RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Name: cydAB
Synonym(s): OP00140
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|.
Evidence: [TAS] Traceable author statement
Reference(s): [1] Cotter PA., et al., 1990
[2] Ramseier TM., et al., 1996
Promoter
Name: cydAp1
+1: 771170
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 288
Sequence: ttgatatttatcaatgtataagtcttggaaatgggcatcaaaaagagataaattgttctcGatcaaattggctgaaaggcg
                         -35                     -10        +1                   
Evidence: [TIM]
Reference(s): [3] Cotter PA., et al., 1997
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-Phosphorylated activator cydAp1 770848 770862 -315.0 ccctgggtgaGTTAATTATAATATAattataagtt nd [AIBSCS], [GEA] [2], [4], [5], [6]
remote ArcA-Phosphorylated activator cydAp1 770859 770873 -304.0 ttaattataaTATAATTATAAGTTAactaaatgtt nd [AIBSCS], [GEA] [2], [4], [5], [6]
remote ArcA-Phosphorylated activator cydAp1 770870 770884 -293.0 ataattataaGTTAACTAAATGTTAatattggcgg nd [AIBSCS], [BPP], [GEA] [2], [3], [4], [5], [6], [7], [8]
proximal ArcA-Phosphorylated activator cydAp1 771079 771093 -84.0 aagttaccttATTGAAACATGATTAacataatttg nd [BCE], [GEA], [HIBSCS] [2], [3], [4], [5], [6], [7], [8]
remote ArcA-Phosphorylated activator cydAp1 771297 771311 135.0 ggatcaatttGAGTTTTTATTAACAtgtttgcaac nd [AIBSCS], [GEA] [2], [4], [5], [6]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 repressor cydAp1 771110 771123 -53.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [AIBSCS], [BPP], [GEA] [2], [3], [6], [7], [9], [10], [11]
proximal FNR repressor cydAp1 771162 771175 -1.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [BPP], [GEA], [HIBSCS] [1], [2], [3], [6], [7], [10], [11]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor cydAp1 nd nd nd nd nd [BPP], [GEA] [13]
[HypT,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd HypT-Met-oxidized activator cydAp1 nd nd nd nd nd [BPP], [GEA] [12]
Note(s): 1Under anaerobiosis, FNR represses cydAB operon expression Salmon K,2003.
1H-NS most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. H-NS regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.5Under anaerobiosis, FNR represses cydAB operon expression Salmon K,2003.
9H-NS most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. H-NS regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|.
Reference(s): [2] Ramseier TM., et al., 1996
Promoter
Name: cydAp3
+1: 771202
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 256
Sequence: gggcatcaaaaagagataaattgttctcgatcaaattggctgaaaggcggtaatttagctAtaaattgatcaccgtcgaaa
                              -35                  -10      +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [10] Govantes F., et al., 2000
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated activator cydAp3 nd nd nd nd nd [AIBSCS], [GEA] [5], [6], [10], [13]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor cydAp3 771110 771123 -85.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [AIBSCS], [BPP], [GEA] [2], [6], [10], [11]
proximal FNR2 repressor cydAp3 771162 771175 -33.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [BPP], [GEA], [HIBSCS] [1], [2], [6], [10], [11]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor cydAp3 nd nd nd nd nd [BPP], [GEA] [13]
Note(s): 2Under anaerobiosis, FNR repress cydAB operon expression Salmon K,2003.1Hns most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. Hns regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.2Under anaerobiosis, FNR repress cydAB operon expression Salmon K,2003.
4Hns most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. Hns regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|.
Reference(s): [2] Ramseier TM., et al., 1996
Promoter
Name: cydAp4
+1: 771213
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 245
Sequence: agagataaattgttctcgatcaaattggctgaaaggcggtaatttagctataaattgatcAccgtcgaaaaatgcaaattt
                         -35                     -10        +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [10] Govantes F., et al., 2000
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated activator cydAp4 nd nd nd nd nd [AIBSCS], [GEA] [5], [6], [10], [13]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR repressor cydAp4 771110 771123 -96.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [AIBSCS], [BPP], [GEA] [2], [6], [10], [11]
proximal FNR2 repressor cydAp4 771162 771175 -44.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [BPP], [GEA], [HIBSCS] [1], [2], [6], [10], [11]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor cydAp4 nd nd nd nd nd [BPP], [GEA] [13]
Note(s): 2Under anaerobiosis, FNR repress cydAB operon expression Salmon K,2003.1H-NS most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. H-NS regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.2Under anaerobiosis, FNR repress cydAB operon expression Salmon K,2003.
4H-NS most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. H-NS regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|.
Reference(s): [2] Ramseier TM., et al., 1996
Promoter
Name: cydAp2
+1: 771284
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 174
Sequence: atgcaaatttgcttcaacaaaaacctgtttattgtaaggattttgcggcgtaatatatacGtgggatcaatttgagttttt
                            -35                    -10      +1                   
Evidence: [HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Cotter PA., et al., 1997
[14] Ogasawara H., et al., 2005
[15] Salgado H, et al., 2012
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-Phosphorylated activator cydAp2 771199 771213 -77.5 cggtaatttaGCTATAAATTGATCAccgtcgaaaa nd [BPP], [GEA], [HIBSCS] [5], [6], [8]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator cydAp2 771110 771123 -167.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [AIBSCS], [BPP], [GEA] [2], [6], [10], [11]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR1 repressor cydAp2 771162 771175 -115.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [BPP], [GEA], [HIBSCS] [1], [2], [6], [10], [11]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor cydAp2 nd nd nd nd nd [BPP], [GEA] [13]
Note(s): 1Under anaerobiosis, FNR repress cydAB operon expression Salmon K,2003.1Hns most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. Hns regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.2Under anaerobiosis, FNR repress cydAB operon expression Salmon K,2003.
4Hns most strongly represses the cydAp4 promoter and has a moderate effect on cydAp1, cydAp2, and cydAp3 promoters. Hns regulates cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis |CITS:[23274360]|. The increased expression under aerobiosis appears to be caused by the transcription factor PhoB |CITS:[23274360]|.
Reference(s): [2] Ramseier TM., et al., 1996
Promoter
Name: cydAp5
+1: 771368
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 90
Sequence: aacatgtttgcaacctttctttacgccgtttttgtgtgcattcacatggtatgatgaaagTgttcaaacaaatttctattg
                             -35                  -10       +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [10] Govantes F., et al., 2000
TF binding sites (TFBSs)
[Cra,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra activator cydAp5 771225 771242 -134.5 cgtcgaaaaaTGCAAATTTGCTTCAACAaaaacctgtt nd [AIBSCS], [BPP], [GEA] [2]
remote Cra activator cydAp5 771254 771271 -105.5 aaacctgtttATTGTAAGGATTTTGCGGcgtaatatat nd [AIBSCS], [BPP], [GEA] [2]


