DcmR and regulation of dcmA expression

Mutants with dcmA and the intergenic region but without complete dcmR express DcmA constitutively. Re-integration of dcmR restores regulation of dcmA expression at the transcriptional level [1]. In addition, it has been shown that the region including dcmR, the intergenic region and dcmA is sufficient to confer a DCM dependent response in genetically engineered Methylobacterium extorquens DM4 [2].

DcmR and DNA-binding

DcmR is thought to be a DNA binding protein as structure predicting software indicates that there is a helix-turn-helix domain at the N-terminal of the protein. Since the region between the two promoters for dcmR and dcmA can be deleted without any effect on regulation it has been suggested that DcmR does not to a secondary regulatory site in between the genes but most likely acts directly on the dcmA promoter itself [1]. In addition, regulated expression of dcmA is not effected when the dcmR and dcmA transcriptional units are placed on separate replicons thereby suggesting that their topology is independent of the regulatory network. It is therefore suggested that DcmR binds the DNA in the intergenic region with the simplest model of its mode of action being as a trans-acting DNA-binding repressor; however this remains to be fully validated [1].

We have therefore proceeded on the assumption that DcmR is directly influenced by the presence or absence of DCM and furthermore that we can use dcmR, the intergenic region and dcmA alone to characterise the regulatory network.

[1] La Roche, S. D., and T. Leisinger. "Identification of dcmR, the regulatory gene governing expression of dichloromethane dehalogenase in Methylobacterium sp. strain DM4." Journal of bacteriology 173.21 (1991): 6714-6721.
[2] Lopes, N., et al “Detection of dichloromethane with a bioluminescent (lux) bacterial bioreporter” J Ind Microbiol Biotechnol (2012) 39:45–53

Characterising the DcmR - DCM - P_dcmA interaction

To find out whether the gene dcmR acts as a repressor or an activator on the promoter of the dcmA gene, we attempted to build the genetic circuit shown above on the right. Having dcmR under inducible TetR expression should allow us to have very good control of the amount of DcmR present. On top of this, attaching the mCherry fluorescence tag will act as another confirmation to the amount of DcmR present.

We then extensively modelled the circuit to discover how the response of the system would differ if it was either of the two circuit systems. Click the modelling bubbles (pink) to find out exactly how we achieved this.

Predicting the mCherry fluorescence

We simplified the first double repression by modelling it as an activation of dcmR by ATC, albeit parameterised by different constants. This assumption is justified by the fact that we are able to precisely control the addition of ATC and measure the fluorescence of the mCherry.

We modelled this first step using both deterministic and stochastic models.

Biochemical equations

The biochemical equations that describe the behaviour of the top half of the genetic circuit are:

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Deterministic

Deterministic models are very powerful tools for synthetic biology. They describe the behaviour of the bacteria at the population level and use Ordinary Differential Equations (ODEs) to relate each activation and repression. By constructing a cascade of differential equations one can build a realistic model of the average behaviour of the system.
The differential equation that descibes this first step of the system is:












Solving this ODE in Matlab (with zero basal transcription rate) predicts the following the response of the system:

This model works assuming that sufficient TetR is always present.

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While the analysis of this circuit is not critical to the successful outcome of this part of the project, it will provide us with very good practice of both obtaining fluorescence time series data and accurately fitting the data to the model. It will also help us develop our methods of predicting future system behaviour. This is because this system is already well documented in the literature and so we should be able to test our methods and responses against well documented results from labs across the world.

As you can clearly see from the graph, the model predicts a large fluorescence increase as the input is added. This is the what we expect from the actual system and is the best approximation that is obtainable before we get experimental data.

In the graph above, the model is set to have a basal transcription rate of zero. This is why there is a zero fluorescence response before the input has been added - this corresponds to the tetO promoter not being leaky at all. This basal rate will be calibrated alongside all of the other parameters in the model.

Stochastic Modelling

Stochastic modelling uses probability theory to predict the behaviour of a system. For our project, we used it to model the expression of GFP from bacteria.

We started with the Gillespie Algorithm, which considers the expression of GFP to be binary; a molecule of GFP is either produced or degraded. We modelled the probability of a molecule of GFP being created using the Michaelis-Menten model, incorporating a basal transcription rate. For the degradation, we assumed a simple proportional relationship; the more you have the more likely it is that a molecule degrades. The constant of proportionality will be a function of the intrinsic life time of the protein in the cell. Because it is not necessary for a reaction to occur at every time interval, before determining the nature of a reaction, the code had to predict whether any reaction would occur at all. We achieved this by using the random number generator on Matlab and comparing the random figure generated to the overall probability of a reaction occurring. To then work out which reaction occurred we compared the relative probabilities of production and degradation, and used the same random number generator to determine the nature of the reaction.

