RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: hlyE
Gene(s): hlyE   Genome Browser M3D Gene expression COLOMBOS
Note(s): SlyA activates hlyE trasnscription by antagonizing the negative action of the H-NS protein Ludwig A,1999. Wyborn NR,2004. H-NS prevents binding of RNA polymerase to the hlyE promoter. On the other hand, SlyA allows binding of RNA polymerase but inhibits binding of H-NS Lithgow JK,2007. The location of the sites for SlyA reported by Lithgow JK,2007 are unusual for typical bacterial transcription. However, it has been shown that some other S. typhimurium genes that are positively regulated by SlyA contain SlyA-binding sites downstream from the transcriptional start site, including pagC and ugtL 15813739. 15208313.
FNR and CRP are in competition for binding at the hlyE regulatory region, and FNR ocuppies the site more frequently than CRP even under aerobic conditions, but under such conditions FNR is not an active protein and so this protein cannot activate trancription of hlyE as efficiently as CRP. The expression of hlyE CRP-mediated activation requires the presence of Hns.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Oscarsson J., et al., 1996
Promoter
Name: hlyEp
+1: 1230466
Distance from start of the gene: 72
Sequence:
Note(s): This promoter was characterized as a class I promoter that could be transcriptionally activated by CRP and/or FNR.
Evidence: [HIPP]
[TIM]
Reference(s): [2] Ludwig A., et al., 1999
[3] Westermark M., et al., 2000
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
proximal CRP-cAMP activator hlyEp 1230517 1230538 -61.5 acattaaacaTTGTTTGATATTTATCATATTAatagaaataa nd [BPP], [CV(SM)], [GEA], [SM] [3], [5]
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 activator hlyEp 1230521 1230534 -61.5 taaacattgtTTGATATTTATCATattaatagaa nd [BPP], [GEA] [3], [5]
[Fis,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fis repressor hlyEp 1230441 1230455 19.0 aagtaaaattTATTAATAGTTGTAAaacaggagtt nd [AIBSCS], [CV(GEA)], [GEA] [4]
proximal Fis repressor hlyEp 1230451 1230465 9.0 gaattagatgAAGTAAAATTTATTAatagttgtaa nd [AIBSCS], [CV(GEA)], [GEA] [4]
proximal Fis repressor hlyEp 1230522 1230536 -63.0 attaaacattGTTTGATATTTATCAtattaataga nd [AIBSCS], [CV(GEA)], [GEA] [4]
remote Fis repressor hlyEp 1230569 1230583 -110.0 aatatcacccGGCTAAAAAATAGAAtagaagcatt nd [AIBSCS], [CV(GEA)], [GEA] [4]
remote Fis repressor hlyEp 1230651 1230665 -192.0 tgcataggctGCTGATTTTTCGTTCtcttatcttg nd [AIBSCS], [CV(GEA)], [GEA] [4]
[H-NS,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal H-NS1 activator hlyEp 1230465 1230479 -6.0 gcccggctaaCTATGAATTAGATGAagtaaaattt nd [BPP], [GEA] [3], [5], [6]
proximal H-NS2 activator hlyEp 1230515 1230529 -56.5 attgtttgatATTTATCATATTAATagaaataaag nd [BPP], [GEA] [3], [5], [6]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal H-NS1 repressor hlyEp 1230465 1230479 -6.0 gcccggctaaCTATGAATTAGATGAagtaaaattt nd [BPP], [GEA] [3], [5], [6]
proximal H-NS2 repressor hlyEp 1230515 1230529 -56.5 attgtttgatATTTATCATATTAATagaaataaag nd [BPP], [GEA] [3], [5], [6]
[SlyA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote SlyA activator hlyEp 1230371 1230382 90.5 gactgaaatcGTTGCAGATAAAacggtagaag nd [BPP], [GEA] [6]
remote SlyA activator hlyEp 1230385 1230396 76.5 aggcgaatgaTTATGACTGAAAtcgttgcaga nd [BPP], [GEA] [6]
remote SlyA activator hlyEp 1230400 1230411 61.5 tttatatattTAAAGAGGCGAAtgattatgac nd [BPP], [GEA] [6]
remote SlyA activator hlyEp 1230409 1230420 52.5 tcattacaatTTATATATTTAAagaggcgaat nd [BPP], [GEA] [6]
proximal SlyA5 activator hlyEp 1230505 1230516 -44.5 tatcatattaATAGAAATAAAGacattgacgc nd [BPP], [GEA] [1], [2], [3], [5], [6]
proximal SlyA activator hlyEp 1230516 1230527 -55.5 tgtttgatatTTATCATATTAAtagaaataaa nd [BPP], [GEA] [2], [5], [6]
Note(s): 1During anaerobic growth Fnr is important for hlyE expression. 1Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.
2Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.
1Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.
2Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.
5The almost-to-40-bp size of the footprinting suggests that two dimers of SlyA are binding.
5During anaerobic growth Fnr is important for hlyE expression.
6Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.

7Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.

9The almost-to-40-bp size of the footprinting suggests that two dimers of SlyA are binding.
10Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.
11Hns modulates the hlyE expression both positively and negatively; this protein enhances the CRP-mediated expression of hlyE , but it inhibits the FNR-mediated hlyE expression.


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [BPP] Binding of purified proteins

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [CV(GEA)] cross validation(GEA)


Reference(s)    

 [1] Oscarsson J., Mizunoe Y., Uhlin BE., Haydon DJ., 1996, Induction of haemolytic activity in Escherichia coli by the slyA gene product., Mol Microbiol 20(1):191-9

 [2] Ludwig A., Bauer S., Benz R., Bergmann B., Goebel W., 1999, Analysis of the SlyA-controlled expression, subcellular localization and pore-forming activity of a 34 kDa haemolysin (ClyA) from Escherichia coli K-12., Mol Microbiol 31(2):557-67

 [3] Westermark M., Oscarsson J., Mizunoe Y., Urbonaviciene J., Uhlin BE., 2000, Silencing and activation of ClyA cytotoxin expression in Escherichia coli., J Bacteriol 182(22):6347-57

 [4] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [5] Wyborn NR., Stapleton MR., Norte VA., Roberts RE., Grafton J., Green J., 2004, Regulation of Escherichia coli hemolysin E expression by H-NS and Salmonella SlyA., J Bacteriol 186(6):1620-8

 [6] Lithgow JK., Haider F., Roberts IS., Green J., 2007, Alternate SlyA and H-NS nucleoprotein complexes control hlyE expression in Escherichia coli K-12., Mol Microbiol 66(3):685-98

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