Assimilation and biosynthetic pathways: molecular tricks and adaptation

When drawing metabolic pathways, we tend to forget that some reactions are unrealistic in the cellular context due to the production of toxic compounds, thermodynamic bottlenecks, or even reactions for which enzymes have not yet been identified. This research axis aims to understand the molecular tricks microbes use to carry out the challenging reactions that allow them to assimilate the basic elements (e.g., carbon, nitrogen, sulfur) they need to synthesize all the cellular building blocks.

The sulfate-assimilation pathway of a marine methanogen is a roaring example of the success of our approach. Here, via a combination of microbial physiology, genome mining, phylogenetic analyses, structural biology, enzymology, and even spectroscopy, we elucidated the entire assimilatory pathway and determined that the reactions eliminating the poisons sulfite (SO32-) and 3´-phosphoadenosine 5´-phosphate are faster than they are produced.

One of our core projects on this axis is the nitrogen-assimilation capability of a hyperthermophilic archaeon. Here, we aim to understand the regulation of the different pathways and how the different enzymatic actors operate.

Selected publications

  • Wissink M, Engilberge S, Leão P, Jansen RS, Jetten MSM, Royant A, Welte CU, Wagner T. Mini-bacterioferritins: Structural insight into a new type of ferritin-like protein from the anaerobic methane-oxidising archaeon Candidatus Methanoperedens sp. BLZ2. Comm. Biol. Accepted. BioRxiv doi: 10.1101/2025.06.06.658376
  • Maslać N, Cadoux C, Bolte P, Murken F, Gu W, Milton RD, Wagner T. Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales. FEBS Journal. 2024. doi: 10.1111/febs.17148.
  • Müller M-C, Lemaire ON, Kurth JM, Welte CU, Wagner T. Differences in the regulation mechanisms of the glutamine synthetase from methanogenic archaea unveiled by structural investigations. Comm. Bio. 2024. doi: 10.1038/s42003-023-05726-w.
  • Cadoux C*, Maslać N*, Luzio LD, Ratcliff D, Gu W, Wagner T, Milton RD. The Mononuclear Metal-Binding Site of Mo-Nitrogenase Is Not Required for Activity. JACS Au. 2023. doi.org/10.1021/jacsau.3c00567
  • Jespersen M, and Wagner T. Assimilatory sulfate-reduction in the marine methanogen Methanothermococcus thermolithotrophicus. Nat Microbiol. 2023. doi.org/10.1038/s41564-023-01398-8
  • Cadoux C, Ratcliff D, Maslać N, Gu W, Tsakoumagkos I, Hoogendoorn S, Wagner T, and Milton RD. Nitrogen Fixation and Hydrogen Evolution by Sterically Encumbered Mo-Nitrogenase. JACS Au. 2023. doi.org/10.1021/jacsau.3c00165 
  • Lemaire ON, Belhamri M., Wagner T. Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Front. Microbiol. 2023. doi.org/10.3389/fmicb.2023.1179204
  • Jespersen M, Pierik AJ, Wagner T. Structures of the sulfite detoxifying F420-dependent enzyme from Methanococcales. Nat Chem Biol. 2023. doi: 10.1038/s41589-022-01232-y.
  • Maslać N, Sidhu C, Teeling H, Wagner T. Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus. mBio. 2022. doi: 10.1128/mbio.02443-22.
  • Lemaire ON, Müller MC, Kahnt J, Wagner T. Structural rearrangements of a dodecameric Ketol-Acid Reductoisomerase isolated from a marine thermophilic methanogen. Biomolecules. 2021. doi: 10.3390/biom11111679.
  • Müller MC, Wagner T. The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales. Int. J. Mol. Sci. 2021. doi.org/10.3390/ijms22168631.
    Wissink M, Engilberge S, Leão P, Jansen RS, Jetten MSM, Royant A, Welte CU, Wagner T. Mini-bacterioferritins: Structural insight into a new type of ferritin-like protein from the anaerobic methane-oxidising archaeon Candidatus Methanoperedens sp. BLZ2. Comm. Biol. Accepted. BioRxiv doi: 10.1101/2025.06.06.658376

External collaborations

  • Pr. Dr. Ross Milton, enzymology (Geneva University)
  • Dr. Wenyu Gu, genetic support (EPFL Lausanne)
  • Dr. Victor Mougel, chemical synthesis (ETH Zurich)
  • Pr. Dr. Markus Reiher, Computational studies (ETH Zurich)
  • Pr. Dr. George Cutsail, spectroscopy (Germany)