RegulonDB RegulonDB 10.6.3: Operon Form
   

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




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


Transcription unit          
Gene(s): lgoR   Genome Browser M3D Gene expression COLOMBOS
Note(s): In the presence of D-glucuronate, the binding affinity of ExuR is higher than that of UxuR to the lgoR/lgoD intergenic region. Under the same conditions, the binding of ExuR to the regulatory region is affected by the presence of UxuR |CITS:[ 27129867]|.
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: lgoRp4
+1: 4595947
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 96
Sequence: aacattcatcgtagacatgattcggctctccactttttgttgccttagatatcaatgaaaAtgaaaaatggcagcggaacg
                             -10                  -35       +1                   
Note(s): Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.055. P-value: 3.792e-5
Evidence: [ICWHO]
Reference(s): [1] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP1 activator lgoRp4 4595902 4595915 40.0 aaaatcttttTTGTGAAAACACACgcataaaaat nd [GEA], [HIBSCS] [2]
[ExuR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ExuR-α-D-galacturonate, α-D-glucuronate repressor lgoRp4 4595807 4595824 132.5 tttacgccacAATGTGATTAACCAGGTCattgatgata nd [BPP] [4]
[UxuR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote UxuR repressor lgoRp4 4595807 4595824 132.5 tttacgccacAATGTGATTAACCAGGTCattgatgata nd [BPP], [GEA] [3], [4]
Note(s): 1CRP is required for lgoR and lgoD transcription in a sugar-independent manner, irrespective of whether the bacteria are grown with glucose or glucuronate as the main carbon source Tutukina MN,2016, and this might be due to its cAMP-independent binding to a nonspecific site leading to only a secondary effect Kolb A, Busby S, Buc H, Garges S, Adhya S,1993.1CRP is required for lgoR and lgoD transcription in a sugar-independent manner, irrespective of whether the bacteria are grown with glucose or glucuronate as the main carbon source Tutukina MN,2016, and this might be due to its cAMP-independent binding to a nonspecific site leading to only a secondary effect Kolb A, Busby S, Buc H, Garges S, Adhya S,1993.


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins


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] Tutukina MN., Potapova AV., Cole JA., Ozoline ON., 2016, Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation., Microbiology 162(7):1220-31

 [3] Suvorova IA., Tutukina MN., Ravcheev DA., Rodionov DA., Ozoline ON., Gelfand MS., 2011, Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria., J Bacteriol 193(15):3956-63

 [4] Tutukina MN., Potapova AV., Vlasov PK., Purtov YA., Ozoline ON., 2016, Structural modeling of the ExuR and UxuR transcription factors of E. coli: search for the ligands affecting their regulatory properties., J Biomol Struct Dyn :1-9

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