In Silico Sequence Analysis, Structure Prediction and Function Annotation of Melanocortin 1 Receptor Gene (MC1R) from the Guppy Poecilia reticulata

Abstract

The common guppy, Poecilia reticulata is one of the most popular aquarium fish used as a model organism in toxicology, embryology and genetical studies. Vibrant colors in males are a secondary sexual character which attracts the females for mating. Pigmentation in guppy is found to be linked with melanin synthesis. Melanocortin genes are involved in the synthesis of melanin pigments. Alteration in Melanocortin 1 Receptor (MC1R) genes results in polymorphism. Analysis of the MC1R gene of Poecilia reticulata revealed a 966 bp open reading frame encoding 322 amino acids. The deduced MC1R protein sequence was predicted to possess three domains: 7TM GPCR (7 transmembrane G-protein-coupled receptor) chemoreceptor Srsx at the N-terminal, 7 TM receptor and the G-protein-coupled chemokine receptor like protein domain at the C-terminal. Predicted mutations in the MC1R protein sequence shows Indel (Insertion and deletion) and block mutations. Phylogenetic analysis revealed that MC1R of Poecilia reticulata and other fish species were separated from other vertebrates. The 3D structure of the 54-105 region of MC1R protein predicted for the first time comprised of two helices namely α1 and α2 from amino acid residues 59-69 and 86-97 respectively. The extracellular region is composed of two loops from amino acid residues 54-58 at the N-terminal and 88-105 at C-terminal. The intracellular region of the receptor contains a beta turn from the amino acid residues 71-73 which connects the α1 and α2 helices by means of a loop. Docking of α-MSH, ligand (Ca²⁺ ions and Cholesterol) interactions and the presence of CRAC domain (Cholesterol Recognition Amino acid Consensus sequence) within the TM region of receptor further reiterates the predicted structure has a definite functional role in pigmentation.