Identification of novel polymorphism and in silico analysis of caprine DNAJB3 gene

Abstract

• DNAJB3, a molecular chaperon, was analysed first time both in vivo and in silico in goat. • In the amplified complete coding sequence of caprine DNAJB3, one nucleotide substitution at 419 th (C > A) position was identified. • In silico structural analysis predicted change in amino acid (Ala > Glu) at 140 th position with minor difference (7%) in three dimensional protein structure. • Computational analysis showed differential interaction of the wild and mutant type DNAJB3 proteins with other stress related proteins. DNAJB3 acts as a cochaperon and stimulates ATPase activity of HSP family genes through its J domain. An in vivo and in silico study was conducted to get comprehensive idea on the role of DNAJB3 gene in goat. The coding sequence of DNAJB3 gene was amplified and searched for polymorphism in three indigenous goat (i.e. Black Bengal, Ganjam and Raighar) populations. One nucleotide substitution at 419th (C > A) position (wild and mutant) with resultant change in amino acid (Ala > Glu) at 140th position was identified. The comparative nucleotide sequence analysis showed 68 variable sites that included 53 parismony informative sites and 15 singleton sites. In silico structural analysis revealed minor difference (7%) in three dimensional protein structure between mutant and wild type DNAJB3 proteins. The protein-protein interactions of DNAJB3 with HSP72, JNK stress kinase, and IKKβ stress kinase were also predicted. The mutant (Raighar) type DNAJB3 protein predicted to interact only with A chain of the JNK stress kinase. Both the wild and mutant type variants of DNAJB3 proteins predicted to interact with A and B chain of hexamer IKKβ stress kinase. This study will be helpful to use DNAJB3 as a molecular marker for thermal tolerance in future.