RegulonDB RegulonDB 10.7: Operon Form
   

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




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


Transcription unit          
Name: ssuEADCB
Gene(s): ssuB, ssuC, ssuD, ssuA, ssuE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] van Der Ploeg JR., et al., 1999
Promoter
Name: ssuEp
+1: 997563
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 51
Sequence: cagaaaaagatacacaaaatttatatttggaattttcttgtctctccgacagactgaccgAattgttatcaatgttaacaa
                           -35                    -10       +1                   
Evidence: [HIPP]
[TIM] ; Method: Primer Extension
[TIM]
Reference(s): [1] van Der Ploeg JR., et al., 1999
TF binding sites (TFBSs)
[Cbl,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cbl activator ssuEp 997598 997637 -54.5 aaagccctttCTTTAGTTTATTTTCAGAAAAAGATACACAAAATTTATATttggaatttt nd [BPP], [GEA] [1], [2]
[CysB,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CysB-O-acetyl-L-serine1 repressor ssuEp 997560 997601 -18.0 cacaaaatttATATTTGGAATTTTCTTGTCTCTCCGACAGACTGACCGAATTgttatcaatg nd [BPP], [GEA] [1], [2]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR1 activator ssuEp nd nd nd nd nd [AIBSCS], [GEA] [3]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF1 activator ssuEp 997691 997703 -134.0 actgaacgagTAATTCATTGATTcaacatctaa nd [APIORCISFBSCS], [BPP], [GEA] [1]
remote IHF2 activator ssuEp 997734 997746 -177.0 gacaaatcttTAATTTATAGATTtcatgaatat nd [APIORCISFBSCS], [BPP], [GEA] [1]
[IHF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF1 repressor ssuEp 997525 997537 33.0 aacaaaaaaaGAACAATTGGTTAtaaggagaga nd [APIORCISFBSCS], [BPP], [GEA] [1]
Note(s): 1CysB appears to modulate in a negative manner the expression of the ssu operon rather than to be a strong repressor of the operon Bykowski T,2002.1By making use of microarray analyses it was concluded that anarobiosis does not affect expression of the ssu operon, although FNR appears to activate it. A putative FNR-binding site, which was not shown in the report, was identified in this operon Salmon K,2003.1We have assigned the positive function for these sites (-77, -134) since IHF normally activates at this distance.
2 We have assigned the positive function for these sites (-177, -134) since IHF normally activates at this distance.
1We have assigned a negative function for this site (+33), since IHF normally represses at this distance.1 We have assigned the positive function for these sites (-177, -134) since IHF normally activates at this distance.

2We have assigned the positive function for these sites (-77, -134) since IHF normally activates at this distance.
4CysB appears to modulate in a negative manner the expression of the ssu operon rather than to be a strong repressor of the operon Bykowski T,2002.
5We have assigned a negative function for this site (+33), since IHF normally represses at this distance.
6By making use of microarray analyses it was concluded that anarobiosis does not affect expression of the ssu operon, although FNR appears to activate it. A putative FNR-binding site, which was not shown in the report, was identified in this operon Salmon K,2003.


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  gcvB unknown unknown activator       [IMP] [4]
[5]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

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


Reference(s)    

 [1] van Der Ploeg JR., Iwanicka-Nowicka R., Bykowski T., Hryniewicz MM., Leisinger T., 1999, The Escherichia coli ssuEADCB gene cluster is required for the utilization of sulfur from aliphatic sulfonates and is regulated by the transcriptional activator Cbl., J Biol Chem 274(41):29358-65

 [2] Bykowski T., van der Ploeg JR., Iwanicka-Nowicka R., Hryniewicz MM., 2002, The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5'-phosphosulphate (APS) as a signalling molecule for sulphate excess., Mol Microbiol 43(5):1347-58

 [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] Eichhorn E., van der Ploeg JR., Leisinger T., 1999, Characterization of a two-component alkanesulfonate monooxygenase from Escherichia coli., J Biol Chem 274(38):26639-46

 [5] Pulvermacher SC., Stauffer LT., Stauffer GV., 2009, Role of the sRNA GcvB in regulation of cycA in Escherichia coli., Microbiology 155(Pt 1):106-14

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