A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.
Identifieur interne : 000931 ( Ncbi/Merge ); précédent : 000930; suivant : 000932A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.
Auteurs : Benedikt M. Beckmann [Allemagne] ; Philipp G. Hoch ; Manja Marz ; Dagmar K. Willkomm ; Margarita Salas ; Roland K. HartmannSource :
- The EMBO journal [ 1460-2075 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA-Directed RNA Polymerases, RNA, Bacterial.
- metabolism : Bacillus subtilis, DNA-Directed RNA Polymerases, RNA, Bacterial.
- Base Sequence, Molecular Sequence Data, Nucleic Acid Conformation, RNA, Untranslated.
Abstract
Bacillus subtilis 6S-1 RNA binds to the housekeeping RNA polymerase (σ(A)-RNAP) and directs transcription of short 'product' RNAs (pRNAs). Here, we demonstrate that once newly synthesized pRNAs form a sufficiently stable duplex with 6S-1 RNA, a structural rearrangement is induced in cis, which involves base-pairing between sequences in the 5'-portion of the central bulge and nucleotides that become available as a result of pRNA invasion. The rearrangement decreases 6S-1 RNA affinity for σ(A)-RNAP. Among the pRNA length variants synthesized by σ(A)-RNAP (up to ∼14 nt), only the longer ones, such as 12-14-mers, form a duplex with 6S-1 RNA that is sufficiently long-lived to induce the rearrangement. Yet, an LNA (locked nucleic acid) 8-mer can induce the same rearrangement due to conferring increased duplex stability. We propose that an interplay of rate constants for polymerization (k(pol)), for pRNA:6S-1 RNA hybrid duplex dissociation (k(off)) and for the rearrangement (k(conf)) determines whether pRNAs dissociate or rearrange 6S-1 structure to trigger 6S-1 RNA release from σ(A)-RNAP. A bioinformatic screen suggests that essentially all bacterial 6S RNAs have the potential to undergo a pRNA-induced structural rearrangement.
DOI: 10.1038/emboj.2012.23
PubMed: 22333917
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Beckmann</name><affiliation wicri:level="3"><nlm:affiliation>Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marburg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marburg</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Giessen</region><settlement type="city">Marbourg</settlement></placeName></affiliation></author><author><name sortKey="Hoch, Philipp G" sort="Hoch, Philipp G" uniqKey="Hoch P" first="Philipp G" last="Hoch">Philipp G. Hoch</name></author><author><name sortKey="Marz, Manja" sort="Marz, Manja" uniqKey="Marz M" first="Manja" last="Marz">Manja Marz</name></author><author><name sortKey="Willkomm, Dagmar K" sort="Willkomm, Dagmar K" uniqKey="Willkomm D" first="Dagmar K" last="Willkomm">Dagmar K. Willkomm</name></author><author><name sortKey="Salas, Margarita" sort="Salas, Margarita" uniqKey="Salas M" first="Margarita" last="Salas">Margarita Salas</name></author><author><name sortKey="Hartmann, Roland K" sort="Hartmann, Roland K" uniqKey="Hartmann R" first="Roland K" last="Hartmann">Roland K. Hartmann</name></author></analytic><series><title level="j">The EMBO journal</title><idno type="eISSN">1460-2075</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacillus subtilis (metabolism)</term><term>Base Sequence</term><term>DNA-Directed RNA Polymerases (chemistry)</term><term>DNA-Directed RNA Polymerases (metabolism)</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>RNA, Bacterial (chemistry)</term><term>RNA, Bacterial (metabolism)</term><term>RNA, Untranslated</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN bactérien ()</term><term>ARN bactérien (métabolisme)</term><term>ARN non traduit</term><term>Bacillus subtilis (métabolisme)</term><term>Conformation d'acide nucléique</term><term>DNA-directed RNA polymerases ()</term><term>DNA-directed RNA polymerases (métabolisme)</term><term>Données de séquences moléculaires</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA-Directed RNA Polymerases</term><term>RNA, Bacterial</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Bacillus subtilis</term><term>DNA-Directed RNA Polymerases</term><term>RNA, Bacterial</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN bactérien</term><term>Bacillus subtilis</term><term>DNA-directed RNA polymerases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>RNA, Untranslated</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN bactérien</term><term>ARN non traduit</term><term>Conformation d'acide nucléique</term><term>DNA-directed RNA polymerases</term><term>Données de séquences moléculaires</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bacillus subtilis 6S-1 RNA binds to the housekeeping RNA polymerase (σ(A)-RNAP) and directs transcription of short 'product' RNAs (pRNAs). Here, we demonstrate that once newly synthesized pRNAs form a sufficiently stable duplex with 6S-1 RNA, a structural rearrangement is induced in cis, which involves base-pairing between sequences in