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

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function
Creator	Berkhout, Ben Lukashov, Vladimir Van Hemert, Formijn
source	Medline; PMC
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.
has issue date	2007-03-07(xsd:dateTime)
bibo:doi	10.1186/1743-422x-4-25
bibo:pmid	17343744
has license	cc-by
sha1sum (hex)	38771dc09043758e9f76b1c8746495874d2a41bc
schema:url	https://doi.org/10.1186/1743-422x-4-25
resource representing a document's title	Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function
has PubMed Central identifier	PMC1828050
has PubMed identifier	17343744
schema:publication	Virol J
resource representing a document's body	covid:38771dc09043758e9f76b1c8746495874d2a41bc#body_text
is schema:about of	named entity 'VIROLOGY' named entity 'astrovirus' named entity 'synonymous mutations' named entity 'SATURATION' named entity 'CERTAIN' »more»

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