RegulonDB RegulonDB 11.1: 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 cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
Evidence: [AS-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: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Cotter PA., et al., 1997
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-phosphorylated activator cydAp1 770848 770862 -315.0 ccctgggtgaGTTAATTATAATATAattataagtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5], [6], [7], [8]
remote ArcA-phosphorylated activator cydAp1 770859 770873 -304.0 ttaattataaTATAATTATAAGTTAactaaatgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5], [6], [7], [8]
remote ArcA-phosphorylated activator cydAp1 770870 770884 -293.0 ataattataaGTTAACTAAATGTTAatattggcgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [5], [6], [7], [8], [9], [10]
proximal ArcA-phosphorylated activator cydAp1 771079 771093 -84.0 aagttaccttATTGAAACATGATTAacataatttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [3], [5], [6], [7], [8], [9], [10]
remote ArcA-phosphorylated activator cydAp1 771297 771311 135.0 ggatcaatttGAGTTTTTATTAACAtgtttgcaac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [5], [6], [7], [8]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor cydAp1 771110 771123 -53.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3], [7], [9], [11], [12], [13]
proximal FNR repressor cydAp1 771162 771175 -1.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3], [7], [9], [12], [13]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor cydAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [15]
[HypT,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd HypT-Met-oxidized activator cydAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14]


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [12] Govantes F., et al., 2000
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-phosphorylated activator cydAp3 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6], [7], [8], [12], [15]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR repressor cydAp3 771110 771123 -85.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12], [13]
proximal FNR repressor cydAp3 771162 771175 -33.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [12], [13]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor cydAp3 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [15]


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [12] Govantes F., et al., 2000
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-phosphorylated activator cydAp4 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [6], [7], [8], [12], [15]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR repressor cydAp4 771110 771123 -96.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12], [13]
proximal FNR repressor cydAp4 771162 771175 -44.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [12], [13]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor cydAp4 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [15]


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
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: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Cotter PA., et al., 1997
[4] Huerta AM., et al., 2003
[16] Ogasawara H., et al., 2005
[17] Salgado H, et al., 2012
TF binding sites (TFBSs)
[ArcA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-phosphorylated activator cydAp2 771199 771213 -77.5 cggtaatttaGCTATAAATTGATCAccgtcgaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7], [8], [10]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR activator cydAp2 771110 771123 -167.5 tttgtaggaaTTGATATTTATCAAtgtataagtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [7], [12], [13]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR repressor cydAp2 771162 771175 -115.5 aagagataaaTTGTTCTCGATCAAattggctgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [7], [12], [13]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor cydAp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [15]


Transcription unit          
Name: cydAB
Gene(s): cydA, cydB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The cydAB operon is upregulated by long-term (8 to 12 h) exposure of E. coli to some biocides Merchel Piovesan Pereira B, Wang X, Tagkopoulos I,2020.
The expression of the gene cydB is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [12] Govantes F., et al., 2000
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[Cra,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra activator cydAp5 771225 771242 -134.5 cgtcgaaaaaTGCAAATTTGCTTCAACAaaaacctgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
remote Cra activator cydAp5 771254 771271 -105.5 aaacctgtttATTGTAAGGATTTTGCGGcgtaatatat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [COMP-HINF] Inferred by a human based on computational evidence

 [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] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [5] 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

 [6] 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

 [7] 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

 [8] Vazquez-Ciros OJ., Alvarez AF., Georgellis D., 2020, Identification of Z nucleotides as an ancient signal for two-component system activation in bacteria., Proc Natl Acad Sci U S A 117(52):33530-33539

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] 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

 [15] 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

 [16] 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

 [17] 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.

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