ArticlePloS one2017
The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
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- An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets.Journal of microbiology (Seoul, Korea) · 2024Article
- Genome and transcriptomic analysis of the adaptation ofComputational and structural biotechnology journal · 2024Review
- A simple and unified protocol to purify all seven Escherichia coli RNA polymerase sigma factors.Journal of applied genetics · 2024Article
- RpoS and the bacterial general stress response.Microbiology and molecular biology reviews : MMBR · 2024Review
- Genomic SELEX Screening of Regulatory Targets of Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Genomic SELEX Reveals Pervasive Role of the Flagella Master Regulator FlhDC in Carbon Metabolism.International journal of molecular sciences · 2023Article
- Disentangling direct from indirect relationships in association networks.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The transcription activator AtxA fromSynthetic biology (Oxford, England) · 2022Article
- TheMicroorganisms · 2021Article
- Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC inMicrobial genomics · 2021Article
- What is in the black box? The discovery of the sigma factor and the subunit structure of E. coli RNA polymerase.The Journal of biological chemistry · 2021Article
- Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors.Biomolecules · 2021Review
- The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.Journal of bacteriology · 2021Review
- σFrontiers in microbiology · 2021Article
- Temperature-Dependent Influence of FliA Overexpression on PHL628Frontiers in cellular and infection microbiology · 2021Article
- Single-Target Regulators Constitute the Minority Group of Transcription Factors inFrontiers in microbiology · 2021Article
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3 authors.
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Abstract
The promoter selectivity of Escherichia coli RNA polymerase (RNAP) is determined by the sigma subunit. The model prokaryote Escherichia coli K-12 contains seven species of the sigma subunit, each recognizing a specific set of promoters. For identification of the "constitutive promoters" that are recognized by each RNAP holoenzyme alone in the absence of other supporting factors, we have performed the genomic SELEX screening in vitro for their binding sites along the E. coli K-12 W3110 genome using each of the reconstituted RNAP holoenzymes and a collection of genome DNA segments of E. coli K-12. The whole set of constitutive promoters for each RNAP holoenzyme was then estimated based on the location of RNAP-binding sites. The first successful screening of the constitutive promoters was achieved for RpoD (σ70), the principal sigma for transcription of growth-related genes. As an extension, we performed in this study the screening of constitutive promoters for four minor sigma subunits, stationary-phase specific RpoS (σ38), heat-shock specific RpoH (σ32), flagellar-chemotaxis specific RpoF (σ28) and extra-cytoplasmic stress-response RpoE (σ24). The total number of constitutive promoters were: 129~179 for RpoS; 101~142 for RpoH; 34~41 for RpoF; and 77~106 for RpoE. The list of constitutive promoters were compared with that of known promoters identified in vivo under various conditions and using varieties of E. coli strains, altogether allowing the estimation of "inducible promoters" in the presence of additional supporting factors.
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