Team:Tokyo Tech/Experiment/Overview of fim inversion system
Overview of fim inversion system
contents
1. Introduction
2. How does fim switch works
2.1. The fim switch(wild-type)
2.2. The fim switch(Tokyo_Tech)
2.2.1. Results of the FimB/FimE assay on the fim switch(Tokyo_Tech)
3. Comparison of other teams’ fim related parts
3.1. FimB(2013_Toronto)
3.2. fim switch(2006_Caltech)-fimE(2006_Caltech)
3.3. fim switch(2013_Michigan)-fimE(2006_Caltech)-hbiF(2012_Michigan)
4. Reference
1. Introduction
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FimB inverts the fim switch in [ON] state to [OFF] state and in [OFF] state to [ON] state with approximately equal probability. FimB enable prisoner coli to select its option (cooperation or defection) randomly (Fig.3-3-1-1.). We showed bidirectional inversion of fim switch by FimB. This is the first case in iGEM to show random inversion of a promoter. |
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Fig.3-3-1-1.In the presence of FimB, promoter in fim switch can be inverted at random. | ||
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On the other hand, FimE inverts the fim switch predominantly in the [ON] state to [OFF] state (McClain, 1991). For implementation of tit-for-tat strategy, the most successful strategy for Prisoner’s Dilemma, we used the FimE (Fig. 3-3-1-2.). |
Fig.3-3-1-2.Prisoner A with tit-for-tat strategy |
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Our biggest achievement is that we have established a tripartite relationship between the three fim related parts, fim switch and FimB/FimE (Fig. 3-3-1-3). |
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Fig.3-3-1-3.Overview of the fim related parts in iGEM |
2. How does fim switch works
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In the wild-type of E.coli K-12, two fim proteins invert the fim switch, which is a specific 314 bp DNA sequence containing a promoter, to modulate its own expressions (Abraham, 1985). The fim switch has two states, ON and OFF. The promoter in the fim switch directs transcription to the right when the fim switch is in [ON] state. In [OFF] state of the fim switch, on the other hand, the promoter directs transcription to the left. |
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Fig.3-3-2-1.The relationship between the fim related genes. |
The fim switch is inverted by two recombinases, FimB(wild-type) (BBa_K1632010) and FimE(wild-type) (BBa_K1632011). These proteins have distinct activities. FimB inverts the fim switch in [ON] state to [OFF] state direction and in [OFF] state to [ON] state direction with approximately equal probability. On the other hand, FimE inverts the fim switch predominantly in [ON] state to [OFF] state direction (McClain, 1991).
We designed two fim switches: the fim switch(wild-type) and the fim switch(Tokyo_Tech) which promoter can be exchanged with an arbitrary promoter.
In the first fim switch, the fim switch(wild-type), the sequence is derived from that of a wild-type. The fim switch(wild-type) we constructed are named fim switch[default ON](wild-type) (BBa_K1632004) and fim switch[default OFF](wild-type) (BBa_K1632005). In the second fim switch, the fim switch(Tokyo_Tech), the promoter of the fim switch(wild-type) is replaced with J23119 promoter(BBa_J23119) and two restriction enzyme cut sites are added in each side of the promoter. Due to this addition of the restriction enzyme cut sites, we were able to replace the J23119 promoter in the fim swtich(Tokyo_Tech). For example, we replaced J23119 promoter with Lac promoter (BBa_K1632006). The fim switch(Tokyo_Tech) we constructed are named fim switch[default ON](Tokyo_Tech/J23119) (BBa_K1632000), fim switch[default OFF](Tokyo_Tech/J23119) (BBa_K1632000), and fim switch[default ON](Tokyo_Tech/B0010) (BBa_K1632006).
2.1 The fim switch(wild-type)
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Fig. 3-3-2-2. The overview of the fim switch(wild-type) |
We designed the fim switch(wild-type). The sequence of our fim switch(wild-type) is derived from that of a wild-type. The fim switch(wild-type) has a sigma 70 promoter which functions constitutively. We submitted two parts, one in the [ON] state (BBa_K1632004) and the other in [OFF] state (BBa_K1632005).
