Genetical approach

Figure XXX: Module 1 overview

Our first module deals with the construction of an E. coli strain, which is able to accept electrons stimulating its metabolism. We regard on different electron transfer systems: direct and indirect electron transfer.
Direct electron transfer in bacteria is a very complex and not completely cleared up so far. So we focused on the indirect electron transfer via a mediators, which is reduced at the electrode in a electrobiochemical reactor and would be reoxidized again by bacterial cells. In gram-negative bacteria E. coli there are two membranes with a periplasmatic space between, which has to break through in the course of electron transfer.
We worked on three different mediators: neutral red, bromphenol blue and cytochromes. Additionally we are going to construct an electrophilic E. coli strain, which grows by the help of electric power because of increased metabolic activity. (Park et al., 1999)
To realize that, several steps and problems in electron transfer has to be resolved. The electron transfer system consists of different steps. First of all the reduced mediator has to cross the outer membrane of E. coli cell. For that we are going to use outer membrane porine OprF (BBa_K1172507) provided by iGEM Team Bielefeld-Germany 2013. Crossing the periplasmatic space, the mediator adsorb at inner membrane of E. coli cell. Electrons has to be transferred into cytoplasm, but the mediator should not enter the cell, because regeneration at the electrode is absolutely necessary. So membrane proteins are required to transfer electrons trough the inner membrane. We looked for different oxidoreductase systems located in bacterial respiration system (shown in figure 1). We focused on respiratory complex II, which contains the succinate dehydrogenase (SDH). This enzyme catalyzes oxidation of succinate into fumarate by transfering electrons to FAD⁺ generating FADH₂. (Iverson et al., 1999; Richardson et al., 1999)
FADH₂ enter the electron transport chain and achieve proton translocation over the inner bacterial membrane. The proton motoric force is used by ATP synthase. Generated ATP effects an increasing metabolic activity. (Gottschalk et al., 1986)
So our aim is to generate a succinate overage in the cytoplasm by increased fumarate reductase activity. The reduced mediator functioned as electron donor for fumarate reductase. Reduction and oxidation between fumarate and succinate creates a loop into the citric acid cycle. In fact electrons are transferred from the mediator to FAD⁺ regenerating ATP via electron transport chain. This concept was successful shown in succinate producing Actinobacillus succinogenes by Park et al., 1999. Naturally E. coli cells release overproduced succinate into the media. This occurs especially under anaerobic conditions because bacteria use fumarate as final electron acceptor instead of oxygen. The resulting succinate would transport out of the cell via C4 carboxylate transporter dcuB. (Janausch, 2001; Unden et al., 1997) In connection to our second module we planed working under oxygen limited condition, hence effective carbon dioxid fixation is possible. Because of that, C4 carboxylate antiporter DcuB has to be knocked out in our E. coli strain.

In conclusion we are going to modify metabolic pathway of fumarate by knockout of C4 carboxylate antiporter DcuB in E. coli and overexpression of different fumarate reductases. Besides outer membrane porine OprF had to be integrated into bacterial chromosome to ensure constitutive expression of OprF and reduce plasmid overload of bacterial cells.

Figure 1: The electron flow in the respiratory chain.

Fumarate Reductase

We worked on expression of different fumarate reductases: Fumarate reductase (Frd) from Escherichia coli and Fumarate reductase (Fum) from Actinobacillus succinogenes both under controll of the T7 promotor in different E. coli strains. In figure 2 our concept is visualized with neutral red as a mediator. Fumarate reductase has a key role in our first module because this enzyme makes sure that electrons are transfered from reduced mediator into bacterial cells. It leads to increased succinate production, which support ATP production and generation of reductive power, for example FADH₂.

Figure 2: The electron flow mediated by redox active mediator in interaction with fumarate reductase in E. coli cell.

