Microbial Energy Conversion and Biotechnology

Prof. Dr. Jörg Simon

Research Interests

Our laboratory studies microbially catalysed and environmentally relevant reactions of the biogeochemical nitrogen and sulfur cycles at the cellular and subcellular levels. We are mainly interested in the physiology and bioenergetics of anaerobic/microaerobic bacteria and focus on the enzymology of anaerobic respiration and the functional architecture of corresponding electron transport chains. Special emphasis is laid on the structure and function of quinone/quinol-reactive membrane-bound proteins and their contribution to the generation of the electrochemical membrane potential.

We use a wide range of methods in cellular and molecular microbiology in combination with genetic engineering of suitable model bacteria, omics techniques, protein biochemistry and structural biology.

Electron micrograph of a W. succinogenes cell and substrate conversions catalysed by respiratory enzymes involved in nitrate ammonification, nitrous oxide and sulfite respiration as well as in nitric oxide and hydroxylamine detoxification. Dehydrogenases (yellow) and reductases (red) are connected via the menaquinone/menaquinol pool and contribute to the generation of a proton motive force (pmf) that drives ATP synthesis. Hyd, Hydrogenase; Fdh, Formate dehydrogenase; Mcc, cytochrome c sulfite reductase; Nap, periplasmic nitrate reductase; Nrf, cytochrome c nitrite reductase; Nos, nitrous oxide reductase.
Exemplary substrate conversions of a W. succinogenes cell – for more information please click on the picture

1. Respiratory reduction of nitrate, nitrite and nitrous oxide

The biogeochemical nitrogen cycle depends on a diverse range of microorganisms that catalyse key reactions such as (i) assimilatory and respiratory (dissimilatory) nitrate and nitrite reduction to ammonium, (ii) denitrification including nitric oxide (NO) production and detoxification as well as nitrous oxide (N2O) respiration, (iii) nitrogen fixation, (iv) nitrification and (v) anaerobic ammonium oxidation (anammox).

An environmentally important intermediate of the nitrogen cycle is nitrous oxide (laughing gas), which is a potent greenhouse gas and an ozone depleting substance. We study the nitrogen metabolism of nitrate/nitrite-ammonifying bacteria that, in addition, are capable to grow by nitrous oxide respiration. A prime example for this type of energy metabolism is the non-pathogenic rumen bacterium Wolinella succinogenes (order Campylobacterales). As this bacterium is known to generate small amounts of nitric oxide (NO) and nitrous oxide during nitrate ammonification, we also explore the enzymology of nitric oxide detoxification and nitrosative stress defence.

The terminal reductase of W. succinogenes nitrous oxide respiration is a cytochrome c nitrous oxide reductase (cNosZ) that belongs to the so-called clade II of NosZ enzymes. We presented evidence that the electron transport chain that oxidizes menaquinol by nitrous oxide depends on a membrane-bound multi-protein nitrous oxide respirasome that might involve an electrogenic Rieske/cytochrome bc complex. Furthermore, transcriptome analysis suggested that nitrous oxide-grown W. succinogenes cells specifically regulate gene expression in response to nitrous oxide.

Over the last century the atmospheric concentration of nitrous oxide has been constantly on the rise. This fact is caused by the invention of man-made nitrogen fixation (the Haber-Bosch process), which led to a drastic intensification of agricultural fertilization practices and a severe anthropogenic imbalance of the global biogeochemical nitrogen cycle. In a biotechnological approach we aim to apply suitable nitrous oxide respiring bacteria to waste water sludge to reduce nitrous oxide emissions (project supported by FIF).

