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Escherichia coli K-12 substr. MG1655 RNA: Spot 42 small regulatory RNA

Gene: spf Accession Numbers: EG30098 (EcoCyc), b3864, ECK3856

Synonyms: Spf RNA, IS197

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

The small regulatory RNA Spot 42 (Spf) was first identified as an abundant RNA in E. coli [Ikemura73, Ikemura73a, Sahagan79, Sahagan79a]. Its first regulatory target, galK, was identified much later [Moller02, Urban07], and additional regulatory targets were identified by [Beisel11, Beisel12, Wright13]. Spot 42 is responsible for selective inhibition of translation of galK within the gal operon mRNA by occluding interaction of the ribosome with the galK Shine-Dalgarno sequence [Moller02]. Spot 42 and CRP form a multi-output feedforward loop during catabolite repression. Both the steady-state level and dynamics of gene regulation are affected [Beisel11, Beisel11a].

Spot 42 does not inhibit translation of the sdhCDAB operon directly. Instead, Spot 42 binds upstream of the translation initiation site and recruits Hfq to its binding site, which occludes the site for binding of the 30S subunit of the ribosome [Desnoyers12].

Spot 42 was shown to be a non-translated RNA [Rice87]. The Hfq protein stabilizes Spot 42 and stimulates pairing of Spf regions with complementary RNA sequences [Moller02a]. Spot 42 appears to be unable to compete effectively for Hfq binding [Moon11].

An spf deletion mutant exhibits a mild growth defect in some, but not all, strain backgrounds [Hatfull86]. Overexpression of Spf RNA results in slow growth, particularly on succinate [Rice82] as well as other carbon sources [Beisel11], and a pronounced growth defect upon transfer from minimal to rich media, compared to wild type [Rice82]. Overexpression also leads to a two-fold increase in 6S RNA abundance [Rice82] and increased DNA polymerase I activity [Polayes88a].

Transcription of spf is negatively regulated by cAMP-CRP [Polayes88]. Spot 42 RNA accumulates to 150-200 copies per cell in glucose-grown cells [Sahagan79a].

Spf: "spot fourty-two"

Reviews: [Inouye88, Wassarman99, Masse03, Storz04, Gottesman04, Gottesman06, Gorke08a, Waters09, Papenfort11, Richards11]

Citations: [Joyce82, Chen02c, Komine91, Windbichler08]

Map Position: [4,047,922 -> 4,048,030] (87.25 centisomes)
Length: 109 bp

Activates: gss Inferred from experiment [Beisel11] , dppB Inferred from experiment [Beisel11]

Inhibits: ytfJ Inferred from experiment [Beisel11] , yjiA Inferred from experiment [Beisel11] , ebgC Inferred from experiment [Beisel11] , lldP Inferred from experiment [Beisel11] , fucK Inferred from experiment [Beisel11] , maeA Inferred from experiment [Beisel11]

Genetic Regulation Schematic: ?

Unification Links: ASAP:ABE-0012621 , CGSC:157 , EchoBASE:EB4261 , EcoGene:EG30098 , EcoliWiki:b3864 , OU-Microarray:b3864 , PortEco:spf , RegulonDB:EG30098

GO Terms:

Biological Process: GO:0045974 - regulation of translation, ncRNA-mediated Inferred from experiment [Moller02]
Molecular Function: GO:0000499 - base pairing with mRNA Inferred from experiment [Beisel12, Beisel11]
GO:0003729 - mRNA binding Inferred from experiment [Moller02]
GO:0005515 - protein binding Inferred from experiment [Moller02a]

MultiFun Terms: information transfer protein related translation
information transfer RNA related antisense RNA
regulation type of regulation posttranscriptional antisense RNA
regulation type of regulation posttranscriptional translation attenuation and efficiency

Regulated Transcription Units (33 total): ?


Gene Local Context (not to scale): ?

Transcription Unit:


10/20/97 Gene b3864 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG30098.

Last-Curated ? 18-Nov-2013 by Keseler I , SRI International


Beisel11: Beisel CL, Storz G (2011). "The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli." Mol Cell 41(3);286-97. PMID: 21292161

Beisel11a: Beisel CL, Storz G (2011). "Discriminating tastes: physiological contributions of the Hfq-binding small RNA Spot 42 to catabolite repression." RNA Biol 8(5);766-70. PMID: 21788732

Beisel12: Beisel CL, Updegrove TB, Janson BJ, Storz G (2012). "Multiple factors dictate target selection by Hfq-binding small RNAs." EMBO J 31(8);1961-74. PMID: 22388518

Chen02c: Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB (2002). "A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome." Biosystems 65(2-3);157-77. PMID: 12069726

Desnoyers12: Desnoyers G, Masse E (2012). "Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq." Genes Dev 26(7);726-39. PMID: 22474262

Gorke08a: Gorke B, Vogel J (2008). "Noncoding RNA control of the making and breaking of sugars." Genes Dev 22(21);2914-25. PMID: 18981470

