A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal
Identifieur interne : 004956 ( Main/Curation ); précédent : 004955; suivant : 004957A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal
Auteurs : Ewan P. Plant ; Gabriela C. Pérez-Alvarado ; Jonathan L. Jacobs ; Bani Mukhopadhyay ; Mirko Hennig ; Jonathan D. DinmanSource :
- PLoS Biology [ 1544-9173 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA, Messenger, RNA, Viral.
- chemical , genetics : RNA, Messenger, RNA, Viral.
- genetics : SARS Virus.
- Animals, Chlorocebus aethiops, Frameshift Mutation, Molecular Sequence Data, Nucleic Acid Conformation, Open Reading Frames, Vero Cells.
Abstract
A wide range of RNA viruses use programmed −1 ribosomal frameshifting for the production of viral fusion proteins. Inspection of the overlap regions between ORF1a and ORF1b of the SARS-CoV genome revealed that, similar to all coronaviruses, a programmed −1 ribosomal frameshift could be used by the virus to produce a fusion protein. Computational analyses of the frameshift signal predicted the presence of an mRNA pseudoknot containing three double-stranded RNA stem structures rather than two. Phylogenetic analyses showed the conservation of potential three-stemmed pseudoknots in the frameshift signals of all other coronaviruses in the GenBank database. Though the presence of the three-stemmed structure is supported by nuclease mapping and two-dimensional nuclear magnetic resonance studies, our findings suggest that interactions between the stem structures may result in local distortions in the A-form RNA. These distortions are particularly evident in the vicinity of predicted A-bulges in stems 2 and 3. In vitro and in vivo frameshifting assays showed that the SARS-CoV frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics.
Url:
DOI: 10.1371/journal.pbio.0030172
PubMed: 15884978
PubMed Central: 1110908
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PMC:1110908Le document en format XML
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Dinman</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS Biology</title><idno type="ISSN">1544-9173</idno><idno type="eISSN">1545-7885</idno><imprint><date when="2005">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Chlorocebus aethiops</term><term>Frameshift Mutation</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Open Reading Frames</term><term>RNA, Messenger (chemistry)</term><term>RNA, Messenger (genetics)</term><term>RNA, Viral (chemistry)</term><term>RNA, Viral (genetics)</term><term>SARS Virus (genetics)</term><term>Vero Cells</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager ()</term><term>ARN messager (génétique)</term><term>ARN viral ()</term><term>ARN viral (génétique)</term><term>Animaux</term><term>Cadres ouverts de lecture</term><term>Cellules Vero</term><term>Conformation d'acide nucléique</term><term>Données de séquences moléculaires</term><term>Mutation avec décalage du cadre de lecture</term><term>Virus du SRAS (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>ARN viral</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Chlorocebus aethiops</term><term>Frameshift Mutation</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Open Reading Frames</term><term>Vero Cells</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN messager</term><term>ARN viral</term><term>Animaux</term><term>Cadres ouverts de lecture</term><term>Cellules Vero</term><term>Conformation d'acide nucléique</term><term>Données de séquences moléculaires</term><term>Mutation avec décalage du cadre de lecture</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A wide range of RNA viruses use programmed −1 ribosomal frameshifting for the production of viral fusion proteins. Inspection of the overlap regions between ORF1a and ORF1b of the SARS-CoV genome revealed that, similar to all coronaviruses, a programmed −1 ribosomal frameshift could be used by the virus to produce a fusion protein. Computational analyses of the frameshift signal predicted the presence of an mRNA pseudoknot containing three double-stranded RNA stem structures rather than two. Phylogenetic analyses showed the conservation of potential three-stemmed pseudoknots in the frameshift signals of all other coronaviruses in the GenBank database. Though the presence of the three-stemmed structure is supported by nuclease mapping and two-dimensional nuclear magnetic resonance studies, our findings suggest that interactions between the stem structures may result in local distortions in the A-form RNA. These distortions are particularly evident in the vicinity of predicted A-bulges in stems 2 and 3. In vitro and in vivo frameshifting assays showed that the SARS-CoV frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lai, Mm" uniqKey="Lai M">MM Lai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marra, Ma" uniqKey="Marra M">MA Marra</name></author><author><name sortKey="Jones, Sj" uniqKey="Jones S">SJ Jones</name></author><author><name sortKey="Astell, Cr" uniqKey="Astell C">CR Astell</name></author><author><name sortKey="Holt, Ra" uniqKey="Holt R">RA Holt</name></author><author><name sortKey="Brooks Wilson, A" uniqKey="Brooks Wilson A">A Brooks-Wilson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rota, Pa" uniqKey="Rota P">PA Rota</name></author><author><name sortKey="Oberste, Ms" uniqKey="Oberste M">MS Oberste</name></author><author><name 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Ono</name></author><author><name sortKey="Fernandez, C" uniqKey="Fernandez C">C Fernandez</name></author><author><name sortKey="Szyperski, T" uniqKey="Szyperski T">T Szyperski</name></author><author><name sortKey="Kainosho, M" uniqKey="Kainosho M">M Kainosho</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dingley, Aj" uniqKey="Dingley A">AJ Dingley</name></author><author><name sortKey="Grzesiek, S" uniqKey="Grzesiek S">S Grzesiek</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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