ArticleProceedings of the National Academy of Sciences of the United States of America2016
Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of E. coli ribosomal RNA promoters.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 62 citations in OpenAlex.
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- Assessing in vivo the impact of gene context on transcription through DNA supercoiling.Nucleic acids research · 2023Article
- A high-throughput dual system to screen polyphosphate kinase mutants for efficient ATP regeneration in L-theanine biocatalysis.Biotechnology for biofuels and bioproducts · 2023Article
- Structural basis of three different transcription activation strategies adopted by a single regulator SoxS.Nucleic acids research · 2022Article
- Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters.Nucleic acids research · 2022Article
- Structural and mechanistic basis of σ-dependent transcriptional pausing.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans.Microbiology spectrum · 2022Article
- Structural and mechanistic basis of reiterative transcription initiation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase.RNA biology · 2021Article
- Promoter-sequence determinants and structural basis of primer-dependent transcription initiation inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter.BMC biology · 2021Article
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- Structural basis of ribosomal RNA transcription regulation.Nature communications · 2021Article
- The secondary messenger ppGpp interferes with cAMP-CRP regulon by promoting CRP acetylation in Escherichia coli.PloS one · 2021Article
- Rewiring of growth-dependent transcription regulation by a point mutation in region 1.1 of the housekeeping σ factor.Nucleic acids research · 2020Article
- TheMicroorganisms · 2020Article
- Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences.Biomolecules · 2020Article
- XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing.Molecular cell · 2020Article
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4 authors at 1 institution in 1 country.
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Abstract
Most Escherichia coli promoters initiate transcription with a purine 7 or 8 nt downstream from the -10 hexamer, but some promoters, including the ribosomal RNA promoter rrnB P1, start 9 nt from the -10 element. We identified promoter and RNA polymerase determinants of this noncanonical rrnB P1 start site using biochemical and genetic approaches including mutational analysis of the promoter, Fe(2+) cleavage assays to monitor template strand positions near the active-site, and Bpa cross-linking to map the path of open complex DNA at amino acid and nucleotide resolution. We find that mutations in several promoter regions affect transcription start site (TSS) selection. In particular, we show that the absence of strong interactions between the discriminator region and σ region 1.2 and between the extended -10 element and σ region 3.0, identified previously as a determinant of proper regulation of rRNA promoters, is also required for the unusual TSS. We find that the DNA in the single-stranded transcription bubble of the rrnB P1 promoter complex expands and is "scrunched" into the active site channel of RNA polymerase, similar to the situation in initial transcribing complexes. However, in the rrnB P1 open complex, scrunching occurs before RNA synthesis begins. We find that the scrunched open complex exhibits reduced abortive product synthesis, suggesting that scrunching and unusual TSS selection contribute to the extraordinary transcriptional activity of rRNA promoters by increasing promoter escape, helping to offset the reduction in promoter activity that would result from the weak interactions with σ.
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