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: ?

Regulation summary diagram for ssrS

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, Kim04f, 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 [Lee85], 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, 237°)
Length: 183 bp

Genetic Regulation Schematic: ?

Genetic regulation schematic for ssrS

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): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


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

Kim04f: 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

Lee85: 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

Lee13a: 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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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