Part:BBa_K2023001
Biosensor device for BTEX detection
Principle of our biosensor and usage
This biosensor was the heart of our iGEM project. This biobrick is composed of the Pr promoter with an Elowitz 1999 RBS (BBa_K2023004) which is a constitutive promoter. This promoter drives to the transcription of the XylR gene (BBa_K2023005) coding for the XylR protein. The XylR protein is able to bind aromatic hydrocarbons that carry a methyl group like toluene and xylene. When XylR bound toluene for instance, it forms a tetramer and is able to regulate the Pu promoter has a transcriptional regulator. Then, Pu is activated and it allows the transcription of the bioluminescent reporter gene GLuc (Pu+GLuc: BBa_K2023003), coding for the Gaussia luciferase. When this enzyme reacts with its substrate which is the Coelenterazine, it emits luminescence.
The more bioluminescence is emit, the more aromatic hydrocarbons are present. Therefore our biosensor is able to detect and quantify some aromatics hydrocarbons such as BTEX (Toluene, Xylene).Those molecules are atmospheric pollutants.
Although air pollution contains only 2% VOCs (mean concentration: 5ng/L), the impact of those pollutants on health and environment is major. These pollutants are persistent in the environment, they bio-accumulate in living tissues and are able spread over long distances. Although their effect on human health are only partially known, scientists have demonstrated their systemic effects (hepatic, hematologic, immunologic), their toxicity on the reproductive systems, their genetic toxicity.
Existing methods for monitoring those pollutants include physical and chemical tools (continuous analysis scanner, integrated measure by active and passive sampling). However, those tools are mainly found in fix weather stations and thus, do not allow a precise quantification of air pollution. Our biosensor can supply rapid and specific results at low cost. Biosensors, as they are easily transportable (minimal size, reduced weight) are perfectly suitable for field measurements.
Our project aimed to integrate this biosensor in bacteria safely contain within a drone able to perform on-field measurement
For more information on our project, visit our website http://2016.igem.org/Team:Ionis_Paris
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 2446
Illegal NheI site found at 2691
Illegal NheI site found at 3102 - 21INCOMPATIBLE WITH RFC[21]Illegal BamHI site found at 2101
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 329
- 1000COMPATIBLE WITH RFC[1000]
Details of the part used
Pr promoter
The Pr promoter is found in the toluene recognition system and is composed of 410 bp. This promoter is available on the iGEM registry at this ID access: BBa_I723018. We chose to use this promoter because it is the specific promoter for the XylR gene. This promoter is naturally constitutive. It leads to the permanent production of the XylR protein. Indeed, the induced luminescence has to be proportional to the pollutant rate. Therefore, when pollutant molecules enter in the bacteria, the XylR protein should be present in sufficient amount.
XylR
The 1704 bp XylR gene, encodes for the XylR protein and is regulated by the Pr promoter in its native context. This gene is available on the iGEM Registry of Standard Biological Parts (BBa_K1834844). The XylR that we designed for our biosensor is a bit different because it is optimized for E.Coli DH5-Alpha and for IDT synthesis.
The XylR protein, mined from Pseudomonas putida, is involved in the transcriptional activation of the toluene recognition system. This regulatory protein allows the detection of aromatic hydrocarbons that carry a methyl group, i.e. xylene, toluene and 1-chloro-3-methyl-benzene. The A domain of the XylR protein (sensing domain), binds to the pollutant molecule. This leads to the formation of a tetramer. The C domain is involved in the dimerization of XylR, which is ATP dependent. The made up tetramer acts as an activator transcriptional factor for the Pu promoter through the DNA binding D domain.
Pu promoter
Pu is a promoter found in the toluene recognition system and is composed of 320 bp. This promoter is available on the iGEM registry at this ID access: BBa_I723020.
We chose to use this promoter because of its sensibility to the transcriptional regulator XylR bound to xylene, toluene or 1-chloro-3-methyl-benzene.
Gaussia luciferase
This gene is found in a well-known organism, the copepod Gaussia princeps. It encodes for the Gaussia luciferase enzyme, also known as GLuc, which is involved in a bioluminescence process. This enzyme degrades its substrate, coelenterazine, into a product, celenteramide. With an optimal substrate level, this step produces energy in the form of light that can be detected with a fixed spectrophotometer at 488nm.
We chose to use the GLuc-His part, a gene of 522 bp, available on the iGEM registry at the (BBa_K1732027) which codes for the Gaussia luciferase followed by 6 histidines and optimized it for a use in E.coli and IDT synthesis. In our plasmid, this gene is positioned after an inducible promoter, the Pu promoter, to report the activation of the toluene recognition system. The Gaussia luciferase needs the addition of substrate to ensure its activity because this molecule is not synthetized by our biosensor. Therefore, in the laboratory, luciferase substrate can be added at the same time in each sample ensuring that every measurement will be taken at the same time. This allow a better consistency between our different results. Also, due to its secreted form, lysing cells in order to assay GLuc activity is not necessary. The Gaussia luciferase is an ideal reporter gene.
