RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
Identifieur interne : 001C78 ( Main/Exploration ); précédent : 001C77; suivant : 001C79RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus
Auteurs : Daniella Ishimaru [États-Unis] ; Ewan P. Plant [États-Unis] ; Amy C. Sims [États-Unis] ; Boyd L. Yount [États-Unis] ; Braden M. Roth [États-Unis] ; Nadukkudy V. Eldho [États-Unis] ; Gabriela C. Pérez-Alvarado [États-Unis] ; David W. Armbruster [États-Unis] ; Ralph S. Baric [États-Unis] ; Jonathan D. Dinman [États-Unis] ; Deborah R. Taylor [États-Unis] ; Mirko Hennig [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2012.
Descripteurs français
- KwdFr :
- ARN viral (), Cinétique, Codon, Conformation d'acide nucléique, Dimérisation, Données de séquences moléculaires, Décalage ribosomique du cadre de lecture, Magnésium (), Mutation, Résonance magnétique nucléaire biomoléculaire, Séquence conservée, Séquence nucléotidique, Séquences répétées inversées, Température, Viabilité microbienne, Virus du SRAS (génétique).
- MESH :
- génétique : Virus du SRAS.
- ARN viral, Cinétique, Codon, Conformation d'acide nucléique, Dimérisation, Données de séquences moléculaires, Décalage ribosomique du cadre de lecture, Magnésium, Mutation, Résonance magnétique nucléaire biomoléculaire, Séquence conservée, Séquence nucléotidique, Séquences répétées inversées, Température, Viabilité microbienne.
English descriptors
- KwdEn :
- Base Sequence, Codon, Conserved Sequence, Dimerization, Frameshifting, Ribosomal, Inverted Repeat Sequences, Kinetics, Magnesium (chemistry), Microbial Viability, Molecular Sequence Data, Mutation, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Conformation, RNA, Viral (chemistry), SARS Virus (genetics), Temperature.
- MESH :
- chemical , chemistry : Magnesium, RNA, Viral.
- chemical : Codon.
- genetics : SARS Virus.
- Base Sequence, Conserved Sequence, Dimerization, Frameshifting, Ribosomal, Inverted Repeat Sequences, Kinetics, Microbial Viability, Molecular Sequence Data, Mutation, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Conformation, Temperature.
Abstract
Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further
Url:
DOI: 10.1093/nar/gks1361
PubMed: 23275571
PubMed Central: 3575852
Affiliations:
- États-Unis
- Caroline du Nord, Caroline du Sud, Illinois, Maryland
- College Park (Maryland), Columbia (Caroline du Sud)
- Université de Caroline du Sud, Université du Maryland
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Le document en format XML
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Pérez-Alvarado</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gks1361-AFF1">Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Armbruster, David W" sort="Armbruster, David W" uniqKey="Armbruster D" first="David W." last="Armbruster">David W. 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Plant</name><affiliation wicri:level="2"><nlm:aff id="gks1361-AFF1">Laboratory of Hepatitis and Related Emerging Agents, Division of Emerging and Transfusion-Transmitted Diseases, Food and Drug Administration, Bethesda, MD 20892, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Hepatitis and Related Emerging Agents, Division of Emerging and Transfusion-Transmitted Diseases, Food and Drug Administration, Bethesda, MD 20892</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Sims, Amy C" sort="Sims, Amy C" uniqKey="Sims A" first="Amy C." last="Sims">Amy C. Sims</name><affiliation wicri:level="2"><nlm:aff id="gks1361-AFF1">Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Yount, Boyd L" sort="Yount, Boyd L" uniqKey="Yount B" first="Boyd L." last="Yount">Boyd L. Yount</name><affiliation wicri:level="2"><nlm:aff id="gks1361-AFF1">Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Roth, Braden M" sort="Roth, Braden M" uniqKey="Roth B" first="Braden M." last="Roth">Braden M. Roth</name><affiliation wicri:level="4"><nlm:aff id="gks1361-AFF1">Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425</wicri:regionArea><placeName><region type="state">Caroline du Sud</region><settlement type="city">Columbia (Caroline du Sud)</settlement></placeName><orgName type="university">Université de Caroline du Sud</orgName></affiliation></author><author><name sortKey="Eldho, Nadukkudy V" sort="Eldho, Nadukkudy V" uniqKey="Eldho N" first="Nadukkudy V." last="Eldho">Nadukkudy V. Eldho</name><affiliation wicri:level="4"><nlm:aff id="gks1361-AFF1">Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425</wicri:regionArea><placeName><region type="state">Caroline du Sud</region><settlement type="city">Columbia (Caroline du Sud)</settlement></placeName><orgName