Microbial enzyme inspiration for chemistry and biotechnology

Microbes are astounding chemists. They perform challenging reactions at high rates under normal temperature and pressure using biochemical energy (e.g., ATP hydrolysis or electron flow). More interestingly, Life uses abundant Earth metals to perform these enzymatic reactions, compared to the expensive and rare metals used in industry. Therefore, microbial enzymes serve as blueprints for chemists, inspiring tailor-made catalysts to fuel technologies urgently required to sustain our modern society.
In this research axis, we snapshot (metallo)enzymes in action to decipher their molecular mechanisms that could provide milestones to chemists (e.g., H2-forming enzyme, CO2-capturing nanomachine…), or explain/improve the molecular fundamentals of biotechnological industries (e.g., isoprenoid synthesis, wastewater treatment degradation process…).

As a recent example, we solved key enzymatic complexes involved in the microbial transformation of industrial waste gases into the biofuel ethanol. Our first target was the CO-processing enzyme called CO-dehydrogenase/Acetyl-CoA synthase complex, which generates reducing power from CO-oxidation (i.e., reduced ferredoxin) and at the same time, produces the cellular building block: acetyl-CoA. The different crystallographic structures, complemented by biochemical characterization, revealed an astonishing reorganization of the complex, allowing a reallocation of CO channels, potentially increasing gas diffusion and thereby improving its capture. Cryo-EM experiments under turnover conditions captured the CO-dehydrogenase/Acetyl-CoA synthase complex’s various conformations and provided a molecular movie of the catalytic cycle of acetyl-CoA production. The second target was the enzymes involved in converting acetate to ethanol, which was proposed to be catalysed by an acetaldehyde ferredoxin oxidoreductase (AFOR, converting acetate to acetaldehyde) and an ethanol dehydrogenase (converting acetaldehyde to ethanol). This hypothesis was controversial because acetate reduction is a highly endergonic process that would not allow high-rate production in cellulo. By isolating and characterizing AFOR, we found that the enzyme is strictly dependent on native ferredoxin to regain full activity. Then, through in vitro enzymatic coupling, we understood that the CO-oxidation reducing power drives the thermodynamically unfavorable first reaction, enabling robust ethanol production.

Selected publications

  • Lemaire ON#, Belhamri M, Schevchenko A, Wagner T#. Carbon monoxide-driven bioethanol production operates via a tungsten-dependent catalyst. Under revision in Nat. Chem. Biol. BioRxiv doi: 10.1101/2024.07.29.605569
  • Jespersen M*, Lorent C*, Lemaire ON, Zebger I, Wagner T#. Structural and spectroscopic insights into catalytic intermediates of a NiFe-hydrogenase from group 3. ChemBioChem. 2025. doi: 10.1002/cbic.202500692
  • Yin MD*, Lemaire ON*, Rosas Jiménez JG, Belhamri M, Shevchenko A, Hummer G#, Wagner T#, Murphy BJ#. Snapshots of acetyl-CoA synthesis, the final step of CO2 fixation in the Wood-Ljungdahl pathway. Science. BioRxiv doi: 10.1101/2024.08.05.606187
  • Lemaire ON, and Wagner T#. An all-in-one CO2 capture and transformation: lessons from formylmethanofuran dehydrogenases. Account of Chemical Research. 2024. doi: 10.1021/acs.accounts.4c00623
  • Sahin S*, Lemaire ON*, Belhamri M, Kurth JM, Welte CU, Wagner T#, Milton RD#. Bioelectrocatalytic CO2 Reduction by Mo-Dependent Formylmethanofuran Dehydrogenase. Angew Chem Int Ed Engl. 2023. doi: 10.1002/anie.202311981.
  • Lemaire ON, Wagner T#. Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum. Biochim. Biophys. Acta Bioenerg. 2021. doi: 10.1016/j.bbabio.2020.148330.
  • Lemaire ON, Jespersen M, Wagner T#. CO2-fixation strategies in energy extremophiles: What can we learn from homoacetogens? Front. Microbiol. 2020. doi: 10.3389/fmicb.2020.00486.
  • Wagner T, Ermler U, Shima S. Formyl-methanofuran dehydrogenase. Encyclopedia of Inorganic and Bioinorganic Chemistry. 2018. Book chapter.
  • Vögeli B, Shima S, Erb TJ, Wagner T#. Crystal structure of archaeal HMG-CoA reductase: insights into structural changes of the C-terminal helix of the class-I enzyme. FEBS Lett. 2019. doi: 10.1002/1873-3468.13331.
  • Vögeli B, Engilberge S, Girard E, Riobé F, Maury O, Erb TJ, Shima S, Wagner T#. Archaeal acetoacetyl-CoA thiolase/HMG-CoA synthase complex channels the intermediate via a fused CoA-binding site. Proc. Natl. Acad. Sci. USA. 2018. doi: 10.1073/pnas.1718649115.

External collaborations

  • Prof. Ross Milton (Geneva University)
  • Dr. Ingo Zebger (TU Berlin)