Characterization : Bioluminescence assays
Protocol and tested concentrations
We used the protocol 13 available on our wiki : http://2016.igem.org/Team:Ionis_Paris/Protocol_13 and decided to test several concentration of toluene (0ng/L, 10ng/L, 100ng/L, 10µg/L and 10mg/L).Bioluminescence assays were realized several times after toluene addition (1h, 3h, 4h30 and 5h30).
Bacteria transformed with our biosensor used in each assays come from the same culture (OD = 0.1). This culture was well mixed and divided in 50 mL falcon. Toluene was then added in each Falcon.
Bioluminescence assays were realized quickly after substrate addition and the bioluminescence intensity was measured using Mithras² LB 943 Monochromator Multimode Reader.This machine was kindly lend by Berthold company for 3 days in order to let us realized the bioluminescence measurement. In addition to bioluminesence intensity, sample's OD was also measured.
All tests were realized in triplicates.
Several negative controls were realized :
We recommend BBa_K2023007(Gluc codig device with Pr) as the positive control to ensure the substrate efficiency.
Preliminary considerations
Effect of toluene on sample's bioluminescence intensity
We determine the effect of adding toluene to cell culture medium on bioluminescence intensity. As shown on the graph below the bioluminescence intensity of the LB + toluene at 10 mg/L (47.71 RLU) do not significantly differ from the bioluminescence intensity of the LB (48.93 RLU). The little bioluminescence found was due to the substrate added in our sample.
Therefore, toluene addition in our samples will not impact their bioluminescence intensity.
Figure 1: Bioluminescence intensity expressed in RLU of LB and LB with toluene at 10mg/L. Mann whitney statistical test was performed to asses the effect of toluene on LB auto-bioluminescence (ns: non significant).
Bacteria E.coli have little auto-bioluminescence
Bacteria transformed with a genetic construction that does not contain Gaussia luciferase gene were used in this study. The auto-bioluminescence of E.coli cells was assessed by comparate E.coli bacteria bioluminescence intensity to LB bioluminescence intensity. As shown on the figure 3, the bioluminescence intensity of E.coli cells (53.14 RLU) was a little superior to LB bioluminescence intensity (48.93 RLU) but not significantly superior. E.coli cells have little auto-bioluminescence. However, this bioluminescence in greatly inferior to the one produce by our biosensor in presence of pollutant (results presented after)
Figure 2: Bioluminescence intensity expressed in RLU of LB and LB + E.coli cells. Mann whitney statistical test was performed (ns: non significant).
Little leakage in Gaussia luciferase expression
We investigate the inductility of the Pu promoter to ensure that the gaussia luciferase is not constitutively produce in our biosensor. To do so we compared the bioluminescence intensity of bacteria containing our biosensor to the bioluminescence intensity of bacteria transformed with a genetic construction that do not contain the Gaussia luciferase gene (BB12 : Pr-RBS-XylR).
The obtained results (figure 3) indicate that the gaussia luciferase gene is not produce in a constitutive manner in the cells. The bioluminescence intensity of our biosensor without toluene injection (158.86 RLU) is a little higher than the bioluminescence intensity of cells transformed with BB12 (53.14 RLU). However this bioluminescence intensity is significantly lower than the bioluminescence intensity of the cells transformed with our biosensor in presence of toluene (results presented in the next section)
Figure 3: Bioluminescence intensity expressed in RLU of E.coli cells transformed with a construction genetic that contain (BB123) or do not contain (BB12) the gaussia gene. A little leakage of the gaussia gene can be seen as the bioluminescence intensity of the sample that contain bacteria transformed with our biosensor is significantly superior to the one that contain bacteria transformed with Pr-RBS-XylR. Mann whitney statistical test was performed (*** : extremely significant).
Data processing
Due to the little LB background noise and leakage in gaussia luciferase synthesis, obtain bioluminescence intensity results were treated as followed. The background noise (LB+toluene) was subtracted to each sample’s bioluminescence intensity. Those latest were then expressed depending on the negative control (bacteria transformed with our biosensor in a medium without toluene, C0).
Results
Investigation of the best measurement time
It was first necessary to determine when, after toluene injection, bioluminescence results were the most relevant. To do so, we determine the bioluminescence intensity of our sample (bacteria transformed with our biosensor within LB medium containing different toluene concentration) several times after toluene addition.
The bioluminescence intensity of the negative control was also determine at each time after toluene addition and bioluminescent results for each assay were normalized on the corresponding negative control bioluminescence intensity. This normalization was necessary as we are dealing with several incubation time. This enable us to handle the bacteria OD increase within our samples and ensure that an increase in sample’s bioluminescence intensity is not correlated with an increase in cells concentration.
