RegulonDB RegulonDB 10.8: Operon Form
   

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




Operon      
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 Johansen J,2008
CRP controls cyaR expression under conditions in which cAMP levels are high De Lay N,2009
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Johansen J., et al., 2008
[2] Wassarman KM., et al., 2001
Promoter
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]
[CV(RS-EPT-CBR/TA)]
[CV(TA/TIM)]
[HTIM]
[RS-EPT-CBR]
[TIM]
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
Terminator(s)
Type: rho-independent
Sequence: gaaccacctcCTTAGCCTGTGTAATCTCCCTTACACGGGCTTATTTTTTacgcgtaata
Reference(s): [3] De Lay N., et al., 2009
TF binding sites (TFBSs)
[CRP,+] Phrase
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], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [1], [3]
[CpxR,-] Phrase
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]


Evidence    

 [AIPP] Automated inference of promoter position

 [CV(RS-EPT-CBR/TA)] cross validation(RS-EPT-CBR/TA)

 [CV(TA/TIM)] cross validation(TA/TIM)

 [HTIM] High-throughput transcription initiation mapping

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [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

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