Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch
Identifieur interne : 000414 ( Pmc/Curation ); précédent : 000413; suivant : 000415Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch
Auteurs : Vamsi Krishna Boyapati [États-Unis] ; Wei Huang [États-Unis] ; Jessica Spedale [États-Unis] ; Fareed Aboul-Ela [États-Unis]Source :
- RNA [ 1355-8382 ] ; 2012.
Abstract
Riboswitches are RNA elements that bind to effector ligands and control gene expression. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. The authors present binding measurements and in-line probing that are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. These findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.
Url:
DOI: 10.1261/rna.032177.111
PubMed: 22543867
PubMed Central: 3358645
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xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802</wicri:regionArea></affiliation></author><author><name sortKey="Spedale, Jessica" sort="Spedale, Jessica" uniqKey="Spedale J" first="Jessica" last="Spedale">Jessica Spedale</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802</wicri:regionArea></affiliation></author><author><name sortKey="Aboul Ela, Fareed" sort="Aboul Ela, Fareed" uniqKey="Aboul Ela F" first="Fareed" last="Aboul-Ela">Fareed Aboul-Ela</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22543867</idno><idno type="pmc">3358645</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358645</idno><idno type="RBID">PMC:3358645</idno><idno type="doi">10.1261/rna.032177.111</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000414</idno><idno type="wicri:Area/Pmc/Curation">000414</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch</title><author><name sortKey="Boyapati, Vamsi Krishna" sort="Boyapati, Vamsi Krishna" uniqKey="Boyapati V" first="Vamsi Krishna" last="Boyapati">Vamsi Krishna Boyapati</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802</wicri:regionArea></affiliation></author><author><name sortKey="Huang, Wei" sort="Huang, Wei" uniqKey="Huang W" first="Wei" last="Huang">Wei Huang</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802</wicri:regionArea></affiliation></author><author><name sortKey="Spedale, Jessica" sort="Spedale, Jessica" uniqKey="Spedale J" first="Jessica" last="Spedale">Jessica Spedale</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802</wicri:regionArea></affiliation></author><author><name sortKey="Aboul Ela, Fareed" sort="Aboul Ela, Fareed" uniqKey="Aboul Ela F" first="Fareed" last="Aboul-Ela">Fareed Aboul-Ela</name><affiliation wicri:level="1"><nlm:aff id="aff1">Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802</wicri:regionArea></affiliation></author></analytic><series><title level="j">RNA</title><idno type="ISSN">1355-8382</idno><idno type="eISSN">1469-9001</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Riboswitches are RNA elements that bind to effector ligands and control gene expression. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. The authors present binding measurements and in-line probing that are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. These findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">RNA</journal-id><journal-id journal-id-type="iso-abbrev">RNA</journal-id><journal-id journal-id-type="publisher-id">RNA</journal-id><journal-title-group><journal-title>RNA</journal-title></journal-title-group><issn pub-type="ppub">1355-8382</issn><issn pub-type="epub">1469-9001</issn><publisher><publisher-name>Cold Spring Harbor Laboratory Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22543867</article-id><article-id pub-id-type="pmc">3358645</article-id><article-id pub-id-type="medline">9509184</article-id><article-id pub-id-type="publisher-id">RA</article-id><article-id pub-id-type="doi">10.1261/rna.032177.111</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch</article-title><alt-title alt-title-type="left-running">Boyapati et al.</alt-title><alt-title alt-title-type="right-running">Riboswitch hybrid conformations</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Boyapati</surname><given-names>Vamsi Krishna</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Spedale</surname><given-names>Jessica</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Aboul-ela</surname><given-names>Fareed</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1">1</xref></contrib></contrib-group><aff id="aff1">Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA</aff><author-notes><fn><p><italic>Abbreviations:</italic> SAM, S-Adenosyl Methionine; AT, antiterminator; MFE, minimum free energy.</p></fn><corresp id="cor1"><label>1</label><bold>Corresponding author.</bold><bold>E-mail <email>fareed@aboulela.com</email>.</bold></corresp></author-notes><pub-date pub-type="ppub"><month>6</month><year>2012</year></pub-date><volume>18</volume><issue>6</issue><fpage>1230</fpage><lpage>1243</lpage><history><date date-type="received"><day>27</day><month>12</month><year>2011</year></date><date date-type="accepted"><day>17</day><month>3</month><year>2012</year></date></history><permissions><copyright-statement>Copyright © 2012 RNA Society</copyright-statement><copyright-year>2012</copyright-year></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="1230.pdf"></self-uri><abstract abstract-type="precis"><p>Riboswitches are RNA elements that bind to effector ligands and control gene expression. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. The authors present binding measurements and in-line probing that are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. These findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.</p></abstract><abstract><p>Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the <italic>Bacillus subtilis yitJ</italic> SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming “hybrid” structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.</p></abstract><kwd-group><kwd>riboswitch</kwd><kwd>aptamer</kwd><kwd>S-adenosyl methionine</kwd><kwd>RNA folding</kwd><kwd>ligand binding</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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