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|
| small RNA |  |
|
|---|---|---|
| Gene name: | omrB 
|
|
| Synonym(s): | PAIR2, PAIR2b, RygB, T59, rygB, small regulatory RNA OmrB, sraE, t59 | |
| Genome position: | 2976304 <-- 2976385 | |
| Strand: | reverse | |
| Sequence: | Get ribonucleotide sequence FastaFormat | |
GC content %: |
47.56 | |
| Note(s): | OmrB is a small RNA that is involved in regulating the protein composition of the outer membrane Guillier M,2006. OmrB was shown to negatively regulate the levels of ompT, cirA, fecA Guillier M,2006, gntP 16717284, ompR Guillier M,2008. 27439713, csgD Holmqvist E,2010, flhDC 22925049, and dgcM 30833291 mRNAs. The effect of OmrB on ompT and cirA abundance is dependent on RNase E and involves direct base pairing at the 5' end of OmrB Guillier M,2008. OmrB 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 OmrB 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. OmrB represses its own synthesis via feedback regulation of its transcriptional activator OmpR 27439713. Interaction between OmrB RNA and Hfq protein has been detected Wassarman KM,2001, and the effect of OmrB 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. OmrB levels increase at the end of exponential phase and decrease after the onset of stationary phase Vogel J,2003. The half life of OmrB in both exponential and stationary phase is 30 minutes Vogel J,2003. Transcription of omrB is regulated by OmpR Guillier M,2006. The 5' end of OmrB 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 omrB inhibits the formation of curli by downregulating CsgD expression Holmqvist E,2010. Bak G,2015. Transcription of omrB is activated by OmpR Guillier M,2006. 27439713. Ryx: RNA of unknown function at X position (10 minute) in the genome Wassarman KM,2001 OmrB: OmpR-regulated sRNA B Guillier M,2006 Reviews: 17055775. 19366629. 25028968 |
|
| Evidence: | [IDA] Inferred from direct assay [IMP] Inferred from mutant phenotype |
|
| Reference(s): | [1] Guillier M., et al., 2006 [2] Guillier M., et al., 2008 [3] Vogel J., et al., 2003 |
|
| External database links: | ||
ECOCYC: |
RYGB-RNA | |
ECOLIWIKI: |
b4445 | |
| M3D: | OmrB |
| 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
|
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
|
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] Guillier M., Gottesman S., 2006, Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs., Mol Microbiol 59(1):231-47