High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2)

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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Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0701572104 ◽

2007 ◽

Vol 104 (16) ◽

pp. 6504-6510 ◽

Cited By ~ 109

Author(s):

S. A. Sawyer ◽

J. Parsch ◽

Z. Zhang ◽

D. L. Hartl

Keyword(s):

Amino Acid ◽

Positive Selection ◽

Neutral Amino Acid

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Tailored amino acid diversity for the evolution of antibody affinity

mAbs ◽

10.4161/mabs.21728 ◽

2012 ◽

Vol 4 (6) ◽

pp. 664-672 ◽

Cited By ~ 7

Author(s):

Andrea González-Muñoz ◽

Evert Bokma ◽

Desmond O’Shea ◽

Kevin Minton ◽

Martin Strain ◽

...

Keyword(s):

Amino Acid ◽

Antibody Affinity ◽

Amino Acid Diversity

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Biochemical characterization of a glucoamylase from Saccharomycopsis fibuligera R64

Biologia ◽

10.2478/s11756-010-0151-2 ◽

2011 ◽

Vol 66 (1) ◽

Cited By ~ 3

Author(s):

Dessy Natalia ◽

Keni Vidilaseris ◽

Pasjan Satrimafitrah ◽

Wangsa Ismaya ◽

Purkan ◽

...

Keyword(s):

Mass Spectrometry ◽

Amino Acid ◽

Amino Acid Sequence Identity ◽

Biochemical Characterization ◽

Saccharomycopsis Fibuligera ◽

Sequence Identity ◽

Ic50 Value ◽

High Amino Acid ◽

Ph Range

AbstractGlucoamylase from the yeast Saccharomycopsis fibuligera R64 (GLL1) has successfully been purified and characterized. The molecular mass of the enzyme was 56,583 Da as determined by mass spectrometry. The purified enzyme demonstrated optimum activity in the pH range of 5.6–6.4 and at 50°C. The activity of the enzyme was inhibited by acarbose with the IC50 value of 5 μM. GLL1 shares high amino acid sequence identity with GLU1 and GLA1, which are Saccharomycopsis fibuligera glucoamylases from the strains HUT7212 and KZ, respectively. The properties of GLL1, however, resemble that of GLU1. The elucidation of the primary structure of GLL1 contributes to the explanation of this finding.

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Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus

PLoS Pathogens ◽

10.1371/journal.ppat.1000254 ◽

2009 ◽

Vol 5 (1) ◽

pp. e1000254 ◽

Cited By ~ 90

Author(s):

Viviane F. Botosso ◽

Paolo M. de A. Zanotto ◽

Mirthes Ueda ◽

Eurico Arruda ◽

Alfredo E. Gilio ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Amino Acid ◽

Positive Selection ◽

G Protein ◽

Protein Gene ◽

Human Respiratory Syncytial Virus ◽

Syncytial Virus

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The Drosophila homeobox gene optix is capable of inducing ectopic eyes by an eyeless-independent mechanism

Development ◽

10.1242/dev.127.9.1879 ◽

2000 ◽

Vol 127 (9) ◽

pp. 1879-1886 ◽

Cited By ~ 7

Author(s):

M. Seimiya ◽

W.J. Gehring

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Gene Family ◽

Eye Development ◽

Ectopic Expression ◽

Amino Acid Sequence Similarity ◽

Sine Oculis ◽

High Amino Acid ◽

Independent Mechanism ◽

Ectopic Eyes

optix is a new member of the Six/so gene family from Drosophila that contains both a six domain and a homeodomain. Because of its high amino acid sequence similarity with the mouse Six3 gene, optix is considered to be the orthologous gene from Drosophila rather than sine oculis, as previously believed. optix expression was detected in the eye, wing and haltere imaginal discs. Ectopic expression of optix leads to the formation of ectopic eyes suggesting that optix has important functions in eye development. Although optix and sine oculis belong to the same gene family (Six/so) and share a high degree of amino acid sequence identity, there are a number of factors which suggest that their developmental roles are different: (1) the expression patterns of optix and sine oculis are clearly distinct; (2) sine oculis acts downstream of eyeless, whereas optix is expressed independently of eyeless; (3) sine oculis functions synergistically with eyes absent in eye development whereas optix does not; (4) ectopic expression of optix alone, but not of sine oculis can induce ectopic eyes in the antennal disc. These results suggest that optix is involved in eye morphogenesis by an eyeless-independent mechanism.

