A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable.
Identifieur interne : 001540 ( PubMed/Checkpoint ); précédent : 001539; suivant : 001541A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable.
Auteurs : Suzanne N. Stammler [États-Unis] ; Song Cao ; Shi-Jie Chen ; David P. GiedrocSource :
- RNA (New York, N.Y.) [ 1469-9001 ] ; 2011.
Descripteurs français
- KwdFr :
- ARN viral (), ARN viral (génétique), Appariement de bases, Conformation d'acide nucléique, Données de séquences moléculaires, Génome viral, Régions 3' non traduites, Réplication virale (génétique), Séquence nucléotidique, Thermodynamique, Virus de l'hépatite murine (génétique), Virus de l'hépatite murine (physiologie), Virus du SRAS (génétique).
- MESH :
- génétique : ARN viral, Réplication virale, Virus de l'hépatite murine, Virus du SRAS.
- physiologie : Virus de l'hépatite murine.
- ARN viral, Appariement de bases, Conformation d'acide nucléique, Données de séquences moléculaires, Génome viral, Régions 3' non traduites, Séquence nucléotidique, Thermodynamique.
English descriptors
- KwdEn :
- 3' Untranslated Regions, Base Pairing, Base Sequence, Genome, Viral, Molecular Sequence Data, Murine hepatitis virus (genetics), Murine hepatitis virus (physiology), Nucleic Acid Conformation, RNA, Viral (chemistry), RNA, Viral (genetics), SARS Virus (genetics), Thermodynamics, Virus Replication (genetics).
- MESH :
- chemical , chemistry : RNA, Viral.
- chemical , genetics : RNA, Viral.
- chemical : 3' Untranslated Regions.
- genetics : Murine hepatitis virus, SARS Virus, Virus Replication.
- physiology : Murine hepatitis virus.
- Base Pairing, Base Sequence, Genome, Viral, Molecular Sequence Data, Nucleic Acid Conformation, Thermodynamics.
Abstract
The 3'-untranslated region (UTR) of the group 2 coronavirus mouse hepatitis virus (MHV) genome contains a predicted bulged stem-loop (designated P0ab), a conserved cis-acting pseudoknot (PK), and a more distal stem-loop (designated P2). Base-pairing to create the pseudoknot-forming stem (P1(pk)) is mutually exclusive with formation of stem P0a at the base of the bulged stem-loop; as a result, the two structures cannot be present simultaneously. Herein, we use thermodynamic methods to evaluate the ability of individual subdomains of the 3' UTR to adopt a pseudoknotted conformation. We find that an RNA capable of forming only the predicted PK (58 nt; 3' nucleotides 241-185) adopts the P2 stem-loop with little evidence for P1(pk) pairing in 0.1 M KCl and the absence of Mg(2+); as Mg(2+) or 1 M KCl is added, a new thermal unfolding transition is induced and assignable to P1(pk) pairing. The P1(pk) helix is only marginally stable, ΔG(25) ≈ 1.2 ± 0.3 kcal/mol (5.0 mM Mg(2+), 100 mM K(+)), and unfolded at 37°C. Similar findings characterize an RNA 5' extended through the P0b helix only (89 nt; 294-185). In contrast, an RNA capable of forming either the P0a helix or the pseudoknot (97 nt; 301-185) forms no P1(pk) helix. Thermal unfolding simulations are fully consistent with these experimental findings. These data reveal that the PK forms weakly and only when the competing double-hairpin structure cannot form; in the UTR RNA, the double hairpin is the predominant conformer under all solution conditions.
DOI: 10.1261/rna.2816711
PubMed: 21799029
Affiliations:
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pubmed:21799029Le document en format XML
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Stammler</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Texas A&M University, College Station, Texas 77843-2128, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, Texas A&M University, College Station, Texas 77843-2128</wicri:regionArea><wicri:noRegion>Texas 77843-2128</wicri:noRegion></affiliation></author><author><name sortKey="Cao, Song" sort="Cao, Song" uniqKey="Cao S" first="Song" last="Cao">Song Cao</name></author><author><name sortKey="Chen, Shi Jie" sort="Chen, Shi Jie" uniqKey="Chen S" first="Shi-Jie" last="Chen">Shi-Jie Chen</name></author><author><name sortKey="Giedroc, David P" sort="Giedroc, David P" uniqKey="Giedroc D" first="David P" last="Giedroc">David P. Giedroc</name></author></analytic><series><title level="j">RNA (New York, N.Y.)</title><idno type="eISSN">1469-9001</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>3' Untranslated Regions</term><term>Base Pairing</term><term>Base Sequence</term><term>Genome, Viral</term><term>Molecular Sequence Data</term><term>Murine hepatitis virus (genetics)</term><term>Murine hepatitis virus (physiology)</term><term>Nucleic Acid Conformation</term><term>RNA, Viral (chemistry)</term><term>RNA, Viral (genetics)</term><term>SARS Virus (genetics)</term><term>Thermodynamics</term><term>Virus Replication (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral ()</term><term>ARN viral (génétique)</term><term>Appariement de bases</term><term>Conformation d'acide nucléique</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Régions 3' non traduites</term><term>Réplication virale (génétique)</term><term>Séquence nucléotidique</term><term>Thermodynamique</term><term>Virus de l'hépatite murine (génétique)</term><term>Virus de l'hépatite murine (physiologie)</term><term>Virus du SRAS (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>3' Untranslated Regions</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Murine hepatitis virus</term><term>SARS Virus</term><term>Virus Replication</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Réplication virale</term><term>Virus de l'hépatite murine</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Virus de l'hépatite murine</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Murine hepatitis virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Genome, Viral</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN viral</term><term>Appariement de bases</term><term>Conformation d'acide nucléique</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Régions 