Single-nucleotide polymorphisms (SNPs) are single genetic code variations
considered one of the most common forms of nucleotide modifications. Such SNPs
can be located in genes associated to immune response and, therefore, they may
have direct implications over the phenotype of susceptibility to infections
affecting the productive sector. In this study, a set of immune-related genes
(cc motif chemokine 19 precursor [ccl19], integrin β2 (itβ2, also named cd18),
glutathione transferase omega-1 [gsto-1], heat shock 70 KDa protein [hsp70],
major histocompatibility complex class I [mhc-I]) were analyzed to identify SNPs
by data mining. These genes were chosen based on their previously reported
expression on infectious pancreatic necrosis virus (IPNV)-infected Atlantic
salmon phenotype. The available EST sequences for these genes were obtained from
the Unigene database. Twenty-eight SNPs were found in the genes evaluated and
identified most of them as transition base changes. The effect of the SNPs
located on the 5'-untranslated region (UTR) or 3'-UTR upon transcription factor
binding sites and alternative splicing regulatory motifs was assessed and ranked
with a low-medium predicted FASTSNP score risk. Synonymous SNPs were found on
itβ2 (c.2275G > A), gsto-1 (c.558G > A), and hsp70 (c.1950C > T) with low
FASTSNP predicted score risk. The difference in the relative synonymous codon
usage (RSCU) value between the variant codons and the wild-type codon (ΔRSCU)
showed one negative (hsp70 c.1950C > T) and two positive ΔRSCU values (itβ2
c.2275G > A; gsto-1 c.558G > A), suggesting that these synonymous SNPs (sSNPs)
may be associated to differences in the local rate of elongation. Nonsynonymous
SNPs (nsSNPs) in the gsto-1 translatable gene region were ranked, using SIFT and
POLYPHEN web-tools, with the second highest (c.205A > G; c484T > C) and the
highest (c.499T > C; c.769A > C) predicted score risk possible. Using homology
modeling to predict the effect of these nonsynonymous SNPs, the most relevant
nucleotide changes for gsto-1 were observed for the nsSNPs c.205A > G, c484T >
C, and c.769A > C. Molecular dynamics was assessed to analyze if these GSTO-1
variants have significant differences in their conformational dynamics,
suggesting these SNPs could have allosteric effects modulating its catalysis.
Altogether, these results suggest that candidate SNPs identified may play a
crucial potential role in the immune response of Atlantic salmon.
