Abstract
Background: Double stranded RNA (dsRNA) dependent protein kinase (PKR) is an interferon (IFN) stimulated antiviral protein. It inhibits protein synthesis by phosphorylation of the eukaryotic translation initiation factor 2-alpha (eIF2-α) by its serine-threonine kinase activity that prevents virus replication. This is the first report on the in silico analysis of PKR coding region and its promoter from a Coldwater fish of the Indian Himalayan region. Snow trout, Schizothorax richardsonii is an important Coldwater food fish. It is being over fished and therefore requires conservation. Being a vulnerable species it is listed under the red list of IUCN. Here we discuss the identification, cloning and sequencing of PKR coding region and its promoter. Results: We have revealed the complete coding region of dsRNA dependent protein kinase (PKR) and its promoter from Schizothorax richardsonii , one of the several species of snow trout inhabiting sub-Himalayan fresh water bodies. An amplicon of 2884bp containing 5ʹ and 3ʹ untranslated regions (UTR) of 234 and 558 bases was obtained while the deduced open reading frame (ORF) of 2076 bases encoded a polypeptide of 691 amino-acids. Snow trout PKR protein contains three double stranded RNA binding motifs (dsRBM) at N terminal, besides possessing a serine/threonine protein kinase and a C terminal catalytic domain. Moreover, a stretch of 791 nucleotide bases was identified as the promoter upstream the ORF. The identified promoter has two interferon stimulated response elements (ISRE) besides the presence of core promoter elements. Moreover, the snow trout PKR promoter has a TATA box but lacks kinase conserved sequence (KCS) that is present in mammalian PKR promoters. Conclusion: The promoter of snow trout was identified as a stretch of 791 nucleotide bases. It has two interferon-stimulated response elements (ISRE) besides core promoter elements. Intriguingly, unlike the mammalian PKR promoter, the snow trout PKR promoter has a TATA box but lacks the conserved kinase sequence (KCS) present in human counterpart. Keywords: Schizothorax richardsonii , Interferon Stimulated Genes, PKR protein, Antiviral state, Homology modeling, dsRNA binding protein kinase
Schizothorax richardsonii dsRNA dependent protein kinase has three double-stranded RNA binding motifs with a promoter lacking conserved kinase sequence