We confirmed the inversion of our fim switch(wild-type) by FimB and by FimE. Considering the experimental results, fimB(wild-type) inverts the fim switch(wild-type) in both [ON] state to [OFF] state and [OFF] state to [ON] state with approximately equal probability. Similarly FimE(wild-type) inverts the fim switch(wild-type) predominantly in [ON] state to [OFF] state. In order to confirm inversion more precisely, we also show the percentage of [ON] state with induction by arabinose and without induction. Also we show inversion in the level of DNA sequencing.
In summary, establishing a tripartite relationship between the fim switch and FimB/FimE is an unprecedented achievement in iGEM.
2.1.1. Result of the FimB/FimE assay on the fim switch(wild-type)
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Fig.3-3-2-3. New plasmids we constructed to confirm the function of fim switch |
The fim switch is inverted by two recombinases, FimB(wild-type) (BBa_K1632010) and FimE(wild-type) (BBa_K1632011). These proteins have distinct activities. FimB inverts the fim switch in both [ON] state to [OFF] state and [OFF] state to [ON] state direction with approximately equal probability. On the other hand, FimE inverts the fim switch predominantly in [ON] state to [OFF] state (McClain, 1991).
In order to assay the function of FimB(wild-type) and FimE(wild-type) for fim switch(wild-type), we added a GFP coding sequence on the downstream of the fim switch.The fim switch[default ON](wild-type)_gfp (BBa_K1632007) emitts fluorescence when expressed, while the fim switch [default OFF](wild-type)_gfp(BBa_K1632008) does not emit florescence when expressed. We also added pBAD/araC (BBa_I0500) on the upstream of both fimB(wild-type) and fimE(wild-type). pBAD/araC_fimB(wild-type) (BBa_K1632012) and pBAD/araC_fimE(BBa_K1632013) can induce the expression of FimB(wild-type) or FimE(wild-type) in the presence of arabinose. We co-transformed a fim switch_gfp and a pBAD/araC_fimB or _fimE in the E. coli DH5alpha strain(Fig. 3-3-2-3.). We measured the fluorescence intensity of the cells induced by different concentraions of arabinose. From the experimental results(Fig. 3-3-2-4), FimB(wild-type) inverted the fim switch[default ON](wild-type) from [ON] state to [OFF] state and the fim switch[defult OFF](wild-type) from [OFF] state to [ON] state, depending on the concentration of arabinose. FimE(wild-type) inverted the fim switch[default ON](wild-type) from [ON] state to [OFF] state but did not invert the fim switch[default OFF](wild-type) from [OFF] state to [ON] state, depending on the concentration of arabinose.
