A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.
Identifieur interne : 002280 ( Main/Exploration ); précédent : 002279; suivant : 002281A 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
Affiliations:
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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><affiliations><list><country><li>Allemagne</li></country><region><li>District de Giessen</li><li>Hesse (Land)</li></region><settlement><li>Marbourg</li></settlement></list><tree><noCountry><name sortKey="Hartmann, Roland K" sort="Hartmann, Roland K" 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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