AMPLIFICATION, SEQUENCING AND BIOINFORMATIC CHARACTERIZATION OF TRANSMEMBRANE PROTEIN 95 GENE (TMEM95) IN MURRAH BUFFALO (Bubalus bubalis)
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Date
2017-01
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SRI VENKATESWARA VETERINARY UNIVERSITY TIRUPATI – 517 502. (A.P) INDIA
Abstract
ABSTRACT:
TMEM95 gene is known to be involved in idiopathic male subfertility in cattle. It is required for the integrity of sperm plasma membrane and thus has a role in fertilization. The present study was aimed at bioinformatic characterization of the Transmembrane protein 95 (TMEM95) gene in Murrah buffalo. The TMEM95 gene was amplified and sequenced in Murrah. Analysis with CodonCode Aligner revealed three heterozygous positions in Murrah sequence at positions 1284 (T and G), 1460 (C and A) and 1897 (G and A) with respect to the 2631 bp reference fragment from the Hereford cattle genome assembly. A 2 bp deletion (at 937 bp) was observed in Murrah buffalo which is causing frame shift mutation. The isoforms were predicted using GeneWise, a comparative gene annotation tool and found that the 2bp deletion resulted in the truncation of isoforms 1, 3 and 4 and were unlikely to form. The transmembrane topology and signal peptide were predicted using Phobius program, and it was observed that the isoforms 1, 2 and 3 doesn’t have any transmembrane domains but the isoform 5 has two transmembrane domains. Analysis of isoforms with MotifScan predicted the presence of Casein kinase II phosphorylation site, which has an important role in sperm morphology. Leucine zipper pattern, N-myristoylation site, protein kinase C phosphorylation site, CHRD domain profile, N-glycosylation site and HIT zinc finger motifs were also predicted. Divergence analysis was carried out for the TMEM95 region across different mammalian species and less divergence was observed among cattle, bison, yak and mithun. Buffalo and sheep are moderately divergent from cattle. Based on the sequence analysis and functional prediction, it was concluded that the TMEM95 gene in Murrah buffalo is likely to have function in male fertility. However there may be some species-specific differences with respect to their function between the two species.