type="university">Université de Caroline du Sud</orgName></affiliation></author><author><name sortKey="Perez Alvarado, Gabriela C" sort="Perez Alvarado, Gabriela C" uniqKey="Perez Alvarado G" first="Gabriela C." last="Pérez-Alvarado">Gabriela C. Pérez-Alvarado</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gks1361-AFF1">Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Armbruster, David W" sort="Armbruster, David W" uniqKey="Armbruster D" first="David W." last="Armbruster">David W. Armbruster</name><affiliation wicri:level="4"><nlm:aff id="gks1361-AFF1">Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425</wicri:regionArea><placeName><region type="state">Caroline du Sud</region><settlement type="city">Columbia (Caroline du Sud)</settlement></placeName><orgName type="university">Université de Caroline du Sud</orgName></affiliation></author><author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S." last="Baric">Ralph S. Baric</name><affiliation wicri:level="2"><nlm:aff id="gks1361-AFF1">Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Caroline du Nord</region></placeName><wicri:cityArea>Departments of Epidemiology and Microbiology and Immunology, University of North Carolina, Chapel Hill</wicri:cityArea></affiliation></author><author><name sortKey="Dinman, Jonathan D" sort="Dinman, Jonathan D" uniqKey="Dinman J" first="Jonathan D." last="Dinman">Jonathan D. Dinman</name><affiliation wicri:level="4"><nlm:aff id="gks1361-AFF1">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation></author><author><name sortKey="Taylor, Deborah R" sort="Taylor, Deborah R" uniqKey="Taylor D" first="Deborah R." last="Taylor">Deborah R. Taylor</name><affiliation wicri:level="2"><nlm:aff id="gks1361-AFF1">Laboratory of Hepatitis and Related Emerging Agents, Division of Emerging and Transfusion-Transmitted Diseases, Food and Drug Administration, Bethesda, MD 20892, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Laboratory of Hepatitis and Related Emerging Agents, Division of Emerging and Transfusion-Transmitted Diseases, Food and Drug Administration, Bethesda, MD 20892</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Hennig, Mirko" sort="Hennig, Mirko" uniqKey="Hennig M" first="Mirko" last="Hennig">Mirko Hennig</name><affiliation wicri:level="4"><nlm:aff id="gks1361-AFF1">Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425</wicri:regionArea><placeName><region type="state">Caroline du Sud</region><settlement type="city">Columbia (Caroline du Sud)</settlement></placeName><orgName type="university">Université de Caroline du Sud</orgName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Codon</term><term>Conserved Sequence</term><term>Dimerization</term><term>Frameshifting, Ribosomal</term><term>Inverted Repeat Sequences</term><term>Kinetics</term><term>Magnesium (chemistry)</term><term>Microbial Viability</term><term>Molecular Sequence Data</term><term>Mutation</term><term>Nuclear Magnetic Resonance, Biomolecular</term><term>Nucleic Acid Conformation</term><term>RNA, Viral (chemistry)</term><term>SARS Virus (genetics)</term><term>Temperature</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral ()</term><term>Cinétique</term><term>Codon</term><term>Conformation d'acide nucléique</term><term>Dimérisation</term><term>Données de séquences moléculaires</term><term>Décalage ribosomique du cadre de lecture</term><term>Magnésium ()</term><term>Mutation</term><term>Résonance magnétique nucléaire biomoléculaire</term><term>Séquence conservée</term><term>Séquence nucléotidique</term><term>Séquences répétées inversées</term><term>Température</term><term>Viabilité microbienne</term><term>Virus du SRAS (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Magnesium</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Codon</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus du SRAS</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Conserved Sequence</term><term>Dimerization</term><term>Frameshifting, Ribosomal</term><term>Inverted Repeat Sequences</term><term>Kinetics</term><term>Microbial Viability</term><term>Molecular Sequence Data</term><term>Mutation</term><term>Nuclear Magnetic Resonance, Biomolecular</term><term>Nucleic Acid Conformation</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN viral</term><term>Cinétique</term><term>Codon</term><term>Conformation d'acide nucléique</term><term>Dimérisation</term><term>Données de séquences moléculaires</term><term>Décalage ribosomique du cadre de lecture</term><term>Magnésium</term><term>Mutation</term><term>Résonance magnétique nucléaire biomoléculaire</term><term>Séquence conservée</term><term>Séquence