Team:Tokyo Tech/Experiment/FimE dependent fim switch state assay

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FimE dependent fim switch state assay

　　

contents

1. Introduction

2. Summary of the Experiment

3. Results

3.1. Arabinose-dependent FimE (wild-type) expression

3.2. Supplemental experiments

4. Materials and Methods

4.1. Construction

4.2. Assay Protocol

4.2.1. Arabinose dependent FimE(wild-type) expression

4.2.2. Supplemental experiments

5. Reference

　　

1. Introduction

　　　　　　

To confirm the function of fim switch in the presence of FimE(wild-type), we constructed two Biobrick parts, BBa_K1632013　(Fig. 3-5-1-1). 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.

　　　　　　

Fig.3-5-1-1. New plasmids we constructed to confirm the function of fim switch

2. Summary of the Experiment

　　　　　　

Our purpose is to confirm that FimE (wild-type) inverts the fim switch (wild-type) from ON to OFF and from OFF to ON (Fig.3-5-2-1). We prepared six plasmids below (Fig.3-5-2-2). We measured the fluorescence intensity from the GFP expression in the presence of arabinose. From the results, we confirmed that our fim switch (wild-type) is inverted from ON to OFF and OFF to ON. From the results we also confirmed our fim switch (wild-type) is not inverted by the endogenous FimB and FimE and that FimE(wild-type) expression doesn’t have effect on the GFP expression.In order to confirm inversion more precisely, we also show the inversion ration of ON and inversion in the level of DNA sequencing

(1) P_BAD/araC_fimE(wild-type) (pSB6A1) + fim switch[default ON](wild-type)_gfp (pSB3K3)
(2) P_BAD/araC_fimE(wild-type) (pSB6A1) + fim switch[default OFF](wild-type) _gfp (pSB3K3)
(3) Positive control 1 : (pSB6A1) + fim switch[default ON](wild-type) _gfp (pSB3K3)
(4) Negative control 1 : (pSB6A1) + fim switch[default OFF](wild-type) _gfp (pSB3K3)
(5) Positive control 2 : P_BAD/araC_fimE(wild-type) (pSB6A1) + Pcon_gfp (pSB3K3)
(6) Negative control 2 : P_BAD/araC_fimE(wild-type) (pSB6A1) + promoter less_gfp (pSB3K3)

Fig.3-5-2-1. Plasmids for the experiment of FimE dependent fim switch state assay

3. Results

3.1. Arabinose dependent FimE(wild-type) expression

　　　　　　

We tried to confirm that fim switch is unidirectionally inverted in the presence of FimE (wild-type) by using GFP as a reporter, under 4 different concentrations of arabinose. In the medium with 0 M arabinose, we supplemented the medium with 1.0 % glucose in order to repress the leakage in the P_BAD/araC promoter. Fig. 3-5-3-1 shows the histograms of the samples measured by the flow cytometer. In the results of the reporter cell (1), when the Induction of FimE(wild-type) expression increases, the fluorescence intensity decreases. From this fact, we confirmed that the fim switch (wild-type) is inverted from ON to OFF by FimE (wild-type). From the result of the reporter cell (2), even when the expression amount of FimE (wild-type) increases, the expression amount of GFP in the reporter cell (2) does not change. From this fact, we confirmed that the fim switch (wild-type) is inverted only from ON to OFF by FimE (wild-type). From the results of the two reporter cells (1) and (2), we successfully confirmed that FimE (wild-type) inverts the fim switch only from ON to OFF.
   　The results of positive control 1 and negative control 1 confirmed that the endogenous FimB and FimE did not invert our fim switch (wild-type). Also, the result of positive control 2 and negative control 2, indicates that the expression of FimE (wild-type) do not have effects on the GFP expression.

Fig. 3-5-3-1. The histogram of the samples measured by flow cytometer

3.2. FLA analysis

　　　　　　

写真とシークエンスデータ

5. Materials and Methods

5.1. Construction

-Strain

　　　　　　

All the samples were DH5alpha strain.