Selected publications

  • S. Hein, J. Simon (2019) Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions. Adv. Microb. Physiol. 75, 137-175
  • S. Hein, S. Witt, J. Simon (2017) Clade II nitrous oxide respiration of Wolinella succinogenes depends on the NosG, -C1, -C2, -H electron transport module, NosB and a Rieske/cytochrome bc complex. Environ. Microbiol. 19, 4913-4925
  • M. Kern, J. Simon (2016) Three transcription regulators of the Nss family mediate the adaptive response induced by nitrate, nitric oxide or nitrous oxide in Wolinella succinogenes. Environ. Microbiol. 18, 2899-2912
  • M. Luckmann, D. Mania, M. Kern, L.R. Bakken, Ǻ. Frostegård, J. Simon (2014) Production and consumption of nitrous oxide in nitrate-ammonifying Wolinella succinogenes cells. Microbiology 160, 1749-1759
  • J. Simon, M.G. Klotz (2013) Diversity and evolution of bioenergetics systems in nitrogen compound transformations. Biochim. Biophys. Acta 1827, 114-135
  • M. Kern, J. Volz, J. Simon (2011) The oxidative and nitrosative stress defence network of Wolinella succinogenes: cytochrome c nitrite reductase mediates the stress response to nitrite, nitric oxide, hydroxylamine and hydrogen peroxide. Environ. Microbiol. 13, 2478-2494
  • J. Simon, R.J.M. van Spanning, D.J. Richardson (2008) The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems. Biochim. Biophys. Acta 1777, 1480-1490

2. MccA-dependent sulphite respiration

In the periplasm of certain Proteobacteria including Wolinella succinogenes sulphite is reduced to sulfide by the octahaem cytochrome c MccA, which is a representative of a new class of highly active cytochrome c sulphite reductases. The high-resolution crystal structure of W. succinogenes MccA revealed an unprecedented haem c-copper active site of sulfite reduction and confirmed the presence of a haem c group bound to a unique CX15CH haem attachment site.

Currently, we explore the constituents of the corresponding electron transport chain and the process of MccA maturation, which is supposed to include the putative copper chaperone MccL.

Selected publications

  • J. Eller, S. Hein, J. Simon (2019) Significance of MccR, MccC, MccD, MccL and 8-methylmenaquinone in sulfite respiration of Wolinella succinogenes. Biochim. Biophys. Acta 1860, 12-21
  • B. Hermann, M. Kern, L. La Pietra, J. Simon, O. Einsle (2015) Octaheme MccA is a heme c:copper sulfite reductase. Nature 520, 706-709
  • J. Simon, P.M.H. Kroneck (2013) Microbial sulfite respiration. Adv. Microb. Physiol. 62, 45-117
  • M. Kern, M.G. Klotz, J. Simon (2011) The Wolinella succinogenes mcc gene cluster encodes an unconventional respiratory sulfite reduction system. Mol. Microbiol. 82, 1515-1530
  • J. Simon, L. Hederstedt (2011) Composition and function of cytochrome c biogenesis system II. FEBS J. 278, 4179-4188

3. Biosynthesis and function of methylated menaquinone derivatives

The membranous quinone/quinol pool is one of the most widespread components of bacterial and archaeal respiratory electron transport chains. Beside the well-known ubiquinone and menaquinone (MK), many bacteria produce mono- and dimethylated MK derivatives such as 8-methyl-MK and 7,8-dimethyl-MK.

We identified and characterized a family of HemN-related class C radical S-adenosylmethionine methyltransferases termed MenK, MenK2 or MqnK that methylate MK specifically at position C-8 (MenK/MqnK) or C-7 (MenK2). The MenK and MenK2 enzymes from Adlercreutzia equolifaciens were functionally produced in Wolinella succinogenes or Escherichia coli cells. We currently explore the reaction mechanism of these enzymes and the cellular function of methylated menaquinones.

Selected publications

  • S. Hein, J. von Irmer, M. Gallei, R. Meusinger, J. Simon (2018) Two dedicated class C radical S-adenosylmethionine methyltransferases concertedly catalyse the synthesis of 7,8-dimethylmenaquinone Biochim. Biophys. Acta 1859, 300-308
  • S. Hein, O. Klimmek, M. Polly, M. Kern, J. Simon (2017) A class C radical S-adenosylmethionine methyltransferase synthesizes 8-methylmenaquinone. Mol. Microbiol. 104, 449-462

Group members

Research group

Recent publications

Publications (tu-biblio)
Literature is available upon request.

Open positions

We are seeking highly motivated students at the BSc, MSc and PhD level. Projects for Bachelor and Master theses for students from Biology, Biochemistry and Biomolecular Engineering are offered in the research areas described above. Please contact Jörg Simon for details on current projects.