Researchers have unveiled the detailed architecture of a massive molecular machine that methane-producing microbes use to generate energy, according to a study published in Nature. The complex, found in the microorganism Methanococcus maripaludis, weighs roughly 8 megadaltons and contains 252 polypeptide chains along with more than 600 redox cofactors, making it one of the largest bioenergetic assemblies characterized to date in these organisms.
Methanogens are archaea responsible for producing the majority of the world's biogenic methane, a potent greenhouse gas, according to the study. At the same time, the researchers note, these microbes represent a potential source of renewable energy. Understanding how they convert simple molecules like hydrogen and carbon dioxide into methane is described as essential both for climate change mitigation and for biotechnology applications.
Using cryogenic electron microscopy, the team resolved the structure of what is called the Hdr–Vhu–Fwd super-assembly, which couples the oxidation of hydrogen with the reduction of carbon dioxide through a process known as flavin-based electron bifurcation. The architecture consists of two hexameric rings — each combining the enzymes HdrABC and Vhu — connected by a tetrameric core built from the Fwd complex, forming what the authors describe as a continuous, circular chain for moving electrons.
A key feature of the structure is a set of 12 polyferredoxin subunits, called VhuB, that physically bridge the two ends of the machine, directly linking the final step of methanogenesis with its first step. Cryo-electron tomography further indicated that this same architecture assembles intact within living cells, the researchers report.
A modular design
The study also identified a variant of the complex in which the hydrogen-processing enzyme Vhu is replaced by a tungsten-containing formate dehydrogenase, called FdhAB. According to the researchers, this substitution points to a flexible design that allows the microbe to swap electron-input components depending on environmental conditions.
Comparing this structure with previously known complexes, the team found that this particular architecture is specific to what are called class I methanogens — a group that includes Methanococcus, Methanopyrus and Methanobacteriales — and is distinct from a smaller version, the Hdr–Fmd complex, found in class II methanogens such as Methanosarcinales.
The authors say their findings reveal that methanogens have evolved lineage-specific, modular bioenergetic machinery, helping explain how different groups of these microbes adapt to a wide range of harsh, energy-limited anaerobic environments.