nucléotidique</term><term>Séquences répétées inversées</term><term>Température</term><term>Viabilité microbienne</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further <italic>in vitro</italic> analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, <italic>in vitro</italic> RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Plant, Ep" uniqKey="Plant E">EP Plant</name></author><author><name sortKey="Perez Alvarado, Gc" uniqKey="Perez Alvarado G">GC Perez-Alvarado</name></author><author><name sortKey="Jacobs, Jl" uniqKey="Jacobs J">JL Jacobs</name></author><author><name sortKey="Mukhopadhyay, B" uniqKey="Mukhopadhyay B">B Mukhopadhyay</name></author><author><name sortKey="Hennig, M" uniqKey="Hennig M">M Hennig</name></author><author><name sortKey="Dinman, Jd" uniqKey="Dinman J">JD Dinman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Su, Mc" uniqKey="Su M">MC Su</name></author><author><name sortKey="Chang, Ct" 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uniqKey="Pardi A">A Pardi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woese, Cr" uniqKey="Woese C">CR Woese</name></author><author><name sortKey="Winker, S" uniqKey="Winker S">S Winker</name></author><author><name sortKey="Gutell, Rr" uniqKey="Gutell R">RR Gutell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Farabaugh, Pj" uniqKey="Farabaugh P">PJ Farabaugh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giedroc, Dp" uniqKey="Giedroc D">DP Giedroc</name></author><author><name sortKey="Theimer, Ca" uniqKey="Theimer C">CA Theimer</name></author><author><name sortKey="Nixon, Pl" uniqKey="Nixon P">PL Nixon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Herold, J" uniqKey="Herold J">J Herold</name></author><author><name sortKey="Siddell, Sg" uniqKey="Siddell S">SG Siddell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paul, Cp" uniqKey="Paul C">CP Paul</name></author><author><name sortKey="Barry, Jk" uniqKey="Barry J">JK Barry</name></author><author><name sortKey="Dinesh Kumar, Sp" uniqKey="Dinesh Kumar S">SP Dinesh-Kumar</name></author><author><name sortKey="Brault, V" uniqKey="Brault V">V Brault</name></author><author><name sortKey="Miller, Wa" uniqKey="Miller W">WA Miller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tajima, Y" uniqKey="Tajima Y">Y Tajima</name></author><author><name sortKey="Iwakawa, Ho" uniqKey="Iwakawa H">HO Iwakawa</name></author><author><name sortKey="Kaido, M" uniqKey="Kaido M">M Kaido</name></author><author><name sortKey="Mise, K" uniqKey="Mise K">K Mise</name></author><author><name sortKey="Okuno, T" uniqKey="Okuno T">T Okuno</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Caroline du Nord</li><li>Caroline du Sud</li><li>Illinois</li><li>Maryland</li></region><settlement><li>College Park (Maryland)</li><li>Columbia (Caroline du Sud)</li></settlement><orgName><li>Université de Caroline du Sud</li><li>Université du Maryland</li></orgName></list><tree><country name="États-Unis"><region name="Caroline du Sud"><name sortKey="Ishimaru, Daniella" sort="Ishimaru, Daniella" uniqKey="Ishimaru D" first="Daniella" last="Ishimaru">Daniella Ishimaru</name></region><name sortKey="Armbruster, David W" sort="Armbruster, David W" uniqKey="Armbruster D" first="David W." last="Armbruster">David W. Armbruster</name><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S." last="Baric">Ralph S. Baric</name><name sortKey="Dinman, Jonathan D" sort="Dinman, Jonathan D" uniqKey="Dinman J" first="Jonathan D." last="Dinman">Jonathan D. Dinman</name><name sortKey="Eldho, Nadukkudy V" sort="Eldho, Nadukkudy V" uniqKey="Eldho N" first="Nadukkudy V." last="Eldho">Nadukkudy V. Eldho</name><name sortKey="Hennig, Mirko" sort="Hennig, Mirko" uniqKey="Hennig M" first="Mirko" last="Hennig">Mirko Hennig</name><name sortKey="Perez Alvarado, Gabriela C" sort="Perez Alvarado, Gabriela C" uniqKey="Perez Alvarado G" first="Gabriela C." last="Pérez-Alvarado">Gabriela C. Pérez-Alvarado</name><name sortKey="Plant, Ewan P" sort="Plant, Ewan P" uniqKey="Plant E" first="Ewan P." last="Plant">Ewan P. Plant</name><name sortKey="Roth, Braden M" sort="Roth, Braden M" uniqKey="Roth B" first="Braden M." last="Roth">Braden M. Roth</name><name sortKey="Sims, Amy C" sort="Sims, Amy C" uniqKey="Sims A" first="Amy C." last="Sims">Amy C. Sims</name><name sortKey="Taylor, Deborah R" sort="Taylor, Deborah R" uniqKey="Taylor D" first="Deborah R." last="Taylor">Deborah R. Taylor</name><name sortKey="Yount, Boyd L" sort="Yount, Boyd L" uniqKey="Yount B" first="Boyd L." last="Yount">Boyd L. Yount</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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