MersV1, Ncbi, Merge, bibRecord, 000C66

Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs--commonalities and differences.

Identifieur interne : 000C66 ( Ncbi/Merge ); précédent : 000C65; suivant : 000C67

Mechanistic 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. Hartmann

Source :

RNA (New York, N.Y.) [ 1469-9001 ] ; 2014.

RBID : pubmed:24464747

Descripteurs français

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

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Le document en format XML

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<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>
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<Abstract><AbstractText>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.</AbstractText>
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<Keyword MajorTopicYN="N">6S-1 RNA</Keyword>
<Keyword MajorTopicYN="N">6S-2 RNA</Keyword>
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<Keyword MajorTopicYN="N">affinity for σA-RNAP</Keyword>
<Keyword MajorTopicYN="N">bsrA</Keyword>
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<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>
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Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs--commonalities and differences.

Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs--commonalities and differences.

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