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Fig.3-3-2-4. The intensity of fluroscence in cells measured using flowcytometer. |
2.1.1.1 FimB dependent fim switch(wild-type) state assay
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We newly constructed plasmid, PBAD/araC_fimB(wild-type) (BBa_K1632012) that produces FimB(wild-type). We also prepared two other new plasmids, (BBa_K1632007 and (BBa_K1632008(Fig. 3-5-1-2). (BBa_K1632012 enables arabinose-inducible expression of FimB(wild-type). In both [ON] state and [OFF] state, fim switch(wild-type) is placed upstream of GFP coding sequence. |
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Fig.3-3-2-5.New plasmids we constructed to confirm the function of fim switch. | ||
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First, we measured the fluorescence intensity from the GFP expression in the presence of arabinose. From the results (Fig. 3-3-2-6.), we confirmed that the fim switch (wild-type) is inverted from both [ON] state to [OFF] state and [OFF] state to [ON] state. | |
Fig. 3-3-2-6.The intensity of fluroscence in cells measured using flowcytometer | ||
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First, we measured the fluorescence intensity from the GFP expression in the presence of arabinose. From the results (Fig. 3-3-2-6.), we confirmed that the fim switch (wild-type) is inverted from both [ON] state to [OFF] state and [OFF] state to [ON] state. Next, in order to confirm inversion more precisely, we also show the percentage of ON state (Fig. 3-3-2-7) and inversion in the level of DNA sequencing (Fig. 3-3-2-8). Fig.3-3-2-7 and Fig.3-3-2-8 clearly shows inversion from both [ON] state to [OFF] state and [OFF] state to [ON] state. E. coli harboring the [ON] fim switch plasmid glows in green fluorescence while E. coli harboring the [OFF] fim switch plasmid does not glow under ultra violet light. Cells transformed by the plasmid mixture extracted from the experiment formed two types of colonies: those with strong fluorescence and those with little background fluorescence. Also, sequence complementarity in the specific region of the fim switch(wild-type) shows intended inversion of the fim switch from [ON] state to [OFF] state. Furthermore, the nearly equal number of the colonies between fluorescent and non-fluorescent suggest random inversion of the fim switch by FimB expression. |
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Fig. 3-3-2-7. Determination of percetage of ON state and colony formation using plasmid mixture extracted cell expressing FimB. |
Fig. 3-3-2-8. DNA sequencing results of fim switch from [ON] state to [OFF] state | |
For more information, see experiment page.
2.1.1.2 FimE dependent fim switch(wild-type) state assay
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To confirm the function of fim switch(wild-type) in the presence of FimE(wild-type), we constructed Biobrick parts, (BBa_K1632013 as Fig. 3-3-2-9. (BBa_K1632013 enables arabinose-inducible expression of the FimE (wild-type). In (BBa_K1632007 and (BBa_K1632008, either the fim switch [default ON] or the fim switch [default OFF] is placed upstream of the GFP coding sequence. |
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Fig.3-3-2-9.New plasmids we constructed to confirm the function of fim switch. | ||
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Our purpose is to confirm that FimE (wild-type) inverts the fim switch (wild-type) from [ON] state to [OFF] state predominantly. First of all, we measured the fluorescence intensity from the GFP expression in the presence of arabinose. From the results (Fig. 3-3-2-10), we confirmed that our fim switch(wild-type) is inverted from [ON] state to [OFF] state predominatly. | |
Fig. 3-3-2-10.The intensity of fluroscence in cells measured using flowcytometer | ||
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Next, in order to confirm inversion more precisely, we also show the percentage of ON state (Fig. 3-3-2-11) and inversion in the level of DNA sequencing (Fig. 3-3-2-12). Fig. 3-3-2-11 shows inversion from [ON] state to [OFF] state predominantly. E. coli harboring the [ON] fim switch(wild-type) plasmid glows in green fluorescence while E. coli harboring the [OFF] fim switch(wild-type) plasmid does not glow under ultra violet light. Cells transformed by the plasmid mixture extracted from the experiment formed two types of colonies: those with strong fluorescence and those with little background fluorescence. Also, sequence complementarity in the specific region of the switch shows intended inversion of the fim switch(wild-type) from [ON] state to [OFF] state. Considering the percentage of [ON] state, FimE(wild-type) inverts the fim switch predominantly in [ON] state to [OFF] state.
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Fig. 3-3-2-11. Determination of percetage of ON state and colony formation using plasmid mixture extracted cell expressing FimE. |
Fig. 3-3-2-12. DNA sequencing results of fim switch. | |
For more information, see experiment page.
2.2. The fim switch(Tokyo_Tech)
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Fig. 3-3-2-13. The overview of fim switch(Tokyo_Tech) |
We designed a fim switch, which promoter can be exchanged with an arbitrary promoter, the fim switch(Tokyo_Tech) (Fig. 3-3-2-13).
