Expression profile and in silico characterization of novel RTF2h gene under oxidative stress in Indian catfish, Clarias magur (Hamilton 1822).

Abstract

During the investigation of genes involved in the hypoxia tolerance, novel transcript, Replication Termination Factor 2 homologue (RTF2h), was found to be differentially expressed in brain of Clarias magur (previous name, C. batrachus) whose function was still undefined. Thus, present study was aimed to examine the transcriptional response of novel RTF2h gene, for its possible involvement in hypoxia tolerance in C. magur. Novel transcripts expressed under hypoxic stress were identified from ESTs obtained from SSH libraries of C. magur. Homology analysis of novel transcript (JK487668) revealed it to have RING superfamily signature and was closely related with RTF2 homologue. To characterize the expression pattern of CmRTF2h gene in different tissues of C. magur, qRT-PCR analysis was performed which showed significant increased expression, in spleen following short-term hypoxia exposure (12H; 2.33-fold), while after long-term hypoxia exposure, significant up-regulation was found three tissues: in spleen (6.57-fold), liver (2.31-fold) and head kidney (2.99-fold) and was down-regulated in brain (3.52-fold). Further, the consensus sequence, obtained from SSH EST sequence and transcripts from hypoxia induced transcriptome data, through multiple sequence alignments, homology modeling and phylogentic analysis together, confirmed it as a novel CmRTF2h gene. In-silico protein-protein interaction and docking studies suggested its closely related function to that of RTF2. The present study reports the expression pattern of CmRTF2h under hypoxia. The up-regulated expression of CmRTF2h under hypoxic conditions may contribute to defense mechanism against induced DNA damage, which in turn may of adaptive significance for hypoxia tolerance in C. magur.