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Persistent Nontumoral High-Amino-Acid Uptake on Brain [11C]Methionine PET/CT in a Patient After Combined Glioma Treatment

Clinical Nuclear Medicine ◽

10.1097/rlu.0000000000003559 ◽

2021 ◽

Vol Publish Ahead of Print ◽

Author(s):

Tatiana Yu. Skvortsova ◽

Zhanna I. Savintceva ◽

Anastasia S. Zhavoronkova ◽

Alexander F. Gurchin ◽

Polina L. Andropova

Keyword(s):

Amino Acid ◽

Amino Acid Uptake ◽

Acid Uptake ◽

Pet Ct ◽

High Amino Acid

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A Single Adaptive Mutation in Sodium Taurocholate Cotransporting Polypeptide Induced by Hepadnaviruses Determines Virus Species Specificity

Journal of Virology ◽

10.1128/jvi.01432-18 ◽

2018 ◽

Vol 93 (5) ◽

Cited By ~ 3

Author(s):

Junko S. Takeuchi ◽

Kento Fukano ◽

Masashi Iwamoto ◽

Senko Tsukuda ◽

Ryosuke Suzuki ◽

...

Keyword(s):

Amino Acid ◽

Virus Infection ◽

Positive Selection ◽

Sodium Taurocholate ◽

Arms Race ◽

Adaptive Mutation ◽

Molecular Evidence ◽

Adaptive Mutations ◽

Wide Range ◽

Coevolutionary Arms Race

ABSTRACTHepatitis B virus (HBV) and its hepadnavirus relatives infect a wide range of vertebrates, from fish to human. Hepadnaviruses and their hosts have a long history of acquiring adaptive mutations. However, there are no reports providing direct molecular evidence for such a coevolutionary “arms race” between hepadnaviruses and their hosts. Here, we present evidence suggesting that the adaptive evolution of the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, has been influenced by virus infection. Evolutionary analysis of the NTCP-encoding genes from 20 mammals showed that most NTCP residues are highly conserved among species, exhibiting evolution under negative selection (dN/dSratio [ratio of nonsynonymous to synonymous evolutionary changes] of <1); this observation implies that the evolution of NTCP is restricted by maintaining its original protein function. However, 0.7% of NTCP amino acid residues exhibit rapid evolution under positive selection (dN/dSratio of >1). Notably, a substitution at amino acid (aa) 158, a positively selected residue, converting the human NTCP to a monkey-type sequence abrogated the capacity to support HBV infection; conversely, a substitution at this residue converting the monkey Ntcp to the human sequence was sufficient to confer HBV susceptibility. Together, these observations suggested a close association of the aa 158 positive selection with the pressure by virus infection. Moreover, the aa 158 sequence determined attachment of the HBV envelope protein to the host cell, demonstrating the mechanism whereby HBV infection would create positive selection at this NTCP residue. In summary, we provide the first evidence in agreement with the function of hepadnavirus as a driver for inducing adaptive mutation in host receptor.IMPORTANCEHBV and its hepadnavirus relatives infect a wide range of vertebrates, with a long infectious history (hundreds of millions of years). Such a long history generally allows adaptive mutations in hosts to escape from infection while simultaneously allowing adaptive mutations in viruses to overcome host barriers. However, there is no published molecular evidence for such a coevolutionary arms race between hepadnaviruses and hosts. In the present study, we performed coevolutionary phylogenetic analysis between hepadnaviruses and the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, combined with virological experimental assays for investigating the biological significance of NTCP sequence variation. Our data provide the first molecular evidence supporting that HBV-related hepadnaviruses drive adaptive evolution in the NTCP sequence, including a mechanistic explanation of how NTCP mutations determine host viral susceptibility. Our novel insights enhance our understanding of how hepadnaviruses evolved with their hosts, permitting the acquisition of strong species specificity.

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Positive Selection on Two Mitochondrial Coding Genes and Adaptation Signals in Hares (Genus Lepus) from China

10.21203/rs.3.rs-80023/v1 ◽

2020 ◽

Author(s):

Asma Awadi ◽

Hichem Ben Slimen ◽

Helmut Schaschl ◽

Felix Knauer ◽

Franz Suchentrunk

Keyword(s):

Amino Acid ◽

Positive Selection ◽

Protein Function ◽

Transmembrane Domain ◽

Proton Translocation ◽

Introgressive Hybridization ◽

Vibrational Entropy ◽

Mutant Type ◽

Selection For ◽

Protein Variants

Abstract Background: Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection. Results: Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, the PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. The statistical model runs indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgresson.Conclusions: Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.

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