RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: dcuD
Gene(s): dcuD   Genome Browser M3D Gene expression COLOMBOS
Note(s): In spite of 0010525738 mentioning that the σ54 promoter consensus and the putative IHF site in the intergenic region were most likely part of the narR promoter, we believe that these correspond to the dcuC gene, based on two points: (1) the orientation of the putative σ54 sequence with the +1 site of the transcriptional start site in the dcuC direction and (2) the way that regulation (with the presence of the σ54 promoter type and IHF regulator at almost the same position and acting positively) is very similar to that of other promoters, such as glnHp2, pspAp, norVp, hycAp, hypAp, pspGp, and ibpBp, which are controlled by both factors.
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: dcuDp2
+1: 3374583
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 286
Sequence: acatcctatcacaggattgaaagtaggggaaaatggcagggttttctctttgtgcctcatCattaccataattaacggaat
                                  -24         -12           +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [HIPP]
Reference(s): [1] Janausch IG., et al., 1999
TF binding sites (TFBSs)
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF activator dcuDp2 3374533 3374545 -44.0 acatcctatcACAGGATTGAAAGtaggggaaaa nd [APIORCISFBSCS] [1]


Transcription unit          
Name: dcuD
Gene(s): dcuD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: dcuDp
+1: 3374766
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 103
Sequence: tacaaaataatcataagcgcatattttttaatgaaaaatcacctcacctacaattaaaaaCacgacatccgcaccataaat
                           -35                   -10        +1                   
Evidence: [HIPP]
TF binding sites (TFBSs)
[PhoP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote PhoP-Phosphorylated1 repressor dcuDp 3374812 3374832 56.5 ataacatcgtTGTTTTCAATCTGCCGTTTATgggattgacc nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [2]
Note(s): 1This regulatory interaction was identified by means of PhoPQ-related microarray experiments, and the analysis checked for the presence of the regulatory motif in the promoter region Monsieurs P,2005. A repressor function for dcuD gene transcription can be clearly anticipated from the localization of the PhoP-binding site, very close to the dcuDp promoter core
region Monsieurs P,20051This regulatory interaction was identified by means of PhoPQ-related microarray experiments, and the analysis checked for the presence of the regulatory motif in the promoter region Monsieurs P,2005. A repressor function for dcuD gene transcription can be clearly anticipated from the localization of the PhoP-binding site, very close to the dcuDp promoter core
region Monsieurs P,2005


Evidence    

 [HIPP] Human inference of promoter position

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [GEA] Gene expression analysis


Reference(s)    

 [1] Janausch IG., Unden G., 1999, The dcuD (former yhcL) gene product of escherichia coli as a member of the DcuC family of C4-dicarboxylate carriers: lack of evident expression, Arch Microbiol 172(4):219-26

 [2] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

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