Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015

Escherichia coli K-12 substr. MG1655 RNA: 6S RNA

Gene: ssrS Accession Numbers: EG30099 (EcoCyc), b2911, ECK2906

Synonyms: ssr

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

The 6S RNA is involved in stationary phase regulation of transcription by the sigma70-holoenzyme [Wassarman00]. The 6S RNA binds to both sigma70 and the beta/beta' subunits of core RNA polymerase and enables stable association between sigma70 and the core RNA polymerase [Wassarman00]. During stationary phase, 6S RNA represses expression from a subset of sigma70-dependent promoters containing an extended -10 promoter element [Wassarman00, Kim04c, Trotochaud04]. 6S RNA also has an effect on the transcription of several sigmaS-dependent promoters [Trotochaud04]. In vitro, 6S RNA alone inhibits both stationary-phase and exponential promoters, suggesting that additional factors are involved in its effects in vivo [Gildehaus07].

The 6S RNA is not required for growth and is not essential for export of proteins [Lee85a], but cells lacking 6S RNA show a stationary phase survival defect and are less competitive during growth [Trotochaud04].

6S RNA secondary structure has been discussed [Vogel87a].

The 6S RNA has been detected in a ribonucleoprotein particle [Lee78].

Regulation has been described [Rice82, Hsu85, Wassarman00]. The 6S RNA is expressed at stationary phase [Wassarman00]. Overexpression of Spot 42 RNA increases the abundance of 6S RNA [Rice82].

The ssrS gene is one of the genes most highly dependent on Eσ70, based on runoff/microarray (ROMA) experiments among genes whose promoters have been characterized [Maciag11].

Reviews: [Wassarman99, Masse03]

Citations: [Brownlee71, Trown73, Sklar75, Somasekhar83]

Map Position: [3,054,005 -> 3,054,187] (65.82 centisomes)
Length: 183 bp

Genetic Regulation Schematic: ?

Unification Links: ASAP:ABE-0009556 , EchoBASE:EB4262 , EcoGene:EG30099 , EcoliWiki:b2911 , OU-Microarray:b2911 , PortEco:ssrS , RegulonDB:EG30099

MultiFun Terms: regulation type of regulation transcriptional level

Gene Local Context (not to scale): ?

Transcription Units:


10/20/97 Gene b2911 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG30099.


Brownlee71: Brownlee GG (1971). "Sequence of 6S RNA of E. coli." Nat New Biol 229(5);147-9. PMID: 4929322

Gildehaus07: Gildehaus N, Neusser T, Wurm R, Wagner R (2007). "Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts." Nucleic Acids Res 35(6):1885-96. PMID: 17332013

Hsu85: Hsu LM, Zagorski J, Wang Z, Fournier MJ (1985). "Escherichia coli 6S RNA gene is part of a dual-function transcription unit." J Bacteriol 161(3);1162-70. PMID: 2579060

Kim04c: Kim EY, Shin MS, Rhee JH, Choy HE (2004). "Factors influencing preferential utilization of RNA polymerase containing sigma-38 in stationary-phase gene expression in Escherichia coli." J Microbiol 42(2);103-10. PMID: 15357303

Lee78: Lee SY, Bailey SC, Apirion D (1978). "Small stable RNAs from Escherichia coli: evidence for the existence of new molecules and for a new ribonucleoprotein particle containing 6S RNA." J Bacteriol 133(2);1015-23. PMID: 342486

Lee85a: Lee CA, Fournier MJ, Beckwith J (1985). "Escherichia coli 6S RNA is not essential for growth or protein secretion." J Bacteriol 161(3);1156-61. PMID: 2579059

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Masse03: Masse E, Majdalani N, Gottesman S (2003). "Regulatory roles for small RNAs in bacteria." Curr Opin Microbiol 6(2);120-4. PMID: 12732300

Rice82: Rice PW, Dahlberg JE (1982). "A gene between polA and glnA retards growth of Escherichia coli when present in multiple copies: physiological effects of the gene for spot 42 RNA." J Bacteriol 152(3);1196-210. PMID: 6183252

Sklar75: Sklar J, Yot P, Weissman SM (1975). "Determination of genes, restriction sites, and DNA sequences surrounding the 6S RNA template of bacteriophage lambda." Proc Natl Acad Sci U S A 72(5);1817-21. PMID: 1098044

Somasekhar83: Somasekhar G, Szybalski W (1983). "Mapping of the Q-utilization site (qut) required for antitermination of late transcription in bacteriophage lambda." Gene 26(2-3);291-4. PMID: 6231216

Trotochaud04: Trotochaud AE, Wassarman KM (2004). "6S RNA function enhances long-term cell survival." J Bacteriol 186(15);4978-85. PMID: 15262935

Trown73: Trown PW, Meyer PL (1973). "Recognition of template RNA by Q polymerase: sequence at the 3'-terminus of Q 6S RNA." Arch Biochem Biophys 154(1);250-62. PMID: 4570237

Vogel87a: Vogel DW, Hartmann RK, Struck JC, Ulbrich N, Erdmann VA (1987). "The sequence of the 6S RNA gene of Pseudomonas aeruginosa." Nucleic Acids Res 15(11);4583-91. PMID: 2438656

Wassarman00: Wassarman KM, Storz G (2000). "6S RNA regulates E. coli RNA polymerase activity." Cell 101(6);613-23. PMID: 10892648

Wassarman99: Wassarman KM, Zhang A, Storz G (1999). "Small RNAs in Escherichia coli." Trends Microbiol 7(1);37-45. PMID: 10068996

Other References Related to Gene Regulation

Chae11a: Chae H, Han K, Kim KS, Park H, Lee J, Lee Y (2011). "Rho-dependent termination of ssrS (6S RNA) transcription in Escherichia coli: implication for 3' processing of 6S RNA and expression of downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase)." J Biol Chem 286(1);114-22. PMID: 21036909

Kim04b: Kim KS, Lee Y (2004). "Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases." Nucleic Acids Res 32(20);6057-68. PMID: 15550566

Lee13c: Lee JY, Park H, Bak G, Kim KS, Lee Y (2013). "Regulation of transcription from two ssrS promoters in 6S RNA biogenesis." Mol Cells 36(3);227-34. PMID: 23864284

Neusser08: Neusser T, Gildehaus N, Wurm R, Wagner R (2008). "Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation." Biol Chem 389(3);285-97. PMID: 18177266

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Tue Jan 27, 2015, BIOCYC14A.