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.