Gottesman04: Gottesman S (2004). "The Small RNA Regulators of Escherichia coli: Roles and Mechanisms*." Annu Rev Microbiol 58;303-28. PMID: 15487940

Gottesman06: Gottesman S, McCullen CA, Guillier M, Vanderpool CK, Majdalani N, Benhammou J, Thompson KM, FitzGerald PC, Sowa NA, FitzGerald DJ (2006). "Small RNA regulators and the bacterial response to stress." Cold Spring Harb Symp Quant Biol 71;1-11. PMID: 17381274

Hatfull86: Hatfull GF, Joyce CM (1986). "Deletion of the spf (spot 42 RNA) gene of Escherichia coli." J Bacteriol 166(3);746-50. PMID: 2940230

Ikemura73: Ikemura T, Dahlberg JE (1973). "Small ribonucleic acids of Escherichia coli. I. Characterization by polyacrylamide gel electrophoresis and fingerprint analysis." J Biol Chem 248(14);5024-32. PMID: 4577761

Ikemura73a: Ikemura T, Dahlberg JE (1973). "Small ribonucleic acids of Escherichia coli. II. Noncoordinate accumulation during stringent control." J Biol Chem 248(14);5033-41. PMID: 4577762

Inouye88: Inouye M, Delihas N (1988). "Small RNAs in the prokaryotes: a growing list of diverse roles." Cell 53(1);5-7. PMID: 2450678

Joyce82: Joyce CM, Grindley ND (1982). "Identification of two genes immediately downstream from the polA gene of Escherichia coli." J Bacteriol 152(3);1211-9. PMID: 6183253

Komine91: Komine Y, Inokuchi H (1991). "Physical map locations of the genes that encode small stable RNAs in Escherichia coli." J Bacteriol 173(17);5252. PMID: 1715853

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

Moller02: Moller T, Franch T, Udesen C, Gerdes K, Valentin-Hansen P (2002). "Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon." Genes Dev 16(13);1696-706. PMID: 12101127

Moller02a: Moller T, Franch T, Hojrup P, Keene DR, Bachinger HP, Brennan RG, Valentin-Hansen P (2002). "Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction." Mol Cell 9(1);23-30. PMID: 11804583

Moon11: Moon K, Gottesman S (2011). "Competition among Hfq-binding small RNAs in Escherichia coli." Mol Microbiol 82(6);1545-62. PMID: 22040174

Papenfort11: Papenfort K, Vogel J (2011). "Sweet business: Spot42 RNA networks with CRP to modulate catabolite repression." Mol Cell 41(3);245-6. PMID: 21292156

Polayes88: Polayes DA, Rice PW, Garner MM, Dahlberg JE (1988). "Cyclic AMP-cyclic AMP receptor protein as a repressor of transcription of the spf gene of Escherichia coli." J Bacteriol 1988;170(7);3110-4. PMID: 2454912

Polayes88a: Polayes DA, Rice PW, Dahlberg JE (1988). "DNA polymerase I activity in Escherichia coli is influenced by spot 42 RNA." J Bacteriol 170(5);2083-8. PMID: 2452153

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

Rice87: Rice PW, Polayes DA, Dahlberg JE (1987). "Spot 42 RNA of Escherichia coli is not an mRNA." J Bacteriol 169(8);3850-2. PMID: 2440852

Richards11: Richards GR, Vanderpool CK (2011). "Molecular call and response: the physiology of bacterial small RNAs." Biochim Biophys Acta 1809(10);525-31. PMID: 21843668

Sahagan79: Sahagan BG, Dahlberg JE (1979). "A small, unstable RNA molecule of Escherichia coli: spot 42 RNA. I. Nucleotide sequence analysis." J Mol Biol 131(3);573-92. PMID: 390161

Sahagan79a: Sahagan BG, Dahlberg JE (1979). "A small, unstable RNA molecule of Escherichia coli: spot 42 RNA. II. Accumulation and distribution." J Mol Biol 131(3);593-605. PMID: 229230

Storz04: Storz G, Opdyke JA, Zhang A (2004). "Controlling mRNA stability and translation with small, noncoding RNAs." Curr Opin Microbiol 7(2);140-4. PMID: 15063850

Urban07: Urban JH, Vogel J (2007). "Translational control and target recognition by Escherichia coli small RNAs in vivo." Nucleic Acids Res 35(3);1018-37. PMID: 17264113

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

Waters09: Waters LS, Storz G (2009). "Regulatory RNAs in bacteria." Cell 136(4);615-28. PMID: 19239884

Windbichler08: Windbichler N, von Pelchrzim F, Mayer O, Csaszar E, Schroeder R (2008). "Isolation of small RNA-binding proteins from E. coli: evidence for frequent interaction of RNAs with RNA polymerase." RNA Biol 5(1);30-40. PMID: 18388495

Wright13: Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013). "Comparative genomics boosts target prediction for bacterial small RNAs." Proc Natl Acad Sci U S A 110(37);E3487-96. PMID: 23980183

Other References Related to Gene Regulation

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

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 Mon Mar 2, 2015, BIOCYC14A.