We later changed this code so that a reaction occurred every time increment, but included a null reaction where no GFP was degraded or created. Although this made the code a lot more data heavy, it allowed for much easier calculation of the mean response of multiple realisations.

Stochastic modelling is useful because it builds in the random effects which are often seen in real bacteria. By calculating the variation of the mean of multiple GFP producing bacteria, we can also work out the standard deviation. If we then assume that the system varies with respect to the normal distribution, we can produce error bounds for the production of GFP. Such that we can say, 90% of the time we can expect the production of GFP from a single bacterium to be within these 2 curves. This could be useful for seeing if results are unexpected, or, if there are multiple outliers, that our model is incorrect. If we average more and more bacteria then the mean curve tend towards the deterministic response. This is to be expected as we are now looking at the system as a whole and fluctuations in the production from individual bacteria are averaged out. Sto for small Det for large What is stochastic modelling? -- Yes How is it useful? Ads/Dis -- Getting there Tending to deterministic -- Yes Modelling activator repressor --? Parameter characterisation/Data matching -- Not yet Matlab graphs – Not yet Improve Gillespie algorithm bit

Matlab graphs

Predicting the sfGFP fluorescence

Introduction

To allow us to characterize the second half of the genetic circuit, we needed to be able to predict the difference in response. To do this, we constructed models by cascading the differential equations according to the respective circuit structures thereby producing two different potential system responses.

To achieve this, we constructed simplified equivalent circuits that were linked by two potential activation-repression relationships.

It is important to understand that these simplified equivalent circuits will not give the correct mCherry response but they will give the correct GFP response after correct parameterisation.

We then set up the differential equations necessary to solve this problem in Matlab. The method and results are as detailed below:

INSERT SENSITIVITY GRAPH HERE

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Conclusion

The bottom graphs illustrate the predicted response of each system to a simultaneous step input of both DCM and ATC. As you can see, there is little difference in the predicted steady-state value of the fluorescence, however, providing the basal transcription rate of GFP is relatively low, there should be a clear difference in the level of fluorescence before either of these inputs are added. This very easily identifiable difference between the two systems will enable us to characterize the genetic circuit present in our particular system.

Calculating the parameters

Calculating the many parameters for this system will be undoubtedly challenging.

How are we calculating the parameters?

Go to the data section where we calculated parameters for this part of the circuit.

Wetlab data showing response in level of mCherry expressed with different concs of ATC

By making a translational fusion of mCherry at the C terminus of the dcmR gene under the tet promoter and tet operator system(see our Construction page for details) we could measure mCherry fluorescence to gain information about dcmR induction by ATC. Expression was induced with various amounts of ATC and the following fluorescence data acquired. Exposure time was 0.2 seconds. As no calibration data was obtained using purified mCherry, the results have been left in fluorescence arbitrary units. Images were analysed using imageJ software.
mCherry fluorescence increases with amount of ATC used confirming that the dcmR gene was expressed under the control of the tet promoter and operator system.



This data was then used to refine and test our models (see below).

Introduction

As you can see from the biochemistry bubble above, our team was only able to obtain fluorescence data for the first half of the genetic circuit (ATC induced mCherry response). On top of this, the wet lab team were unable to obtain data that measured how the fluorescence of a single culture changed with time, again because of time constraints. This is slightly limiting because it means that we don’t have any dynamic data for any part of our system, and therefore can’t test the modelling predictions of the speed of the biosensor’s response.

The original data is shown on the right with error bars showing the standard error of the measurements.

Standard error is calculated as the average standard deviation divided by the square root of the total number of readings.

How we used the model

However, to demonstrate the power of the computer models that we’ve built, we made our model simulate the same graph (mean fluorescence against ATC concentration added). To build this, we started from the graph shown in the first modelling bubble on this page, shown here with a small basal rate (see where did these equations come from? ). This graph shows how the predicted fluorescence of the cells changes with time in response to an addition of ATC halfway along the time scale. At this stage, all input values, model parameters and therefore results are arbitrary.



We then ran the model for the correct amount of time (2 hours 20mins incubation with ATC) and ran it for lots of different concentrations of ATC over the range that the wet-lab team tried. The parameters are still arbitrary at this point (the same as above) and the results of the graphs are therefore arbitrary are as well, but the input values are now correct. The graphic below shows how we used the existing model to obtain the same graphs as the wet-lab team had obtained.

