Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch
Identifieur interne : 000526 ( Main/Exploration ); précédent : 000525; suivant : 000527Basis 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
Affiliations:
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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><wicri:noRegion>Louisiana 70802</wicri:noRegion></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><wicri:noRegion>Louisiana 70802</wicri:noRegion></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><wicri:noRegion>Louisiana 70802</wicri:noRegion></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><idno type="wicri:Area/Pmc/Checkpoint">000438</idno><idno type="wicri:Area/Ncbi/Merge">000305</idno><idno type="wicri:Area/Ncbi/Curation">000305</idno><idno type="wicri:Area/Ncbi/Checkpoint">000305</idno><idno 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70802</wicri:noRegion></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><wicri:noRegion>Louisiana 70802</wicri:noRegion></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><wicri:noRegion>Louisiana 70802</wicri:noRegion></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><wicri:noRegion>Louisiana 70802</wicri:noRegion></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><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Boyapati, Vamsi Krishna" sort="Boyapati, Vamsi Krishna" uniqKey="Boyapati V" first="Vamsi Krishna" last="Boyapati">Vamsi Krishna Boyapati</name></noRegion><name sortKey="Aboul Ela, Fareed" sort="Aboul Ela, Fareed" uniqKey="Aboul Ela F" first="Fareed" last="Aboul-Ela">Fareed Aboul-Ela</name><name sortKey="Huang, Wei" sort="Huang, Wei" uniqKey="Huang W" first="Wei" last="Huang">Wei Huang</name><name sortKey="Spedale, Jessica" sort="Spedale, Jessica" uniqKey="Spedale J" first="Jessica" last="Spedale">Jessica Spedale</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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