The complete sequence of the bovine torovirus genome.
Identifieur interne : 001144 ( Ncbi/Curation ); précédent : 001143; suivant : 001145The complete sequence of the bovine torovirus genome.
Auteurs : Ryan Draker [Canada] ; Rachel L. Roper ; Martin Petric ; Raymond TellierSource :
- Virus research [ 0168-1702 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA Replicase, Serine Endopeptidases.
- genetics : Open Reading Frames, Torovirus.
- Amino Acid Sequence, Genome, Viral, Molecular Sequence Data, Nucleic Acid Conformation, Sequence Alignment.
Abstract
Viruses in the family Coronaviridae have elicited new interest, with the outbreaks caused by SARS-HCoV in 2003 and the recent discovery of a new human coronavirus, HCoV-NL63. The genus Torovirus, within the family Coronaviridae, is less well characterized, in part because toroviruses cannot yet be grown in cell culture (except for the Berne virus). In this study, we determined the sequence of the complete genome of Breda-1 (BoTV-1), a bovine torovirus. This is the first complete torovirus genome sequence to be reported. BoTV-1 RNA was amplified using long RT-PCR and the amplicons sequenced. The genome has a length of 28.475 kb and consisted mainly of the replicase gene ( approximately 20.2 kb) which contains two large overlapping ORFs, ORF1a and ORF1b, encoding polyproteins pp1a and pp1b, respectively. Sequence analysis identified conserved domains within the predicted sequences of pp1a and pp1b. Sequence alignments and protein secondary structure prediction data suggest the presence of a 3C-like serine protease domain with similarity to the arterivirus 3C-like serine protease and a single papain-like cysteine protease domain with similarity to the picornavirus leader protease. The ADRP (APPR-1'') domain - unique to the Coronaviridae - was also located in BoTV pp1a. In addition, several hydrophobic domains were identified that are typical of a nidovirus replicase. Within the pp1b sequence the polymerase and helicase domains were identified, as well as sequences predicted to be involved in ribosomal frameshifting, including the conserved slippery sequence UUUAAAC and two potential pseudoknot structures.
DOI: 10.1016/j.virusres.2005.07.005
PubMed: 16137782
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :002558
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :002558
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :001F60
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :001144
Links to Exploration step
pubmed:16137782Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The complete sequence of the bovine torovirus genome.</title>
<author><name sortKey="Draker, Ryan" sort="Draker, Ryan" uniqKey="Draker R" first="Ryan" last="Draker">Ryan Draker</name>
<affiliation wicri:level="4"><nlm:affiliation>Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ont., Canada.</nlm:affiliation>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ont.</wicri:regionArea>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Roper, Rachel L" sort="Roper, Rachel L" uniqKey="Roper R" first="Rachel L" last="Roper">Rachel L. Roper</name>
</author>
<author><name sortKey="Petric, Martin" sort="Petric, Martin" uniqKey="Petric M" first="Martin" last="Petric">Martin Petric</name>
</author>
<author><name sortKey="Tellier, Raymond" sort="Tellier, Raymond" uniqKey="Tellier R" first="Raymond" last="Tellier">Raymond Tellier</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2006">2006</date>
<idno type="RBID">pubmed:16137782</idno>
<idno type="pmid">16137782</idno>
<idno type="doi">10.1016/j.virusres.2005.07.005</idno>
<idno type="wicri:Area/PubMed/Corpus">002558</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002558</idno>
<idno type="wicri:Area/PubMed/Curation">002558</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002558</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001F60</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F60</idno>
<idno type="wicri:Area/Ncbi/Merge">001144</idno>
<idno type="wicri:Area/Ncbi/Curation">001144</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">The complete sequence of the bovine torovirus genome.</title>
<author><name sortKey="Draker, Ryan" sort="Draker, Ryan" uniqKey="Draker R" first="Ryan" last="Draker">Ryan Draker</name>
