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| Operon |  |
|---|---|
| Name: | fimAICDFGH |
| This page displays every known transcription unit of this operon and their known regulation. | |
| 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 2863818 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 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) Dorman CJ,1987 lrp, the leucine-responsive regulatory protein Gally DL,1994 and hns, the histone-like protein H1 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 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 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 Blumer C,2005|. The mRNA that contains the fimI gene has been observed mainly in the cellular membrane 31540875. |
| 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 operon2863818. 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 2863818. 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 2863818. 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 |
| 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 | [APIORCISFBSCS], [CV(GEA)], [GEA] | [4], [5], [6], [7] |
| remote | IHF2 | activator | fimAp | 4542764 | 4542776 | 77.0 | aaaaagcatcTAACTGTTTGATAtgtaaattat | nd | [APIORCISFBSCS], [CV(GEA)], [GEA] | [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], [CV(SM)], [SM] | [8] |
| remote | Lrp2 | activator | fimAp | 4542890 | 4542904 | 204.0 | ccacctcatgCAATATAAACATCTAtaaataaaga | nd | [APIORCISFBSCS], [BPP], [CV(SM)], [SM] | [8], [9] |
| remote | Lrp3 | activator | fimAp | 4542921 | 4542935 | 235.0 | aagataacaaTAGAATATTAAGCCAacaaataaac | nd | [APIORCISFBSCS], [BPP], [CV(SM)], [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 16855224 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 16855224 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 16855224 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 16855224 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] | [12] [13] |
||||
| omrA | antisense | post-transcriptional regulation | repressor | [IMP] | [12] [13] |
||||
| 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 |
| 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) |
|
|---|---|
[HIPP] Human inference of promoter position