Key interactions of RNA polymerase with 6S RNA and secondary channel factors during pRNA synthesis.
Biochim Biophys Acta Gene Regul Mech
; 1867(2): 195032, 2024 Jun.
Article
in En
| MEDLINE
| ID: mdl-38692564
ABSTRACT
Small non-coding 6S RNA mimics DNA promoters and binds to the σ70 holoenzyme of bacterial RNA polymerase (RNAP) to suppress transcription of various genes mainly during the stationary phase of cell growth or starvation. This inhibition can be relieved upon synthesis of short product RNA (pRNA) performed by RNAP from the 6S RNA template. Here, we have shown that pRNA synthesis depends on specific contacts of 6S RNA with RNAP and interactions of the σ finger with the RNA template in the active site of RNAP, and is also modulated by the secondary channel factors. We have adapted a molecular beacon assay with fluorescently labeled σ70 to analyze 6S RNA release during pRNA synthesis. We found the kinetics of 6S RNA release to be oppositely affected by mutations in the σ finger and in the CRE pocket of core RNAP, similarly to the reported role of these regions in promoter-dependent transcription. Secondary channel factors, DksA and GreB, inhibit pRNA synthesis and 6S RNA release from RNAP, suggesting that they may contribute to the 6S RNA-mediated switch in transcription during stringent response. Our results demonstrate that pRNA synthesis depends on a similar set of contacts between RNAP and 6S RNA as in the case of promoter-dependent transcription initiation and reveal that both processes can be regulated by universal transcription factors acting on RNAP.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Sigma Factor
/
Transcription, Genetic
/
DNA-Directed RNA Polymerases
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RNA, Bacterial
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Escherichia coli Proteins
Language:
En
Journal:
Biochim Biophys Acta Gene Regul Mech
/
Biochim. Biophys. Acta Gene. Regul. Mech
/
Biochimica et biophysica acta. Gene regulatory mechanisms (Online)
Year:
2024
Document type:
Article
Affiliation country:
Country of publication: