RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: cyoABCDE
Synonym(s): OP00141
Gene(s): cyoE, cyoD, cyoC, cyoB, cyoA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of this operon is enhanced during and after the switch from aerobic to anaerobic growth conditions Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J,2011
The expression of the gene cyoA is increased under acidic growth conditions in aerobiosis but it is decreased in microaerobiosis under acidic growth conditions Marzan LW,2013
In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid modified the expression of cyoABCDE Li Y, Liu B, Guo J, Cong H, He S, Zhou H, Zhu F, Wang Q, Zhang L,2019.
CpxR represses transcription of the nuo and cyo operons in enteropathogenic Escherichia coli (EPEC), and these complexes confer adaptation to stresses that compromise envelope integrity Guest RL, Wang J, Wong JL, Raivio TL,2017
Reference(s): [1] Cotter PA., et al., 1992
[2] Tseng CP., et al., 1996
Promoter
Name: cyoAp
+1: 451653
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 43
Sequence: tccaagtaacaggaatttaatcatgtttacagtaatgtaaccttcccgtaaaatgcccacAcactttaaacgccaccagat
                               -35                    -10   +1                   
Note(s): Like pdhRp, ndhp and cyoAp are repressed by PdhR and derepressed by the addition of pyruvate Ogasawara H,2007
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Huerta AM., et al., 2003
[4] Minagawa J., et al., 1990
[5] Ogasawara H., et al., 2007
[6] 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
remote ArcA-phosphorylated repressor cyoAp 451846 451860 -200.0 ataattatttGTTAAATAATTGTTTtatttcacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [10], [11], [12]
[CRP,+] 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 CRP-cyclic-AMP activator cyoAp 451680 451701 -37.5 caagtaacagGAATTTAATCATGTTTACAGTAatgtaacctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [16]
remote CRP-cyclic-AMP activator cyoAp 451834 451855 -191.5 tatttgttaaATAATTGTTTTATTTCACATTGgttataccaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [16]
[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 repressor cyoAp 451913 451930 -268.5 aattctatttTTCTTACACGATTCAGCTaatgagtctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[CusR,+] 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 CusR-phosphorylated activator cyoAp 451577 451593 69.5 tcaggaaataCAATAAAAGTTTGGGATggttgtcatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [17]
[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 cyoAp 451839 451852 -192.5 ttgttaaataATTGTTTTATTTCAcattggttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [8], [13], [14], [15]
[Fis,+] 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 Fis activator cyoAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [19]
[Fur,-] 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 Fur-Fe2+ repressor cyoAp 451857 451875 -213.0 gttgtcactcTAATGATAATTATTTGTTAaataattgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [8], [9]
[GadE,+] 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 GadE activator cyoAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [18]
[HprR,-] 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 HprR-phosphorylated repressor cyoAp 451576 451594 69.5 ctcaggaaatACAATAAAAGTTTGGGATGgttgtcatta nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [17]
[PdhR,-] 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 PdhR repressor cyoAp 451822 451838 -177.0 ttttatttcaCATTGGTTATACCAATTgcccgcccag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-CHIP] high throughput ChIP-chip evidence

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence

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

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

 [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-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] 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

 [2] Tseng CP., Albrecht J., Gunsalus RP., 1996, Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli., J Bacteriol 178(4):1094-8

 [3] 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

 [4] Minagawa J., Nakamura H., Yamato I., Mogi T., Anraku Y., 1990, Transcriptional regulation of the cytochrome b562-o complex in Escherichia coli. Gene expression and molecular characterization of the promoter., J Biol Chem 265(19):11198-203

 [5] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol 189(15):5534-41

 [6] 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.

 [7] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

 [8] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [9] Stojiljkovic I., Baumler AJ., Hantke K., 1994, Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay., J Mol Biol 236(2):531-45

 [10] Federowicz S., Kim D., Ebrahim A., Lerman J., Nagarajan H., Cho BK., Zengler K., Palsson B., 2014, Determining the control circuitry of redox metabolism at the genome-scale., PLoS Genet 10(4):e1004264

 [11] 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

 [12] Salmon KA., Hung SP., Steffen NR., Krupp R., Baldi P., Hatfield GW., Gunsalus RP., 2005, Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA., J Biol Chem 280(15):15084-96

 [13] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [14] 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

 [15] Spiro S., Guest JR., 1991, Adaptive responses to oxygen limitation in Escherichia coli., Trends Biochem Sci 16(8):310-4

 [16] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [17] Urano H., Umezawa Y., Yamamoto K., Ishihama A., Ogasawara H., 2015, Cooperative regulation of the common target genes between H2O2-sensing YedVW and Cu2+-sensing CusSR in Escherichia coli., Microbiology 161(Pt 4):729-38

 [18] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [19] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

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