We could not confirm the inversion of the fim switch(Tokyo_Tech) by FimE(wild-type). From the experimental results, FimB(wild-type) inverts the fim switch in both [ON] state to [OFF] state and [OFF] state to [ON] state as expected. However, FimE(wild-type) unexpectedly did not invert the fim switch(Tokyo_Tech) predominantly in [ON] state to [OFF] state. Instead, FimE(wild-type) inverted the fim switch(Tokyo_Tech) in both [ON] state to [OFF] state and in [OFF] state to [ON] state. In other words, FimE(wild-type) worked in the same way as FimB(wild-type).
Basically, the design of the fim switch(Tokyo_Tech) is similar to the fim switch(wild-type). The only difference is that we inserted restriction cut enzyme sites to fim switch(Tokyo_Tech). In detail, in fim switch(Tokyo_Tech), the sigma 70 promoter is exchanged to the J23119 promoter(BBa_J23119) and there are two restriction enzyme cut sites inserted each in the front (SalI and BamHI) and in the back (BglII and MluI) of the promoter. Due to the insertion of the restriction enzyme cut sites, fim switch(Tokyo_Tech) has a promoter which can we exchanged with an arbitrary promoter. We actually changed J23119 promoter in the fim switch(Tokyo_Tech) to Lac promoter(BBa_K1632006) as shown in the Fig. 3-3-2-14.
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Fig. 3-3-2-14. The flow of changing the promoter in fim switch(Tokyo_Tech) |
2.2.1. Results of the FimB/FimE assay on the fim switch(Tokyo_Tech)
As with assays of fim swtich(wild-type), in order to assay the function of FimB(wild-type) and FimE(wild-type) for fim switch(Tokyo_Tech), we added a GFP coding sequence on the downstream of the fim switch(Tokyo_Tech). The fim switch[default ON](Tokyo_Tech/J23119)_gfp (BBa_K1632003) emitts fluorescence when expressed, while the fim switch [default OFF](Tokyo_Tech/J23119)_gfp(BBa_K1632004) does not emit florescence when expressed. We also added pBAD/araC(BBa_I0500) on the upstream of both FimB(wild-type) and FimE(wild-type). pBAD/araC_fimB (BBa_K1632012) and pBAD/araC_fimE(BBa_K1632013) can induce the expression of FimB(wild-type) or FimE(wild-type) in the presence of arabinose. We co-transformed a fim switch(Tokyo_Tech)_gfp and a pBAD/araC_fimB or _fimE in the E. coli DH5alpha strain. We measured the fluorescence intensity of the cells induced by different concentraions of arabinose. We could not confirm the inversion of the fim switch(Tokyo_Tech) by FimE(wild-type). From the experimental results, FimB(wild-type) inverts the fim switch(Tokyo_Tech) in both [ON] state to [OFF] state and [OFF] state to [ON] state as expected. However, FimE(wild-type) unexpectedly did not invert the fim switch(Tokyo_Tech) predominantly in [ON] state to [OFF] state. Instead, FimE(wild-type) inverted the fim switch(Tokyo_Tech) in both [ON] state to [OFF] state and [OFF] state to [ON] state. In other words, FimE(wild-type) worked in the same way as FimB(wild-type).
For more information, see the parts registry page(FimB_dependent_fim_switch_state_assay).
3. Comparison other team’s fim switch
Our biggest achievement is that we have established a tripartite relationship between the three fim related parts, the fim switch and FimB/FimE.
In this chapter, the novelty of constructing and assaying all three fim related parts (the fim switch, FimB, and FimE) is shown by comparison to the past iGEM teams’ fim related parts. Some teams have submitted fim related parts. However the information of the fim related parts are so complicated that we felt that it is necessary to clarify the situation.
These submitted parts which show some data, are divided into three groups as shown in the figure below (Fig. 3-3-3-1.)
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Fig. 3-3-3-1. All past iGEM teams’ fim related parts. |
From the results of each group, we evaluated each group’s data as shown below.
From these evaluations, we concluded that our establishment of a tripartite relationship between the fim switch and FimB/FimE, is an unprecedented achievement in iGEM.
