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

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FimB dependent fim switch state assay

　　

contents

1. Introduction

2. Summary of the Experiment

3. Results

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

3.2. FLA analysis

4. Discussion

5. Materials and Methods

5.1. Construction

5.2. Assay Protocol

5.2.1 Arabinose dependent FimB expression

5.2.2. FLA analysis

6. Reference

　　

1. Introduction

　　　　　　 　　　　

In order to enable a prisoner coli to randomly select its option between cooperation and defection, we noticed that a fim switch(wild-type), which can invert a promoter sequence bidirectionally in the presence of FimB (wild-type) recombinase, is the part we need (Fig. 3-4-1-1).
	Fig. 3-4-1-1. In the presence of FimB(wild-type) recombinase, the fim switch which is a promoter containing repeated DNA sequence, is invert at random.

　　　　　　

For implementation of Decision making coli, we newly constructed plasmid, P_BAD/araC_rbs_fimB(wild-type) (BBa_K1632012) that produces FimB (wild-type). We also prepared two other new plasmids, BBa_K1632007 and BBa_K1632008 (Fig. 3-4-1-2). BBa_K1632012 enables arabinose-inducible expression of FimB (wild-type). In BBa_K1632007 and BBa_K1632008, either [ON] or [OFF] fim switch (wild-type) is placed upstream of GFP coding sequence.

　　　　　　

Fig.3-4-1-2. New plasmids we constructed to confirm the function of BBa_K1632012 plasmid for Decision making coli.

2. Summary of the Experiment

　　　　　　

Our purpose is to confirm that FimB (wild-type) inverts the fim switch (wild-type) from ON to OFF and from OFF to ON (Fig.3-4-2-1). We prepared six plasmids below. (Fig.3-4-2-2). 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 FimB expression doesn’t affect 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_fimB(wild-type) (pSB6A1)+ fim switch[default ON](wild-type)_GFP (pSB3K3)
(2) P_BAD/araC_fimB(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_fimB (wild-type) (pSB6A1)+Pcon_GFP (pSB3K3)
(6)Negative control 2 : P_BAD/araC_fimB (wild-type) (pSB6A1)+promoter less_GFP (pSB3K3)

Fig.3-4-2-1. Plasmids for the experiment of FimB dependent fim switch state assay

3. Results

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

　　　　　　

We tried to confirm that fim switch is bidirectically inverted in the presence of FimB (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 0.5 % glucose in order to repress the leakage in the P_BAD/araC promoter. Fig. 3-4-3-1 shows the histograms of the samples measured by the flow cytometer. In the results of the reporter cell (1), when the Induction of FimB(wild-type) expression increases, the fluorescence intensity decreases. From this fact, we confirmed that the fim switch is inverted from ON to OFF by FimB (wild-type). From the result of the reporter cell (2), when the expression amount of FimB(wild-type) increases, the expression amount of GFP in the reporter cell (2) increases. From this fact, we confirmed that the fim switch is inverted from OFF to ON by FimB(wild-type). From the results of the two reporter cells (1) and (2), we successfully confirmed that FimB (wild-type) inverts the fim switch from ON to OFF and from OFF to ON.
   　The results of positive control 1 and negative control 1 confirmed that the endogenous FimB and FimE did not invert our fim switch (wild-tyoe). Also, the result of negative control 2, indicates that the expression of FimB (wild-type) do not have effects on the gfp expression. The reason the fluorescence intensity of the positive control 2 is increasing in proportion to the arabinose concentration is described in 4. Discussion section.

Fig. 3-4-3-1. Histogram of the samples measured by flow cytometer

3.2. FLA analysis

　　　　　　

写真とシークエンスデータ

4. Discussion

When the concentration of FimB (wild-type) increased by increasing the concentration of arabinose, we confirmed that the fluorescence intensity decreased in both ON to OFF process and OFF to ON process.    The result of the reporter cell (2) shows that when the concentration of arabinose is increased to 0〜20 microM, the fluorescence intensity increases. This shows the function of FimB (wild-type) inverting the fim switch (wild-type) from OFF to ON. However, when the arabinose concentration is excess amount, (5mM)、the fluorescence intensity decreases (Fig.3-4-4-1). According to [1], this is caused by the excess increase of the inversion rate of the fim switch. When the inversion rate is too high, there is not enough time for transcription initiation. Consequently, the GFP expression decreases.

Fig.3-4-4-1. Histogram of reporter cell (2)

	Even though there is no fim switch (wild-type) in the plasmid of positive control 2, similar increase of fluorescence intensity dependent on the expression of FimB (wild-type) was found in our positive control 2 (Fig.3-4-4-1) This unpredictable increase of fluorescence intensity is caused by the decrease of dilution rate of proteins inside cells. The FimB (wild-type) expression, depending on the arabinose induction, inhibits cell division that decreases protein concentration inside the individual cells. Therefore, the concentration of GFP in individual cell increases.
Fig.3-4-4-2. The histogram of positive control 2

5. Materials and Methods

5.1. Construction

-Strain

　　　　　　

All the samples were DH5alpha strain.

-Plasmids

　　　　　　

A. P_BAD/araC_fimB(pSB6A1)+ fim switch[default ON](wild-type)_gfp (pSB3K3)

Fig. 3-4-5-1.

　　　　　　

B. P_BAD/araC_fimB(pSB6A1)+ fim switch[default OFF](wild-type)_gfp (pSB3K3)

Fig. 3-4-5-2.

　　　　　　

C. Posigive control1:(pSB6A1)+ fim switch[default ON](wild-type)_gfp(pSB3K3)

Fig. 3-4-5-3.

　　　　　　

D. Negative control2: (pSB6A1)+ fim switch[default OFF](wild-type)_gfp(pSB3K3)

Fig. 3-4-5-4.

　　　　　　

E. Pbad/araC-fimB (pSB6A1) +J23119 promoter_gfp (pSB3K3)…Positive control2

Fig. 3-4-5-5.

　　　　　　

F. Pbad/araC-fimB (pSB6A1) +promoter less gfp (pSB3K3)…Negative control2

Fig. 3-4-5-6.

5.2. Assay Protocol

5.2.1. Arabinose dependent FimB expression

1. Prepare overnight cultures for each sample in 3 mL of LB medium containing ampicillin (50 microg / mL), kanamycin (30 microg / mL) and glucose (final concentration is 0.5 %) at 37 ℃, shaking at 180 rpm for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp, Kan and glucose (final concentration of mass of glucose is 0.5 %).
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 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 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 of mass of glucose is 0.5 percent) and 30 microL of sterile water.
   ② 3 mL of LB containing Amp, Kan and 30 microL of 2 mM arabinose (final concentration of arabinose is 20 microM)
   ③ 3 mL of LB containing Amp, Kan and 30 microL of 20 mM arabinose (final concentration of arabinose is 200 microM)
   ④ 3 mL of LB containing Amp, Kan and 30 microL of 500 mM arabinose (final concentration of arabinose is 5 mM)
   ※ As for C and D, the suspension were added only in medium ① and ④.
12. Incubate the samples at 37 ℃, shaking at 180 rpm for 6.5 hours. (Measure 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.)

5.2.2. FLA analysis

1. After the assay of “Arabinose dependent FimE 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℃.

6. Reference

　　　　　　

1. Hung M. et al. (2014) Modulating the frequency and bias of stochastic switching to control phenotypic variation. Nat Commun 5:4574. doi:10.1038/ncomms5574

　　　　　　

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