Non-synonymous Amino Acid Substitutions Research Articles

A Haplotype-Based Analysis of the PTPN22 Locus in Type 1 Diabetes

A recent addition to the list of widely confirmed type 1 diabetes risk loci is the PTPN22 gene encoding a lymphoid-specific phosphatase (Lyp). However, evidence supporting a role for PTPN22 in type 1 diabetes derives entirely from the study of just one coding single nucleotide polymorphism, 1858C/T. In the current study, the haplotype structure of the PTPN22 region was determined, and individual haplotypes were tested for association with type 1 diabetes in family-based tests. The 1858T risk allele occurred on only a single haplotype that was strongly associated with type 1 diabetes (P = 7.9 x 10(-5)). After controlling for the effects of this allele, two other haplotypes were observed to be weakly associated with type 1 diabetes (P < 0.05). Sequencing of the coding region of PTPN22 on these haplotypes revealed a novel variant (2250G/C) predicted to result in a nonsynonymous amino acid substitution. Analysis of PTPN22 transcripts from a subject heterozygous for this variant indicated that it interfered with normal mRNA splicing, resulting in a premature termination codon after exon 17. These results support the conclusion that the 1858C/T allele is the major risk variant for type 1 diabetes in the PTPN22 locus, but they suggest that additional infrequent coding variants at PTPN22 may also contribute to type 1 diabetes risk.

Coding region polymorphisms in T cell signal transduction genes. Prevalence and association to development of multiple sclerosis

We systematically assessed 53 genes involved in T cell signaling, among which 72 SNPs in 32 genes were reported in databases as causing non-synonymous amino acid substitutions. Screening of 41 of these SNPs in DNA pools from 4000 Norwegian controls showed that only 12 SNPs (29%) were polymorphic. These were tested for association to MS in DNA pools from 364 Norwegian MS patients. To eliminate sources of variance introduced by DNA pooling, the SNPs in the best-ranked PLCG1 as well as the PTPN22 gene were thereafter genotyped in individual MS and control samples, however, without finding evidence for association to MS.

Polymorphisms of the porcine dopamineβ‐hydroxylase gene and their relation to reproduction and piglet survivability in an Iberian × Meishan F2 intercross

The goals of this study were to sequence and physically map the porcine dopaminebeta-hydroxylase (DBH) gene, as well as to perform an association study between polymorphisms of this gene and the reproductive performance and piglet survivability of F(2) pigs from an Iberian x Meishan cross. The porcine DBH gene was positioned by RH mapping near the telomere of chromosome 1q2.13, close to markers SSC10D08 and SW1301. Sequencing of DBH cDNAs from 10 pigs revealed the existence of six nucleotide polymorphisms, two of which led to non-synonymous amino acid substitutions within exon 3 at positions 463A>G and 616A>G that corresponded to Thr155Ala and Lys206Glu respectively. Three haplotypes segregated in an Iberian x Meishan population: DBH(X) (A(436)-A(616)), DBH(Y) (A(436)-G(616)) and DBH(Z) (G(436)-G(616)). The DBH haplotypes significantly affected rectal temperatures 1 h after birth (P = 0.002) and have a suggestive effect on the time to first colostrum intake (P = 0.019) and on birth weight (P = 0.019).

Antigenic and molecular characterization of isolates of the Italy 02 infectious bronchitis virus genotype

