RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: dcuR
Gene(s): dcuR   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: dcuRp
+1: 4350565
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 531
Sequence: acgatcccacgaatttatgaataaattgcatgtgattctcggattattgcatctgaagagTtataagcagttggaagatta
                       -35                        -10       +1                   
Note(s): The dcuRp promoter is positively regulated by CRP-cAMP under both aerobic and anaerobic conditions Oyamada T,2007.
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Oyamada T., et al., 2007
TF binding sites (TFBSs)
[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 dcuRp 4350612 4350633 -57.5 tgctgacgcaCTTCGTGAACGATCCCACGAATttatgaataa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]


Transcription unit          
Name: dcuSR
Gene(s): dcuR, dcuS   Genome Browser M3D Gene expression COLOMBOS
Note(s): The dcuSR operon is constitutively expressed in the absence of nitrate Oyamada T,2007 however, when nitrate is present, the operon is regulated by NarL. NarL binds to a region from positions -25 to -75, upstream the transcriptional start site of dcuS, where there are two consensus sequences. These sequences were identified as the NarL-binding site Goh EB,2005
Based on β-galactosidase and Western blot analyses, it was shown that the expression of the dcuSR operon is positively regulated during the growth phase but it is not σS dependent Abo-Amer AE, Altalhi AD,2009 In addition, the results suggest that other growth phase-dependent regulatory mechanisms, such as DcuSR and CRP, could be involved during postexponential dcuSR expression Abo-Amer AE, Altalhi AD,2009
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [3] Salmon K., et al., 2003
Promoter
Name: dcuSp
+1: 4351685
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 23
Sequence: atatagccaatcattcttactccctttgaattacccgcctcatcagagataatgcttaagAaatttgtcacacaaggaagc
                               -35                   -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Goh EB., et al., 2005
[1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[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
nd FNR activator dcuSp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [3]
[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 repressor dcuSp 4351713 4351719 -31.0 ttactcccttTGAATTAcccgcctcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal NarL-phosphorylated repressor dcuSp 4351722 4351728 -40.0 caatcattctTACTCCCtttgaattac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [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

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

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

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


Reference(s)    

 [1] 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

 [2] Oyamada T., Yokoyama K., Morinaga M., Suzuki M., Makino K., 2007, Expression of Escherichia coli DcuS-R two-component regulatory system is regulated by the secondary internal promoter which is activated by CRP-cAMP., J Microbiol 45(3):234-40

 [3] 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

 [4] Goh EB., Bledsoe PJ., Chen LL., Gyaneshwar P., Stewart V., Igo MM., 2005, Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system., J Bacteriol 187(14):4890-9

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