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small RNA | ![]() ![]() |
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Gene name: | rybB ![]() |
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Synonym(s): | P25, RybB | |
Genome position: | 887979 <-- 888057 | |
Strand: | reverse | |
Sequence: | Get ribonucleotide sequence FastaFormat | |
GC content %: |
48.1 | |
Note(s): | RybB is a small regulatory RNA whose expression increases in stationary phase, when its half life is 8 minutes Wassarman KM,2001. Vogel J,2003. RybB expression is dependent on the alternative sigma factor σE, which is activated by cell envelope stress Johansen J,2006. Thompson KM,2007. Indirect repression of σE synthesis by RybB creates an autoregulatory loop Thompson KM,2007. An efficient interaction between RybB RNA and Hfq protein has been detected Wassarman KM,2001, and the specific contacts between RybB and Hfq have been probed using Salmonella components 22645344. RybB also interacts with the RNA chaperone ProQ. The RbsZ RNA was discovered in an RNA-RNA interactome screen, where RybB-RbsZ was the most abundant pair found on ProQ. RbsZ appears to act as a sponge that lowers the leves of RybB, while ProQ protects RybB against downregulation/degradation by Hfq and RNase III Melamed S,2020. A number of regulatory targets of RybB were identified Gogol EB,2011. Prediction of regulatory targets of RybB can be improved by considering accessible regions in both the sRNA and its target 22767260; comparative genomics was subsequently used to predict regulatory targets Wright PR,2013. A candidate RybB regulon was inferred by integrating information on experimentally supported targets and sRNA-mRNA interactions with transcription datasets 32487739. New targets were identified by an affinity purification method Lalaouna D,2015. This method also identified direct interactions of RybB with the 3' external transcribed spacer (ETS) sequence of a tRNA-encoding operon, |FRAME: TU00512|. In this context, the 3'ETSleuZ is thought to function as a sponge that absorbs transcriptional noise while RybB expression is not induced Lalaouna D,2015. Translation of WaaR may be downregulated by RybB 22021036. Overexpression of rybB causes increased expression of rpoS in minimal media Wassarman KM,2001 and decreased levels of ompC, ompW Johansen J,2006, rpoE, and rybB itself Thompson KM,2007. Overexpression of either MicA or RybB rescues the growth and viability phenotypes of σE depletion Gogol EB,2011 and also leads to increased cell lysis in stationary phase 22251246. Overexpression of RybB decreases biofilm formation and expression of type I fimbriae Bak G,2015. A rybB deletion mutant is less sensitive to cell envelope stress than wild type Hobbs EC,2010, appears unable to establish long-term stationary phase Nagamitsu H,2013, and shows increased frequency of persister cell waking 31608580. Expression of rybB is induced in complex medium at stationary phase Wassarman KM,2001. Vogel J,2003. RybB accumulates in the absence of |FRAME: CPLX0-3521| 18203924. Proper regulation of rybB expression by σE is critical Nicoloff H,2017. The transcripts of many RybB targets are decreased after σE induction as expected Lacoux C,2020. The |FRAME: RNA0-413| acts as a sponge for RybB Adams PP,2021. Reviews: 12654996. 15487940. 17055775. Papenfort K, Vogel J,2009. De la Cruz MA,2010. Azam MS,2015. 26618164. Frohlich KS,2018. 32213244 |
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Evidence: | [IEP] Inferred from expression pattern [IMP] Inferred from mutant phenotype |
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Reference(s): | [1] El-Mowafi SA., et al., 2014 [2] Gogol EB., et al., 2011 [3] Guo MS., et al., 2014 [4] Johansen J., et al., 2006 [5] Lalaouna D., et al., 2015 [6] Leiser OP., et al., 2012 [7] Malecka EM., et al., 2015 [8] Mihailovic MK., et al., 2018 [9] Serra DO., et al., 2016 [10] Thompson KM., et al., 2007 [11] Wassarman KM., et al., 2001 |
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External database links: | ||
ECOCYC: |
RYBB-RNA | |
ECOLIWIKI: |
b4417 | |
M3D: | small regulatory RNA RybB |
Regulation exerted by the small RNA | ![]() |
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Target | Mechanism | Function | Target Type | Binding Site | Evidence Code |
Reference(s) | |||
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LeftPos | RightPos | Sequence | |||||||
MRNA-DEGRADATION
|
repressor
|
Gene
|
755153
|
755164
|
AAGAACAGCAUG
|
||||
repressor
|
TU
|
1103278
|
1103285
|
GCACUGCU
|
|||||
repressor
|
TU
|
1103278
|
1103285
|
GCACUGCU
|
|||||
repressor
|
TU
|
2461288
|
2461304
|
AUCAUUGAGGUUAUGGU
|
|||||
repressor
|
TU
|
841601
|
841615
|
GCCACUGUUAAUCCC
|
|||||
repressor
|
TU
|
576806
|
576834
|
GCCACUGUUAAUUUUUUCAUCGUGAGCCC
|
|||||
repressor
|
TU
|
2312750
|
2312782
|
GUUAUUAACCCUCUGUUAUAUGCCUUUAUUUGC
|
|||||
repressor
|
TU
|
2312750
|
2312782
|
GUUAUUAACCCUCUGUUAUAUGCCUUUAUUUGC
|
|||||
repressor
|
TU
|
2312750
|
2312782
|
GUUAUUAACCCUCUGUUAUAUGCCUUUAUUUGC
|
|||||
repressor
|
TU
|
987018
|
987042
|
GCCACUGCCGUCAAUAAGUUCUGUC
|
|||||
repressor
|
TU
|
987018
|
987042
|
GCCACUGCCGUCAAUAAGUUCUGUC
|
|||||
repressor
|
TU
|
1314007
|
1314039
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CGACGGAGCGGAUAUGAAAAAGUUAACAGUGGC
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|||||
repressor
|
Gene
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3936196
|
3936213
|
GAUCGUCAAAGCGGUGGU
|
|||||
repressor
|
Gene
|
2736007
|
2736026
|
GCCAUAUAUACUGCUUCUUC
|
|||||
repressor
|
TU
|
432020
|
432038
|
GCCACUGUUUGAAAAUCCC
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|||||
repressor
|
TU
|
432020
|
432038
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GCCACUGUUUGAAAAUCCC
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|||||
activator
|
TU
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Evidence: |
[IEP] Inferred from expression pattern [SM] Site mutation [IMP] Inferred from mutant phenotype [IPI] Inferred from physical interaction [AH] Author hypothesis [IDA] Inferred from direct assay |
Reference(s) |
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