The graphs presented below represent the bioluminescence intensity of the sample depending on the time after a toluene addition for a fix concentration of toluene injected.
Figure 4: Evolution of bioluminescence intensity at different times after toluene addition (10ng/L). The bioluminescence intensity of each sample is normalized on the bioluminescence intensity of the corresponding negative control. Mann whitney statistical test was performed (ns : non significant, * : significant, ** : very significant, *** : extremely significant)
Figure 5: Evolution of bioluminescence intensity at different times after toluene addition (100ng/L). The bioluminescence intensity of each sample is normalized on the bioluminescence intensity of the corresponding negative control. Mann whitney statistical test was performed (ns : non significant, * : significant, ** : very significant, *** : extremely significant)
Figure 6: Evolution of bioluminescence intensity at different times after toluene addition (10µg/L). The bioluminescence intensity of each sample is normalized on the bioluminescence intensity of the corresponding negative control. Mann whitney statistical test was performed (ns : non significant, * : significant, ** : very significant, *** : extremely significant)
Figure 7: Evolution of bioluminescence intensity at different times after toluene addition (10mg/L). The bioluminescence intensity of each sample is normalized on the bioluminescence intensity of the corresponding negative control. Mann whitney statistical test was performed (ns : non significant, * : significant, ** : very significant, *** : extremely significant)
The bioluminescence intensity of all our samples was compared to the bioluminescence intensity of the negative control for each time after toluene injection. Mann Whitney statistics test were realized to determine whether the bioluminescence intensity of the sample was significantly higher than the bioluminescence intensity of the negative control.
On the graphics we can notice that the bioluminescence intensity increase as the time after toluene injection increase. However, for the highest concentration (10 mg/L), a decrease in the bioluminescence intensity can be notice 5h30 after toluene injection. It is due to the accumulation of gaussia luciferase and the impact of toluene on the cell metabolism and especially protein synthesis (see http://2016.igem.org/Team:Ionis_Paris/E.coli for more information).
Therefore, it is essential to realize our bioluminescence test at a precise time after sampling. As we want to detect environmental toluene concentration (less than 20ng/L), it is to be suitable to wait 5h30 before proceeding to the bioluminescence test. We did not incubate our bacteria with toluene for a longer time because of the effect of toluene on E.coli cells. We though that this effect will decrease our biosensor sensitivity and precision.
Investigation of detectable concentration 5h30 after toluene addition to the cells medium
As we determined that it was preferable to wait 5h30 before realizing the bioluminescence assay, we decided to focus on the results obtain for this time after toluene addition in the cells medium. We studied the evolution of the bioluminescence intensity according to the toluene concentration added in the cells medium 5h30 before. Those tests were realize in triplicates.
First of all, we wanted to ensure that the OD of the different samples is the same 5h30 after bacteria inoculation in presence of toluene. As shown on the Figure 8, the sample’s ODs are quite similar going from 1.464 to 1.61.
Figure 8: Sample's ODs depending on the toluene concentration added 5h30 before.
The bioluminescence intensity of each samples was then determined and shown depending on the toluene concentration. As we are dealing with extremely different toluene concentration, it was preferable to give our results in function of the logarithm of the toluene concentration. The bioluminescence intensity data in RLU for each replicates (R1, R2, R3) are given in the table below and represented on the Figure 9.
Toluene concentration |
Logarithm of toluene concentration |
Mean - R1 (RLU) |
SD - R1 |
Mean - R2 (RLU) |
SD - R2 |
Mean - R3 (RLU) |
SD - R3 |
0 ng/L |
0 |
180.2 |
16.0 |
146.5 |
23.4 |
167.9 |
11.8 |
10 ng/L |
1 |
1007.3 |
210.2 |
337.7 |
39.3 |
1041.9 |
139.4 |
100 ng/L |
2 |
754.4 |
150.4 |
762.4 |
77.9 |
1823.1 |
243.1 |
10 µg/L |
4 |
1110.4 |
150.0 |
1373.8 |
162.4 |
2073.7 |
202.9 |
10 mg/L |
7 |
882.8 |
131.6 |
2485.4 |
259.5 |
1247.2 |
151.4 |
Figure 9: Evolution of bioluminescence intensity for each replicate depending on the logarithm of the toluene concentration injected 5h30 before.
As shown on the graph, the obtained data differ from one replicates to another due to difference in the metabolism which is normal when working with living organism. However the curve profile stay is the same : the bioluminescence intensity of the sample increases until a toluene concentration of 10 µg/, then it reaches a plateau for two replicates and continues to increase for the other replicate.
Those results were pooled in order to draw a standard curve and being able to predict toluene concentration in a sample according to the bioluminescence intensity.