The numerical inputs that were used to model this data set were therefore:





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Parameters

As all results are arbitrary up to this point, it is now time to calculate the parameters that will make the model’s response match up with the wet-lab data. The purpose of doing this is that the model will be able to give relatively accurate predictions of the response of the bacteria to further testing, therefore making the development of the biosensor much more efficient. The amount of data here will not allow us to calculate the parameters to a high level of accuracy, but it should be able to give us some very good approximations of what we can expect.



The parameters that we need to calculate are the constants in the differential equation that governs the behaviour of the first half of the genetic circuit. This half of the system is shown again here to remind the reader which part we are considering.

These parameters are:

α1 = expression rate constant of dcmR

k1 = Michaelis - Menten constant of dcmR

d1 = degradation constant of dcmR

β1 = Basal transcription rate of dcmR

Remember that because the mCherry gene is tagged (translational fusion) onto the end of the dcmR gene, the mCherry fluorescence will be the same as the amount of DcmR protein present. However, there is not very comprehensive data in the literature about the values that we can expect from the behaviour of the dcmR gene and its stability in vivo.

Degradation constant

The initial steady state of the system (before ATC has been added) is determined by two constants in the model. These constants are the degradation constant of DcmR and the basal transcription rate of the system. Due to the lack of numerical information in the literature on the behaviour of the dcmR gene, the way of calculating these two parameters is by using the single basal rate data point from the wet-lab data (fluorescence value when 0ng of ATC has been added).

If we assume that the half-life of the dcmR protein is 3 hours [1] (180 minutes), we can calculate the degradation constant for our model. The exponential protein decay is therefore described by:

Basal transcription rate

At the basal steady state, the rate of change of DcmR (and therefore fluorescence) is zero. As no ATC has been added to the system yet, the value of [ATC] is also zero.

This simplifies the equation to:

As we want our model to accurately predict the fluorescence, we will substitute the fluorescence value in place of the [DcmR] and rearrange:

Substituting in the value for δ1 that we found above and the basal steady state fluorescence level from the data (471 to 3 s.f.) gives the basal transcription rate as:

Expression rate constant and Michaelis - Menten constant

After the ATC has been added to the system, the value of [ATC] becomes non-zero. This means that the expression constant and the Michaelis – Menten constant start to affect the system.

To find the parameters that make the model’s output match the data values, we turned to the code that we had developed for parameter calibration.

How are we calculating the parameters?

This code gave the parameters as:

α1 = expression rate constant of dcmR

= 16.5 (fluorescence/min)

k1 = Michaelis - Menten constant of dcmR

= 0.015 (1/ng)

Entering the correct parameters

When the parameters that had been calculated above were entered into the model:

alongside the correct inputs:

The graph below shows the model's predictions plotted in the same figure as the data points that the wet-lab team obtained for the system:

Plotting the model's output as a by interpolating between the calculated values makes the graph clearer:

Sensitivity

An important part of building mathematical models is sensitivity analysis of the results. This can be basically explained as wiggling all of the input values and parameters to see how much variations in each of these values affects the system output. This is especially important for finding parameters to describe the system as it is important to know what level of accuracy the values need to be found to provide a reasonable degree of prediction accuracy.

On top of this, it is possible to find what range of values the system is especially sensitive to. An example of this analysis is shown with a simple example that is relevant to our system below:

Stability

In our Engineering studies we have learnt detailed control theory. Control theory is an interdisciplinary branch of engineering and mathematics that deals with the behaviour of dynamical systems with inputs, and how their behavior is modified by feedback. The usual objective of control theory is to control a system so that its output follows a desired control signal, called the reference, which may be a fixed or changing value. This important because many dynamic systems can go unstable if they are given an unsafe set of input values and/or operating conditions.

However, as there are no feedback loops in this synthetic circuit, control theory analysis of this system isn't necessary.

Future experiment ideas from an Engineering design perspective

To see details about how the wet lab team then used this model to guide their work see our optimisation page.

Reference

[1] Dr George Wadhams by personal communication (14/10/2014)

The first data readings that we managed to obtain from the completed genetic circuit were qualitative sfGFP fluorescence readings. The results of these are shown here:

First system tested

The first system that we tested is shown here. This is the bottom level of our synthetic circuit. Testing just this plasmid allowed us to obtain some important information to allow us to characterise the genetic system.

The GFP fluorescence of this system was high and this is the basal transcription rate of the PdcmA promoter.

Second system tested

The second system that we tested was the whole synthetic system without any DCM added. This allowed us to analyse just the effect of DcmR on the PdcmA promoter when it was compared to the result from system 1.

The fluorescence was much lower than the basal transcription rate of the PdcmA. This strongly suggests that the DcmR protein acts as a repressor of the PdcmA.

The next step is to prove that adding DCM represses this repression and increases the sfGFP fluorescence of the system.