-Plasmids

　　　　　　

(1) P_BAD/araC_fimE(wild-type) (pSB6A1)+ fim switch[default ON](wild-type)_gfp (pSB3K3)

Fig. 3-5-4-1.

　　　　　　

(2) P_BAD/araC_fimE(wild-type) (pSB6A1)+ fim switch[default OFF](wild-type)_gfp (pSB3K3)

Fig. 3-5-4-2.

　　　　　　

(3) Positive control 1 : (pSB6A1) + fim switch[default ON](wild-type) _gfp (pSB3K3)

Fig. 3-5-4-3.

　　　　　　

(4) Negative control 1 : (pSB6A1) + fim switch[default OFF](wild-type) _gfp (pSB3K3)

Fig. 3-5-4-4.

　　　　　　

(5) Positive control 2 : P_BAD/araC_fimE (wild-type) (pSB6A1) + Pcon_gfp (pSB3K3)

Fig. 3-5-4-5.

　　　　　　

(6) Negative control 2 : P_BAD/araC_fimE (wild-type) (pSB6A1) + promoter less_gfp (pSB3K3)

Fig. 3-5-4-6.

4.2. Assay Protocol

4.2.1. Arabinose dependent FimE expression

1. Prepare overnight cultures for the each sample in 3 ml LB medium, containing ampicillin (50 microg / mL), kanamycin (30 microg / mL) and glucose (final concentration is 1.0 percent) at 37 ℃ for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp, Kan and glucose (final concentration is 1.0 %).
3. Incubate the cells at 37 ℃, shaking at 180 rpm until the observed OD590 reaches 0.4 (Fresh Culture).
4. After the incubation, take 1 mL of the samples, and centrifuge at 5000x g, 1 min, 25 ℃.
5. Remove the supernatant.
6. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃.
7. Remove the supernatant.
8. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃.
9. Remove the supernatant.
10. Suspend the pellet in 1 mL of LB containing Amp and Kan.
11. Add 30 microL of suspension in the following medium.
   ① 3 mL of LB containing Amp, Kan, glucose (final concentration is 1.0 %) and 30 microL sterile water
   ② 3 mL of LB containing Amp, Kan and 30 microL of 500microM arabinose (final concentration of arabinose is 5 microM)
   ③ 3 mL of LB containing Amp, Kan and 30 microL of 1 mM arabinose (final concentration of arabinose is 10 microM)
   ④ 3 mL of LB containing Amp, Kan and 30 microL of 2 mM arabinose (final concentration of arabinose is 20 microM)
   ※ As for (3) and (4), the suspension were added only in medium ① and ④. 12. Incubate the samples at 37 ℃ for 6 hours, shaking at 180 rpm.(Measure the OD590 of all the samples every hour.)
13. After the incubation, take the samples, and centrifuge at 9000x g, 1min, 4℃.
14. Remove the supernatant.
15. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3)
16. Dispense all of each suspension into a disposable tube through a cell strainer.
17. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)

4.2.2. FLA analysis

1. After the assay of “Arabinose dependent FimB expression”, miniprep cell culture (A,B, ,C and D) of leftover as here.(http://parts.igem.org/Help:Protocols/Miniprep)
2. Turn on water bath to 42℃.
3. Take competent DH5alpha strain from -80℃ freezer and leave at rest on ice.
4. Add 3 µl of each plasmids in a 1.5 ml tube.
5. Put 25 µl competent cell into each 1.5 ml tubes with plasmid.
6. Incubate on ice for 15 min.
7. Put tubes with DNA and competent cells into water bath at 42℃ for 30 seconds.
8. Put tubes back on ice for 2 minutes.
9. Add 125 µl of SOC medium. Incubate tubes for 30 minutes at 37℃.
10. Make a 1:5 dilution in 150µl of fresh SOC medium.
11. Spread about 100 µl of the resulting culture of LB plate containing kanamycin.
12. Incubate LB plate for 14-15 hours at 37℃.

5. Reference

　　　　　　

1. Timothy S. Ham et al. (2006) A Tightly Regulated Inducible Expression System Utilizing the fim Inversion Recombination Switch. Biotechnol Bioeng 94(1):1-4