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Filamentous enzymes have been found in all domains of life, but the advantage of filamentation is often elusive1. Some anaerobic, autotrophic bacteria have an unusual filamentous enzyme for CO2 fixation—hydrogen-dependent CO2 reductase (HDCR)2,3—which directly converts H2 and CO2 into formic acid. HDCR reduces CO2 with a higher activity than any other known biological or chemical catalyst4,5, and it has therefore gained considerable interest in two areas of global relevance: hydrogen storage and combating climate change by capturing atmospheric CO2. However, the mechanistic basis of the high catalytic turnover rate of HDCR has remained unknown. Here we use cryo-electron microscopy to reveal the structure of a short HDCR filament from the acetogenic bacterium Thermoanaerobacter kivui. The minimum repeating unit is a hexamer that consists of a formate dehydrogenase (FdhF) and two hydrogenases (HydA2) bound around a central core of hydrogenase Fe-S subunits, one HycB3 and two HycB4. These small bacterial polyferredoxin-like proteins oligomerize through their C-terminal helices to form the backbone of the filament. By combining structure-directed mutagenesis with enzymatic analysis, we show that filamentation and rapid electron transfer through the filament enhance the activity of HDCR. To investigate the structure of HDCR in situ, we imaged T. kivui cells with cryo-electron tomography and found that HDCR filaments bundle into large ring-shaped superstructures attached to the plasma membrane. This supramolecular organization may further enhance the stability and connectivity of HDCR to form a specialized metabolic subcompartment within the cell.
Background: In times of global warming there is an urgent need to replace fossil fuel-based energy vectors by less carbon dioxide (CO2)-emitting alternatives. One attractive option is the use of molecular hydrogen (H2) since its combustion emits water (H2O) and not CO2. Therefore, H2 is regarded as a non-polluting fuel. The ways to produce H2 can be diverse, but steam reformation of conventional fossil fuel sources is still the main producer of H2 gas up to date. Biohydrogen production via microbes could be an alternative, environmentally friendly and renewable way of future H2 production, especially when the flexible and inexpensive C1 compound formate is used as substrate.
Results: In this study, the versatile compound formate was used as substrate to drive H2 production by whole cells of the thermophilic acetogenic bacterium Thermoanaerobacter kivui which harbors a highly active hydrogen-dependent CO2 reductase (HDCR) to oxidize formate to H2 and CO2 and vice versa. Under optimized reaction conditions, T. kivui cells demonstrated the highest H2 production rates (qH2 = 685 mmol g−1 h−1) which were so far reported in the literature for wild-type organisms. Additionally, high yields (Y(H2/formate)) of 0.86 mol mol−1 and a hydrogen evolution rate (HER) of 999 mmol L−1 h−1 were observed. Finally, stirred-tank bioreactor experiments demonstrated the upscaling feasibility of the applied whole cell system and indicated the importance of pH control for the reaction of formate-driven H2 production.
Conclusions: The thermophilic acetogenic bacterium T. kivui is an efficient biocatalyst for the oxidation of formate to H2 (and CO2). The existing genetic tool box of acetogenic bacteria bears further potential to optimize biohydrogen production in future and to contribute to a future sustainable formate/H2 bio-economy.
Hydrogen is a promising fuel in a carbon-neutral economy, and many efforts are currently undertaken to produce hydrogen. One of the challenges is to store and transport the highly explosive gas in a safe and easy way. One option that is intensively analyzed by chemists and biologists is the conversion of hydrogen and CO2 to formic acid, the liquid organic hydrogen carrier. Here, we demonstrate for the first time that a bio-based system, using Acetobacterium woodii as the biocatalyst, allows multiple cycles of bi-directional hydrogenation of CO2 to formic acid in one bioreactor. The process was kept running over 2 weeks producing and oxidizing 330 mM formic acid in total. Unwanted side-product formation of acetic acid was prevented through metabolic engineering of the organism. The demonstrated process design can be considered as a future “bio-battery” for the reversible storage of electrons in the form of H2 in formic acid, a versatile compound.