ArticleRNA (New York, N.Y.)2012
E. coli 6S RNA release from RNA polymerase requires σ70 ejection by scrunching and is orchestrated by a conserved RNA hairpin.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 38 citations in OpenAlex.
- 6S-1 pRNA 9-mers are a prominent length species during outgrowth ofRNA biology · 2025Article
- A general RNA-templated RNA extension activity ofRNA (New York, N.Y.) · 2025Article
- RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria.Nucleic acids research · 2024Article
- RpoS and the bacterial general stress response.Microbiology and molecular biology reviews : MMBR · 2024Review
- Processing and decay of 6S-1 and 6S-2 RNAs inRNA (New York, N.Y.) · 2023Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Probing the conformational changes ofFrontiers in molecular biosciences · 2023Article
- Article
- Structural and Functional Insight into the Mechanism ofNon-coding RNA · 2022Article
- Ms1 RNA Interacts With the RNA Polymerase Core inFrontiers in microbiology · 2022Article
- Insights into 6S RNA in lactic acid bacteria (LAB).BMC genomic data · 2021Article
- Structured RNA Contaminants in Bacterial Ribo-Seq.mSphere · 2020Article
- 6S RNA, a Global Regulator of Transcription.Microbiology spectrum · 2018Review
- 6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype.RNA biology · 2017Article
- 6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase.Molecular cell · 2017Article
- Ribonucleoprotein purification and characterization using RNA Mango.RNA (New York, N.Y.) · 2017Article
- Small regulatory bacterial RNAs regulating the envelope stress response.Biochemical Society transactions · 2017Review
- Bacillus subtilis 6S-2 RNA serves as a template for short transcripts in vivo.RNA (New York, N.Y.) · 2016Article
- Maturation of 6S regulatory RNA to a highly elongated structure.The FEBS journal · 2015Article
- In vitro characterization of 6S RNA release-defective mutants uncovers features of pRNA-dependent release from RNA polymerase in E. coli.RNA (New York, N.Y.) · 2014Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 6S RNA in Escherichia coli suppresses housekeeping transcription by binding to RNA polymerase holoenzyme (core polymerase + σ⁷⁰) under low nutrient conditions and rescues σ⁷⁰-dependent transcription in high nutrient conditions by the synthesis of a short product RNA (pRNA) using itself as a template. Here we characterize a kinetic intermediate that arises during 6S RNA release. This state, consisting of 6S RNA and core polymerase, is related to the formation of a top-strand "release" hairpin that is conserved across the γ-proteobacteria. Deliberately slowing the intrinsic 6S RNA release rate by nucleotide feeding experiments reveals that σ⁷⁰ ejection occurs abruptly once a pRNA length of 9 nucleotides (nt) is reached. After σ⁷⁰ ejection, an additional 4 nt of pRNA synthesis is required before the 6S:pRNA complex is finally released from core polymerase. Changing the E. coli 6S RNA sequence to preclude formation of the release hairpin dramatically slows the speed of 6S RNA release but, surprisingly, does not alter the abruptness of σ⁷⁰ ejection. Rather, the pRNA size required to trigger σ⁷⁰ release increases from 9 nt to 14 nt. That a precise pRNA length is required to trigger σ⁷⁰ release either with or without a hairpin implicates an intrinsic "scrunching"-type release mechanism. We speculate that the release hairpin serves two primary functions in the γ-proteobacteria: First, its formation strips single-stranded "-10" 6S RNA interactions away from σ⁷⁰. Second, the formation of the hairpin accumulates RNA into a region of the polymerase complex previously associated with DNA scrunching, further destabilizing the 6S:pRNA:polymerase complex.
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