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

Gene: omrA Accession Numbers: G0-8868 (EcoCyc), b4444, ECK2833

Synonyms: psrA12, rygA, PAIR2a, t59, sraE

Superclasses: a regulatory RNA

Regulation Summary Diagram: ?

Regulation summary diagram for omrA

OmrA is a small RNA of approximately 88 nt in length [Argaman01, Wassarman01] that is involved in regulating the protein composition of the outer membrane [Guillier06]. OmrA was shown to negatively regulate the levels of ompT, cirA, fecA, fepA [Guillier06], ompR [Guillier08], csgD [Holmqvist10], and flhDC [De12] mRNAs. The effect of OmrA on ompT and cirA abundance is dependent on RNase E and involves direct base pairing at the 5' end of OmrA [Guillier08]. A set of targets for regulation by OmrA has been predicted, but only a small percentage of those possible targets was supported by microarray data [Tjaden06].

Interaction between OmrA RNA and Hfq protein has been detected [Wassarman01], and the effect of OmrA on ompT and cirA expression is dependent on Hfq [Guillier08].

OmrA and OmrB were first recognized as an intergenic duplication (PAIR2) containing sites that resemble Rho-independent terminators [Rudd99]. The 5' and 3' ends of OmrA and OmrB are nearly identical, but their central regions differ.

OmrA is highly abundant in stationary phase cells grown in LB medium [Argaman01, Wassarman01, Zhang03c]. The half life of OmrA in stationary phase is 16 minutes [Vogel03]. Transcription of omrA is regulated by OmpR [Guillier06].

The 5' end of OmrA is required for the regulatory function of the small RNA [Guillier08]. An omrAB deletion mutant shows a change in the protein composition of the outer membrane [Guillier06]. Overexpression of omrA inhibits the formation of curli by downregulating CsgD expression [Holmqvist10].

SraE: "small RNA", PsrA12: "predicted small RNA" [Argaman01]

Ryx: "RNA of unknown function at X position (10 minute) in the genome" [Wassarman01]

OmrA: "OmpR-regulated sRNA A" [Guillier06]

Reviews: [Vogel06, Papenfort09]

Citations: [Rivas01, Moon11]

Map Position: [2,974,124 <- 2,974,211] (64.1 centisomes, 231°)
Length: 88 bp

Genetic Regulation Schematic: ?

Genetic regulation schematic for omrA

Unification Links: ASAP:ABE-0047264 , EchoBASE:EB4530 , EcoliWiki:b4444 , PortEco:omrA , RegulonDB:G0-8868

GO Terms:

Biological Process: GO:0040033 - negative regulation of translation, ncRNA-mediated Inferred from experiment [Holmqvist10]
Molecular Function: GO:0000499 - base pairing with mRNA Inferred from experiment [Guillier08]
GO:0005515 - protein binding Inferred from experiment [Wassarman01]

MultiFun Terms: information transfer RNA related antisense RNA
information transfer RNA related RNA degradation

Regulated Transcription Units (5 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Last-Curated ? 11-Jul-2013 by Keseler I , SRI International


Argaman01: Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S (2001). "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli." Curr Biol 11(12);941-50. PMID: 11448770

De12: De Lay N, Gottesman S (2012). "A complex network of small non-coding RNAs regulate motility in Escherichia coli." Mol Microbiol 86(3);524-38. PMID: 22925049

Guillier06: Guillier M, Gottesman S (2006). "Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs." Mol Microbiol 59(1);231-47. PMID: 16359331

Guillier08: Guillier M, Gottesman S (2008). "The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator." Nucleic Acids Res 36(21):6781-94. PMID: 18953042

Holmqvist10: Holmqvist E, Reimegard J, Sterk M, Grantcharova N, Romling U, Wagner EG (2010). "Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis." EMBO J 29(11);1840-50. PMID: 20407422

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

Papenfort09: Papenfort K, Vogel J (2009). "Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level." Res Microbiol 160(4):278-87. PMID: 19366629

Rivas01: Rivas E, Klein RJ, Jones TA, Eddy SR (2001). "Computational identification of noncoding RNAs in E. coli by comparative genomics." Curr Biol 11(17);1369-73. PMID: 11553332

Rudd99: Rudd KE (1999). "Novel intergenic repeats of Escherichia coli K-12." Res Microbiol 150(9-10);653-64. PMID: 10673004

Tjaden06: Tjaden B, Goodwin SS, Opdyke JA, Guillier M, Fu DX, Gottesman S, Storz G (2006). "Target prediction for small, noncoding RNAs in bacteria." Nucleic Acids Res 34(9);2791-802. PMID: 16717284

Vogel03: Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A, Wagner EG (2003). "RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria." Nucleic Acids Res 31(22);6435-43. PMID: 14602901

Vogel06: Vogel J, Papenfort K (2006). "Small non-coding RNAs and the bacterial outer membrane." Curr Opin Microbiol 9(6);605-11. PMID: 17055775

Wassarman01: Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S (2001). "Identification of novel small RNAs using comparative genomics and microarrays." Genes Dev 15(13);1637-51. PMID: 11445539

Zhang03c: Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003). "Global analysis of small RNA and mRNA targets of Hfq." Mol Microbiol 50(4);1111-24. PMID: 14622403

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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 19.0 on Wed Oct 7, 2015, BIOCYC14A.