Quantification of environmentally relevant toluene concentration
The Figure 10 shows the evolution of the bioluminescence intensity depending on the logarithm of toluene concentration. For a toluene concentration inferior to 10 µg/L (10,000 ng/L : log(4)) the curve increases steadily, then the curve reach a plateau. This can be due to gaussia accumulation in the cells.
We were able to detect environmentally relevant toluene concentration and as the standard curve is linear for a toluene concentration inferior to 10µg/L, we are able to quantify the toluene concentration of a given sample.
0 ng/L |
10 ng/L |
100 ng/L |
10 µg/L |
10 mg/L |
|
Mean (RLU) |
164,84 |
795,63 |
1139,88 |
1519,28 |
1538,45 |
Standard deviation |
17,62 |
129,73 |
146,68 |
171,75 |
180,84 |
Induction percentage |
383% |
592% |
822% |
833% |
Figure 10: Evolution of bioluminescence intensity for pooled of the replicate depending on the logarithm of the toluene concentration injected 5h30 before. Correlation between toluene concentration in the cell culture medium and the bioluminescence intensity.
Comparison with existing methods
5h30 after toluene injection, our biosensor is able to detect environmentally relevant toluene concentration (10ng/L). This way of pollutant detection is environmentally friendly as the bacteria only required the appropriate molecules in its culture medium to grow and quantify pollutant. In addition, the use of a biosensor, even if it requires an expensive machine (a luminometer) for results analysis, is cheapper compared to others physical chemical existings methods.
Find out more informations about existing methods of pollutant detection here : http://2016.igem.org/Team:Ionis_Paris/Design
However, our biosensor is only a prototype and we present below the different improvement that should be made.
Perspectives and improvement
Based on the results present above, we though about improvement and future experiments that should be realize. First of all, the standard curve drawn is based on few toluene concentration. We can improve this standard curve by focusing on low toluene concentration and realize bioluminescence assay for more low toluene concentration.
Then we have to determine the lowest concentration that our biosensor can detect while ensuring precise and reproductible results.Moreover,CelloCad software http://2016.igem.org/Team:Ionis_Paris/Measurement can be use to optimize our genetic circuit.
We have pointed out the variation between our different replicates for bioluminescence assay. Those variations are due to metabolism variations of living organisms. Several measurements have to be realize for each toluene concentration and the
reproductibility of the results have to be assess on more experiments.
Also, we did not have the time to optimize our bioluminescence assay protocol and to test the different parameters of the luminometer.
We did not performed tests with others pollutants such as the xylene. Therefore, the sensibility of our biosensor to those pollutants should be assesses in future experiments. For a convenient reason and as we could not evaporate toluene within our laboratory, we only performed bioluminescence assay using liquid toluene. Future work could consist in the creation of an isolated and hermetic room in which gazeous toluene could be add ad our drone flight to perform air sampling.
Click here http://2016.igem.org/Team:Ionis_Paris/Demonstrate
References
Hernandez C.A., Osma, J.F. (2014). Whole cell biosensors. In M. Stoytcheva & J.F. Osma (Eds.). Biosensors: Recent Advances and Mathematical Challenges. Barcelona: OmniaScience, pp. 51-96.
Rawson, D.M., Willmer, A.J., and Turner, A.P. (1989). Whole-cell biosensors for environmental monitoring. Biosensors 4, 299–311.
Behzadian, F., Barjeste, H., Hosseinkhani, S., and Zarei, A.R. (2011). Construction and Characterization of Escherichia coli Whole-Cell Biosensors for Toluene and Related Compounds. Current Microbiology 62, 690–696.
Abril, M. A., Michan, C., Timmis, K. N., & Ramos, J. (1989). Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway.Journal of bacteriology, 171(12), 6782-6790.
Fernández, S., Lorenzo, V., and Pérez-Martin, J. (1995). Activation of the transcriptional regulator XylR of Pseudomonas putida by release of repression between functional domains. Molecular Microbiology 16, 205–213.
Nunes-Halldorson, V. da S., and Duran, N.L. (2003). Bioluminescent bacteria: lux genes as environmental biosensors. Brazilian Journal of Microbiology 34.
Wu, N., Rathnayaka, T., and Kuroda, Y. (2015). Bacterial expression and re-engineering of Gaussia princeps luciferase and its use as a reporter protein. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1854, 1392–1399.
AIRPARIF, association for air quality monitoring in Ile de France (France)
7 million premature deaths annually linked to air pollution, WHO , 2015
//cds/reporter
//cds/transcriptionalregulator/activator
//chassis/prokaryote/ecoli
//function/reporter/light
| control | BBa_K2023007 is the positive control for GLuc |
| emit | 488 nm |
| input_s | BTEX (Toluene, Xylene...) |
| positive_regulators | Pr, Pu |
| protein | XylR |
| signalling_molecule | Gaussia Luciferase |