Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites

AbstractComparison of relative fixation rates of synonymous (silent) and nonsynonymous (amino acid-altering) mutations provides a means for understanding the mechanisms of molecular sequence evolution. The nonsynonymous/synonymous rate ratio (ω = dN/dS) is an important indicator of selective pressure at the protein level, with ω = 1 meaning neutral mutations, ω < 1 purifying selection, and ω > 1 diversifying positive selection. Amino acid sites in a protein are expected to be under different selective pressures and have different underlying ω ratios. We develop models that account for heterogeneous ω ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences. These models are useful for testing for adaptive molecular evolution and identifying amino acid sites under diversifying selection. Ten data sets of genes from nuclear, mitochondrial, and viral genomes are analyzed to estimate the distributions of ω among sites. In all data sets analyzed, the selective pressure indicated by the ω ratio is found to be highly heterogeneous among sites. Previously unsuspected Darwinian selection is detected in several genes in which the average ω ratio across sites is <1, but in which some sites are clearly under diversifying selection with ω > 1. Genes undergoing positive selection include the β-globin gene from vertebrates, mitochondrial protein-coding genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to the specific distributional form assumed for ω and can be achieved using any of several models we implement. However, we encountered difficulties in estimating the precise distribution of ω among sites from real data sets.

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The role of HLA typing in rheumatic diseases

Molecular and experimental biology in medicine ◽

10.33602/mebm.3.1.1 ◽

2020 ◽

Vol 3 (1) ◽

pp. 1-8

Author(s):

Luca Mascaretti ◽

Elena Bevilacqua

Keyword(s):

Rheumatoid Arthritis ◽

Juvenile Idiopathic Arthritis ◽

Amino Acid ◽

Ankylosing Spondylitis ◽

Hla Class I ◽

Acid Sites ◽

Hla Typing ◽

Erosive Disease ◽

Complex Cases

Association between HLA-DR4 and rheumatoid arthritis (RA) has been known for 4 decades, and amino acid sites within HLA-DRB1 (11/13, 71, 74) are highly associated with RA. HLA is not useful for diagnosis or prognosis, but it may help predict severe and erosive disease. Since 90% of patients with ankylosing spondylitis (AS) and 50-70% of other spondyloarthritis (SpA) patients are HLA-B*27 positive, HLA is a stronghold of diagnostic algorithms. Genetic predisposition to juvenile idiopathic arthritis (JIA) is mainly due to HLA class II, and to a lesser extent to HLA class I. Although HLA plays a role in rheumatic disorders, its clinical relevance is not homogeneous. When classical biomarkers are lacking or in complex cases, HLA typing may provide support for the management of patients.

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Capsid Assembly is Regulated by Amino Acid Residues Asparagine 47 and 48 in The VP2 Protein of Porcine Parvovirus

10.21203/rs.3.rs-72147/v1 ◽

2020 ◽

Author(s):

Jucai Wang ◽

Yunchao Liu ◽

Yumei Chen ◽

Teng Zhang ◽

Aiping Wang ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Vaccine Development ◽

