RegulonDB RegulonDB 10.7: Operon Form

cyaR operon and associated TUs in Escherichia coli K-12 genome

Name: cyaR
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit          
Name: cyaR
Gene(s): cyaR   Genome Browser M3D Gene expression COLOMBOS
Note(s): A stem-loop of the ρ-independent terminator for the cyaR gene was predicted by Johansen et al. (2008). However, the terminator is inside of the cyaR gene |CITS:[18619465]|.
CRP controls cyaR expression under conditions in which cAMP levels are high |CITS:[18978044]|.

Evidence: [BTEI] Boundaries of transcription experimentally identified
[ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
[LTED] Length of transcript experimentally determined
Reference(s): [1] Johansen J., et al., 2008
[2] Wassarman KM., et al., 2001
Name: cyaRp
+1: 2167114
Sigma Factor: Sigma24, Sigma70, Sigma38
Distance from start of the gene: 0
Sequence: tggaaaattcttagaaaccgatcacatacagctgcatttattaaggttatcatccgtttcGctgaaaaacataacccataa
                          -35                   -10         +1                   
Note(s): cyaRp could be transcribed from EσE, since cyaR expression is up-regulated in response to an increase in the activity of σE. Furthermore, a small group of σE-regulated factors is also regulated by σ70. Another issue is the fact that the -10 and -35 boxes of cyaR match with the ecfFp2 boxes, which are under control of σE. In addition, cyaRp contains in the upstream region an AU-rich region which may have a role in recognition of the alternative RNA polymerases Johansen J,2008
Evidence: [AIPP]
[TIM] ; Method: Primer Extension
Reference(s): [3] De Lay N., et al., 2009
[1] Johansen J., et al., 2008
[4] Maciag A., et al., 2011
[5] Salgado H, et al., 2012
Type: rho-independent
Reference(s): [3] De Lay N., et al., 2009
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator cyaRp 2167061 2167082 -42.5 ggatggaaaaTTCTTAGAAACCGATCACATACagctgcattt nd [AIBSCS], [BPP], [GEA], [SM] [1], [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd CpxR-Phosphorylated repressor cyaRp nd nd nd nd nd [BPP], [GEA] [6]


 [1] 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

 [2] 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

 [3] 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

 [4] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [6] Vogt SL., Evans AD., Guest RL., Raivio TL., 2014, The Cpx envelope stress response regulates and is regulated by small noncoding RNAs., J Bacteriol 196(24):4229-38