3' non traduites</term><term>Séquence nucléotidique</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The 3'-untranslated region (UTR) of the group 2 coronavirus mouse hepatitis virus (MHV) genome contains a predicted bulged stem-loop (designated P0ab), a conserved cis-acting pseudoknot (PK), and a more distal stem-loop (designated P2). Base-pairing to create the pseudoknot-forming stem (P1(pk)) is mutually exclusive with formation of stem P0a at the base of the bulged stem-loop; as a result, the two structures cannot be present simultaneously. Herein, we use thermodynamic methods to evaluate the ability of individual subdomains of the 3' UTR to adopt a pseudoknotted conformation. We find that an RNA capable of forming only the predicted PK (58 nt; 3' nucleotides 241-185) adopts the P2 stem-loop with little evidence for P1(pk) pairing in 0.1 M KCl and the absence of Mg(2+); as Mg(2+) or 1 M KCl is added, a new thermal unfolding transition is induced and assignable to P1(pk) pairing. The P1(pk) helix is only marginally stable, ΔG(25) ≈ 1.2 ± 0.3 kcal/mol (5.0 mM Mg(2+), 100 mM K(+)), and unfolded at 37°C. Similar findings characterize an RNA 5' extended through the P0b helix only (89 nt; 294-185). In contrast, an RNA capable of forming either the P0a helix or the pseudoknot (97 nt; 301-185) forms no P1(pk) helix. Thermal unfolding simulations are fully consistent with these experimental findings. These data reveal that the PK forms weakly and only when the competing double-hairpin structure cannot form; in the UTR RNA, the double hairpin is the predominant conformer under all solution conditions.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21799029</PMID><DateCompleted><Year>2011</Year><Month>10</Month><Day>17</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-9001</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>9</Issue><PubDate><Year>2011</Year><Month>Sep</Month></PubDate></JournalIssue><Title>RNA (New York, N.Y.)</Title><ISOAbbreviation>RNA</ISOAbbreviation></Journal><ArticleTitle>A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable.</ArticleTitle><Pagination><MedlinePgn>1747-59</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1261/rna.2816711</ELocationID><Abstract><AbstractText>The 3'-untranslated region (UTR) of the group 2 coronavirus mouse hepatitis virus (MHV) genome contains a predicted bulged stem-loop (designated P0ab), a conserved cis-acting pseudoknot (PK), and a more distal stem-loop (designated P2). Base-pairing to create the pseudoknot-forming stem (P1(pk)) is mutually exclusive with formation of stem P0a at the base of the bulged stem-loop; as a result, the two structures cannot be present simultaneously. Herein, we use thermodynamic methods to evaluate the ability of individual subdomains of the 3' UTR to adopt a pseudoknotted conformation. We find that an RNA capable of forming only the predicted PK (58 nt; 3' nucleotides 241-185) adopts the P2 stem-loop with little evidence for P1(pk) pairing in 0.1 M KCl and the absence of Mg(2+); as Mg(2+) or 1 M KCl is added, a new thermal unfolding transition is induced and assignable to P1(pk) pairing. The P1(pk) helix is only marginally stable, ΔG(25) ≈ 1.2 ± 0.3 kcal/mol (5.0 mM Mg(2+), 100 mM K(+)), and unfolded at 37°C. Similar findings characterize an RNA 5' extended through the P0b helix only (89 nt; 294-185). In contrast, an RNA capable of forming either the P0a helix or the pseudoknot (97 nt; 301-185) forms no P1(pk) helix. Thermal unfolding simulations are fully consistent with these experimental findings. These data reveal that the PK forms weakly and only when the competing double-hairpin structure cannot form; in the UTR RNA, the double hairpin is the predominant conformer under all solution conditions.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stammler</LastName><ForeName>Suzanne N</ForeName><Initials>SN</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Texas A&M University, College Station, Texas 77843-2128, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Song</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Shi-Jie</ForeName><Initials>SJ</Initials></Author><Author ValidYN="Y"><LastName>Giedroc</LastName><ForeName>David P</ForeName><Initials>DP</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>GM063732</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 AI067416</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>AI067416</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM063732</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>AI040187</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 AI040187</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>07</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>RNA</MedlineTA><NlmUniqueID>9509184</NlmUniqueID><ISSNLinking>1355-8382</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020413">3' Untranslated Regions</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020413" MajorTopicYN="Y">3' Untranslated Regions</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020029" MajorTopicYN="N">Base Pairing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="Y">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006517" MajorTopicYN="N">Murine hepatitis virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013816" 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sort="Cao, Song" uniqKey="Cao S" first="Song" last="Cao">Song Cao</name><name sortKey="Chen, Shi Jie" sort="Chen, Shi Jie" uniqKey="Chen S" first="Shi-Jie" last="Chen">Shi-Jie Chen</name><name sortKey="Giedroc, David P" sort="Giedroc, David P" uniqKey="Giedroc D" first="David P" last="Giedroc">David P. Giedroc</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Stammler, Suzanne N" sort="Stammler, Suzanne N" uniqKey="Stammler S" first="Suzanne N" last="Stammler">Suzanne N. Stammler</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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