothorax richardsonii. The sequenced elongation factor 1A (SrEF1A) consisted of 1290 bp long partial ORF, which included a start codon (ATG) and 430 deduced amino acids. The SrEF1A sequence showed high homology (≥90%) with other teleosts and higher vertebrates. Phylogenetic analysis, multiple sequence alignment and prediction of conserved residues indicated a close evolutionary relationship among the cyprinids and conservation of SrEF1A protein across the vertebrate class. The deduced SrEF1A protein did not contain any signal peptide, but had two potential N-glycosylation motifs at 284th and 314th amino acid residue. Presence of many serine, threonine and tyrosine phosphorylation sites was also predicted, suggesting a potential post-translational regulation of the SrEF1A protein. In silico predictions of sub-cellular localization, function and protein-protein network illustrate the role of SrEF1A in the protein synthesis machinery of the cell. Finally, a reliable tertiary structure of SrEF1A protein was predicted with ten helixes and nineteen beta sheets. Ligand (GDP) binding sites in the tertiary structure were predicted at 15-22, 154, 156, 157 and 194-196 amino acid residues.