As part of an epidemiological surveillance of infectious bronchitis virus (IBV) in Spain, four Spanish field isolates showed high S1 spike sequence similarities with an IBV sequence from the GenBank database named Italy 02. Given that little was known about this new emergent IBV strain we have characterized the four isolates by sequencing the entire S1 part of the spike protein gene and have compared them with many reference IBV serotypes. In addition, cross-virus neutralization assays were conducted with the main IBV serotypes present in Europe. The four Spanish field strains and the Italy 02 S1 sequence from the NCBI database were established as a new genotype that showed maximum amino acid identities with the 4/91 serotype (81.7% to 83.7%), the D274 group that included D207, D274 and D3896 strains (79.8% to 81.7%), and the B1648 serotype (79.3% to 80%). Furthermore, on the basis of these results, it was demonstrated that the Italy 02 genotype had been circulating in Spain since as early as 1997. Based on the average ratio of synonymous:non-synonymous (dS/dN) amino acid substitutions within Italy 02 sequences, no positive selection pressures were related with changes observed in the S1 gene. Moreover, phylogenetic analysis of the S1 gene suggested that the Italy 02 genotype has undergone a recombination event. Virus neutralization assays demonstrated that little antigenic relatedness (less than 35%) exists between Italy 02 and some of the reference IBV serotypes, and indicated that Italy 02 is likely to be a new serotype.

Intraspecific variation in the rainbow trout mitochondrial DNA genome

Four complete mitochondrial DNA genomes for rainbow trout, Oncorhynchus mykiss, were sequenced and compared to the previously reported complete mitochondrial sequence. Analyses revealed 13 additional bp and 31 insertion/deletion (indels) sites between the four new sequences and the previously published sequence. Twenty-eight indels were single base pairs while the remaining were multiple base pair insertions, two in the ATPase6 gene, one of three bases and one of nine bases, and a two base insert in the control region. Indels in the new genomes were compared to a wide range of salmonid species and corresponded with sequences in closely related species, indicating that errors were likely incorporated into the previously published sequence. Although variable nucleotide positions were observed throughout the newly sequenced genomes, non-synonymous amino acid substitutions were observed in only six of seven ND genes. While there were only 14 amino acid substitutions between genomes, K a/ K s ratios ranged between 0 and 1. A single amino acid deletion in the ND1 coding region unique to rainbow trout was also detected. Using complete mitochondrial genomes for all sequenced Salmonidae species, a phylogenetic analysis was performed to establish a salmonid mitochondrial phylogeny revealing support for Salvelinus, rather than Salmo, as the sister taxa to Oncorhynchus.

Lrrk2 pathogenic substitutions in Parkinson's disease

Leucine-rich repeat kinase 2 (LRRK2) mutations have been implicated in autosomal dominant parkinsonism, consistent with typical levodopa-responsive Parkinson's disease. The gene maps to chromosome 12q12 and encodes a large, multifunctional protein. To identify novel LRRK2 mutations, we have sequenced 100 affected probands with family history of parkinsonism. Semiquantitative analysis was also performed in all probands to identify LRRK2 genomic multiplication or deletion. In these kindreds, referred from movement disorder clinics in many parts of Europe, Asia, and North America, parkinsonism segregates as an autosomal dominant trait. All 51 exons of the LRRK2 gene were analyzed and the frequency of all novel sequence variants was assessed within controls. The segregation of mutations with disease has been examined in larger, multiplex families. Our study identified 26 coding variants, including 15 nonsynonymous amino acid substitutions of which three affect the same codon (R1441C, R1441G, and R1441H). Seven of these coding changes seem to be pathogenic, as they segregate with disease and were not identified within controls. No multiplications or deletions were identified.

Combined monogenic hypercholesterolemia and hypoalphalipoproteinemia caused by mutations in LDL-R and LCAT genes