Fumarate reductase is part of the anaerobic fumarate respiration in E. coli. It catalyzes the reaction from fumarate into succinate using fumarate as final electron acceptor in anaerobic fumarate respiration. The related enzyme in aerobic respiration is succinate dehydrogenase, which catalyse the reaction from succinate to fumarate. The electrons were transferred from to FADH₂ producing fumarate. Succinat dehydrogenase is also a membrane enzyme and it is part of the citric acid cycle. They both belong to respiration complex II. (Iverson et al., 1999)
Fumarate reductase catalyses the reverse reaction of succinate dehydrogenase, so there isn´t activity of both enzymes at the same time in E. coli cells. Electrons were transferred under anaerobic conditions from intermediates of electron transport chain to fumarate. Resulting succinate is secreted into the media to take electrons out of the cell.
In our project we use fumarate reductase in combination with an extracellular mediator as electron donor to transfer electrons into bacterial cells. The reduced mediator cross the outer membrane of E. coli through outer membrane porine OprF (BBa_K1172507). Mediators adsorb at inner membrane and transfer electrons to fumarate reductase. After that the reduced fumarate reductase transfer electrons to fumarate producing succinate. This process has been shown for fumarate reductase in Actinobacillus succinogenes by Park et al..
Preventing succinate excretion succinate can serve as substrate for succinate dehydrogenase, which catalyzes oxidation of succinate into fumarate again. So we create a loop in the citric acid cycle between fumarate and succinate generating FADH₂ as reductive power in the cell. Electrons are transferred to FAD+, which generate proton translocation from cytosol into the periplasmatic space. The proton motoric force achieve ATP production. So mediator-dependent activity of fumarate reductase could serve as energy source for bacterial cells.
We are going to compare activity of fumarate reductases (Frd) from Escherichia coli KRX and fumarate reductase (Fum)from Actinobacillus succinogenes working with different mediators, for example neutral red oder bromphenol blue, as electron donor.

C4 Carboxylate Antiporter DcuB

Under anaerobic conditions E. coli cells use different alternative electron acceptors instead of oxygen. In part the bacteria use fumarate respiration, whereby fumarate is reduced into succinate. There are also other potential less-oxidizing substances for bacteria to release their electrons, for example anorganic compounds like nitrate (NO₃^-) or sulfate (SO₄^2-).(Gottschalk et al., 1986) Fumarate respiration leads to succinate excretion through C4 carboxylate transporter DcuB. It is an antiporter which exchange fumarate against succinate under anaerobic conditions. Under aerobic condition there is usually no succinate release observed. In connection to our second module we planed working under oxygen limited condition, hence effective carbon dioxid fixation is possible. Because of that, C4 carboxylate antiporter DcuB has to be knocked out in our E. coli strain.
A further important point in our project is the transport of the electrochemical reduced mediator into bacterial cells. First of all the reduced mediator has to cross the outer membrane of E. coli cell. For that we are going to use outer membrane porine OprF (BBa_K1172507) provided by iGEM Team Bielefeld-Germany 2013.
We planed a targeted knockout of dcuB gene in E. coli KRX using Genebridge Red/ET-System. In the same step we are going to integrate the outer membrane porine OprF (BBa_K1172507) into bacterial chromosome under controll of a constitutive promotor (BBa_J23104). This ensure the permeability of outer membrane and avoid a plasmid overload of the bacteria, because for our system the outer membrane porines are indispensable.

Cytochromes

Besides the intention of using a mediator for indirect electron transfer we additionally focused on the electron transfer via cytochromes. Although the exact mechanism of electron transfer by cytochromes is not clarified up to now there are a few basic approaches that indicate which ones could have an important function. The basic idea of this attempt is to bring a periplasmatic cytochrome which is essential for electron uptake in E. coli and use it as an intermediate electron acceptor. Therefore we decided to work with a key-type cytochrome c of Geobacter sulfurreducens because it has been shown that biofilms of this organism are capable of accepting electrons from an electrode. Furthermore it has been demonstrated that the mechanism of electron delivery and electron uptake varies in view of involved proteins. In this case the deletion of the corresponding gene GSU 3274 inhibits the electron uptake completly
Figure 3 shows the general principle of the electron flow.

Figure 1: The electron flow mediated by redox active molecules.

Therefore the periplasmatic cytochrome leaves the periplasm through the porins in the outer membrane, gets reduced at the cathode and enters the periplasm again. There the fumarate reductase which is located in the inner phospholipid membrane oxidized the cytochrome again and is thereby the connective element which transfers the electrons into the cell. These supplied electrons increase the succinate production and together with the succinate dehydrogenase the metabolic activity of the cells should be enhanced.

References

• Iverson et al., 1999. Structure of the Escherichia coli Fumarate Reductase Respiratory Complex. Science, vol. 284, pp. 1961-1966
• Janausch, 2001. Rekonstitution des Fumaratsensors DcuS in Liposomen und Transport von Fumarat und Succinat in Escherichia coli. Doctoral dissertation at Johannes Gutenberg-Universität Mainz, Germany
• Gottschalk et al., 1986. Bacterial Metabolism. Springer-Verlag, New York, Berlin, Heidelberg, Tokyo
• Park et al., 1999. Utilization of Electrically Reduced Neutral Red byActinobacillus succinogenes: Physiological Function of Neutral Red in Membrane-Driven Fumarate Reduction and Energy Conservation. Journal of Bacteriology, vol. 181, pp. 2403-2410
• Richardson et al., 1999. Bacterial respiration: a flexible process for a changing environment. Microbiology, vol. 146, pp. 551-571
• Unden et al., 1997. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochimica et Biophysica Acta, vol. 1320, pp. 217-234