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small RNA | ![]() ![]() |
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Gene name: | cyaR ![]() |
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Synonym(s): | CyaR, RyeE | |
Genome position: | 2167114 --> 2167200 | |
Strand: | forward | |
Sequence: | Get ribonucleotide sequence FastaFormat | |
GC content %: |
42.53 | |
Note(s): | CyaR is a small RNA that promotes degradation of the ompX Johansen J,2008. De Lay N,2009, yqaE, nadE, luxS De Lay N,2009 and rpoS Kim W,2020 mRNAs. Additional targets of CyaR have been identified by comparative genomics Wright PR,2013 and by an affinity purification method Lalaouna D,2018. A candidate CyaR regulon was inferred by integrating information on experimentally supported targets and sRNA-mRNA interactions with transcription datasets 32487739. Regulation depends on the presence of Hfq Johansen J,2008. Hfq and CyaR interact Wassarman KM,2001, and Hfq may stabilize CyaR Johansen J,2008. CyaR also impacts the function of RyhB by competing for Hfq Chen J,2021. In an hfq mutant, significantly less CyaR accumulates than in wild type Moon K,2011; CyaR is also more unstable in a |FRAME: EG10743 pnp| mutant 21527671. |FRAME: EG10743-MONOMER PNPase| and |FRAME: EG10863-MONOMER| together stabilize CyaR during exponential growth; during stationary phase, CyaR is relatively stable independent of PNPase or RNase PH 27698082. The processed form of the |FRAME: SRAH-RNA| downregulates CyaR levels by base-pairing and mediating its RNase E-dependent degradation Kim W,2020 or by acting as a sponge Iosub IA,2020. CyaR expression is increased by cAMP-CRP and subject to catabolite repression Johansen J,2008. De Lay N,2009 and is regulated by the CpxAR two-component system Vogt SL,2014. CyaR is expressed at higher levels when cells are grown in pyruvate compared to glucose 31363904. Johansen J,2008 observed that CyaR expression was upregulated by the alternative sigma factor of the envelope stress response, σE; however, this regulatory effect was not observed by Guo MS,2014. Overexpression of CyaR decreases curli expression Bak G,2015. Ryx: RNA of unknown function at X position (10 minute) in the genome Wassarman KM,2001 CyaR: cyclic AMP-activated RNA Johansen J,2008 Reviews: Gottesman S,2001. 12654996. Papenfort K, Vogel J,2009. De la Cruz MA,2010. 21843668. Frohlich KS,2018. 32213244 |
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Evidence: | [EXP-IMP] Inferred from mutant phenotype | |
Reference(s): | [1] De Lay N., et al., 2009 [2] Johansen J., et al., 2008 [3] Mihailovic MK., et al., 2018 [4] Sylwan L., et al., 2010 |
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External database links: | ||
ECOCYC: |
RYEE-RNA | |
ECOLIWIKI: |
b4438 | |
M3D: | small regulatory RNA CyaR |
Regulation exerted by the small RNA | ![]() |
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Target | Mechanism | Function | Target Type | Binding Site | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Sequence | ||||||||
MRNA-DEGRADATION
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repressor
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TU
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850441
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850451
|
GAGGUGGUUAU
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W
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MRNA-DEGRADATION
|
repressor
|
TU
|
2867671
|
2867685
|
AAAAUGCAAGCGUGU
|
S
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||||
MRNA-DEGRADATION
|
repressor
|
TU
|
850441
|
850451
|
GAGGUGGUUAU
|
W
|
||||
TRANSLATION-BLOCKING, MRNA-DEGRADATION
|
repressor
|
TU
|
3656985
|
3656994
|
GGGUGGUUCU
|
S
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||||
TRANSLATION-BLOCKING, MRNA-DEGRADATION
|
repressor
|
TU
|
3656985
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3656994
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GGGUGGUUCU
|
S
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||||
repressor
|
TU
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2814731
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2814745
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CAUUUAGCCACCUCC
|
S
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|||||
repressor
|
TU
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1822447
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1822460
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GGAGGGGUUCAAUG
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S
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|||||
repressor
|
TU
|
W
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||||||||
repressor
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Gene
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1907574
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1907616
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ACUGAAAAUGCCACACAUAAACAGAACUGUACCUCGUUUAACC
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S
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|||||
repressor
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TU
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2797013
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2797032
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UUCUCCAGAAACCCAUAUGU
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S
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Reference(s) |
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