We studied a three generation family with co-dominant monogenic hypercholesterolemia and hypoalphalipoproteinemia. The proband, a 48 year-old male, was found to be heterozygous for a previously reported mutation in LDL receptor ( LDL-R) gene (IVS15–3 c>a) and a novel mutation in exon 6 of lecithin cholesterol acyltransferase ( LCAT) gene (c.803 G>A) causing a non-synonymous amino acid substitution (p.R244H). These mutations segregated independently in the family. The LDL-R mutation was associated with high levels of LDL-C (6.20–9.85 mmol/L) and apo B (170–255 mg/dL), comparable to those previously reported in carriers of the same mutation. The LCAT mutation was associated with low levels of HDL-C (0.67–0.80 mmol/L) and apo A-I (96–110 mg/dL). The proband had reduced LCAT function, as measured by cholesterol esterification rate (29 nmol/(mL/h) versus 30–60 nmol/(mL/h)), LCAT activity (10 nmol/(mL/h) versus 20–55 nmol/(mL/h)) and LCAT mass (2.87 μg/mL versus 3.1–6.7 μg/mL). Carriers of LCAT mutation had lower LCAT activity and a tendency to reduced cholestrol esterification rate (CER) and LCAT mass as compared to non-carrier family members. The LCAT mutation was not found in 80 control subjects and 60 patients with primary hypoalphalipoproteinemia. Despite the unfavourable lipoprotein profile, the proband had only mild clinical signs of atherosclerosis. This unexpected finding is probably due to the intensive lipid lowering treatment the patient has been on over the last decade.

Complexity and diversity of hepatitis C virus RNA in african americans and whites: analysis of the envelope-coding domain.

African Americans infected with hepatitis C virus (HCV) are less responsive than whites to interferon-based therapy. HCV quasi species have been implicated. Quasi-species complexity and diversity were evaluated in matched African American and white individuals. Complexity and diversity in the first hypervariable region were similar in the 2 groups. Both the frequency of nonsynonymous amino acid substitutions and the mean ratio of nonsynonymous mutations to synonymous mutations were greater in clones derived from white patients. Racial differences in amino acid usage at otherwise conserved positions were observed. Differences in amino acid representation at key positions are suggestive of immunologic and functional selection along racial lines.

Identification of NAD +-dependent isocitrate dehydrogenase 3 γ-like (IDH3GL) gene and its genetic polymorphisms

We have identified a novel human gene designated as IDH3GL (isocitrate dehydrogenase 3 γ-like) that is expressed specifically in human testis. The gene corresponds in sequence to an EST (expressed sequence tag) A1476435 that was first detected by differential expression analysis using a microarray assay. The full-length cDNA sequence (1037 bp) was isolated from the human testis 5′-3′-RACE cDNA libraries and found to have 83% nucleotide sequence identity with part of the IDH3G ( isocitrate dehydrogenase 3 γ). The IDH3GL gene consists of 3 exons spanning approximately 220 kb within the region of the NELL1 gene on chromosome 11p15.1. Sequence analysis of the IDH3GL cDNA revealed the presence of a premature stop codon at nucleotide positions 337–339 that results in a truncated peptide with 112 amino acids. This stop codon is conserved in various human ethnic populations and in the chimpanzee ( Pan troglodytes). In order to assess the functional status of IDH3GL, especially in relation to the presence of the putative premature stop codon, single nucleotide polymorphisms (SNPs) were screened in the upstream, coding and non-coding regions of the IDH3GL gene in a Japanese population. As a result, a total of 10 SNPs were identified, seven were novel and one of them was a non-synonymous amino acid substitution from Leu to Val. We conclude that the IDH3GL gene sequence is a splice variant of the NELL1 gene and that it probably evolved from a transposed pseudogene of the IDH3 gene.

The HLA-DOB gene displays limited polymorphism with only one amino acid substitution.

The HLA-DO molecule is a non-classical class II heterodimer composed of alpha and beta chains. We have previously recognized that all eight of the allelic variations of the HLA-DOA gene represent non-synonymous amino acid substitution. In the present study, to analyze genetic polymorphism and allelic variation of the HLA-DOB gene which may affect the efficiency of class II restricted antigen presentation thereby being involved in the susceptibility of HLA associated diseases, we conducted direct DNA sequencing of HLA-DOB in 36 HLA class II homozygous typing cells and identified six new allelic variations (DOB*0101101, *0101102, *01012, *01022, *0104101 and *0104102) including five single nucleotide polymorphisms with only one amino acid substitution. Furthermore, strong linkage disequilibrium was detected between DOB*01022 and DRB1*1502 only, with no linkage disequilibrium between the DOA and the DOB genes. The HLA-DOB gene has been identified in other mammals, and their nucleotide sequences are well conserved. These facts suggest that limited polymorphism in the DOB gene is profitable to execute their unique function as a co chaperone and so strong selective pressure is operating to prevent generic variation against the DOB molecule interacting with the DM molecule and thus maintaining the specified immunological function of regulating antigen presentation.

