Functional in silico analysis of a non-synonymous SNP located in the coding region of the FASN gene in Korean native cattle

Abstract

Bovine fatty acid synthase, an enzyme encoded by the FASN gene in cattle, is a multi-enzyme protein that catalyses fatty acid synthesis. This cytosolic enzyme catalyzes the synthesis of palmitate from acetylcoenzyme A and malonyl-coenzyme A in the presence of nicotinamide adenine dinucleotide phosphate (NADPH). However, there is no previous verification study that each allele of SNPs related to lipid synthesis were impact on protein function in Korean native cattle and nsSNPs for the FASN gene have not yet been verified by computer analysis. Given the role of the FASN gene in beef quality traits in cattle, the study aimed to use computational analysis to narrow down the candidate nsSNPs for FASN that may affect protein structure and/or function, which may play an important role in lipid synthesis. These results predicted that the g.16039 T>C nsSNP at position R1957Y of FASN was functionally 'Deleterious' and 'PROBABLY DAMAGING' in non-synonymous SNP functional analysis, and the g.16039 T>C and g.17924 A>G nsSNPs at positions R1957Y and T2266A decrease the stability of a FASN protein and have two PTM sites for proteolytic cleavage and amidation. In addition, the R1957Y and T2266A variants of FASN were shown to have a direct effect on altering the protein structure. Therefore, we suggested that our results could be used as fundamental data for further studies related to functional verification of nsSNPs based on bovine cells.