RegulonDB RegulonDB 10.10: 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. Bartoli J,2020. 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 Navarre WW, Halsey TA, Walthers D, Frye J, McClelland M, Potter JL, Kenney LJ, Gunn JS, Fang FC, Libby SJ,2005. Shi Y, Latifi T, Cromie MJ, Groisman EA,2004.
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:
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-cyclic-AMP activator hlyEp 1230517 1230538 -61.5 acattaaacaTTGTTTGATATTTATCATATTAatagaaataa nd [GEA], [BPP], [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 FNR activator hlyEp 1230521 1230534 -61.5 taaacattgtTTGATATTTATCATattaatagaa nd [GEA], [BPP] [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 [GEA], [AIBSCS] [4]
proximal Fis repressor hlyEp 1230451 1230465 9.0 gaattagatgAAGTAAAATTTATTAatagttgtaa nd [GEA], [AIBSCS] [4]
proximal Fis repressor hlyEp 1230522 1230536 -63.0 attaaacattGTTTGATATTTATCAtattaataga nd [GEA], [AIBSCS] [4]
remote Fis repressor hlyEp 1230569 1230583 -110.0 aatatcacccGGCTAAAAAATAGAAtagaagcatt nd [GEA], [AIBSCS] [4]
remote Fis repressor hlyEp 1230651 1230665 -192.0 tgcataggctGCTGATTTTTCGTTCtcttatcttg nd [GEA], [AIBSCS] [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-NS activator hlyEp 1230465 1230479 -6.0 gcccggctaaCTATGAATTAGATGAagtaaaattt nd [GEA], [BPP] [3], [5], [6]
proximal H-NS activator hlyEp 1230515 1230529 -56.5 attgtttgatATTTATCATATTAATagaaataaag nd [GEA], [BPP] [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-NS repressor hlyEp 1230465 1230479 -6.0 gcccggctaaCTATGAATTAGATGAagtaaaattt nd [GEA], [BPP] [3], [5], [6]
proximal H-NS repressor hlyEp 1230515 1230529 -56.5 attgtttgatATTTATCATATTAATagaaataaag nd [GEA], [BPP] [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 1230376 1230377 90.5 aaatcgttgcAgataaaacgg nd [GEA], [BPP] [6], [7]
remote SlyA activator hlyEp 1230390 1230391 76.5 aatgattatgActgaaatcgt nd [GEA], [BPP] [6], [7]
remote SlyA activator hlyEp 1230405 1230406 61.5 atatttaaagAggcgaatgat nd [GEA], [BPP] [6], [7]
remote SlyA activator hlyEp 1230414 1230415 52.5 acaatttataTatttaaagag nd [GEA], [BPP] [6], [7]
proximal SlyA activator hlyEp 1230510 1230511 -44.5 tattaatagaAataaagacat nd [GEA], [BPP] [1], [2], [3], [5], [6], [7]
proximal SlyA activator hlyEp 1230521 1230522 -55.5 gatatttatcAtattaataga nd [GEA], [BPP] [2], [5], [6], [7]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp activation hlyEp nd   [GEA] [7]
Evidence: [GEA] Gene expression analysis
Reference(s): [7] Bartoli J., et al., 2020


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences


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

 [7] Bartoli J., Viala JP., Bouveret E., 2020, SlyA Transcriptional Regulator Is Not Directly Affected by ppGpp Levels., Front Microbiol 11:1856

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