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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Brandão</name><affiliation wicri:level="1"><nlm:affiliation>Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil. paulo7926@usp.br</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22903606</idno><idno type="pmid">22903606</idno><idno type="doi">10.1007/s00239-012-9515-2</idno><idno type="wicri:Area/PubMed/Corpus">001316</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001316</idno><idno type="wicri:Area/PubMed/Curation">001316</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001316</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.</title><author><name sortKey="Brandao, Paulo E" sort="Brandao, Paulo E" uniqKey="Brandao P" first="Paulo E" last="Brandão">Paulo E. Brandão</name><affiliation wicri:level="1"><nlm:affiliation>Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil. paulo7926@usp.br</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of molecular evolution</title><idno type="eISSN">1432-1432</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Chickens (virology)</term><term>Codon</term><term>Coronavirus (genetics)</term><term>Genetic Drift</term><term>Membrane Glycoproteins (genetics)</term><term>Models, Genetic</term><term>Phylogeny</term><term>Selection, Genetic</term><term>Spike Glycoprotein, Coronavirus</term><term>Viral Envelope Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Codon</term><term>Coronavirus (génétique)</term><term>Dérive génétique</term><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></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Glycoproteins</term><term>Viral Envelope Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Codon</term><term>Spike Glycoprotein, Coronavirus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term><term>Glycoprotéines membranaires</term><term>Protéines de l'enveloppe virale</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Poulets</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Chickens</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Genetic Drift</term><term>Models, Genetic</term><term>Phylogeny</term><term>Selection, Genetic</term></keywords><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><term>Phylogénie</term><term>Sélection génétique</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22903606</PMID><DateCompleted><Year>2013</Year><Month>03</Month><Day>22</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-1432</ISSN><JournalIssue CitedMedium="Internet"><Volume>75</Volume><Issue>1-2</Issue><PubDate><Year>2012</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Journal of molecular evolution</Title><ISOAbbreviation>J. Mol. Evol.</ISOAbbreviation></Journal><ArticleTitle>Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.</ArticleTitle><Pagination><MedlinePgn>19-24</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00239-012-9515-2</ELocationID><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></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Brandão</LastName><ForeName>Paulo E</ForeName><Initials>PE</Initials><AffiliationInfo><Affiliation>Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil. paulo7926@usp.br</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>08</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>J Mol 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