RegulonDB RegulonDB 10.8: smallRNA Form
   

CyaR small RNA in Escherichia coli K-12 genome


Gene local context to scale (view description)

trhP ogrK cyaR CRP cyaRp cyaRp
small RNA      
Gene name: cyaR    Texpresso search in the literature
Synonym(s): RyeE, ryeE, small regulatory RNA CyaR
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, and luxS mRNAs De Lay N,2009. Additional targets of CyaR have been identified by comparative genomics Wright PR,2013 and by an affinity purification method 29294085. 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.
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.
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. 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. 19366629. De la Cruz MA,2010. 21843668. Frohlich KS,2018
Evidence: [IDA] Inferred from direct assay
[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
[5] Wassarman KM., et al., 2001
External database links:  
ECOCYC:
RYEE-RNA
ECOLIWIKI:
b4438
M3D: CyaR


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
850441
850449
-5
AGGTGGTT
 
 
 
antisense
post-transcriptional regulation
repressor
2797013
2797032
6
ACATATGGGTTTCTGGAGA
 
 
antisense
post-transcriptional regulation
repressor
2814731
2814745
-5
GGAGGTGGCTAAAT
 
 
antisense
post-transcriptional regulation
repressor
1822447
1822460
-5
GAGGGGTTCAATG
 
Evidence: [IMP] Inferred from mutant phenotype


Reference(s)    

 [1] De Lay N., Gottesman S., 2009, The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior., J Bacteriol 191(2):461-76

 [2] Johansen J., Eriksen M., Kallipolitis B., Valentin-Hansen P., 2008, Down-regulation of Outer Membrane Proteins by Noncoding RNAs: Unraveling the cAMP-CRP- and sigma(E)-Dependent CyaR-ompX Regulatory Case., J Mol Biol 383(1):1-9

 [3] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084

 [4] Sylwan L., Frumerie C., Haggard-Ljungquist E., 2010, Identification of bases required for P2 integrase core binding and recombination., Virology 404(2):240-5

 [5] 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


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