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Fig. 3-3-3-2. Summary of the fim related parts in iGEM. |
3.1. fimB (2013 Toronto) : No data about inversion
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Fig. 3-3-3-3. Overview of the fim related parts in iGEM. |
FimB
| Gene Name | Year | College | Parts Number | Sequence Confirmation |
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| FimB | 2013 | Toronto | BBa_K1019000 | None |
Fig. 3-3-3-4. Lists of submitted fim parts.
2013_Toronto submitted fimB (BBa_K1019000) and showed some data. However, their data clearly did not relate to the inversion of fim switch. Their experimental result is to search the difference of certain parameters like OD600, in the condition of FimB (+) and FimB (-). Therefore, it can be concluded that the results of 2013_Toronto did not show any data referring to the inversion of the fim switch.
For detailed information, see Team:Toronto
3.2. fim switch(2008_Caltech)-fimE(2008_Caltech) : No data about inversion
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Fig. 3-3-3-5. Overview of the fim related parts in iGEM. |
FimE
| Gene Name | Year | College | Parts Number | Sequence Confirmation |
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| FimE | 2008 | Caltech | BBa_K137007 | None |
fim switch
Gene Name |
Year | College | Parts Number | Sequence Confirmation |
|---|---|---|---|---|
| FimE IRR | 2008 | Caltech | BBa_K137008 | None |
| FimE IRL | 2008 | Caltech | BBa_K137010 | None |
| GFP fimE switch with 150 bp tetR promoter | 2008 | Caltech | BBa_K137057 | None |
| GFP fimE switch with 250 bp tetR promoter | 2008 | Caltech | BBa_K137058 | None |
| GFP fimE switch with 350 bp tetR promoter | 2008 | Caltech | BBa_K137059 | None |
| GFP fimE switch with 450 bp tetR promoter | 2008 | Caltech | BBa_K137060 | None |
| GFP fimE switch with 550 bp tetR promoter | 2008 | Caltech | BBa_K137061 | None |
| GFP fimE switch with 650 bp tetR promoter | 2008 | Caltech | BBa_K137062 | None |
Fig.3-3-3-6.Lists of submitted fim parts.
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Fig. 3-3-3-7. The experimental result of 2008_Caltech |
2008_Caltech only submitted fimE (BBa_K137007) and showed data about inversion (Fig. 3-3-3-7.). 2008_Caltech wanted to determine the range of length in which fimE (BBa_K137007) will function and to determine how the length affects the activities of FimE. Thus they tested how the length of the recombination site affects FimE’s ability to detect the two flanking binding sites. Therefore, GFP fluorescence / OD600 was observed in each sample in which the length of the inversion site differs.
However their data cannot be trusted completely with respect to inversion of fim switch. There are several reasons. First of all, they did not set Positive controls and Negative controls. Because of the lack of controls, we cannot confirm that FimE inverts the fim switch in [ON] state to [OFF] state predominantly. Secondly, they didn’t write down the information of plasmids used in the experiments. The nucleotide sequence of 2008_Caltech’s fimE (BBa_K137007) and FimE(wild type) which was obtained from Ecogene did not match. Therefore, we designed FimE(wild-type) (BBa_K1632010) ) whose nucleotide sequence completely matchs that of the wild type’s fimE. Comparing these two parts, two differences were confirmed. First, FimE of 2008_Caltech lacks the nucleotide sequence of N-terminal 15 residues. Second, FimE of 2008_Caltech differs from the nucleotide sequence of FimE(wild-type) by C-terminal 2 residues as shown in Fig. 3-3-3-8.
