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Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function.

van Hemert FJ, Lukashov VV, Berkhout B - Virol. J. (2007)

Bottom Line: Deviant patterns of synonymous substitutions are found in the capsid structural genes.Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS.Integrin recognition may play a key role in astrovirus to target cell attachment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands. f.j.vanhemert@amc.uva.nl

ABSTRACT

Background: Complete genome sequences of the Astroviridae include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species.

Results: We analyzed the complete Astroviridae family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non-human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/dS ratio that may indicate site-specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species.

Conclusion: Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/dS are prominent at domains in charge of environmental communication (f.i. VP27 and domain 4 in ORF1a) more than at domains dedicated to intrinsic virus functions (f.i. VP34 and ORF1b (the virus polymerase)). Integrin recognition may play a key role in astrovirus to target cell attachment.

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Related in: MedlinePlus

Routing of astrovirus sequence data from GenBank to PAML input data files. Main features of astrovirus genomes are given at the top. Numbers in parentheses indicate the length of an ORF in nucleotides. RFS points to the ribosomal frame shift signal between ORF1a and ORF1b. In GenBank, the number of complete ORF2 sequences surpasses those of ORF1a or ORF1b. At the ultimate right side, resources are boxed to indicate the actions undertaken and results obtained.
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Figure 4: Routing of astrovirus sequence data from GenBank to PAML input data files. Main features of astrovirus genomes are given at the top. Numbers in parentheses indicate the length of an ORF in nucleotides. RFS points to the ribosomal frame shift signal between ORF1a and ORF1b. In GenBank, the number of complete ORF2 sequences surpasses those of ORF1a or ORF1b. At the ultimate right side, resources are boxed to indicate the actions undertaken and results obtained.

Mentions: Sequences of astroviruses were obtained from GenBank and annotated previously [10]. Recently obtained sequences of mink [3] and human serotypes 4 and 5 [34] were also included in the present study. GenBank accession numbers are mentioned in Table 1 (Results section). The genomes of the astrovirus species include many human species with high sequence homology and few non-human mammalian and avian species, which are very divergent. Initial charges of PAML 3.14 for the estimation of (non-) synonymous rates of mutation in astrovirus genes demonstrated the need of a proper alignment of astrovirus sequences to avoid unconnected Markov chains, likelihood convergence problems and a collapse of the substitution model. Therefore, a novel strategy was developed to obtain properly aligned astrovirus sequences (Fig 4). In order to avoid overrepresentation of human astrovirus species (ORF2 analyses only), we included one specimen per human serotype except for human serotype 1. Besides a few point mutations, the human virus species Z25771 differs from L23513 (and from the other astrovirus species as well) by the presence of the oligopeptide that was reported to be deleted by cell culture adaptation of astrovirus [25]. Multiple sequence comparison by log-expectation (MUSCLE) [35] was used for the alignment of the polypeptide chains encoded by each astrovirus reading frame. A multi-step procedure was used. Firstly, three separate protein alignments were generated from the human, non-human mammalian and avian virus species, respectively. Secondly, these three alignments were combined into a single alignment file for each astrovirus ORF by means of the profile-profile operation of MUSCLE. Thirdly, refinements were introduced manually (BioEdit) [36] with special attention to sites near alignment gaps. An amino acid neighbor-joining tree was constructed in MEGA [37] and stored in newick format.


Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function.

van Hemert FJ, Lukashov VV, Berkhout B - Virol. J. (2007)

Routing of astrovirus sequence data from GenBank to PAML input data files. Main features of astrovirus genomes are given at the top. Numbers in parentheses indicate the length of an ORF in nucleotides. RFS points to the ribosomal frame shift signal between ORF1a and ORF1b. In GenBank, the number of complete ORF2 sequences surpasses those of ORF1a or ORF1b. At the ultimate right side, resources are boxed to indicate the actions undertaken and results obtained.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1828050&req=5

Figure 4: Routing of astrovirus sequence data from GenBank to PAML input data files. Main features of astrovirus genomes are given at the top. Numbers in parentheses indicate the length of an ORF in nucleotides. RFS points to the ribosomal frame shift signal between ORF1a and ORF1b. In GenBank, the number of complete ORF2 sequences surpasses those of ORF1a or ORF1b. At the ultimate right side, resources are boxed to indicate the actions undertaken and results obtained.
Mentions: Sequences of astroviruses were obtained from GenBank and annotated previously [10]. Recently obtained sequences of mink [3] and human serotypes 4 and 5 [34] were also included in the present study. GenBank accession numbers are mentioned in Table 1 (Results section). The genomes of the astrovirus species include many human species with high sequence homology and few non-human mammalian and avian species, which are very divergent. Initial charges of PAML 3.14 for the estimation of (non-) synonymous rates of mutation in astrovirus genes demonstrated the need of a proper alignment of astrovirus sequences to avoid unconnected Markov chains, likelihood convergence problems and a collapse of the substitution model. Therefore, a novel strategy was developed to obtain properly aligned astrovirus sequences (Fig 4). In order to avoid overrepresentation of human astrovirus species (ORF2 analyses only), we included one specimen per human serotype except for human serotype 1. Besides a few point mutations, the human virus species Z25771 differs from L23513 (and from the other astrovirus species as well) by the presence of the oligopeptide that was reported to be deleted by cell culture adaptation of astrovirus [25]. Multiple sequence comparison by log-expectation (MUSCLE) [35] was used for the alignment of the polypeptide chains encoded by each astrovirus reading frame. A multi-step procedure was used. Firstly, three separate protein alignments were generated from the human, non-human mammalian and avian virus species, respectively. Secondly, these three alignments were combined into a single alignment file for each astrovirus ORF by means of the profile-profile operation of MUSCLE. Thirdly, refinements were introduced manually (BioEdit) [36] with special attention to sites near alignment gaps. An amino acid neighbor-joining tree was constructed in MEGA [37] and stored in newick format.

Bottom Line: Deviant patterns of synonymous substitutions are found in the capsid structural genes.Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS.Integrin recognition may play a key role in astrovirus to target cell attachment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands. f.j.vanhemert@amc.uva.nl

ABSTRACT

Background: Complete genome sequences of the Astroviridae include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species.

Results: We analyzed the complete Astroviridae family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non-human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/dS ratio that may indicate site-specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species.

Conclusion: Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/dS are prominent at domains in charge of environmental communication (f.i. VP27 and domain 4 in ORF1a) more than at domains dedicated to intrinsic virus functions (f.i. VP34 and ORF1b (the virus polymerase)). Integrin recognition may play a key role in astrovirus to target cell attachment.

Show MeSH
Related in: MedlinePlus