RpoN

The gene rpoN (RNA polymerase, nitrogen-limitation N) encodes the sigma factor sigma-54 (σ54, sigma N, or RpoN), a protein in Escherichia coli and other species of bacteria. RpoN antagonizes RpoS sigma factors.^[1]

RNA polymerase sigma-54 factor
Identifiers
Organism	?
Symbol	RpoN
UniProt	P24255
Search for Structures Swiss-model Domains InterPro

Biological role

Originally identified as a regulator of genes involved in nitrogen metabolism and assimilation under nitrogen limiting conditions,^[2] E. coli σ54 has since been shown to play important regulatory roles in a variety of other cellular processes. Similarly, σ54 homologues in other species regulate a wide range of processes, including flagellar synthesis and virulence.^[3]

Sequence specificity and mechanism of action

Sigma-54 factor, Activator interacting domain
Identifiers
Symbol	Sigma54_AID
Pfam	PF00309
InterPro	IPR000394
PROSITE	PS50044
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary PDB 5BYH

σ54 promoter elements consist of conserved nucleotides located at −12 and −24 with respect to the transcription start site.^[4] This contrasts with members of the σ70 family, which recognize conserved promoter elements located at roughly −10 and −35 with respect to the transcription start site.^[5] Unlike the members of the σ70 family, σ54 proteins have been shown to bind promoter DNA independent of core RNAPin vitro.^[6] Another distinguishing characteristic of σ54 proteins is their absolute requirement for activator proteins, known as bacterial enhancer binding proteins (bEBPs), to initiate transcription.^[4][7] Thus, both active and inactive forms of RNAP:σ54 are bound at promoters.^[8]

The RpoN-regulated promoter elements have the consensus sequence as follows: TTGGCACGGTTTTTGCT.^[9]