High pass filters

Promoter mutation sites The wild type promoter from registry BBa_R0062 is mutated using site directed mutagenesis. The library shows the site of directed mutagenesis

Comparison of the sensitivity of the wild type promoter and the mutated luxR promoter
For the wild type we got :EC50=4.45nM, R2=0.80, n=1.7
For the pLuxR variant we got :EC50=17814nM, R2=0.93, n=0.8

The detection of different OHHL levels depending on the number of mines needs to have filters in our detection system. We decided to create a high pass filter library by doing site directed mutagenesis of the wild type [http://parts.igem.org/Part:BBa_R0062 BBa_R0062 PluxR]. The sites for mutagenisis were chosen from literature (2) (see Figure 1).
We were able to isolate a promoter having a lower expression level and being less sensitive than the wild type promoter (Figure 2). The promoter is called [http://parts.igem.org/Part:BBa_K1216007?title=Part:BBa_K1216007 PluxR variant BBa_K1216007] (G1, according to its initial position in the deep well plate.
Those two different promoters are used to created two different high pass filter to detect the different OHHL concentrations. The two promoters were analyzed not only by 96-well plate assay and single cell analysis (FACS) but also for E.coli grown in liquid culture and on agar plate. Interestingly the EC₅₀ sensitivity (half maximal effective concentration, EC₅₀) is different between cells in liquid culture and cells in agar plates.

Site directed saturation mutagenesis PCR of the BBa_R0062 PluxR

Figure 1: Promoter mutation sites The wild type promoter from registry BBa_R0062 was mutated using site directed saturation mutagenesis. The library shows the targeted sites for site directed saturation mutagenesis. The sequences for the library, the BBa_R0062, the BBa_K1216007 and the wild type luxR promoter from literature(2) are given.

We did site directed saturation mutagenisis of specific sites of the lux box according to the results taken from literature (2)(see Figure 2).
We mutated the promoter directly in the BBa_J09855 construct and cloned into a eGFP gene as a reporter to be able to screen for differences in the dose response curves. In the end we isolated one mutated promoter which shows a shift in sensitivity (see section below)

Fluorescence data analysis

The fitting of the following graphs was performed using this equation :

Output = eGFP levels [au]
Top = maximal eGFP level [au]("full induction")
Bottom = minimal eGFP level [au](“leakiness”)
n = Hill coefficient (“cooperativity”)
EC₅₀ = Half-maximal effective concentration (“sensitivity”)
[AHL]=OHHL concentration [nM]

Native OHHL tests using microtiter plates

Figure 2: Sensivity curve of the wild type promoter and G1 mutant. The OHHL concentration range is plotted against the standarized fluorescence (au).
For the wild type : EC₅₀=5.86, R₂= 0.87,n=1.7
Fore the G1 mutant : EC₅₀=1'341, R₂= 0.98,n=0.8

In order to select mutated luxR promoters we need to know about the sensitivity.Thus, we carried out dose response cruves using the Tecan Infinite M200 plate reader. The test range was inspired form literature (1).

The results are shown in Figure 2.

Dose response curves of luxR promoters under single cell analysis

Liquid culture and agar plate OHHL detection comparison

To gain precise data out of our fluorescence analysis, to better characterize the different promoters, we use the single analysis to obtain data.
The protocol was the following :
From overnight cultures we inoculate 50 mL Falcon™ tubes containing 5mL LB media, 5 μL OHHL and the antibiotic. We evaluate a range of 10 different concentrations from
10^-4nM OHHL to 10⁵nM OHHL by a 10 fold increase, according to the results of the plate reader analysis. The measurements were done in duplicates.

Here we employed single cell flow cytometry to obtain high quality fluorescence data of each promoter under different OHHL concentrations.we started by analyzing cells grown in liquid culture, then we shifted to agar plate format in order to fit to our project. We obtained different EC₅₀ values between cells in liquid culture and in agar plates for each luxR promoter (see Figure 3, 4 and 5).See methods for the protocol

Figure 3: Sensitivity curve of the wild type BBa_R0062 on agar plates and liquid culture For the liquid culture we got :EC₅₀=0.02nM, R²=0.84, n=1.7; For the agar plates we got :EC₅₀=4.45nM, R²=0.80, n=1.7

Figure 4: Single cell data of the wild type BBa_R0062 promoter vs. the pluxR mutant The histogram plots of eGFP levels for each tested OHHL concentration, culturing condition and corresponding promoter.In orange experiments on agar plates. In black experiments in liquid cultures.On the top the data of the wild type luxR promoter. On the bottom the data of the luxR promoter variant.

Figure 5: Sensitivity curve of the G1 (pluxR variant BBa_K1216007) on agar plates and liquid culture
For the liquid culture we got :EC₅₀=6482nM, R²=0.97, n=0.8;
For the agar plates we got :EC₅₀=17814nM, R²=0.93, n=0.8

In liquid culture

The direct plot of both sensitivity curves (Figure 6) shows the shifted sensitivity of the luxR promoter in comparison to the wild type BBa_R0062 promoter. The EC₅₀ shifted from 0.02nM for the wild type BBA_R0062 to 6'250 nM for the luxR variant promoter which is equal to a 312'500 fold increase.

Figure 6: Comparison of the Wild Type pluxR and the pluxR mutant sensitivity curves in liquid culture using the BD LSRFortessa™ Flow Cytometer System
For the wild type :EC₅₀=0.02nM, R²=0.84, n=1.7
For G1 we got :EC₅₀=6482nM, R²=0.97, n=0.8

On agar plates

The direct plot of both sensitivity curves (Figure 6) shows the shifted sensitivity of the luxR promoter in comparison to the wild type BBa_R0062 promoter. The EC₅₀ shifted from 4.45nM for the wild type BBA_R0062 to 17'814 nM for the luxR variant promoter which is equal to a 4000 fold increase. Therefore, comparing with the results from cells growing in liquid culture an increase of 220 and 3 times for wild type BBa_R0062 and pluxR variant respectively. If you want to know more about the methods please click here

Figure 7: Comparison of the sensivity of the wild type promoter and the mutated luxR promoter on agar plates
For the wild type we got :EC50=4.45nM, R2=0.80, n=1.7
For the pLuxR variant we got :EC₅₀=17814nM, R2=0.93, n=0.8

References

(1) M Geske G.D.,Evaluation of a focused library of N-aryl L-homoserine lactones reveals a new set of potent quorum sensing modulators.
(2) Luis Caetano A Mutational Analysis Defines Vibrio fischeri LuxR Binding Sites