Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Salmo salar)

Abstract

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 b2 (itb2, 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 itb2 (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 (DRSCU) showed one negative (hsp70 c.1950C > T) and two positive DRSCU values (itb2 c.2275G > A; gsto-1 c.558G > A), suggesting that these

Carvacrol, Thymol, and Garlic Essential Oil Promote Skin Innate Immunity in Gilthead Seabream (Sparus aurata) Through the Multifactorial Modulation of the Secretory Pathway and Enhancement of Mucus Protective Capacity

“…GSTK1 belongs to the as Glutathione S-Transferase (GST) superfamily of oxidative stress enzymes, which are mainly known for their important role in cellular detoxification (116). GSTs have been used as markers for fish antioxidative capacity (117), including the evaluation of phytogenics in aquafeeds (118). Under stress-imposed conditions or injury, the transcription of skin gst is usually decreased and associated to immunosuppression in gilthead seabream (33).…”

Diet, Immunity, and Microbiota Interactions: An Integrative Analysis of the Intestine Transcriptional Response and Microbiota Modulation in Gilthead Seabream (Sparus aurata) Fed an Essential Oils-Based Functional Diet

“…Furthermore, glutathione plays important roles in nutrient metabolism and in the regulation of cellular events, such as gene expression, DNA and protein synthesis, cell proliferation and apoptosis, immune response, among others ( 67 ). Glutathione S-transferase is one of the key enzymes involved in the second phase of xenobiotics' metabolism and cellular detoxification, catalyzing the conjugation of reduced glutathione to various substances; thus, suggesting a key role in the host immune response modulation ( 68 ). Accordingly, in our transcriptional analysis, the glutathione S-transferase theta 2B ( gstt2b ) gene was observed to be upregulated in the intestine of gilthead seabream following the administration of dietary EOs.…”

Polymorphisms in Fc Gamma Receptors and Susceptibility to Malaria in an Endemic Population

“…The simplest approach uses the polymerase chain reaction (PCR) in combination with restriction enzyme digestion; this process is known as allelespecific restriction enzyme digestion (ASRED) and is able to differentiate alleles and single nucleotide polymorphisms (SNPs) or single nucleotide variants (SNVs). A SNP is a substitution occurring in at least 1% in the general population and an SNV is a variation of a single nucleotide without limitation of frequency (52)(53)(54). The advantages of this method are that it is relatively inexpensive and easy to perform (55).…”