Genome Property Definition Page

NameSigma-54 (RpoN) systems
DescriptionA sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PMID:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
JCVI RoleTranscription factors
Parent PropertyGenProp0197: protein biosynthesis
Literature References
[ 1 ]Merrick MJ  In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N).  Mol Microbiol. 1993 Dec;10(5):903-9.  PMID 7934866
[ 2 ]Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD  The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor.  J Bacteriol. 2000 Aug;182(15):4129-36.  PMID 10894718
[ 3 ]Reitzer L, Schneider BL  Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli.  Microbiol Mol Biol Rev. 2001 Sep;65(3):422-44, table of contents.  PMID 11528004

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
Sigma-54 interacting protein, activatorS54-depYESPF00158 (HMM): sigma-54 interaction domain
Sigma-54 (RpoN)Sigma-54YESTIGR02395 (HMM): RNA polymerase sigma-54 factor

Parent Properties
GenProp0197protein biosynthesis

Sibling Properties
GenProp0016selenocysteine system
GenProp0132transcription termination - antitermination Nus factors
GenProp0148release factor 2 programmed frameshift
GenProp0174ribosome, bacterial, large subunit
GenProp0175ribosome, bacterial, small subunit
GenProp0188GatABC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase complex
GenProp0189tRNA-Gln direct aminoacylation
GenProp0211tmRNA trans-translation system
GenProp0258tRNA aminoacylation
GenProp0259tRNA-Asn direct aminoacylation
GenProp0304cysteine biosynthesis, tRNA-dependent
GenProp0692selenouridine-containing tRNA
GenProp0704tRNA U34 carboxymethylaminomethyl modification
GenProp0740translation initiation, bacterial
GenProp0741translation elongation, bacterial
GenProp0746translation termination, bacterial
GenProp0812rho-dependent termination