RegulonDB RegulonDB 10.6.3: 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 |CITS:[8878036]|. 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 |CITS:[2863818]|. Recombination of the fim switch requires the fimB and fimE gene products, considered to be the fim recombinases |CITS:[8878036]|. 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 |CITS:[8101185]|. 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) |CITS:[2886490]|, lrp, the leucine-responsive regulatory protein |CITS:[7916011]|, and hns, the histone-like protein H1 |CITS:[1648076]|. 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 |CITS:[9515701]|. 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 |CITS:[9515701]|. 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 |CITS: [16855224]|.
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 |CITS: [16207912]|.
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: [HIPP]
[TIM]
Reference(s): [3] Olsen PB., et al., 1994
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS activator fimAp nd nd nd nd nd [BPP], [GEA] [10]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 activator fimAp 4542636 4542648 -52.0 aggtttgattTAACTTATTGATAataaagttaa nd [GEA], [HIBSCS] [4], [5], [6], [7]
remote IHF2 activator fimAp 4542764 4542776 77.0 aaaaagcatcTAACTGTTTGATAtgtaaattat nd [GEA], [HIBSCS] [4], [5], [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Lrp1 activator fimAp 4542859 4542873 173.0 gacgcatcttCCTCATTCTTCTCTCcaaaaaccac nd [BPP], [SM] [8]
remote Lrp2 activator fimAp 4542890 4542904 204.0 ccacctcatgCAATATAAACATCTAtaaataaaga nd [BPP], [HIBSCS], [SM] [8], [9]
remote Lrp3 activator fimAp 4542921 4542935 235.0 aagataacaaTAGAATATTAAGCCAacaaataaac nd [BPP], [HIBSCS], [SM] [8], [9]
Note(s): 1IHF plays a dual role in controlling fimA expression: it is required both for inversion of the fimA control region and for efficient expression from the fimA promoter.
This transcription factor-binding site (TFBS) for IHF is very close to a 314-bp invertible region whose inversion is necessary to activate ("on" orientation) or to inactivate ("off" orientation) the fimA promoter Blomfield IC,1997 The sequence in the database is shown in the off orientation, in which this TFBS is located at bp -52 from the transcriptional start site (TSS). When the region is inverted to the on orientation, this TFBS is moved to the correct position (-341 bp from the TSS) to be functional and activate fimA promoter Blomfield IC,1997. Dorman CJ,1987

2IHF plays a dual role in controlling fimA expression: it is required both for inversion of the fimA control region and for efficient expression from the fimA promoter.

The transcription factor-binding site (TFBS) for IHF is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate ("on" orientation) or to inactivate ("off" orientation) the fimA promoter Blomfield IC,1997 The sequence in the database is that of the off orientation, and thus the TFBS is located downstream of the transcriptional start site (TSS), at position +77, and its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (bp -76 from the TSS) and correct orientation (TATCAAACAGTTA) to be functional for activation of the fimA promoter Blomfield IC,1997. Dorman CJ,1987

