Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs--commonalities and differences.
Identifieur interne : 001B73 ( Main/Exploration ); précédent : 001B72; suivant : 001B74Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs--commonalities and differences.
Auteurs : Olga Y. Burenina ; Philipp G. Hoch ; Katrin Damm ; Margarita Salas ; Timofei S. Zatsepin ; Marcus Lechner ; Tatiana S. Oretskaya ; Elena A. Kubareva ; Roland K. HartmannSource :
- RNA (New York, N.Y.) [ 1469-9001 ] ; 2014.
Descripteurs français
- KwdFr :
- ARN bactérien (), ARN bactérien (génétique), ARN bactérien (métabolisme), ARN non traduit, Bacillus subtilis (génétique), Bacillus subtilis (métabolisme), Conformation d'acide nucléique, DNA-directed RNA polymerases (métabolisme), Protéines virales (métabolisme), Réaction de polymérisation en chaîne, Régions promotrices (génétique) (génétique), Test de retard de migration électrophorétique, Transcription génétique.
- MESH :
- génétique : ARN bactérien, Bacillus subtilis, Régions promotrices (génétique).
- métabolisme : ARN bactérien, Bacillus subtilis, DNA-directed RNA polymerases, Protéines virales.
- ARN bactérien, ARN non traduit, Conformation d'acide nucléique, Réaction de polymérisation en chaîne, Test de retard de migration électrophorétique, Transcription génétique.
English descriptors
- KwdEn :
- Bacillus subtilis (genetics), Bacillus subtilis (metabolism), DNA-Directed RNA Polymerases (metabolism), Electrophoretic Mobility Shift Assay, Nucleic Acid Conformation, Polymerase Chain Reaction, Promoter Regions, Genetic (genetics), RNA, Bacterial (chemistry), RNA, Bacterial (genetics), RNA, Bacterial (metabolism), RNA, Untranslated, Transcription, Genetic, Viral Proteins (metabolism).
- MESH :
- chemical , chemistry : RNA, Bacterial.
- chemical , genetics : RNA, Bacterial.
- chemical , metabolism : DNA-Directed RNA Polymerases, RNA, Bacterial, Viral Proteins.
- genetics : Bacillus subtilis, Promoter Regions, Genetic.
- metabolism : Bacillus subtilis.
- Electrophoretic Mobility Shift Assay, Nucleic Acid Conformation, Polymerase Chain Reaction, RNA, Untranslated, Transcription, Genetic.
Abstract
Bacterial 6S RNAs bind to the housekeeping RNA polymerase (σ(A)-RNAP in Bacillus subtilis) to regulate transcription in a growth phase-dependent manner. B. subtilis expresses two 6S RNAs, 6S-1 and 6S-2 RNA, with different expression profiles. We show in vitro that 6S-2 RNA shares hallmark features with 6S-1 RNA: Both (1) are able to serve as templates for pRNA transcription; (2) bind with comparable affinity to σ(A)-RNAP; (3) are able to specifically inhibit transcription from DNA promoters, and (4) can form stable 6S RNA:pRNA hybrid structures that (5) abolish binding to σ(A)-RNAP. However, pRNAs of equal length dissociate faster from 6S-2 than 6S-1 RNA, owing to the higher A,U-content of 6S-2 pRNAs. This could have two mechanistic implications: (1) Short 6S-2 pRNAs (<10 nt) dissociate faster instead of being elongated to longer pRNAs, which could make it more difficult for 6S-2 RNA-stalled RNAP molecules to escape from the sequestration; and (2) relative to 6S-1 RNA, 6S-2 pRNAs of equal length will dissociate more rapidly from 6S-2 RNA after RNAP release, which could affect pRNA turnover or the kinetics of 6S-2 RNA binding to a new RNAP molecule. As 6S-2 pRNAs have not yet been detected in vivo, we considered that cellular RNAP release from 6S-2 RNA might occur via 6S-1 RNA displacing 6S-2 RNA from the enzyme, either in the absence of pRNA transcription or upon synthesis of very short 6S-2 pRNAs (∼ 5-mers, which would escape detection by deep sequencing). However, binding competition experiments argued against these possibilities.
