On the biased nucleotide composition of the human coronavirus RNA genome
Identifieur interne : 001036 ( Ncbi/Merge ); précédent : 001035; suivant : 001037On the biased nucleotide composition of the human coronavirus RNA genome
Auteurs : Ben Berkhout ; Formijn Van HemertSource :
- Virus Research [ 0168-1702 ] ; 2015.
Descripteurs français
- KwdFr :
- ARN viral (génétique), Biosynthèse des protéines, Composition en bases nucléiques, Coronavirus du syndrome respiratoire du Moyen-Orient (génétique), Coronavirus du syndrome respiratoire du Moyen-Orient (physiologie), Génome viral, Humains, Nucléotides (génétique), Protéines virales (biosynthèse), Virus du SRAS (génétique), Virus du SRAS (physiologie).
- MESH :
- biosynthèse : Protéines virales.
- génétique : ARN viral, Coronavirus du syndrome respiratoire du Moyen-Orient, Nucléotides, Virus du SRAS.
- physiologie : Coronavirus du syndrome respiratoire du Moyen-Orient, Virus du SRAS.
- Biosynthèse des protéines, Composition en bases nucléiques, Génome viral, Humains.
English descriptors
- KwdEn :
- Base Composition, Genome, Viral, Humans, Middle East Respiratory Syndrome Coronavirus (genetics), Middle East Respiratory Syndrome Coronavirus (physiology), Nucleotides (genetics), Protein Biosynthesis, RNA, Viral (genetics), SARS Virus (genetics), SARS Virus (physiology), Viral Proteins (biosynthesis).
- MESH :
- chemical , biosynthesis : Viral Proteins.
- chemical , genetics : Nucleotides, RNA, Viral.
- genetics : Middle East Respiratory Syndrome Coronavirus, SARS Virus.
- physiology : Middle East Respiratory Syndrome Coronavirus, SARS Virus.
- Base Composition, Genome, Viral, Humans, Protein Biosynthesis.
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.
Url:
DOI: 10.1016/j.virusres.2014.11.031
PubMed: 25656063
PubMed Central: 7114406
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Links to Exploration step
PMC:7114406Le document en format XML
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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><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term><term>Genome, Viral</term><term>Humans</term><term>Middle East Respiratory Syndrome Coronavirus (genetics)</term><term>Middle East Respiratory Syndrome Coronavirus (physiology)</term><term>Nucleotides (genetics)</term><term>Protein Biosynthesis</term><term>RNA, Viral (genetics)</term><term>SARS Virus (genetics)</term><term>SARS Virus (physiology)</term><term>Viral Proteins (biosynthesis)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Biosynthèse des protéines</term><term>Composition en bases nucléiques</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (génétique)</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (physiologie)</term><term>Génome viral</term><term>Humains</term><term>Nucléotides (génétique)</term><term>Protéines virales (biosynthèse)</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (physiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Nucleotides</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Nucléotides</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Composition</term><term>Genome, Viral</term><term>Humans</term><term>Protein Biosynthesis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biosynthèse des protéines</term><term>Composition en bases nucléiques</term><term>Génome viral</term><term>Humains</term></keywords></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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Turner</name></author></analytic></biblStruct></listBibl></div1></back></TEI><double pmid="25656063"><pmc><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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Turner</name></author></analytic></biblStruct></listBibl></div1></back></TEI></pmc><pubmed><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><affiliation wicri:level="4"><nlm:affiliation>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands. Electronic address: b.berkhout@amc.uva.nl.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam</wicri:regionArea><placeName><settlement type="city">Amsterdam</settlement><region>Hollande-Septentrionale</region></placeName><orgName type="university">Université d'Amsterdam</orgName></affiliation></author><author><name sortKey="Van Hemert, Formijn" sort="Van Hemert, Formijn" uniqKey="Van Hemert F" first="Formijn" last="Van Hemert">Formijn Van Hemert</name><affiliation wicri:level="4"><nlm:affiliation>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam</wicri:regionArea><placeName><settlement type="city">Amsterdam</settlement><region>Hollande-Septentrionale</region></placeName><orgName type="university">Université d'Amsterdam</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25656063</idno><idno type="pmid">25656063</idno><idno type="doi">10.1016/j.virusres.2014.11.031</idno><idno type="wicri:Area/PubMed/Corpus">001705</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001705</idno><idno type="wicri:Area/PubMed/Curation">001705</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001705</idno><idno type="wicri:Area/PubMed/Checkpoint">001416</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001416</idno></publicationStmt><sourceDesc><biblStruct><analytic><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><affiliation wicri:level="4"><nlm:affiliation>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands. Electronic address: b.berkhout@amc.uva.nl.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam</wicri:regionArea><placeName><settlement type="city">Amsterdam</settlement><region>Hollande-Septentrionale</region></placeName><orgName type="university">Université d'Amsterdam</orgName></affiliation></author><author><name sortKey="Van Hemert, Formijn" sort="Van Hemert, Formijn" uniqKey="Van Hemert F" first="Formijn" last="Van Hemert">Formijn Van Hemert</name><affiliation wicri:level="4"><nlm:affiliation>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam</wicri:regionArea><placeName><settlement type="city">Amsterdam</settlement><region>Hollande-Septentrionale</region></placeName><orgName type="university">Université d'Amsterdam</orgName></affiliation></author></analytic><series><title level="j">Virus research</title><idno type="eISSN">1872-7492</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term><term>Genome, Viral</term><term>Humans</term><term>Middle East Respiratory Syndrome Coronavirus (genetics)</term><term>Middle East Respiratory Syndrome Coronavirus (physiology)</term><term>Nucleotides (genetics)</term><term>Protein Biosynthesis</term><term>RNA, Viral (genetics)</term><term>SARS Virus (genetics)</term><term>SARS Virus (physiology)</term><term>Viral Proteins (biosynthesis)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Biosynthèse des protéines</term><term>Composition en bases nucléiques</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (génétique)</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (physiologie)</term><term>Génome viral</term><term>Humains</term><term>Nucléotides (génétique)</term><term>Protéines virales (biosynthèse)</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (physiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Nucleotides</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Nucléotides</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Composition</term><term>Genome, Viral</term><term>Humans</term><term>Protein Biosynthesis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biosynthèse des protéines</term><term>Composition en bases nucléiques</term><term>Génome viral</term><term>Humains</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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. </div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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