The anaerobic fungus Caecomyces churrovis produces H ₂ via a non-bifurcating NADH-dependent enzyme complex

Hydrogenosomes are mitochondrion-derived organelles that produce ATP and H ₂ to support energy metabolism in anaerobic eukaryotes. H ₂ production allows reoxidation of reduced cofactors generated during fermentative metabolism; however, the metabolic mechanisms for H ₂ production in anaerobic eukaryotes remain incompletely understood. In particular, it remains unclear whether anaerobic fungi (AF) hydrogenosomes use a ferredoxin-dependent pathway or a distinct mechanism to regenerate NAD(P) ⁺ and link electron transfer to H ₂ formation. Here, by combining genomic search, proteomic analysis, and enzymology, we reveal the molecular mechanism for H ₂ production in the AF Caecomyces churrovis . Our enzyme assays on the organelle fraction of C. churrovis revealed the activity of H ₂ :NAD ⁺ oxidoreductase but not pyruvate:ferredoxin oxidoreductase, which is usually linked to H ₂ formation. We identified genes encoding [FeFe] hydrogenase (Hyd) and NADH dehydrogenase subunits E and F (NuoE and NuoF) in C. churrovis and confirmed their expression in the isolated hydrogenosomal fractions by proteomic analysis. Combining the individually purified enzymes, we found Hyd and NuoEF proteins formed H ₂ directly from NADH independently of ferredoxin, functioning as a non-bifurcating NADH-dependent enzyme rather than an electron-bifurcating enzyme known from anaerobic prokaryotes. We identified homologs of hydrogenosomal NuoE, NuoF, and Hyd in many other AF, indicating this pathway is commonly shared among the AF. This work demonstrates the existence of a non-bifurcating NADH-dependent enzyme complex for H ₂ production in eukaryotes. Moreover, this complex could potentially be exploited as a target for controlling AF H ₂ production and altering fungal metabolism.

IMPORTANCE

H ₂ production is a prominent feature of anaerobic energy metabolism, yet our understanding of eukaryotic mechanisms remains limited. Anaerobic fungi (AF) are key decomposers of lignocellulose and contribute to hydrogen flux in anaerobic environments. Although it has been more than 40 years since the H ₂ production in Neocallimastix was first reported, the molecular mechanism for hydrogenosomal H ₂ production and redox balance remains unclear. We demonstrate that AF produce H ₂ from NADH utilizing a non-bifurcating NADH-dependent enzyme complex rather than an electron-bifurcating, ferredoxin-dependent variant. We show that this enzyme complex is conserved across multiple AF lineages and thus demonstrate the occurrence of a non-bifurcating NADH-dependent enzyme in eukaryotes. This discovery expands our understanding of eukaryotic hydrogenosomal metabolism, reveals a previously unknown strategy for redox balancing, and highlights potential targets for manipulating H ₂ production. These insights have broad implications for microbial energy metabolism, anaerobic ecosystems, and bioengineering of H ₂ -producing systems.