Fueling CO2-fixation by detoxifying CO, what are the secrets behind the electron-bifurcating hydrogenase/formate dehydrogenase from homoacetogens?

• Applicant: Dr. Tristan Wagner
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms ; Biochemistry ; Biological and Biomimetic Chemistry ; Structural Biology
• Term: from 2019 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 428142598

• Final Report Year: 2023

Final Report Abstract

This work comprises two topics focused on the Fe-S cluster biogenesis and Fe-S cluster enzymes found in energy extremophiles. The core project is to investigate how the acetogenic bacterium Clostridium autoethanogenum converts synthetic gases composed of carbon monoxide (CO), CO2 and H2 into biofuels. We use C. autoethanogenum grown on CO to depict the molecular details of the enzymes orchestrating (i) the capture and utilisation of CO, (ii) the entry point of carbon fixation in the central metabolism, and (iii) ethanol biosynthesis. We first unveiled the structure of the CO- dehydrogenase/Acetyl-CoA synthase (CODH/ACS) complex and described how the enzyme is so performant for CO detoxification. Numerous gas channels within the enzyme enhance the gas diffusion to catalytic sites. The CODH catalyses the CO-oxidation to CO2 and transfers electrons to the ferredoxin, while the ACS consumes CO as one of the substrates to build up acetyl-CoA, the turntable of the central carbon metabolism. Reduced ferredoxin and CO2 produced by the CODH are the substrates of another enzyme: the NADP-dependent electron-bifurcating [FeFe]-Hydrogenase/formate dehydrogenase (Hyt/Fdh) complex. By combining biophysics and biochemistry, we found that Hyt/Fdh is insensitive to CO, allowing the reduction of CO2 to formate while dissipating the excess of reduced ferredoxin generated by CODH via H2-generation. The formate is then captured by the formyltetrahydrofolate synthetase (Fts) and processed through the central carbon metabolism. Its resting state structure illustrates how the synthetase prepares to activate formate with ATP. Finally, we targeted the key enzyme involved in ethanol production called the aldehyde-oxidoreductase (AOR). Here, we discovered that the activation of this tungstopterin-containing enzyme depends on the ferredoxin binding. The second project relates to the Fe-S biogenesis in methanogenic archaea and flourished during the COVID pandemic restrictions. We elucidated how a methanogenic archaeon turns sulfate into sulfide, one of the building blocks for Fe-S cluster synthesis. While the first two steps proceed via enzymes common to other organisms, the further steps are catalysed by uncanonical ones belonging to new classes. For instance, the sulfite-reductase generating the end product sulfide relies on reduced F420 as an electron source for the reaction instead of NAD(P)H or reduced ferredoxin. We used electron paramagnetic resonance, enzymology and X-ray crystallography to describe how the electrons flow through the Fe-S cluster relay and why the enzyme is so efficient in reducing sulfite. Finally, we teamed up with experts from the consortium to deepen our knowledge of the F420-reduction through H2-oxidation, a reaction performed by the [NiFe]- containing hydrogenase. Most of these studied proteins have Fe-S clusters and tungstopterin cofactors. The FeS-for-Life consortium provided their knowledge and skills to support us in describing the enzymes.

Publications

• Latest thinking video. How Can Acetogenic Bacteria Process Carbon Monoxide?
  Lemaire O.N.
  
• Sulphite detoxification fuelled by hydrogen. Published by FEBS Open bio
  Jespersen M.
  
• CO2-Fixation Strategies in Energy Extremophiles: What Can We Learn From Acetogens?. Frontiers in Microbiology, 11(c(2020, 4, 3)).
  Lemaire, Olivier N.; Jespersen, Marion & Wagner, Tristan
  
• Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1862(1), 148330.
  Lemaire, Olivier N. & Wagner, Tristan
  
• Structural insights into the AOR from a carbon monoxide devourer. Presented as a poster at the MoTEC 2021 (12th Molybdenum and Tungsten Enzymes Conference)
  Lemaire O.N.; Belhamri M. & Wagner T.
  
• The electron-bifurcating hydrogenase/formate dehydrogenase complex a key nano-machine for carbon fixation and energy conversion. Presented as a poster at the MoTEC 2021 (12th Molybdenum and Tungsten Enzymes Conference)
  Jespersen M.; Lemaire O.N.; Stripp S. & Wagner T.
  
• Activation of different methyl-compounds by a methanogen: one methyl group, different chemistry. Presentation at the Gordon Research Conference Molecular Basis of Microbial One-Carbon Metabolism 2022 (Poster)
  Lemaire O.N; Lorent C.; Alansson N.; Kurth J.M.; Engilberge S.; Royant A.; Ullmann M.; Zebger I.; Welte C. & Wagner T.
  
• How a methanogen assimilates sulfate: Structural and functional elucidation of the complete sulfate-reduction pathway. American Geophysical Union (AGU).
  Jespersen, Marion & Wagner, Tristan
  
• Hydrogenase Lectures 2022. Hydrogenases that fuel carbon-processing in energy-limited microorganisms
  Jespersen M.
  
• Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Frontiers in Microbiology, 14(c(2023, 5, 11)).
  Lemaire, Olivier N.; Belhamri, Mélissa & Wagner, Tristan
  
• Structures of the sulfite detoxifying F420-dependent enzyme from Methanococcales. Nature Chemical Biology, 19(6), 695-702.
  Jespersen, Marion; Pierik, Antonio J. & Wagner, Tristan