Team:Dundee/Project/ProductionExport

The ToxiMop is an engineered E. coli bacterium that expresses PP1 and can be used as a molecular mop to remove microcystin from contaminated water. Central to successfully engineering this machine was to better understand PP1 production and export. This was crucial as we hypothesised that microcystin binding would predominantly take place with periplasmic PP1.

We explored both the Twin Arginine Translocase (Tat) and General Secretory (Sec) pathways as potential export routes for PP1. However, initial Western blot results indicated that PP1 was exported into the periplasm much more successfully via the Tat pathway than via Sec. Therefore, production and export based on Tat transport, was selected as a modelling focus to allow us to optimise the construction of our prototype ToxiMop.

Building a Model for Tat Transport

The Tat machinery is a biological pathway that transports folded proteins from the cytoplasm into the periplasm. It consists of three small membrane proteins; TatA, TatB and TatC.

TatB and TatC together form a TatB-C complex. The protein destined for transport has a signal sequence at its N-terminus which is recognised by and binds to the TatB-C complex. This positions the protein ready for export. TatA proteins then polymerise and form a ring structure surrounding the protein allowing it to penetrate the membrane and pass into the periplasm. The signal peptide is cleaved off and this frees up the TatB-C complex and TatA proteins for further transport.

Figure 1: Processes involved in Tat transport.

Tat-dependent Transport of PP1

PP1 has a molecular mass of 37kDa. Reasonably assuming that PP1 is spherical, it would require 20 TatA proteins to form a ring large enough to accommodate it and enable it to penetrate the membrane [1]. We define this structure as a TatA assembly.

For transport, PP1 in the cytoplasm (PP1_cyto) binds to TatB-C, forming a PP1 TatB-C complex (PP1B-C). The TatA assembly then surrounds the PP1 TatB-C complex. We define this product as PP1_export. PP1_export is then exported into the periplasm (PP1_peri), releasing the TatA assembly and TatB-C back into the membrane to assist in further rounds of transport.

We make the following further assumptions:

• TatA assemblies are pre-formed from TatA proteins
• PP1 exported to the periplasm remains in the periplasm
• All other processes are reversible

Figure 2: Ring structures formed by polymerisation of TatA proteins. Taken from Rodriguez et al. [2]

Hence we have the following framework for Tat transport of PP1:

Production

Before transport, PP1 first needed to be produced. This involved inserting the PP1-encoding gene into a plasmid vector and transforming the plasmid into host cells. These cells then expressed the gene.

We now consider the transcription and translation required for this gene expression. This simple production scheme is derived by assuming that both mRNA and protein can degrade. Due to the heterologous nature of PP1, its degradation constant is particular significant.

Using the law of mass action and appropriate rate constants, we created a mathematical system that represents each reaction. These values and equations are shown below:

Reaction name	Constant	Value
Transcription	KTc	0.03833 nM.s-1
mRNA degradation	Kmdeg	0.0077 s-1
Translation	KTl	0.75 s-1
PP1 degradation	Kpdeg	0.0192 s-1

Table 1: PP1 production rate constants [3].

Our team developed a series of MATLAB programs to solve the models discussed here. The code for these programs along with further analysis is available at this repository [4]. The program v1_odes_solver_PP1Production solves this system numerically.

Our model predicts that we will produce approximately 1200 net PP1 in steady state in the cytoplasm of each E. coli chassis. This gives an initial indication of how many cells are required to mop up given concentrations of microcystin. We used this information to examine the practicality of the ToxiMop. For example, if we assume all the PP1 is exported to the periplasm and exploit the one-to-one binding of microcystin with PP1, then 0.6g of cells are required to clean up one litre of contaminated water that is classified as unsafe by World Health Organisation (WHO) regulations. The production of this mass of cells was easily achievable by our Wet Team.

Production & Export

Combining our separate schemes for protein production (2) and Tat transport (1), we built a model that describes PP1 Production & Export.

Reaction name	Constant	Value
Transcription	KTc	0.03833 nM.s-1
mRNA degradation	Kmdeg	0.0077 s-1
Translation	KTl	0.75 s-1
PP1 degradation	Kpdeg	0.0192 s-1
Recognition binding	K1	8E3 M-1s-1
Recognition unbinding	K2	8E3 M-1.s-1
Assembly association	K3	200E4 M-1s-1
Assembly disassociation	K4	0.00167 s-1
Export	K5	10 s-1

Table 2: PP1 production & export rate constants [3].

Deterministic Model

To solve the system of ODEs (5), we applied the appropriate initial conditions. The only non-zero initial conditions are the number of TatB-C complexes and TatA proteins. It is known that there are approximately 15 TatB-C complexes and 600 TatA proteins in a regular E. coli cell [5]. Hence, in our model we use 15 TatB-C complexes and 30 TatA assemblies.

The program v1_odes_solver_PP1_TatProduction_export solves this system. The deterministic model predicted that approximately 200 PP1 molecules would be exported to the periplasm. This was less than we anticipated. Indeed, based on these figures, 3.3g of cells would be required to clean up one litre of contaminated water as defined by WHO regulations.

Stochastic Model

In order to check whether these deterministic results were reasonable, we next considered a stochastic modelling approach. Some of the components in the ODE model above are in low abundance. To examine whether low copy number had a significant effect on PP1 numbers, we formulated and analysed a stochastic model.

