RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: fimAICDFGH
Gene(s): fimA, fimI, fimC, fimD, fimF, fimG, fimH   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of genes for type 1 fimbriae (fimAICDFGH) is subject to a mode of regulatory control known as phase variation Gally DL,1996. In phase variation, individual cells switch between a state of expression (fimbriate) and nonexpression (afimbriate) and thereby produce a population of mixed cell types. Phase variation of type 1 fimbriae in Escherichia coli is influenced by the orientation of the fim switch, fimS, a 314-bp invertible DNA element Abraham JM, Freitag CS, Clements JR, Eisenstein BI,1985. Recombination of the fim switch requires the fimB and fimE gene products, considered to be the fim recombinases Gally DL,1996. Mutation deletion analyses of fimB and fimE mutants indicates that fimB is able to mediate recombination in both directions (on-to-off and off-to-on) while fimE only stimulates recombination in the on-to-off direction McClain MS, Blomfield IC, Eberhardt KJ, Eisenstein BI,1993. Inversions of the fim switch at normal frequencies also requires the expression of himA and himD, which are the genes for the two subunits of integration host factor (IHF) Dorman CJ,1987, lrp, the leucine-responsive regulatory protein Gally DL,1994, and hns, the histone-like protein H1 Kawula TH, Orndorff PE,1991. Lrp recognizes and binds to three DNA-binding sites located within the fim switch, with central positions 204 (site 1), 235 (site 2), and 173 (site 3) bp from the transcriptional start site of the fim operon. The binding of Lrp to site 1 and site 2 favors the inversion process of the invertible region with a bias toward the "on" orientation, but when Lrp binds to site 3, the inversion is inhibited Roesch PL,1998. When leucine binds to Lrp, a dissociation of Lrp from site 3 is observed; thus, the inversion of the invertible DNA element is promoted by leucine Roesch PL,1998. In addition to the role that Lrp plays in the inversion process, it also seems to be required to keep the inversion trapped in the state of expression Kelly A, Conway C, O Cróinín T, Smith SG, Dorman CJ,2006.
By means of gene expression and mutation analysis, it was determined that the LrhA protein regulator regulates positively fimE expression, leading to the repression of the fimA operon through the on-off switch at fimA Blumer C,2005.
The mRNA that contains the fimI gene has been observed mainly in the cellular membrane Kannaiah S, Livny J, Amster-Choder O,2019.
Reference(s): [1] Dove SL., et al., 1997
[2] Schwan WR., et al., 1994
Promoter
Name: fimAp
+1: 4542694
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 421
Sequence: tttaacttattgataataaagttaaaaaaacaaataaatacaagacaattggggccaaacTgtccatatcataaataagtt
Note(s): The fimAp promoter is located in a region that is part of a 314-bp invertible region whose inversion is necessary to activate ("on" orientation) or inactivate (" off" orientation) the transcription of the fimAICDFGH operonAbraham JM, Freitag CS, Clements JR, Eisenstein BI,1985. Olsen PB,1994. The sequence is shown in the off orientation in the database, and therefore the -10 and -35 boxes are located downstream of the transcriptional start site (TSS), and their sequences are shown in the inverted direction Abraham JM, Freitag CS, Clements JR, Eisenstein BI,1985. Olsen PB,1994. When the region is inverted, the boxes are located in the correct position (upstream of the TSS) and correct orientation (-10 box TATGAT, -35 box TTGAGA) to be functional and activate the fim operon Abraham JM, Freitag CS, Clements JR, Eisenstein BI,1985. Olsen PB,1994.
fimA transcription is regulated by the growth phase. and its repression requires the alternative σ factor, RpoS, during entry to stationary phase. Although the mechanism by which RpoS achieves negative control is unknown, it is possible that the effect on fimA is exerted indirectly Dove SL,1997 .
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
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 activator fimAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [13]
[IHF,+] 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
proximal IHF activator fimAp 4542636 4542648 -52.0 aggtttgattTAACTTATTGATAataaagttaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [6], [7], [8]
remote IHF activator fimAp 4542764 4542776 77.0 aaaaagcatcTAACTGTTTGATAtgtaaattat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [6], [7], [8]
[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
remote Lrp activator fimAp 4542859 4542873 173.0 gacgcatcttCCTCATTCTTCTCTCcaaaaaccac nd [EXP-IEP-RNA-SEQ], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9], [10]
remote Lrp activator fimAp 4542890 4542904 204.0 ccacctcatgCAATATAAACATCTAtaaataaaga nd [EXP-IEP-MICROARRAY], [EXP-IEP-RNA-SEQ], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9], [10], [11], [12]
remote Lrp activator fimAp 4542921 4542935 235.0 aagataacaaTAGAATATTAAGCCAacaaataaac nd [EXP-IEP-RNA-SEQ], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9], [10], [12]
[QseB,+] 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 QseB-Phosphorylated activator fimAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [14]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.8 4545001 4545046 gcgcacttacCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCgcctgaataa
  anti-terminator -5.9 4544998 4545021 atggcgcactTACCCCCAAAATGACGGGCGTAAtggaataacg
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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-CHIP] high throughput ChIP-chip evidence


Reference(s)    

 [1] Dove SL., Smith SG., Dorman CJ., 1997, Control of Escherichia coli type 1 fimbrial gene expression in stationary phase: a negative role for RpoS., Mol Gen Genet 254(1):13-20

 [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] Blomfield IC., Kulasekara DH., Eisenstein BI., 1997, Integration host factor stimulates both FimB- and FimE-mediated site-specific DNA inversion that controls phase variation of type 1 fimbriae expression in Escherichia coli., Mol Microbiol 23(4):705-17

 [6] Dorman CJ., Higgins CF., 1987, Fimbrial phase variation in Escherichia coli: dependence on integration host factor and homologies with other site-specific recombinases., J Bacteriol 169(8):3840-3

 [7] Dove SL., Dorman CJ., 1996, Multicopy fimB gene expression in Escherichia coli: binding to inverted repeats in vivo, effect on fimA gene transcription and DNA inversion., Mol Microbiol 21(6):1161-73

 [8] Kulasekara HD., Blomfield IC., 1999, The molecular basis for the specificity of fimE in the phase variation of type 1 fimbriae of Escherichia coli K-12., Mol Microbiol 31(4):1171-81

 [9] Kroner GM., Wolfe MB., Freddolino PL., 2019, Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes., J Bacteriol 201(3)

 [10] 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

 [11] Cho BK., Barrett CL., Knight EM., Park YS., Palsson BO., 2008, Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli., Proc Natl Acad Sci U S A 105(49):19462-7

 [12] 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

 [13] Schembri MA., Olsen PB., Klemm P., 1998, Orientation-dependent enhancement by H-NS of the activity of the type 1 fimbrial phase switch promoter in Escherichia coli., Mol Gen Genet 259(3):336-44

 [14] Gou Y., Liu W., Wang JJ., Tan L., Hong B., Guo L., Liu H., Pan Y., Zhao Y., 2019, CRISPR-Cas9 knockout of qseB induced asynchrony between motility and biofilm formation in Escherichia coli., Can J Microbiol 65(9):691-702

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