1This transcription factor-binding site (TFBS) called site 3 for Lrp is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate (on orientation) or to inactivate ("off" orientation) the fimA promoter. The sequence of site 3 in the database is shown in the off orientation. It is located downstream of the transcriptional start site (TSS) at position +173, and its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (-174 from the TSS) and correct orientation (GAGAGAAGAATGAGG). In the presence of leucine, the recombination that causes sequence inversion is stimulated by disruption of the binding of Lrp to this TFBS (site 3)Roesch PL,1998
2This transcription factor-binding site (TFBS) called site 1 for Lrp is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate (on orientation) or to inactivate ("off" orientation) the fimA promoter Gally DL,1994 Lrp binding to site 1 and site 2 is required to bias inversion to the on orientation of the invertible region Kelly A, Conway C, O Cróinín T, Smith SG, Dorman CJ,2006 The sequence of site 1 in the database is shown in the off orientation, and therefore it is located downstream of the transcriptional start site (TSS) at position +204, and its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (bp -203 from the TSS) and correct orientation (TAGATGTTTATATTG) Gally DL,1994
3The transcription factor-binding site (TFBS) for Lrp, called site 2, is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate (" on" orientation) or to inactivate ("off" orientation) the fimA promoter Gally DL,1994 Lrp binding to site 1 and site 2 is required to bias inversion to the on orientation of the invertible region Kelly A, Conway C, O Cróinín T, Smith SG, Dorman CJ,2006 The sequence of site 2 in the database is shown in the off orientation, and therefore it is located downstream of the transcriptional start site (TSS) at the bp +235 position; its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (-234 from the TSS) and correct orientation (TGGCTTAATATTCTA) Gally DL,19941IHF plays a dual role in controlling fimA expression: it is required both for inversion of the fimA control region and for efficient expression from the fimA promoter.
This transcription factor-binding site (TFBS) for IHF is very close to a 314-bp invertible region whose inversion is necessary to activate ("on" orientation) or to inactivate ("off" orientation) the fimA promoter Blomfield IC,1997 The sequence in the database is shown in the off orientation, in which this TFBS is located at bp -52 from the transcriptional start site (TSS). When the region is inverted to the on orientation, this TFBS is moved to the correct position (-341 bp from the TSS) to be functional and activate fimA promoter Blomfield IC,1997. Dorman CJ,1987

2IHF plays a dual role in controlling fimA expression: it is required both for inversion of the fimA control region and for efficient expression from the fimA promoter.

The transcription factor-binding site (TFBS) for IHF is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate ("on" orientation) or to inactivate ("off" orientation) the fimA promoter Blomfield IC,1997 The sequence in the database is that of the off orientation, and thus the TFBS is located downstream of the transcriptional start site (TSS), at position +77, and its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (bp -76 from the TSS) and correct orientation (TATCAAACAGTTA) to be functional for activation of the fimA promoter Blomfield IC,1997. Dorman CJ,1987


3This transcription factor-binding site (TFBS) called site 3 for Lrp is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate (on orientation) or to inactivate ("off" orientation) the fimA promoter. The sequence of site 3 in the database is shown in the off orientation. It is located downstream of the transcriptional start site (TSS) at position +173, and its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (-174 from the TSS) and correct orientation (GAGAGAAGAATGAGG). In the presence of leucine, the recombination that causes sequence inversion is stimulated by disruption of the binding of Lrp to this TFBS (site 3)Roesch PL,1998
4This transcription factor-binding site (TFBS) called site 1 for Lrp is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate (on orientation) or to inactivate ("off" orientation) the fimA promoter Gally DL,1994 Lrp binding to site 1 and site 2 is required to bias inversion to the on orientation of the invertible region Kelly A, Conway C, O Cróinín T, Smith SG, Dorman CJ,2006 The sequence of site 1 in the database is shown in the off orientation, and therefore it is located downstream of the transcriptional start site (TSS) at position +204, and its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (bp -203 from the TSS) and correct orientation (TAGATGTTTATATTG) Gally DL,1994
5The transcription factor-binding site (TFBS) for Lrp, called site 2, is in a region that is part of a 314-bp invertible region whose inversion is necessary to activate (" on" orientation) or to inactivate ("off" orientation) the fimA promoter Gally DL,1994 Lrp binding to site 1 and site 2 is required to bias inversion to the on orientation of the invertible region Kelly A, Conway C, O Cróinín T, Smith SG, Dorman CJ,2006 The sequence of site 2 in the database is shown in the off orientation, and therefore it is located downstream of the transcriptional start site (TSS) at the bp +235 position; its sequence is shown in the inverted direction. When the region is inverted, this TFBS is located in the correct position (-234 from the TSS) and correct orientation (TGGCTTAATATTCTA) Gally DL,1994


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  omrB antisense post-transcriptional regulation repressor       [IMP] [11]
[12]
  omrA antisense post-transcriptional regulation repressor       [IMP] [11]
[12]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [13] null null
  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"




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] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [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] 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

 [10] 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

 [11] Guillier M., Gottesman S., 2006, Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs., Mol Microbiol 59(1):231-47

 [12] Guillier M., Gottesman S., 2008, The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator., Nucleic Acids Res 36(21):6781-94

 [13] null, null, null, null


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