Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus
Identifieur interne : 001710 ( Main/Exploration ); précédent : 001709; suivant : 001711Acquisition 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Nucleocapsid Proteins, Viral Proteins.
- chemical , genetics : Nucleocapsid Proteins, Viral Proteins.
- chemistry : SARS Virus.
- genetics : SARS Virus.
- Genes, Overlapping, Genes, Viral, Humans, Models, Molecular, Protein Conformation, Protein Structure, Tertiary.
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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type="abstract" xml:lang="en"><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></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Rancurrel, C" uniqKey="Rancurrel C">C Rancurrel</name></author><author><name sortKey="Khosravi, M" uniqKey="Khosravi M">M Khosravi</name></author><author><name sortKey="Dunker, Ak" uniqKey="Dunker A">AK Dunker</name></author><author><name sortKey="Romero, P" uniqKey="Romero P">P Romero</name></author><author><name sortKey="Karlin, D" uniqKey="Karlin D">D Karlin</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Belshaw, R" uniqKey="Belshaw R">R Belshaw</name></author><author><name sortKey="Pybus, Og" uniqKey="Pybus O">OG Pybus</name></author><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A 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uniqKey="Weiss S">SR Weiss</name></author><author><name sortKey="Masters, Ps" uniqKey="Masters P">PS Masters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Senanayake, Sd" uniqKey="Senanayake S">SD Senanayake</name></author><author><name sortKey="Brian, Da" uniqKey="Brian D">DA Brian</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Calvo, E" uniqKey="Calvo E">E Calvo</name></author><author><name sortKey="Dediego, Ml" uniqKey="Dediego M">ML DeDiego</name></author><author><name sortKey="Garcia, P" uniqKey="Garcia P">P Garcia</name></author><author><name sortKey="Lopez, Ja" uniqKey="Lopez J">JA Lopez</name></author><author><name sortKey="Perez Brena, P" uniqKey="Perez Brena P">P Perez-Brena</name></author><author><name sortKey="Falcon, A" uniqKey="Falcon A">A Falcon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chang, C" uniqKey="Chang C">C Chang</name></author><author><name sortKey="Hou, Mh" uniqKey="Hou M">MH Hou</name></author><author><name sortKey="Chang, Cf" uniqKey="Chang C">CF Chang</name></author><author><name sortKey="Hsiao, Cd" uniqKey="Hsiao C">CD Hsiao</name></author><author><name sortKey="Huang, Th" uniqKey="Huang T">TH Huang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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 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