DOI: 10.1261/rna.042077.113
PubMed: 24464747
Affiliations:
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Burenina</name></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="Damm, Katrin" sort="Damm, Katrin" uniqKey="Damm K" first="Katrin" last="Damm">Katrin Damm</name></author><author><name sortKey="Salas, Margarita" sort="Salas, Margarita" uniqKey="Salas M" first="Margarita" last="Salas">Margarita Salas</name></author><author><name sortKey="Zatsepin, Timofei S" sort="Zatsepin, Timofei S" uniqKey="Zatsepin T" first="Timofei S" last="Zatsepin">Timofei S. Zatsepin</name></author><author><name sortKey="Lechner, Marcus" sort="Lechner, Marcus" uniqKey="Lechner M" first="Marcus" last="Lechner">Marcus Lechner</name></author><author><name sortKey="Oretskaya, Tatiana S" sort="Oretskaya, Tatiana S" uniqKey="Oretskaya T" first="Tatiana S" last="Oretskaya">Tatiana S. Oretskaya</name></author><author><name sortKey="Kubareva, Elena A" sort="Kubareva, Elena A" uniqKey="Kubareva E" first="Elena A" last="Kubareva">Elena A. Kubareva</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">RNA (New York, N.Y.)</title><idno type="eISSN">1469-9001</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacillus subtilis (genetics)</term><term>Bacillus subtilis (metabolism)</term><term>DNA-Directed RNA Polymerases (metabolism)</term><term>Electrophoretic Mobility Shift Assay</term><term>Nucleic Acid Conformation</term><term>Polymerase Chain Reaction</term><term>Promoter Regions, Genetic (genetics)</term><term>RNA, Bacterial (chemistry)</term><term>RNA, Bacterial (genetics)</term><term>RNA, Bacterial (metabolism)</term><term>RNA, Untranslated</term><term>Transcription, Genetic</term><term>Viral Proteins (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN bactérien ()</term><term>ARN bactérien (génétique)</term><term>ARN bactérien (métabolisme)</term><term>ARN non traduit</term><term>Bacillus subtilis (génétique)</term><term>Bacillus subtilis (métabolisme)</term><term>Conformation d'acide nucléique</term><term>DNA-directed RNA polymerases (métabolisme)</term><term>Protéines virales (métabolisme)</term><term>Réaction de polymérisation en chaîne</term><term>Régions promotrices (génétique) (génétique)</term><term>Test de retard de migration électrophorétique</term><term>Transcription génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Bacterial</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA-Directed RNA Polymerases</term><term>RNA, Bacterial</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacillus subtilis</term><term>Promoter Regions, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN bactérien</term><term>Bacillus subtilis</term><term>Régions promotrices (génétique)</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Bacillus subtilis</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN bactérien</term><term>Bacillus subtilis</term><term>DNA-directed RNA polymerases</term><term>Protéines virales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Electrophoretic Mobility Shift Assay</term><term>Nucleic Acid Conformation</term><term>Polymerase Chain Reaction</term><term>RNA, Untranslated</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN bactérien</term><term>ARN non traduit</term><term>Conformation d'acide nucléique</term><term>Réaction de polymérisation en chaîne</term><term>Test de retard de migration électrophorétique</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Bacterial 6S RNAs bind to the housekeeping RNA polymerase (σ(A)-RNAP in Bacillus subtilis) to regulate transcription in a growth phase-dependent manner. B. subtilis expresses two 6S RNAs, 6S-1 and 6S-2 RNA, with different expression profiles. We show in vitro that 6S-2 RNA shares hallmark features with 6S-1 RNA: Both (1) are able to serve as templates for pRNA transcription; (2) bind with comparable affinity to σ(A)-RNAP; (3) are able to specifically inhibit transcription from DNA promoters, and (4) can form stable 6S RNA:pRNA hybrid structures that (5) abolish binding to σ(A)-RNAP. However, pRNAs of equal length dissociate faster from 6S-2 than 6S-1 RNA, owing to the higher A,U-content of 6S-2 pRNAs. This could have two mechanistic implications: (1) Short 6S-2 pRNAs (<10 nt) dissociate faster instead of being elongated to longer pRNAs, which could make it more difficult for 6S-2 RNA-stalled RNAP molecules to escape from the sequestration; and (2) relative to 6S-1 RNA, 6S-2 pRNAs of equal length will dissociate more rapidly from 6S-2 RNA after RNAP release, which could affect pRNA turnover or the kinetics of 6S-2 RNA binding to a new RNAP molecule. As 6S-2 pRNAs have not yet been detected in vivo, we considered that cellular RNAP release from 6S-2 RNA might occur via 6S-1 RNA displacing 6S-2 RNA from the enzyme, either in the absence of pRNA transcription or upon synthesis of very short 6S-2 pRNAs (∼ 5-mers, which would escape detection by deep sequencing). However, binding competition experiments argued against these possibilities.</div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Burenina, Olga Y" sort="Burenina, Olga Y" uniqKey="Burenina O" first="Olga Y" last="Burenina">Olga Y. Burenina</name><name sortKey="Damm, Katrin" sort="Damm, Katrin" uniqKey="Damm K" first="Katrin" last="Damm">Katrin Damm</name><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="Kubareva, Elena A" sort="Kubareva, Elena A" uniqKey="Kubareva E" first="Elena A" last="Kubareva">Elena A. Kubareva</name><name sortKey="Lechner, Marcus" sort="Lechner, Marcus" uniqKey="Lechner M" first="Marcus" last="Lechner">Marcus Lechner</name><name sortKey="Oretskaya, Tatiana S" sort="Oretskaya, Tatiana S" uniqKey="Oretskaya T" first="Tatiana S" last="Oretskaya">Tatiana S. Oretskaya</name><name sortKey="Salas, Margarita" sort="Salas, Margarita" uniqKey="Salas M" first="Margarita" last="Salas">Margarita Salas</name><name sortKey="Zatsepin, Timofei S" sort="Zatsepin, Timofei S" uniqKey="Zatsepin T" first="Timofei S" last="Zatsepin">Timofei S. Zatsepin</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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