Acetone carboxylation as a model reaction for hydrocarbon activation
In this project, we study the biochemistry and physiology of bacteria which degrade acetone in the absence of oxygen. Our interest focuses on the elucidation of the reaction mechanism by which acetone is activated in nitrate-reducing, sulfate-reducing, and fermenting bacteria.
In earlier studies on anaerobic degradation of acetone by nitrate-reducing bacteria, we could document for the first time that acetone was carboxylated to acetoacetate; and a similar mechanism was assumed to operate in sulfate-reducing and fermenting bacteria which cooperate syntrophically with methanogens.
The acetone-carboxylating enzyme systems described so far for aerobic and phototrophic bacteria invest two ATP equivalents into this reaction, and the same appears to be true also for the nitrate-reducing bacteria studied in our lab. Different from those, sulfate-reducing and fermenting bacteria are extremely energy-limited and cannot afford to spend so much energy in this activation reaction. First experimental evidence indicates that these bacteria employ a basically different strategy which requires substantially less energy expenditure.
The expected novel mechanisms for acetone activation by carboxylation or alternative reactions will help to provide models for a better understanding of similar reactions that appear to underly also the activation of phenols, aniline, and aromatic hydrocarbons by different types of anaerobic bacteria.
Anaerobic phosphite oxidation
Project leader: Dr. Diliana D. Simeonova
The main objective of this project is to analyze the biochemistry of phosphite oxidation in the energy metabolism of anaerobic bacteria.
Microorganisms are active in redox transformations of many elements in nature, including C, N, S, H, O, Fe, Mn and other metals. Phosphorus, which is an important element in microbial nutrition and metabolism, is usually considered as an element which does not change its redox state. This element is mainly present in biochemistry in the redox state of phosphate (P[+V]). Nevertheless, small amounts can be found also in the redox state of phosphite (P[+III] or hypophosphite (P[+I]).
In our laboratory, a strictly anaerobic bacterium Desulfotignum phosphitoxidans has been isolated which couples phosphite oxidation with sulfate reduction or with the homoacetogenic reduction of CO2 to acetate. The ability of this strain to use reduced phosphorus substrates in its energy metabolism was the first evidence of dissimilatory anaerobic phosphite oxidation (Schink, and Friedrich, 2000; Schink et al., 2002).
Recently, we have identified a new protein specifically induced only in the presence of phosphite, a new NAD(P)-dependent epimerase/dehydratase (Simeonova et al. 2009). Furthermore, we have successfully identified the entire locus (ptxED-ptdFCGHI) involved in anaerobic dissimilatory phosphite oxidation in D. phosphitoxidans, which encompasses four entirely new genes – the ptdF, ptdC, ptdH and ptdI. Four of the genes (ptxD-ptdFCG) were cloned and heterologously expressed. They were sufficient to confer phosphite uptake and oxidation ability to the host strain, but did not allow use of phosphite as an electron donor for chemolithotrophic growth (Simeonova et al., 2010).
Our further studies on Desulfotignum phosphitoxidans will contribute to reveal a new type of bacterial energy metabolism.
Microbial degradation of synthetic polymers
In nature, polymers are being synthesized for a broad variety of applications, such as catalytically active polymers (proteins, nucleic acids), storage polymers (starch, glycogen, poly-ß-hydroxybutyric acid) or structural polymers (cellulose, hemicelluloses, keratin, lignin). Chemically synthesized (synthetic) plastics are usually not biodegradable because they do not contain the linkages typical of biological polymers (peptide linkages, glycosidic linkages, ester linkages) that can be hydrolytically cleaved by specific enzymes. Biodegradability is a feature of interest especially for packaging material which enters the waste treatment process after a comparably short turnaround time. The development of biodegradable plastics and other synthetic polymers has to combine the knowledge on microbial biodegradation strategies with the skills of specific polymer synthesis and the desired properties of the polymeric product (rigidity, water resistance etc.). Since waste material in dump sites, compost heaps etc. are to be decomposed preferentially under conditions of oxygen limitation we are specifically interested in the development of polymer materials that are degradable in the absence of oxygen.
This project is carried out in cooperation with a partner in chemical industry.