Acid Sites ◽

Site Directed Mutagenesis ◽

Porcine Parvovirus ◽

Capsid Assembly ◽

Structural Protein ◽

Native Page ◽

Vp2 Protein

Abstract Background: Porcine parvovirus (PPV) is a major cause of reproductive failure in swine, and has caused huge losses throughout the world. Viral protein 2 (VP2) of PPV is a major structural protein that can self-assemble into virus-like particles (VLP) with hemagglutination (HA) activity. In order to identify the essential residues involved in the mechanism of capsid assembly and to further understand the function of HA, we analyzed a series of deletion mutants and site-directed mutations within the N-terminal of VP2 in the Escherichia coli (E. coli) system. Results: Our results showed that deletion of first 47 amino acids from the N-terminal of VP2 protein did not affect capsid assembly, and further truncation to residue 48 Asparagine (Asn, N) caused detrimental effects. Site-directed mutagenesis experiments demonstrated that residue 47Asn reduced the assembly efficiency of PPV VLP, while residue 48Asn destroyed the stability, hemagglutination, and self-assembly characteristics of the PPV VP2 protein. These findings indicated that the residues 47Asn and 48Asn are important amino acid sites to capsid assembly and HA activity. Results from Native PAGE inferred that macromolecular polymers were critical intermediates of the VP2 protein during the capsid assembly process. Site-directed mutation at 48Asn did not affect the association of monomers to form into oligomers, but destroyed the ability of oligomers to assemble into macromolecular particles, influencing both capsid assembly and HA activity. Conclusions: These results demonstrated that PPV capsid assembly is a complex process that is regulated by amino acids 47Asn and 48Asn, which are located at the N-terminal of VP2 and closely related to the association of macromolecular particles. Our findings provide valuable information on the mechanisms of PPV capsid assembly and the possibility of chimeric VLP vaccine development by replacing as much as 47 amino acids at the N-terminal of VP2 protein.

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Biosynthesis of a phosphatidylinositol-glycan-linked membrane protein: signals for posttranslational processing of the Ly-6E antigen

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3369-3376.1989 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3369-3376

Author(s):

B Su ◽

A L Bothwell

Keyword(s):

Amino Acid ◽

Surface Protein ◽

Proteolytic Cleavage ◽

Acid Sites ◽

Cell Surface Protein ◽

Mutant Proteins ◽

Cos Cells ◽

Amino Acid Peptide ◽

Peripheral T Cells ◽

Carboxy Terminal

The Ly-6E/A protein is a murine cell surface protein expressed at high levels on activated peripheral T cells. The only linkage known to be responsible for its association with the plasma membrane is a phosphatidylinositol-glycan (PI-G) moiety. To examine the biosynthesis of this structure, we constructed a series of mutants of Ly-6E that were expressed in COS cells by using transient-transfection procedures. When 12 or 20 carboxy-terminal residues were deleted from the primary translation product, the PI-G modification was completely abolished and the mutant proteins became secreted. Addition of the PI-G tail was partially inhibited when the charged 12-amino-acid peptide found as a cytoplasmic tail on the transmembrane form of LFA-3 was added to the COOH terminus of the Ly-6E protein. Proteolytic cleavage occurred on this mutant protein, but the PI-G moiety was added to only 50% of the molecules. Changing an Asn residue to a Lys at the hypothetical cleavage site resulted in a PI-G-linked protein having a detectable alteration in electrophoretic mobility. This finding raises the possibility that proteolytic cleavage at other amino acid sites may occur and that PI-G attachment can occur at this new site. A model identifying two regions that may act as necessary signals for the biosynthesis of the PI-G tail is presented.

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Combing Transcriptomes for Secrets of Deep-Sea Survival: Environmental Diversity Drives Patterns of Protein Evolution

Integrative and Comparative Biology ◽

10.1093/icb/icz063 ◽

2019 ◽

Vol 59 (4) ◽

pp. 786-798 ◽

Cited By ~ 3

Author(s):

J R Winnikoff ◽

W R Francis ◽

E V Thuesen ◽

S H D Haddock

Keyword(s):

Amino Acid ◽

Amino Acid Level ◽

Hydrophobic Effect ◽

Extreme Environments ◽

Environmental Parameters ◽

Acid Sites ◽

Temperature Adaptation ◽

Environmental Diversity ◽

Cofactor Binding ◽

Ideal System

AbstractCtenophores, also known as comb jellies, live across extremely broad ranges of temperature and hydrostatic pressure in the ocean. Because various ctenophore lineages adapted independently to similar environmental conditions, Phylum Ctenophora is an ideal system for the study of protein adaptation to extreme environments in a comparative framework. We present such a study here, using a phylogenetically-informed method to compare sequences of four essential metabolic enzymes across gradients of habitat depth and temperature. This method predicts convergent adaptation to these environmental parameters at the amino acid level, providing a novel view of protein adaptation to extreme environments and demonstrating the power and relevance of phylogenetic comparison applied to multi-species transcriptomic datasets from early-diverging metazoa. Across all four enzymes analyzed, 46 amino acid sites were associated with depth-adaptation, 59 with temperature-adaptation, and 56 with both. Sites predicted to be depth- and temperature-adaptive occurred consistently near Rossmann fold cofactor binding motifs and disproportionately in solvent-exposed regions of the protein. These results suggest that the hydrophobic effect and ligand binding may mediate efficient enzyme function at different hydrostatic pressures and temperatures. Using predicted adaptive site maps, such mechanistic hypotheses can now be tested via mutagenesis.

