Predicting the effects of non-synonymous amino acid variants on protein function in prolactin receptor of cattle and chicken using the MEGA-MD algorithm

Abstract

Prolactin receptor (PRLR) is a single transmembrane protein belonging to the  cytokine receptor super family through which prolactin plays a wide variety of  physiological roles such as mammary gland development, milk production,  reproduction and immune function in vertebrates. Many non synonymous single nucleotide polymorphisms (nsSNPs) at the PRLR locus in  vertebrates are suspected to impact protein function. This study, therefore, aimed at predicting the likelihood of non synonymous (amino acid change) coding SNPs to cause functional impact on protein at the PRLR locus of cattle and chicken using the MEGA MD bioinformatics tool. In cattle, sixteen out of the first twenty non synonymous amino substitutions obtained: V5A, T9V, T12I, N18S, T19V, C20S, L26S, E32K, F34V, R49E, T52A, S61T, R66K, M72I, I79K and H87Y were beneficial, one was likely neutral, two were deleterious while one was likely deleterious. However, in chicken, L131V, E132N, A134T, V135L, I157A and T161S mutations were found harmless, three were likely neutral, eight were deleterious while three were likely deleterious. This was  substantiated by the Evod (–10.70 65.32 versus 0.00-80.03), PolyPhen 2 (0.000- 0.859 versus 0.000-0.990) and SIFT  (0.16-1.00 versus 0.00-1.00) values in cattle and chicken, respectively. Theoretically, the harmful amino acid substitutions  would result in altered spatial structure and functions of the PRLR molecules. Further studies, however, are required to determine whether the beneficial amino acid substitutions obtained will affect the milk yield, reproductive and immune  functions of Nigerian livestock species.

Keywords: prolactin receptor; non-synonymous substitutions; bioinformatics tool; protein function; livestock.