<affiliation wicri:level="4"><nlm:affiliation>Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ont., Canada.</nlm:affiliation>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ont.</wicri:regionArea>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Roper, Rachel L" sort="Roper, Rachel L" uniqKey="Roper R" first="Rachel L" last="Roper">Rachel L. Roper</name>
</author>
<author><name sortKey="Petric, Martin" sort="Petric, Martin" uniqKey="Petric M" first="Martin" last="Petric">Martin Petric</name>
</author>
<author><name sortKey="Tellier, Raymond" sort="Tellier, Raymond" uniqKey="Tellier R" first="Raymond" last="Tellier">Raymond Tellier</name>
</author>
</analytic>
<series><title level="j">Virus research</title>
<idno type="ISSN">0168-1702</idno>
<imprint><date when="2006" type="published">2006</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Genome, Viral</term>
<term>Molecular Sequence Data</term>
<term>Nucleic Acid Conformation</term>
<term>Open Reading Frames (genetics)</term>
<term>RNA Replicase (genetics)</term>
<term>Sequence Alignment</term>
<term>Serine Endopeptidases (genetics)</term>
<term>Torovirus (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences</term>
<term>Cadres ouverts de lecture (génétique)</term>
<term>Conformation d'acide nucléique</term>
<term>Données de séquences moléculaires</term>
<term>Génome viral</term>
<term>RNA replicase (génétique)</term>
<term>Serine endopeptidases (génétique)</term>
<term>Séquence d'acides aminés</term>
<term>Torovirus (génétique)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA Replicase</term>
<term>Serine Endopeptidases</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Open Reading Frames</term>
<term>Torovirus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cadres ouverts de lecture</term>
<term>RNA replicase</term>
<term>Serine endopeptidases</term>
<term>Torovirus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Genome, Viral</term>
<term>Molecular Sequence Data</term>
<term>Nucleic Acid Conformation</term>
<term>Sequence Alignment</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term>
<term>Conformation d'acide nucléique</term>
<term>Données de séquences moléculaires</term>
<term>Génome viral</term>
<term>Séquence d'acides aminés</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Viruses in the family Coronaviridae have elicited new interest, with the outbreaks caused by SARS-HCoV in 2003 and the recent discovery of a new human coronavirus, HCoV-NL63. The genus Torovirus, within the family Coronaviridae, is less well characterized, in part because toroviruses cannot yet be grown in cell culture (except for the Berne virus). In this study, we determined the sequence of the complete genome of Breda-1 (BoTV-1), a bovine torovirus. This is the first complete torovirus genome sequence to be reported. BoTV-1 RNA was amplified using long RT-PCR and the amplicons sequenced. The genome has a length of 28.475 kb and consisted mainly of the replicase gene ( approximately 20.2 kb) which contains two large overlapping ORFs, ORF1a and ORF1b, encoding polyproteins pp1a and pp1b, respectively. Sequence analysis identified conserved domains within the predicted sequences of pp1a and pp1b. Sequence alignments and protein secondary structure prediction data suggest the presence of a 3C-like serine protease domain with similarity to the arterivirus 3C-like serine protease and a single papain-like cysteine protease domain with similarity to the picornavirus leader protease. The ADRP (APPR-1'') domain - unique to the Coronaviridae - was also located in BoTV pp1a. In addition, several hydrophobic domains were identified that are typical of a nidovirus replicase. Within the pp1b sequence the polymerase and helicase domains were identified, as well as sequences predicted to be involved in ribosomal frameshifting, including the conserved slippery sequence UUUAAAC and two potential pseudoknot structures.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/SrasV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001144 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 001144 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= SrasV1 |flux= Ncbi |étape= Curation |type= RBID |clé= pubmed:16137782 |texte= The complete sequence of the bovine torovirus genome. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:16137782" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \ | NlmPubMed2Wicri -a SrasV1
This area was generated with Dilib version V0.6.33. |