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Positively selected amino acid sites in the entire coding region of hepatitis C virus subtype 1b

Gene ◽

10.1016/s0378-1119(01)00640-0 ◽

2001 ◽

Vol 276 (1-2) ◽

pp. 83-87 ◽

Cited By ~ 15

Author(s):

Yoshiyuki Suzuki ◽

Takashi Gojobori

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Amino Acid ◽

Acid Sites ◽

Coding Region ◽

Subtype 1B ◽

Virus Subtype

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Identification of the key amino acid sites of the carbofuran hydrolase CehA from a newly isolated carbofuran-degrading strain Sphingbium sp. CFD-1

Ecotoxicology and Environmental Safety ◽

10.1016/j.ecoenv.2019.109938 ◽

2020 ◽

Vol 189 ◽

pp. 109938 ◽

Cited By ~ 5

Author(s):

Wankui Jiang ◽

Qinqin Gao ◽

Lu Zhang ◽

Hui Wang ◽

Mingliang Zhang ◽

...

Keyword(s):

Amino Acid ◽

Acid Sites

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Intra-Protein Coevolution Is Increasingly Functional with Greater Proximity to Fertilization

Cytogenetic and Genome Research ◽

10.1159/000509584 ◽

2020 ◽

Vol 160 (6) ◽

pp. 295-308

Author(s):

Marcel Kwiatkowski ◽

Abdul R. Asif ◽

Julia Schumacher ◽

Bertram Brenig ◽

Hans Zischler ◽

...

Keyword(s):

Amino Acid ◽

Potential Effect ◽

Acid Sites ◽

Cellular Level ◽

Node Degree ◽

Entire Body ◽

Reproductive Proteins ◽

Sperm Proteins ◽

Postcopulatory Selection ◽

And Function

Intramolecular coevolution of amino acid sites has repeatedly been studied to improve predictions on protein structure and function. Thereby, the focus was on bacterial proteins with available crystallographic data. However, intramolecular coevolution has not yet been compared between protein sets along a gradient of functional proximity to fertilization. This is especially true for the potential effect of external selective forces on intraprotein coevolution. In this study, we investigated both aspects in equally sized sets of mammalian proteins representing spermatozoa, testis, entire body, and liver. For coevolutionary analyses, we derived the proportion of covarying sites per protein from amino acid alignments of 10 mammalian orthologues each. In confirmation of the validity of our coevolution proxy, we found positive associations with the nonsynonymous or amino acid substitution rate in all protein sets. However, our coevolution proxy negatively correlated with the number of protein interactants (node degree) in male reproductive protein sets alone. In addition, a negative association of our coevolution proxy with protein hydrophobicity was significant in sperm proteins only. Accordingly, the restrictive effect of protein interactants was most pronounced in male reproductive proteins, and the tendency of sperm proteins to form internal structures decreased the more coevolutionary sites they had. Both aspects illustrate that the share of outward and thus functional coevolution increases with greater proximity to fertilization. We found this conclusion confirmed by additional comparisons within sperm proteins. Thus, sperm proteins with high hydrophobicity had the lowest proportions of covarying sites and, according to gene annotations, localized more frequently to internal cellular structures. They should therefore be less exposed to postcopulatory forms of sexual selection. Their counterparts with low hydrophobicity had larger proportions of covarying sites and more often resided at the cell membrane or were secreted. At the cellular level, they are thus closer to externally induced forces of postcopulatory selection which are known for their potential to increase substitution rates. In addition, we show that the intermediary status of the testicular protein set in correlation analyses is probably due to a special combination of reproductive and somatic involvements.

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