RegulonDB RegulonDB 10.9: 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: [CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] 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: [ICWHO]
[TIM]
Reference(s): [1] Cook GM., et al., 1997
[4] Huerta AM., et al., 2003
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-phosphorylated1 activator cydDp 931068 931083 -44.0 gcaaaataatTTTACAAATCAGTAACaaaagtaaag nd [AIBSPD], [CCE], [EME], [GEA] [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR activator cydDp 931115 931128 -90.5 catggcagcaCTTGATGCGGAACGCtacctcgatg nd [APIORCISFBSCS], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-phosphorylated activator cydDp 931108 931114 -80.0 atgcggaacgCTACCTCGatggtttagc nd [APIORCISFBSCS], [GEA] [1]
remote NarL-phosphorylated activator cydDp 931154 931160 -126.0 cgccaggccaTTACTTCGgccggtacag nd [APIORCISFBSCS], [GEA] [1]
Note(s): 1Under microaerobic conditions, ArcA activates cydD expression.
Growth Condition-chip-Experiment: Escherichia coli MG1655/arcA-8myc/M9 minimal medium/glucose 0.2%; ammonium chloride 0.1%; potassium nitrate 20 mmol/anaerobiosis/37°C/exponential phase Federowicz S,2014
Growth Conditions_GeneExpression_CONTROL: Escherichia coli MG1655/arcA knockout mutant/M9 minimal medium/glucose 0.2%; ammonium chloride 0.1%/anaerobiosis/37°C/exponential phase Federowicz S,2014
4Under microaerobic conditions, ArcA activates cydD expression.
Growth Condition-chip-Experiment: Escherichia coli MG1655/arcA-8myc/M9 minimal medium/glucose 0.2%; ammonium chloride 0.1%; potassium nitrate 20 mmol/anaerobiosis/37°C/exponential phase Federowicz S,2014
Growth Conditions_GeneExpression_CONTROL: Escherichia coli MG1655/arcA knockout mutant/M9 minimal medium/glucose 0.2%; ammonium chloride 0.1%/anaerobiosis/37°C/exponential phase Federowicz S,2014
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 [IEP] [5]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [8] Merino E, et al., 2005
  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"




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

 [8] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.


RegulonDB