the 5'-portion of the central bulge and nucleotides that become available as a result of pRNA invasion. The rearrangement decreases 6S-1 RNA affinity for σ(A)-RNAP. Among the pRNA length variants synthesized by σ(A)-RNAP (up to ∼14 nt), only the longer ones, such as 12-14-mers, form a duplex with 6S-1 RNA that is sufficiently long-lived to induce the rearrangement. Yet, an LNA (locked nucleic acid) 8-mer can induce the same rearrangement due to conferring increased duplex stability. We propose that an interplay of rate constants for polymerization (k(pol)), for pRNA:6S-1 RNA hybrid duplex dissociation (k(off)) and for the rearrangement (k(conf)) determines whether pRNAs dissociate or rearrange 6S-1 structure to trigger 6S-1 RNA release from σ(A)-RNAP. A bioinformatic screen suggests that essentially all bacterial 6S RNAs have the potential to undergo a pRNA-induced structural rearrangement.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22333917</PMID><DateCompleted><Year>2012</Year><Month>06</Month><Day>04</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1460-2075</ISSN><JournalIssue CitedMedium="Internet"><Volume>31</Volume><Issue>7</Issue><PubDate><Year>2012</Year><Month>Apr</Month><Day>04</Day></PubDate></JournalIssue><Title>The EMBO journal</Title><ISOAbbreviation>EMBO J.</ISOAbbreviation></Journal><ArticleTitle>A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.</ArticleTitle><Pagination><MedlinePgn>1727-38</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/emboj.2012.23</ELocationID><Abstract><AbstractText>Bacillus subtilis 6S-1 RNA binds to the housekeeping RNA polymerase (σ(A)-RNAP) and directs transcription of short 'product' RNAs (pRNAs). Here, we demonstrate that once newly synthesized pRNAs form a sufficiently stable duplex with 6S-1 RNA, a structural rearrangement is induced in cis, which involves base-pairing between sequences in the 5'-portion of the central bulge and nucleotides that become available as a result of pRNA invasion. The rearrangement decreases 6S-1 RNA affinity for σ(A)-RNAP. Among the pRNA length variants synthesized by σ(A)-RNAP (up to ∼14 nt), only the longer ones, such as 12-14-mers, form a duplex with 6S-1 RNA that is sufficiently long-lived to induce the rearrangement. Yet, an LNA (locked nucleic acid) 8-mer can induce the same rearrangement due to conferring increased duplex stability. We propose that an interplay of rate constants for polymerization (k(pol)), for pRNA:6S-1 RNA hybrid duplex dissociation (k(off)) and for the rearrangement (k(conf)) determines whether pRNAs dissociate or rearrange 6S-1 structure to trigger 6S-1 RNA release from σ(A)-RNAP. A bioinformatic screen suggests that essentially all bacterial 6S RNAs have the potential to undergo a pRNA-induced structural rearrangement.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Beckmann</LastName><ForeName>Benedikt M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marburg, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hoch</LastName><ForeName>Philipp G</ForeName><Initials>PG</Initials></Author><Author ValidYN="Y"><LastName>Marz</LastName><ForeName>Manja</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Willkomm</LastName><ForeName>Dagmar K</ForeName><Initials>DK</Initials></Author><Author ValidYN="Y"><LastName>Salas</LastName><ForeName>Margarita</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Hartmann</LastName><ForeName>Roland K</ForeName><Initials>RK</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2012</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>EMBO J</MedlineTA><NlmUniqueID>8208664</NlmUniqueID><ISSNLinking>0261-4189</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C411065">6S RNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012329">RNA, Bacterial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D022661">RNA, Untranslated</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.7.6</RegistryNumber><NameOfSubstance UI="D012321">DNA-Directed RNA 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uniqKey="Hartmann R" first="Roland K" last="Hartmann">Roland K. Hartmann</name><name sortKey="Hoch, Philipp G" sort="Hoch, Philipp G" uniqKey="Hoch P" first="Philipp G" last="Hoch">Philipp G. Hoch</name><name sortKey="Marz, Manja" sort="Marz, Manja" uniqKey="Marz M" first="Manja" last="Marz">Manja Marz</name><name sortKey="Salas, Margarita" sort="Salas, Margarita" uniqKey="Salas M" first="Margarita" last="Salas">Margarita Salas</name><name sortKey="Willkomm, Dagmar K" sort="Willkomm, Dagmar K" uniqKey="Willkomm D" first="Dagmar K" last="Willkomm">Dagmar K. Willkomm</name></noCountry><country name="Allemagne"><region name="Hesse (Land)"><name sortKey="Beckmann, Benedikt M" sort="Beckmann, Benedikt M" uniqKey="Beckmann B" first="Benedikt M" last="Beckmann">Benedikt M. Beckmann</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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