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rpoN RNA polymerase sigma factor RpoN [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 947714, updated on 6-Jul-2026
Official Symbol
rpoN
Official Full Name
RNA polymerase sigma factor RpoN
Primary source
ECOCYC:EG10898
Locus tag
b3202
See related
ASAP:ABE-0010514
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage
Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as
ECK3191; glnF; ntrA
Summary
RpoN, aslo called sigma N, was originally identified as the sigma factor for nitrogen-controlled genes. [More information is available at EcoGene: EG10898]. Sigma 54 controls expression of nitrogen-related genes, directing |FRAME: [More information is available at EcoCyc: EG10898].
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Sequence:
NC_000913.3 (3344717..3346150)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene lipopolysaccharide transport system protein LptC Neighboring gene lipopolysaccharide transport system protein LptA Neighboring gene lipopolysaccharide transport system ATP binding protein LptB Neighboring gene ribosome hibernation-promoting factor Neighboring gene phosphotransferase system enzyme IIA(Ntr)

Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Related articles in PubMed

  1. RNA polymerase binding using a strongly acidic hydrophobic-repeat region of sigma 54. Tintut Y, et al. Proc Natl Acad Sci U S A, 1994 Mar 15. PMID 8134358, Free PMC Article
  2. Investigating protein-protein interfaces in bacterial transcription complexes: a fragmentation approach. Burrows PC. Bioessays, 2003 Dec. PMID 14635249
  3. Action of prokaryotic enhancer over a distance does not require continued presence of promoter-bound sigma54 subunit. Bondarenko V, et al. Nucleic Acids Res, 2002 Feb 1. PMID 11809874, Free PMC Article
  4. Dual regulation of mucoidy in Pseudomonas aeruginosa and sigma factor antagonism. Boucher JC, et al. Mol Microbiol, 2000 Apr. PMID 10792721
  5. Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering. Svergun DI, et al. J Biol Chem, 2000 Feb 11. PMID 10660585

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli.
    Title: Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli.
  2. DNA melting is an active process initiated in closed promoter complex (RPc) and that the RNAP conformations of intermediates are significantly different from that of RPc and open promoter complex.
    Title: Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.
  3. Upregulation of fliZ by NtrC-sigma(N) was shown to be indirect and required an intact flagellar regulator flhDC.
    Title: σ(N) -dependent control of acid resistance and the locus of enterocyte effacement in enterohemorrhagic Escherichia coli is activated by acetyl phosphate in a manner requiring flagellar regulator FlhDC and the σ(S) antagonist FliZ.
  4. Data suggest a direct binding mechanism, in which sigma(54)RNA polymerase (rpoN) reaches the local vicinity of promoters by 3D diffusion.
    Title: RNA polymerase approaches its promoter without long-range sliding along DNA.
  5. Expression of the flagellar sigma(F) factor (FliA), another sigma(70) family protein, is controlled positively by RpoN but negatively by RpoS.
    Title: Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli.
  6. These observations suggest a novel mechanism for negative regulation in bacterial enhancer binding proteins such as NorR in which the GAF domain targets the sigma(54)-interaction surface to prevent access of the AAA+ domain to the sigma factor.
    Title: Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR.
  7. Results inidicate that there are 70 sigma(54) promoters in total in the entire Escherichia coli genome.
    Title: Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis.
  8. Analyses of promoter mutants obtained by in vitro chemical mutagenesis of the atoDAEB promoter verified both the importance of AtoC binding for the inducibility of the promoter by acetoacetate and the sigma54 dependence of atoDAEB expression.
    Title: Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon.
  9. Identified as new member of the polyamine modulon together with Cra and H-NS.
    Title: Enhancement of the synthesis of RpoN, Cra, and H-NS by polyamines at the level of translation in Escherichia coli cultured with glucose and glutamate.
  10. We propose a passive model for ppGpp/DksA regulation of sigma54-dependent transcription that depends on the potent negative effects of these regulatory molecules on transcription from powerful stringently regulated sigma70 promoters.
    Title: The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription.
Submit: New GeneRIF Correction See all GeneRIFs (11)
Products Interactant Other Gene Complex Source Pubs Description

Homology

Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription activator activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription activator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables DNA-binding transcription activator activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sigma factor activity IEA
Inferred from Electronic Annotation
more info
  
enables transcription cis-regulatory region binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription cis-regulatory region binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription cis-regulatory region binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables transcription cis-regulatory region binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription initiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cell motility NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in nitrate assimilation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription initiation IEA
Inferred from Electronic Annotation
more info
  
involved_in submerged biofilm formation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of protein-DNA complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein-DNA complex IEA
Inferred from Electronic Annotation
more info
  
part_of protein-DNA complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of protein-DNA complex IPI
Inferred from Physical Interaction
more info
 PubMed 
Preferred Names
RNA polymerase sigma factor RpoN

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Genome Annotation

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

Reference assembly

Genomic

  1. NC_000913.3 Reference assembly

    Range
    3344717..3346150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_417669.1 RNA polymerase sigma factor RpoN

    See identical proteins and their annotated locations for NP_417669.1

    Status: REVIEWED

    UniProtKB/TrEMBL
    E1CBR4
    Conserved Domains (1) summary
    PRK05932
    Location:1 → 476
    PRK05932; RNA polymerase factor sigma-54; Reviewed
Nucleotide Protein
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