The stochastic model, although better representing the random nature associated with such processes, did not produce significantly different results. Instead the model showed that because the high and low fluctuations cancel each other out, the deterministic solutions were a good approximation of the stochastic means for PP1cyto and PP1peri.

Figure 9: PP1_cyto Stochastic realisations & Deterministic Solution [8]

Figure 10: 2PP1_peri Stochastic realisations & Deterministic Solution [8]

Model Predicts Failure of Basic Mop

As discussed above, the model predicts that 3.3g of the basic mop would be required to clean up one litre of contaminated water as defined by WHO regulations. This equates to an impractically large quantity. Moreover, with these basic cells the Wet Team started testing the ToxiMop. Their initial experiment involved taking 20 µl from a 100 µg/ml microcystin solution and mixing it into a beaker with 200ml of TBS. 1g of ToxiMop cells was then added to the solution in a dialysis bag. Early results indicated that the ToxiMop was ineffective in mopping up the microcystin. We tried to get an understanding of why the tests were unsuccessful.

As detailed in (6), the model predicted that 5.75g of cells would be required to clean up the toxin present in the experimental sample. Hence the 1g of cells used was vastly insufficient. We recommended the use of 5.75g of cells in a repetition of the same experiment. However, this was viewed as being unpractical and hence the Team decided to pursue ways of improving the efficiency of the mop.

Enhancing the Tat Machinery

We next used our model to investigate how PP1 export could be enhanced. Our first thought was that this could be achieved by increasing the amount of Tat machinery per cell as the existing model predicted that in steady state, a significant proportion of the PP1 molecules were retained within the cytoplasm and thus cold not assist in he the binding of microsystin. By increasing the Tat machinery, we hypothesised that augmented transport from this bank of proteins to periplasm would have the desired effect. The options we considered were; increasing TatA assemblies, increasing TatB-C complexes or simultaneously increasing both TatA assemblies & TatB-C complexes.

All of these options were simulated to examine their effects on the number of PP1 being exported. This allowed us to determine the best option to pursue in the Wet Lab.

Experimentally, this increase could be achieved by inserting selected genes into a plasmid with a copy number of 20. This would allow us to obtain 20 extra copies of the selected Tat machinery proteins. Therefore our cells could theoretically produce 20 times the quantity of targeted proteins. The simulations below show the effect of increasing the machinery above the default level (30 TatA assemblies & 15 TatB-C complexes) to 20 times these values.

Increasing TatA assemblies

Increasing TatB-C complexes

As shown in the figures above, increasing the number of TatB-C complexes, predicts a 3-fold increase in the number of PP1 molecules exported into the periplasm. This change is sufficient to improve the efficiency of our ToxiMop cells - with such an increase, the mass of cells required for clean-up is reduced by a factor of three.

Increasing TatA assemblies & TatB-C

Increasing both the number of TatA assemblies and TatB-C complexes increases the number of PP1 in the periplasm by a factor of almost four. Of the possible options, this gives us the greatest increase in PP1 exported with the associated reduction in the number of cells required to effectively deal with a given microcystin load.

In conclusion, the model predicted that increasing TatA assemblies alone does not provide a sufficient change in the number of exported PP1. Combining this with an increased TatB-C complex number is predicted to produce the highest potential for PP1 export. Therefore, for our ToxiMop experiments, we recommended this option. However, we suggested to the Wet Team that they take into account the stress being placed upon the cells with these multiple enhancements and hence if only one variation could be viably introduced, then they should select the TatB-C pathway.

References

• 1. Leake, Mark C., et al. "Variable stoichiometry of the TatA component of the twin-arginine protein transport system observed by in vivo single-molecule imaging." Proceedings of the National Academy of Sciences 105.40 (2008): 15376-15381.


• 2. Rodriguez,Fernanda, et al. “Structural model for the protein-translocating element of the twin-arginine transport system.” Proceedings of the National Academy of Sciences 110( 2013). 1092-101.
  
• 3. Stamatakis, Michail, and Nikos V. Mantzaris. "Comparison of Deterministic and Stochastic Models of the lac Operon Genetic Network." Biophysical journal 96.3 (2009): 887-906.


• 4. MATLAB program repository: https://github.com/cdjohnston/CraigiGEM-MATLAB


• 5. Palmer, Tracy, and Ben C. Berks. "The twin-arginine translocation (Tat) protein export pathway." Nature Reviews Microbiology 10.7 (2012): 483-496.


• 6. Higham, Desmond J. "Modeling and simulating chemical reactions." SIAM review 50.2 (2008): 347-368.


• 7. https://github.com/cdjohnston/CraigiGEM-MATLAB/blob/master/Production%20%26%20Export/Stochastic%20Models/v1_ssa_PP1_TATproduction_export.m


• 8. https://github.com/cdjohnston/CraigiGEM-MATLAB/blob/master/Production%20%26%20Export/Stochastic%20Models/v2_ssa_PP1_TATproduction_export.m


• 9. https://github.com/cdjohnston/CraigiGEM-MATLAB/blob/master/Production%20%26%20Export/Stochastic%20Models/v6_ssa_PP1_TATproduction_export.m


• 10. https://github.com/cdjohnston/CraigiGEM-MATLAB/blob/master/Production%20%26%20Export/Stochastic%20Models/v7_ssa_PP1_TATproduction_export.m


• 11. https://github.com/cdjohnston/CraigiGEM-MATLAB/blob/master/Production%20%26%20Export/Stochastic%20Models/v8_ssa_PP1_TATproduction_export.m