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Fig. 3-3-3-8. The difference of nucleotide sequence between BBa_K137007) and BBa_K1632011) . |
For detailed information, see 2008_Caltech wiki)
3.3. fim switch(2013_Michigan)-fimE(2008_Caltech)-hbiF(2012_Michigan) : Not enough data about inversion
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Fig. 3-3-3-9. Overview of the fim related parts in iGEM. |
FimE
| Gene Name | Year | College | Parts Number | Sequence Confirmation |
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| FimE | 2008 | Caltech | BBa_K137007 | None |
HbiF
| Gene Name | Year | College | Parts Number | Sequence Confirmation |
|---|---|---|---|---|
| HbiF | 2012 | Michigan | BBa_K88000 | None |
fim switch
| Gene Name | Year | College | Parts Number | Sequence Confirmation |
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| fim switch inverted repeat left IRL natural | 2012 | Michigan | BBa_K1077000 | Inconsistent |
| fim switch inverted repeat left IRR natural | 2012 | Michigan | BBa_K1077001 | Inconsistent |
| J23100 fim switch b0034 GFP | 2012 | Michigan | BBa_K1077003 | Inconsistent |
| J23100 fim switch b0034 GFP | 2012 | Michigan | BBa_K1077005 | Inconsistent |
| J23100 fim switch b0034 amilCP ON orientation | 2012 | Michigan | BBa_K1077007 | Inconsistent |
Fig. 3-3-3-10.Lists of submitted fim parts.
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Fig. 3-3-3-11. Overview of the fim related parts in iGEM. |
The characteristic of the part (BBa_K1077002) ) constructed by Michigan, is that it can be inverted in [ON] state to [OFF] state direction or in [OFF] state to [ON] state done-sidedly with induction of aTc or AHL. The repression of the tet promoter by the tet repressor is weakened by the addition of aTc. Therefore, fimE (BBa_K137007) ), which is on the downstream of the tet promoter is expressed by inducing aTc. As a result, the fim switch is inverted from [ON] state to [OFF] state. In other words, the target gene which is on the downstream of the fim switch, is not expressed.
On the other hand, by the addition of AHL, lux promoter is activated. Therefore, hbiF (BBa_K880000) ), which is on the downstream of the lux promoter, is expressed. HbiF inverts the fim switch in [OFF] state to [ON] state. As a result, the target gene which is on the downstream of the fim switch, is expressed.
There are two immense issues to their system, judging from their experimental results. First of all, we could not conclude that their fim switch and fimE is functioning correctly, because the results were only shown for the fim switch[default ON] in their wiki and parts registry. In other words, the data of fim switch[default OFF] was not shown. Without the data of fim switch[default OFF], we can’t conclude that FimE (BBa_K137007) ) inverts the fim switch in [ON] state to [OFF] state predominantly.
Second of all, the results of Team Michigan, lack reproducibility because they have failed to set Positive controls and Negative controls in all of their experiments.
It was impossible to verify the reproducibility because the nucleotide sequence of this part (BBa_K1077002) ) was completely different between the distribution from the HQ and the information shown on the parts registry.
For detailed information, see 2013_Michigan wiki).
4. Reference
1. McClain MS et al. (1991) Roles of fimB and fimE in site-specific DNA inversion associated with phase variation of type 1 fimbriae in Escherichia coli. J Bacteriol 173(17):5308-14.
2. John M. Abraham et al. (1985) An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli. Proc Natl Acad Sci USA 82(17):5724-7
3. Ian C. Blomfield et al. (1997) Integration host factor stimulates both FimB- andFimE-mediated site-specific DNA inversion that controls phase variation of type 1 fimbriae expression in Escherichia coli. Molecular Microbiology 23(4), 705–717
4. Matthew P. McCusker et al. (2008) DNA sequence heterogeneity in Fim tyrosine-integrase recombinase-binding elements and functional motif asymmetries determine the directionality of the fim genetic switch in Escherichia coli K-12. Molecular Microbiology 67(1): 171–187
5. D L Gally et al. (1993) Environmental regulation of the fim switch controlling type 1 fimbrial phase variation in Escherichia coli K-12: effects of temperature and media. J Bacteriol. Oct; 175(19): 6186–6193.