Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.
Identifieur interne : 001316 ( PubMed/Curation ); précédent : 001315; suivant : 001317Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.
Auteurs : Paulo E. Brandão [Brésil]Source :
- Journal of molecular evolution [ 1432-1432 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Membrane Glycoproteins, Viral Envelope Proteins.
- chemical : Codon, Spike Glycoprotein, Coronavirus.
- genetics : Coronavirus.
- virology : Chickens.
- Amino Acid Sequence, Animals, Genetic Drift, Models, Genetic, Phylogeny, Selection, Genetic.
Abstract
This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.
DOI: 10.1007/s00239-012-9515-2
PubMed: 22903606
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<term>Coronavirus (genetics)</term>
<term>Genetic Drift</term>
<term>Membrane Glycoproteins (genetics)</term>
<term>Models, Genetic</term>
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<term>Glycoprotéine de spicule des coronavirus</term>
<term>Glycoprotéines membranaires (génétique)</term>
<term>Modèles génétiques</term>
<term>Phylogénie</term>
<term>Poulets (virologie)</term>
<term>Protéines de l'enveloppe virale (génétique)</term>
<term>Sélection génétique</term>
<term>Séquence d'acides aminés</term>
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<term>Animals</term>
<term>Genetic Drift</term>
<term>Models, Genetic</term>
<term>Phylogeny</term>
<term>Selection, Genetic</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Codon</term>
<term>Dérive génétique</term>
<term>Glycoprotéine de spicule des coronavirus</term>
<term>Modèles génétiques</term>
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<front><div type="abstract" xml:lang="en">This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.</div>
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<ArticleTitle>Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.</ArticleTitle>
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<Abstract><AbstractText>This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.</AbstractText>
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<ForeName>Paulo E</ForeName>
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