On the biased nucleotide composition of the human coronavirus RNA genome
Identifieur interne : 000D55 ( Pmc/Checkpoint ); précédent : 000D54; suivant : 000D56On the biased nucleotide composition of the human coronavirus RNA genome
Auteurs : Ben Berkhout ; Formijn Van HemertSource :
- Virus Research [ 0168-1702 ] ; 2015.
Abstract
The nucleotide composition of a coronaviral RNA genome is biased (high U, low C). This bias is a relatively stable property along the viral genome, but less prominent in the last 1/3 of the genome. This bias is even more pronounced in the single-stranded, unpaired RNA domains. The bias dictates the atypical codon usage of the coronaviruses. The RNA genome of the zoonotic viruses MERS and SARS is extremely biased.
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DOI: 10.1016/j.virusres.2014.11.031
PubMed: 25656063
PubMed Central: 7114406
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">On the biased nucleotide composition of the human coronavirus RNA genome</title><author><name sortKey="Berkhout, Ben" sort="Berkhout, Ben" uniqKey="Berkhout B" first="Ben" last="Berkhout">Ben Berkhout</name></author><author><name sortKey="Van Hemert, Formijn" sort="Van Hemert, Formijn" uniqKey="Van Hemert F" first="Formijn" last="Van Hemert">Formijn Van Hemert</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25656063</idno><idno type="pmc">7114406</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114406</idno><idno type="RBID">PMC:7114406</idno><idno type="doi">10.1016/j.virusres.2014.11.031</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">001198</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001198</idno><idno type="wicri:Area/Pmc/Curation">001198</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001198</idno><idno type="wicri:Area/Pmc/Checkpoint">000D55</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000D55</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">On the biased nucleotide composition of the human coronavirus RNA genome</title><author><name sortKey="Berkhout, Ben" sort="Berkhout, Ben" uniqKey="Berkhout B" first="Ben" last="Berkhout">Ben Berkhout</name></author><author><name sortKey="Van Hemert, Formijn" sort="Van Hemert, Formijn" uniqKey="Van Hemert F" first="Formijn" last="Van Hemert">Formijn Van Hemert</name></author></analytic><series><title level="j">Virus Research</title><idno type="ISSN">0168-1702</idno><idno type="eISSN">1872-7492</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Highlights</title><p><list list-type="simple" id="lis0005"><list-item id="lsti0005"><label>•</label><p id="par0005">The nucleotide composition of a coronaviral RNA genome is biased (high U, low C).</p></list-item><list-item id="lsti0010"><label>•</label><p id="par0010">This bias is a relatively stable property along the viral genome, but less prominent in the last 1/3 of the genome.</p></list-item><list-item id="lsti0015"><label>•</label><p id="par0015">This bias is even more pronounced in the single-stranded, unpaired RNA domains.</p></list-item><list-item id="lsti0020"><label>•</label><p id="par0020">The bias dictates the atypical codon usage of the coronaviruses.</p></list-item><list-item id="lsti0025"><label>•</label><p id="par0025">The RNA genome of the zoonotic viruses MERS and SARS is extremely biased.</p></list-item></list></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bennetzen, J L" uniqKey="Bennetzen J">J.L. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virus Res</journal-id><journal-id journal-id-type="iso-abbrev">Virus Res</journal-id><journal-title-group><journal-title>Virus Research</journal-title></journal-title-group><issn pub-type="ppub">0168-1702</issn><issn pub-type="epub">1872-7492</issn><publisher><publisher-name>Elsevier B.V.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25656063</article-id><article-id pub-id-type="pmc">7114406</article-id><article-id pub-id-type="publisher-id">S0168-1702(15)00044-1</article-id><article-id pub-id-type="doi">10.1016/j.virusres.2014.11.031</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>On the biased nucleotide composition of the human coronavirus RNA genome</article-title></title-group><contrib-group><contrib contrib-type="author" id="aut0005"><name><surname>Berkhout</surname><given-names>Ben</given-names></name><email>b.berkhout@amc.uva.nl</email><xref rid="cor0005" ref-type="corresp">⁎</xref></contrib><contrib contrib-type="author" id="aut0010"><name><surname>van Hemert</surname><given-names>Formijn</given-names></name></contrib></contrib-group><aff id="aff0005">Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands</aff><author-notes><corresp id="cor0005"><label>⁎</label>Corresponding author. Tel.: +31 205664822. <email>b.berkhout@amc.uva.nl</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>2</day><month>2</month><year>2015</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><day>16</day><month>4</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>2</day><month>2</month><year>2015</year></pub-date><volume>202</volume><fpage>41</fpage><lpage>47</lpage><permissions><copyright-statement>Copyright © 2015 Elsevier B.V. All rights reserved.</copyright-statement><copyright-year>2015</copyright-year><copyright-holder>Elsevier B.V.</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract abstract-type="author-highlights" id="abs0005"><title>Highlights</title><p><list list-type="simple" id="lis0005"><list-item id="lsti0005"><label>•</label><p id="par0005">The nucleotide composition of a coronaviral RNA genome is biased (high U, low C).</p></list-item><list-item id="lsti0010"><label>•</label><p id="par0010">This bias is a relatively stable property along the viral genome, but less prominent in the last 1/3 of the genome.</p></list-item><list-item id="lsti0015"><label>•</label><p id="par0015">This bias is even more pronounced in the single-stranded, unpaired RNA domains.</p></list-item><list-item id="lsti0020"><label>•</label><p id="par0020">The bias dictates the atypical codon usage of the coronaviruses.</p></list-item><list-item id="lsti0025"><label>•</label><p id="par0025">The RNA genome of the zoonotic viruses MERS and SARS is extremely biased.</p></list-item></list></p></abstract><abstract id="abs0010"><p>We investigated the nucleotide composition of the RNA genome of the six human coronaviruses. Some general coronavirus characteristics were apparent (e.g. high U, low C count), but we also detected species-specific signatures. Most strikingly, the high U and low C proportions are quite variable and act like communicating vessels, C goes down when U goes up and vice versa. U ranges among virus isolates from 30.7% to 40.3%, and C makes the opposite movement from 20.0% to 12.9%, respectively. The nucleotide biases are more pronounced in the unpaired regions of the structured RNA genome, which may suggest a certain biological function for these distinctive sequence signatures. Coronaviruses have an atypical codon usage that has been linked to mutational events operating on the viral RNA genome on an evolutionary time scale. We suggest that the atypical nucleotide bias may serve a distinct biological function and that it is the direct cause of the characteristic codon usage in these viruses. The relevance for evolution of the novel human pathogens MERS and SARS is discussed.</p></abstract><kwd-group id="kwd0005"><title>Keywords</title><kwd>Coronavirus</kwd><kwd>RNA genome</kwd><kwd>Nucleotide signature</kwd><kwd>MERS</kwd><kwd>SARS</kwd></kwd-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Berkhout, Ben" sort="Berkhout, Ben" uniqKey="Berkhout B" first="Ben" last="Berkhout">Ben Berkhout</name><name sortKey="Van Hemert, Formijn" sort="Van Hemert, Formijn" uniqKey="Van Hemert F" first="Formijn" last="Van Hemert">Formijn Van Hemert</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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