Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus
Identifieur interne : 000925 ( Pmc/Checkpoint ); précédent : 000924; suivant : 000926Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus
Auteurs : Aditi Shukla [Allemagne] ; Rolf Hilgenfeld [Allemagne]Source :
- Virus Genes [ 0920-8569 ] ; 2014.
Abstract
Acquisition of new proteins by viruses usually occurs through horizontal gene transfer or through gene duplication, but another, less common mechanism is the usage of completely or partially overlapping reading frames. A case of acquisition of a completely new protein through introduction of a start codon in an alternative reading frame is the protein encoded by open reading frame (orf) 9b of SARS coronavirus. This gene completely overlaps with the nucleocapsid (N) gene (orf9a). Our findings indicate that the orf9b gene features a discordant codon-usage pattern. We analyzed the evolution of orf9b in concert with orf9a using sequence data of betacoronavirus-lineage b and found that orf9b, which encodes the overprinting protein, evolved largely independent of the overprinted orf9a. We also examined the protein products of these genomic sequences for their structural flexibility and found that it is not necessary for a newly acquired, overlapping protein product to be intrinsically disordered, in contrast to earlier suggestions. Our findings contribute to characterizing sequence properties of newly acquired genes making use of overlapping reading frames.
The online version of this article (doi:10.1007/s11262-014-1139-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1007/s11262-014-1139-8
PubMed: 25410051
PubMed Central: 7089080
Affiliations:
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duplication, but another, less common mechanism is the usage of completely or partially overlapping reading frames. A case of acquisition of a completely new protein through introduction of a start codon in an alternative reading frame is the protein encoded by open reading frame (orf) 9b of SARS coronavirus. This gene completely overlaps with the nucleocapsid (N) gene (orf9a). Our findings indicate that the orf9b gene features a discordant codon-usage pattern. We analyzed the evolution of orf9b in concert with orf9a using sequence data of betacoronavirus-lineage b and found that orf9b, which encodes the overprinting protein, evolved largely independent of the overprinted orf9a. We also examined the protein products of these genomic sequences for their structural flexibility and found that it is not necessary for a newly acquired, overlapping protein product to be intrinsically disordered, in contrast to earlier suggestions. Our findings contribute to characterizing sequence properties of newly acquired genes making use of overlapping reading frames.
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virus Genes</journal-id><journal-id journal-id-type="iso-abbrev">Virus Genes</journal-id><journal-title-group><journal-title>Virus Genes</journal-title></journal-title-group><issn pub-type="ppub">0920-8569</issn><issn pub-type="epub">1572-994X</issn><publisher><publisher-name>Springer US</publisher-name><publisher-loc>Boston</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25410051</article-id><article-id pub-id-type="pmc">7089080</article-id><article-id pub-id-type="publisher-id">1139</article-id><article-id pub-id-type="doi">10.1007/s11262-014-1139-8</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Shukla</surname><given-names>Aditi</given-names></name><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Hilgenfeld</surname><given-names>Rolf</given-names></name><address><phone>+49-451-500-4060</phone><phone>+49-177-2412455</phone><email>hilgenfeld@biochem.uni-luebeck.de</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff3">3</xref></contrib><aff id="Aff1"><label>1</label><institution-wrap><institution-id institution-id-type="GRID">grid.4562.5</institution-id><institution-id institution-id-type="ISNI">0000000100572672</institution-id><institution>Institute of Biochemistry, Center for Structural and Cell Biology in Medicine,</institution><institution>University of Lübeck,</institution></institution-wrap>Ratzeburger Allee 160, 23538 Lübeck, Germany</aff><aff id="Aff2"><label>2</label><institution-wrap><institution-id institution-id-type="GRID">grid.4562.5</institution-id><institution-id institution-id-type="ISNI">0000000100572672</institution-id><institution>Graduate School for Computing in Medicine & Life Sciences,</institution><institution>University of Lübeck,</institution></institution-wrap>Lübeck, Germany</aff><aff id="Aff3"><label>3</label><institution-wrap><institution-id institution-id-type="GRID">grid.4562.5</institution-id><institution-id institution-id-type="ISNI">0000000100572672</institution-id><institution>German Center for Infection Research (DZIF),</institution><institution>University of Lübeck,</institution></institution-wrap>Lübeck, Germany</aff></contrib-group><pub-date pub-type="epub"><day>20</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="ppub"><year>2015</year></pub-date><volume>50</volume><issue>1</issue><fpage>29</fpage><lpage>38</lpage><history><date date-type="received"><day>17</day><month>7</month><year>2014</year></date><date date-type="accepted"><day>25</day><month>10</month><year>2014</year></date></history><permissions><copyright-statement>© Springer Science+Business Media New York 2014</copyright-statement><license><license-p>This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.</license-p></license></permissions><abstract id="Abs1"><p>Acquisition of new proteins by viruses usually occurs through horizontal gene transfer or through gene duplication, but another, less common mechanism is the usage of completely or partially overlapping reading frames. A case of acquisition of a completely new protein through introduction of a start codon in an alternative reading frame is the protein encoded by open reading frame (orf) 9b of SARS coronavirus. This gene completely overlaps with the nucleocapsid (N) gene (orf9a). Our findings indicate that the orf9b gene features a discordant codon-usage pattern. We analyzed the evolution of orf9b in concert with orf9a using sequence data of betacoronavirus-lineage b and found that orf9b, which encodes the overprinting protein, evolved largely independent of the overprinted orf9a. We also examined the protein products of these genomic sequences for their structural flexibility and found that it is not necessary for a newly acquired, overlapping protein product to be intrinsically disordered, in contrast to earlier suggestions. Our findings contribute to characterizing sequence properties of newly acquired genes making use of overlapping reading frames.
</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1007/s11262-014-1139-8) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>SARS coronavirus</kwd><kwd>Accessory proteins</kwd><kwd>Overlapping reading frames</kwd><kwd>Orf9b</kwd><kwd>Nucleocapsid</kwd><kwd>Evolution</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© Springer Science+Business Media New York 2015</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>Allemagne</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Shukla, Aditi" sort="Shukla, Aditi" uniqKey="Shukla A" first="Aditi" last="Shukla">Aditi Shukla</name></noRegion><name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name><name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name><name sortKey="Shukla, Aditi" sort="Shukla, Aditi" uniqKey="Shukla A" first="Aditi" last="Shukla">Aditi Shukla</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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