RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: fimE
Gene(s): fimE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Schwan WR., et al., 1992
[2] Schwan WR., et al., 1994
Promoter
Name: fimEp
+1: 4541871
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 166
Sequence: actggaagttaatccactgcaatctattgttatattgaatcaaatcaatgaaaatagatgTtgtcacatcagtgatatttt
                           -35                    -10       +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Olsen PB., et al., 1994
Terminator(s)
Type: rho-dependent
Sequence: tgtggctcgaCGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCtataaataaa
Reference(s): [5] Hinde P., et al., 2005
TF binding sites (TFBSs)
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor fimEp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [9]
[LrhA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd LrhA activator fimEp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[Lrp,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Lrp activator fimEp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7], [8]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -14.6 4541922 4541958 taattgactgATAGCCACATCACTCCGTGTGTGGTTATCTTTTTATctattgggct
  anti-terminator -11.9 4541867 4541933 atgaaaatagATGTTGTCACATCAGTGATATTTTATTTTTGTATGATATTTAATGTAATTGACTGATAGCCACATCactccgtgtg
  anti-anti-terminator -10.1 4541860 4541897 caaatcaatgAAAATAGATGTTGTCACATCAGTGATATTTTATTTTTgtatgatatt
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Schwan WR., Seifert HS., Duncan JL., 1992, Growth conditions mediate differential transcription of fim genes involved in phase variation of type 1 pili., J Bacteriol 174(7):2367-75

 [2] Schwan WR., Seifert HS., Duncan JL., 1994, Analysis of the fimB promoter region involved in type 1 pilus phase variation in Escherichia coli., Mol Gen Genet 242(5):623-30

 [3] 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

 [4] Olsen PB., Klemm P., 1994, Localization of promoters in the fim gene cluster and the effect of H-NS on the transcription of fimB and fimE., FEMS Microbiol Lett 116(1):95-100

 [5] Hinde P., Deighan P., Dorman CJ., 2005, Characterization of the detachable Rho-dependent transcription terminator of the fimE gene in Escherichia coli K-12., J Bacteriol 187(24):8256-66

 [6] Blumer C., Kleefeld A., Lehnen D., Heintz M., Dobrindt U., Nagy G., Michaelis K., Emody L., Polen T., Rachel R., Wendisch VF., Unden G., 2005, Regulation of type 1 fimbriae synthesis and biofilm formation by the transcriptional regulator LrhA of Escherichia coli., Microbiology 151(Pt 10):3287-98

 [7] Gally DL., Rucker TJ., Blomfield IC., 1994, The leucine-responsive regulatory protein binds to the fim switch to control phase variation of type 1 fimbrial expression in Escherichia coli K-12., J Bacteriol 176(18):5665-72

 [8] Roesch PL., Blomfield IC., 1998, Leucine alters the interaction of the leucine-responsive regulatory protein (Lrp) with the fim switch to stimulate site-specific recombination in Escherichia coli., Mol Microbiol 27(4):751-61

 [9] Olsen PB., Schembri MA., Gally DL., Klemm P., 1998, Differential temperature modulation by H-NS of the fimB and fimE recombinase genes which control the orientation of the type 1 fimbrial phase switch., FEMS Microbiol Lett 162(1):17-23

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