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  ryhB antisense post-transcriptional regulation repressor       [IMP] [16]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [BCE] Binding of cellular extracts

 [HIBSCS] Human inference based on similarity to consensus sequences

 [HIPP] Human inference of promoter position

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


Reference(s)    

 [1] Cotter PA., Chepuri V., Gennis RB., Gunsalus RP., 1990, Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in Escherichia coli is regulated by oxygen, pH, and the fnr gene product., J Bacteriol 172(11):6333-8

 [2] Ramseier TM., Chien SY., Saier MH., 1996, Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli., Curr Microbiol 33(4):270-4

 [3] Cotter PA., Melville SB., Albrecht JA., Gunsalus RP., 1997, Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation., Mol Microbiol 25(3):605-15

 [4] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [5] Mondragon V., Franco B., Jonas K., Suzuki K., Romeo T., Melefors O., Georgellis D., 2006, pH-dependent activation of the BarA-UvrY two-component system in Escherichia coli., J Bacteriol 188(23):8303-6

 [6] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli., Metab Eng 7(5-6):364-74

 [7] Cotter PA., Gunsalus RP., 1992, Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli., FEMS Microbiol Lett 70(1):31-6

 [8] Lynch AS., Lin EC., 1996, Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters., J Bacteriol 178(21):6238-49

 [9] Fu HA., Iuchi S., Lin EC., 1991, The requirement of ArcA and Fnr for peak expression of the cyd operon in Escherichia coli under microaerobic conditions., Mol Gen Genet 226(1-2):209-13

 [10] Govantes F., Albrecht JA., Gunsalus RP., 2000, Oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon: roles of multiple promoters and the Fnr-1 and Fnr-2 binding sites., Mol Microbiol 37(6):1456-69

 [11] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [12] Gebendorfer KM., Drazic A., Le Y., Gundlach J., Bepperling A., Kastenmuller A., Ganzinger KA., Braun N., Franzmann TM., Winter J., 2012, Identification of a Hypochlorite-specific Transcription Factor from Escherichia coli., J Biol Chem 287(9):6892-903

 [13] Govantes F., Orjalo AV., Gunsalus RP., 2000, Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon., Mol Microbiol 38(5):1061-73

 [14] Ogasawara H., Teramoto J., Yamamoto S., Hirao K., Yamamoto K., Ishihama A., Utsumi R., 2005, Negative regulation of DNA repair gene (uvrA) expression by ArcA/ArcB two-component system in Escherichia coli., FEMS Microbiol Lett 251(2):243-9

 [15] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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.

 [16] Masse E., Vanderpool CK., Gottesman S., 2005, Effect of RyhB small RNA on global iron use in Escherichia coli., J Bacteriol 187(20):6962-71

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