rpoD RNA polymerase sigma factor RpoD [Escherichia coli str. K-12 substr. MG1655] - Gene

Summary

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Official Symbol: rpoD
Official Full Name: RNA polymerase sigma factor RpoD
Primary source: ECOCYC:EG10896
Locus tag: b3067
See related: ASAP:ABE-0010070
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as: alt; ECK3057
Summary: Sigma 70 is the primary sigma factor during exponential growth, targeting |FRAME: [More information is available at EcoCyc: EG10896].
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Genomic context

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Sequence:: NC_000913.3 (3213047..3214888)

NC_000913.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A single rare sigma70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82.
Title: A single rare σ70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82.
Bases immediate upstream of the TATAAT box of the sigma 70 promoter of Escherichia coli significantly influence the activity of a model promoter by altering the bending angle of DNA.
Title: Bases immediate upstream of the TATAAT box of the sigma 70 promoter of Escherichia coli significantly influence the activity of a model promoter by altering the bending angle of DNA.
Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria.
Title: Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria.
Alternative transcription cycle that allows RNA polymerase to reinitiate without dissociating from DNA.
Title: Alternative transcription cycle for bacterial RNA polymerase.
RpoD Rna polymerase on an intrinsic terminator generally releases RNA transcript without departing from DNA template, and the remaining RpoD one-dimensionally diffuses on DNA in both directions and even reinitiates transcription at a nearby promoter.
Title: Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA.
this study determined the cryo-EM structures of the E. coli RNAP sigma(70) holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 A resolutions, respectively, to reveal native conformations of RNAP and DNA.
Title: Cryo-EM structure of Escherichia coli σ(70) RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation.
Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution.
Title: Regulatory network structure determines patterns of intermolecular epistasis.
Overexpression of recombinant inhibitor of host bacterial RNA polymerase (Gp2) in exponentially growing E. coli induces changes in RNAP behavior at single molecule level and induces global alterations in the transcriptional programme.
Title: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli.
In contrast to NusG, which freely binds to RNA polymerase, RfaH exists in a structurally distinct autoinhibitory state in which the RNA polymerase-binding site is buried at the interface between two RfaH domains.
Title: Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor.
A promoter's responsiveness to indirect regulation by sigma factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.
Title: Effects of σ factor competition are promoter initiation kinetics dependent.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by EcoCyc

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sigma factor activity	IDA Inferred from Direct Assay more info	PubMed
enables sigma factor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA-templated transcription initiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to heat	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
part_of cytosolic DNA-directed RNA polymerase complex	IPI Inferred from Physical Interaction more info	PubMed
part_of sigma factor antagonist complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: RNA polymerase sigma factor RpoD

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_000913.3 Reference assembly

Range

3213047..3214888

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NP_417539.1 RNA polymerase sigma factor RpoD [Escherichia coli str. K-12 substr. MG1655]

See identical proteins and their annotated locations for NP_417539.1

Status: PROVISIONAL

UniProtKB/TrEMBL

A0A2X1NW71, A0A376JS16

Conserved Domains (1) summary

PRK05658
Location:1 → 613

PRK05658; RNA polymerase sigma factor RpoD; Validated