Team:Tokyo Tech/Projects/Urea-cooler/data
From 2011.igem.org
Assay Method and Results
1. Characterization of rocF and Arg box
1.1 Materials
Expression plasmids used in this study are shown in Table 1.
Designation | pSB3K3 | pSB1C3 |
---|---|---|
mock | PlacIQ | Alcohol-dehydrogenase(promoter-less) |
rocF | Ptrc-rocF | Alcohol-dehydrogenase(promoter-less) |
rocF + Arg box | Ptrc-rocF | Arg box |
1.2 Methods
1.2.1 Preparation of samples for urea concentration assay
- A single colony of cells transformed with engineered plasmids (mock, rocF or rocF+Arg box) was inoculated into 3 mL of LB with appropriate antibiotics and grown to saturation at 37°C.
- The saturated culture was diluted 50-fold, grown till the log phase (OD600 = 0.5).
- The culture was induced with 1 mM IPTG at 37°C for 1 hour.
- 1.5 mL of culture was centrifuged at 9,000 rpm for 1 minute and the supernatant fluid was used as a sample for urea concentration assay.
1.2.2 Urea concentration assay
Urea concentrations of the samples were determined colorimetrically with DIUR-500 -QuantiChrom™ Urea Assay Kit obtained from BioAssay Systems.
Detailed methods are as follows.
- 10 µL of the supernatant fluid from each sample, 10 µL blank(LB),and 10 µL standard (10 mg/dL urea LB) were transferred to wells of clear bottom 96-well plates.
- 200 µL working reagent for coloring reaction from DIUR-500 -QuantiChrom™ Urea Assay Kit was added and the wells were taped lightly to mix.
- The mixture was incubated for 20 munites at room temperature.
-
Optical density at 450 nm was read and urea concentration (mg/dL) of the sample was calculated as
.
ODSAMPLE, ODBLANK and ODSTANDARD are OD450 values of sample, standard and blank, respectively.
Linear plot of OD450 vs. urea concentraion
To test linearlity between OD450 vs. urea concentraion, 0, 0.5, 1.0, 2.5, 7.5, 10 mg/dL urea LB were assayed in triplicate with this urea assay kit in the same way as our bacterial samples. Plot of OD450 values vs. urea concentraions we tested showed very good linearlity as shown in Fig. 1.
![Standard curve for coloring reaction in urea assay](https://static.igem.org/mediawiki/2011/8/81/Linear_plot.png)
fig. 1 Linear plot of OD450 vs. urea concentraion
1.3 Results
Each sample was assayed in duplicate urea concentration detected in each sample is shown in Table 2. fig. 2 shows the average of these 2 values.
Colony No. | mock | rocF | rocF + Arg box |
---|---|---|---|
#1 | 1.9 | 4.9 | 7.3 |
#2 | 0.75 | 4.3 | 7.2 |
Average | 1.3 | 4.6 | 7.2 |
S.D. | 0.80 | 0.44 | 0.080 |
![](https://static.igem.org/mediawiki/2011/c/cb/Arg_box_on_1C3.png)
2. Characterization of Ptrc-RBS-rocF-Argbox
2.1 Materials
Expression plasmids used in this study are listed in table 1.
Designation | Parent vector | Introduced sequence(s) |
---|---|---|
Mock (3K3) | pSB3K3 | PlacIQ |
rocF (3K3) | pSB3K3 | Ptrc-rocF |
rocF + Arg box (3K3) | pSB3K3 | Ptrc-rocF-Arg box |
Mock (6A1) | pSB6A1 | gfp (promoter-less) |
rocF (6A1) | pSB6A1 | Ptrc-rocF |
rocF + Arg box (6A1) | pSB6A1 | Ptrc-rocF-Arg box |
In one experiment, MG1655 (argR +) and JE6852 (argR -) were respectively transformed with either mock(3K3), rocF(3K3) or rocF-Arg box(3K3). In another experiment, MG1655 (argR +) and JD24293 (argR -) were respectively transformed with either mock(6A1), rocF(6A1) or rocF-Arg box(6A1). Both JE6852 and JD24293 were obtained from National Institute of Genetics.
2.2 Methods
2.2.1 Preparation of samples for urea concentration assay
- A single colony of cells transformed with engineered plasmids (mock, rocF or rocF+Arg box) was inoculated into 3 mL of LB with appropriate antibiotics and grown to saturation at 37°C.
- The saturated culture was diluted 50-fold, grown till the log phase (OD600 = 0.5).
- The culture was induced with 1 mM IPTG at 37°C for 1 hour.
- 1.5 mL of culture was centrifuged at 9,000 rpm for 1 minute and the supernatant fluid was used as a sample for urea concentration assay.
2.2.2 Urea concentration assay
Urea concentrations of the samples were determined colorimetrically with DIUR-500 -QuantiChrom™ Urea Assay Kit obtained from BioAssay Systems.
Detailed methods are as follows.
- 10 µL of the supernatant fluid from each sample, 10 µL blank(LB),and 10 µL standard (10 mg/dL urea LB) were transferred to wells of clear bottom 96-well plates.
- 200 µL working reagent for coloring reaction from DIUR-500 -QuantiChrom™ Urea Assay Kit was added and the wells were taped lightly to mix.
- The mixture was incubated for 20 munites at room temperature.
-
Optical density at 450 nm was read and urea concentration (mg/dL) of the sample was calculated as
.
ODSAMPLE, ODBLANK and ODSTANDARD are OD450 values of sample, standard and blank, respectively.
Linear plot of OD450 vs. urea concentraion
To test linearlity between OD450 vs. urea concentraion, 0, 0.5, 1.0, 2.5, 7.5, 10 mg/dL urea LB were assayed in triplicate with this urea assay kit in the same way as our bacterial samples. Plot of OD450 values vs. urea concentraions we tested showed very good linearlity as shown in Fig. 1.
![Standard curve for coloring reaction in urea assay](https://static.igem.org/mediawiki/2011/8/81/Linear_plot.png)
fig. 3 Linear plot of OD450 vs. urea concentraion
2.3 Results
![](https://static.igem.org/mediawiki/2011/b/bc/RocF_and_Arg_box_on_3K3.png)
![](https://static.igem.org/mediawiki/2011/0/01/RocF_and_Arg_box_on_6A1_%283%29.png)
Similar results were obtained in both the experiment with samples on pSB3K3 and the experiment with samples on pSB6A1. In MG1655(argR +), addition of Trc promoter-rocF led to production of more urea compared to mock as expected. These results show that insertion of rocF resulted in arginase production, therefore completing the urea cycle in E. coli. In the same strain, however, addition of Arg box sequence led to little change in urea production. The reason why the effect of Arg boxes was not apparent is probably that both pSB3K3 and pSB6A1 are low-copy-number plasmids. Low-copy-number plasmids are not capable of introducing enough number of Arg boxes to effectively deactivate the arginine repressor. Both of the plasmids containing rocF gene in the strains with argR(a gene which codes arginine repressor) a loss-of-function mutation produce urea more efficiently than those in MG1655(argR +).
These results are in line with the fact that for strains with argR a loss-of-function mutation, deactivation of arginine repressor by Arg boxes is not needed and addition of the Arg box does not result in a significant increase of urea production.