Primate DAX1, SRY, and SOX9: Evolutionary Stratification of Sex-Determination Pathway

The molecular evolution of DAX1, SRY, and SOX9, genes involved in mammalian sex determination, was examined in six primate species. DAX1 and SRY have been added to the X and Y chromosomes, respectively, during mammalian evolution, whereas SOX9 remains autosomal. We determined the genomic sequences of DAX1, SRY, and SOX9 in all six species, and calculated K(a), the number of nonsynonymous substitutions per nonsynonymous site, and compared this with the K(s), the number of synonymous substitutions per synonymous site. Phylogenetic trees were constructed by means of the DAX1, SRY, and SOX9 coding sequences, and phylogenetic analysis was performed using maximum likelihood. Overall measures of gene and protein similarity were closer for DAX1 and SOX9, but DAX1 exhibited nonsynonymous amino acid substitutions at an accelerated frequency relative to synonymous changes, similar to SRY and significantly higher than SOX9. We conclude that, at the protein level, DAX1 and SRY are under less selective pressure to remain conserved than SOX9, and, therefore, diverge more across species than does SOX9. These results are consistent with evolutionary stratification of the mammalian sex determination pathway, analogous to that for sex chromosomes.

Identification of 167 polymorphisms in 88 genes from candidate neurodegeneration pathways.

Catalogs of intra-gene polymorphisms are needed to facilitate wide-ranging candidate gene-based association studies in common complex diseases. With this in mind, we have scanned multiple alignments of expressed sequence tags and of genomic DNA sequences (PCR products from four to eight unrelated individuals) to find polymorphisms in 195 genes putatively involved in neurodegenerative illness (including components of oxidative stress, excitotoxicity, inflammation, apoptosis and aging). This led to the discovery of 167 polymorphisms in 88 genes. These comprised 163 single nucleotide polymorphisms, one insertion/deletion, and three other variations involving more than one base pair. The polymorphisms were distributed in the exons (87), introns (70), and gene flanking regions (10). Of the exonic polymorphisms, 17 would give rise to non-synonymous amino acid substitutions. These findings now provide a valuable resource for association studies in neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease.

Limited polymorphism in the HLA-DOA gene.

The HLA-DO molecule, a heterodimer consisting of two novel members of the class II gene family, DOA and DOB, has recently been suggested to function as an important modulator in the HLA class II restricted antigen presentation pathway by interaction with the HLA-DM molecule. In this study, we have analyzed genetic polymorphism and allelic variation of the HLA-DOA gene in 37 HLA class II homozygous typing cells using the direct DNA sequencing technique. As a result, we recognized at least eight allelic variations, DOA*01011, *0101201, *0101202, *0101203, *01013, *0101401, *0101402 and *01015. None of them, however, result in amino acid substitution. The HLA-DOA gene has been identified in other mammals as well, and the nucleotide sequences were well conserved among these species. These results suggest that the DOA molecule has undergone strong selective pressure to preserve functional structure and conformation required for interaction with the DM molecule, preventing non-synonymous amino acid substitution.

Terms of service--1805

<h3>Abstract</h3> Genomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27^th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins, in which 9 unique locations were detected relative to the global strains, including 516E&gt;Q in the boundary of the ACE2 binding region. The most dominated variant G614 (95%) based in spike protein is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%. <h3>Highlights</h3> We have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh. A total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected. The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year. Nine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative to the global SARS-CoV-2 strains.