RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: yjbE
Gene(s): yjbE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [1] Ferrieres L., et al., 2007
Promoter
Name: yjbEp1
+1: 4235858
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 48
Sequence: catcgctaattccccgcgccgtaattcgcatgctttagttgtgtatactcgatcccgcccGaaatgtttttgggtaaatct
                     -35                    -10             +1                   
Evidence: [TIM]
Reference(s): [2] Ionescu M., et al., 2011
Terminator(s)
Type: rho-independent
Sequence: taaagtatgtATCCCCAAAATAATTCGAGTCATTGCATCTGTGGCTAGAAGTATGAAGGGAttaaccataa
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
remote IHF activator yjbEp1 4235719 4235731 -133.0 tgtttttattTTAAGTTTATGATttttattgtt nd [APIORCISFBSCS], [BPP] [3]
[RcsAB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RcsAB activator yjbEp1 4235642 4235656 -209.0 aatcataccgTGAGGTTAATCCTAAaatagatttt nd [APIORCISFBSCS], [CV(GEA)], [GEA] [1]


Transcription unit          
Name: yjbEFGH
Gene(s): yjbE, yjbF, yjbG, yjbH   Genome Browser M3D Gene expression COLOMBOS
Note(s): The yjbEFGH operon was previously shown to be involved in exopolysaccharide synthesis Ferrieres L,2007, biofilm formation, and the Rcs phosphorelay system 14651646. It is induced by osmotic stress 12024246 and is under positive control of the RpoS-regulated general stress response of E. coli 15184550. Weber H,2005. Nevertheless, it has been shown that RpoS has a negative and indirect effect on it 17957352.
Induction of yjbEFGH is restricted to relatively low cell densities and is positively affected by slow growth rates and a high oxygen concentration 17957352.
The expression of the operon yjbEFGH is increased when colicin (at 30 ng/ml) is added to the medium 23421615.
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[CV(PM)] cross validation(PM)
[LTED] Length of transcript experimentally determined
[PAGTSBP] Products of adjacent genes in the same biological process
[PM] Polar mutation
Reference(s): [1] Ferrieres L., et al., 2007
Promoter
Name: yjbEp1
+1: 4235858
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 48
Sequence: catcgctaattccccgcgccgtaattcgcatgctttagttgtgtatactcgatcccgcccGaaatgtttttgggtaaatct
                     -35                    -10             +1                   
Evidence: [TIM]
Reference(s): [2] Ionescu M., et al., 2011
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
remote IHF activator yjbEp1 4235719 4235731 -133.0 tgtttttattTTAAGTTTATGATttttattgtt nd [APIORCISFBSCS], [BPP] [3]
[RcsAB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote RcsAB activator yjbEp1 4235642 4235656 -209.0 aatcataccgTGAGGTTAATCCTAAaatagatttt nd [APIORCISFBSCS], [CV(GEA)], [GEA] [1]


Transcription unit       
Name: yjbEFGH
Gene(s): yjbE, yjbF, yjbG, yjbH   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of this operon is increased when colicin (at 30 ng/ml) is added to the medium 23421615.
Evidence: [CV(LTED/PM)] cross validation(LTED/PM)
[CV(PM)] cross validation(PM)
[LTED] Length of transcript experimentally determined
[PAGTSBP] Products of adjacent genes in the same biological process
[PM] Polar mutation
Reference(s): [1] Ferrieres L., et al., 2007
Promoter
Name: yjbEp2
+1: 4235872
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 34
Sequence: cgcgccgtaattcgcatgctttagttgtgtatactcgatcccgcccgaaatgtttttgggTaaatctccattcattcaatg
                         -35                     -10        +1                   
Note(s): Two transcription start sites were identified for the yjbEp2 promoter, at -33 and -34 (T/A) upstream of the yjbE ATG Ionescu M,2011
Evidence: [TIM]
Reference(s): [2] Ionescu M., et al., 2011


Transcription unit       
Gene(s): yjbF, yjbG, yjbH   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


Evidence    

 [TIM] Transcription initiation mapping

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

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


Reference(s)    

 [1] Ferrieres L., Aslam SN., Cooper RM., Clarke DJ., 2007, The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production., Microbiology 153(Pt 4):1070-80

 [2] Ionescu M., Elgrably-Weiss M., Elad T., Rasouly A., Yagur-Kroll S., Belkin S., 2011, Negative regulation of σ(70)-driven promoters by σ(70)., Res Microbiol 162(5):461-9

 [3] Murtin C., Engelhorn M., Geiselmann J., Boccard F., 1998, A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell., J Mol Biol 284(4):949-61

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