RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: cydDC
Gene(s): cydC, cydD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Cook GM., et al., 1997
[2] Georgiou CD., et al., 1987
[3] Poole RK., et al., 1993
Promoter
Name: cydDp
+1: 931031
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 69
Sequence: aaaataattttacaaatcagtaacaaaagtaaagaaggcgacaccatgcgactatgggtcGcctttattttttccccgttg
                                  -35                  -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Cook GM., 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
proximal ArcA-phosphorylated activator cydDp 931068 931083 -44.0 gcaaaataatTTTACAAATCAGTAACaaaagtaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-DAP-SEQ] S [6], [7]
[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 activator cydDp 931115 931128 -90.5 atggcagcacTTGATGCGGAACGCtacctcgatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
[NarL,+] 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 NarL-phosphorylated activator cydDp 931108 931114 -80.0 tgcggaacgcTACCTCGatggtttagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
remote NarL-phosphorylated activator cydDp 931154 931160 -126.0 gccaggccatTACTTCGgccggtacag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA FnrS cydDC repressor nd nd nd nd [EXP-IEP] [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -19.1 931018 931058 caaaagtaaaGAAGGCGACACCATGCGACTATGGGTCGCCTTTATTTTTTccccgttgta
  anti-terminator -11.63 931041 931110 gaacgctaccTCGATGGTTTAGCTGACGCAAAATAATTTTACAAATCAGTAACAAAAGTAAAGAAGGCGACACCATGCGactatgggtc
  anti-anti-terminator -9.4 931091 931124 cagcacttgaTGCGGAACGCTACCTCGATGGTTTAGCTGACGCaaaataattt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [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

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

 [EXP-IEP] Inferred from expression pattern


Reference(s)    

 [1] Cook GM., Membrillo-Hernandez J., Poole RK., 1997, Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors., J Bacteriol 179(20):6525-30

 [2] Georgiou CD., Fang H., Gennis RB., 1987, Identification of the cydC locus required for expression of the functional form of the cytochrome d terminal oxidase complex in Escherichia coli., J Bacteriol 169(5):2107-12

 [3] Poole RK., Hatch L., Cleeter MW., Gibson F., Cox GB., Wu G., 1993, Cytochrome bd biosynthesis in Escherichia coli: the sequences of the cydC and cydD genes suggest that they encode the components of an ABC membrane transporter., Mol Microbiol 10(2):421-30

 [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] Boysen A., Moller-Jensen J., Kallipolitis B., Valentin-Hansen P., Overgaard M., 2010, Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli., J Biol Chem 285(14):10690-702

 [6] 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

 [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

RegulonDB