Genome Property Definition Page

Name6S RNA (eubacterial RNA polymerase regulator)
Description6S RNA is a structural RNA widely distributed in bacteria. It is considered non-coding, but in many Proteobacteria such as Escherichia coli its ssrS gene is cotranscribed with ygfA, a putative methenyltetrahydrofolate synthetase gene found immediately downstream. 6S RNA functions by binding to the sigma-70 RNA polymerase holoenzyme during stationary phase and suppressing transcription from a subset of sigma-70-dependent promoters. In alpha- and gamma-proteobacteria, the ygfA gene, encoding a putative methylenetetrahydrofolate synthetase, regularly is found immediately downstream of ssrS in a conserved operon. While the meaning of this association is unclear, other than coordination in gene expression, ygfA is included as an optional element for this genome property.
JCVI RoleAdaptations to atypical conditions
Parent PropertyGenProp0462: response to stress
GenProp0819: RNA metabolism
Literature References
[ 1 ]Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR  6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.  RNA 2005 May;11(5):774-84.  PMID 15811922
[ 2 ]Willkomm DK, Minnerup J, Huttenhofer A, Hartmann RK  Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog.  Nucleic Acids Res 2005 Apr 6;33(6):1949-60.  PMID 15814812
[ 3 ]Trotochaud AE, Wassarman KM  6S RNA regulation of pspF transcription leads to altered cell survival at high pH.  J Bacteriol. 2006 Jun;188(11):3936-43.  PMID 16707685

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
6S structural RNA6SYES6SRNA (RNA)
ygfA linked geneygfANOTIGR02727 (HMM-CLUST): 5-formyltetrahydrofolate cyclo-ligase

Parent Properties
GenProp0462response to stress
GenProp0819RNA metabolism

Sibling Properties
GenProp0211tmRNA trans-translation system
GenProp0648phage shock protein regulon
GenProp0258tRNA aminoacylation
GenProp0262RNA polymerase, bacterial
GenProp0677queuosine (Q-tRNA) biosynthesis from preQ0
GenProp0692selenouridine-containing tRNA
GenProp0704tRNA U34 carboxymethylaminomethyl modification
GenProp0898RNA ligase/unknown protein pair
GenProp0948RNA repair, Hen1/Pnkp system
GenProp1060tRNA N6-threonylcarbamoyladenosine modification
GenProp1077tRNA(Pro) cmo5UGG modification
GenProp108216S rRNA C1402 m(4)Cm modification