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|
| small RNA |  |
|
|---|---|---|
| Gene name: | omrA 
|
|
| Synonym(s): | PAIR2, PAIR2a, PsrA12, RygA, SraE, T59, psrA12, rygA, small regulatory RNA OmrA, sraE, t59 | |
| Genome position: | 2976102 <-- 2976189 | |
| Strand: | reverse | |
| Sequence: | Get ribonucleotide sequence FastaFormat | |
GC content %: |
50.0 | |
| Note(s): | OmrA is a small RNA of approximately 88 nt in length Argaman L,2001. Wassarman KM,2001 that is involved in regulating the protein composition of the outer membrane Guillier M,2006. OmrA was shown to negatively regulate the levels of ompT, cirA, fecA Guillier M,2006, fepA Guillier M,2006. 28918899, ompR Guillier M,2008. 27439713, csgD Holmqvist E,2010, flhDC 22925049, and dgcM 30833291 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 Guillier M,2008. OmrA affects DgcM translation by competing with the ribosome for binding to the dgcM mRNA that has been restructured by Hfq 30833291. 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 16717284. Binding site features for OmrA were identified by high-throughput in vivo mapping Mihailovic MK,2018. OmrA represses its own synthesis via feedback regulation of its transcriptional activator OmpR 27439713. Interaction between OmrA RNA and Hfq protein has been detected Wassarman KM,2001, and the effect of OmrA on ompT and cirA expression is dependent on Hfq Guillier M,2008. OmrA and OmrB were first recognized as an intergenic duplication (PAIR2) containing sites that resemble Rho-independent terminators Rudd KE.,1999. 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 Argaman L,2001. Wassarman KM,2001. Zhang A,2003. The half life of OmrA in stationary phase is 16 minutes Vogel J,2003. Transcription of omrA is regulated by OmpR Guillier M,2006 and by σS Peano C,2015. The 5' end of OmrA is required for the regulatory function of the small RNA Guillier M,2008. An omrAB deletion mutant shows a change in the protein composition of the outer membrane Guillier M,2006. Overexpression of omrA inhibits the formation of curli by downregulating CsgD expression Holmqvist E,2010. Overexpression of OmrA decreases biofilm formation, swimming and swarming motility, and curli expression Bak G,2015. Transcription of omrA is activated by OmpR Guillier M,2006. 27439713. SraE: small RNA, PsrA12: predicted small RNA Argaman L,2001 Ryx: RNA of unknown function at X position (10 minute) in the genome Wassarman KM,2001 OmrA: OmpR-regulated sRNA A Guillier M,2006 Reviews: 17055775. 19366629. 25028968 |
|
| Evidence: | [IDA] Inferred from direct assay [IMP] Inferred from mutant phenotype |
|
| Reference(s): | [1] Argaman L., et al., 2001 [2] Guillier M., et al., 2006 [3] Guillier M., et al., 2008 [4] Holmqvist E., et al., 2010 [5] Moon K., et al., 2011 [6] Rivas E., et al., 2001 [7] Wassarman KM., et al., 2001 |
|
| External database links: | ||
ECOCYC: |
SRAE-RNA | |
ECOLIWIKI: |
b4444 | |
| M3D: | OmrA |
| Regulation exerted by the small RNA | |
|---|
| Target | Regulation Type | Mechanism | Function | Binding Site | Evidence Code |
Reference(s) | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Distance to the gene |
Sequence | |||||||
antisense
|
post-transcriptional regulation
|
repressor
|
2246779
|
2246804
|
-22
|
ATTTTATTTTCGTAGTTACCTCATG
|
||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
585614
|
585645
|
4
|
TGGAGAACTTTTATGCGGGCGAAACTTCTGG
|
||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
||||||||
antisense
|
post-transcriptional regulation
|
activator
|
||||||||
antisense
|
post-transcriptional regulation
|
activator
|
||||||||
antisense
|
post-transcriptional regulation
|
activator
|
||||||||
antisense
|
post-transcriptional regulation
|
activator
|
||||||||
antisense
|
post-transcriptional regulation
|
activator
|
||||||||
antisense
|
post-transcriptional regulation
|
activator
|
||||||||
antisense
|
post-transcriptional regulation
|
repressor
|
3536595
|
3536613
|
-20
|
ATTGTTGCGAACCTTTGG
|
||||
repressor
|
||||||||||
| Evidence: | [IMP] Inferred from mutant phenotype |
| Reference(s) |
|
|---|---|
[1] 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