Energy extraction from air: structural basis of atmospheric hydrogen oxidation

Abstract

Diverse aerobic bacteria use atmospheric H2 as an energy source for growth and survival. This recently discovered yet globally significant process regulates the composition of the atmosphere, enhances soil biodiversity, and drives primary production in certain extreme environments. Atmospheric H2 oxidation has been attributed to still uncharacterised members of the [NiFe]-hydrogenase superfamily. However, it is unresolved how these enzymes overcome the extraordinary catalytic challenge of selectively oxidizing picomolar levels of H2 amid ambient levels of the catalytic poison O2, and how the derived electrons are transferred to the respiratory chain. Here we determined the 1.52 angstroms resolution CryoEM structure of the mycobacterial hydrogenase Huc and investigated its mechanism by integrating kinetics, electrochemistry, spectroscopy, mass spectrometry, and molecular dynamics simulations. Purified Huc is an oxygen-insensitive enzyme that couples the oxidation of atmospheric H2 at its large subunit to the hydrogenation of the respiratory electron carrier menaquinone at its small subunit. The enzyme uses a narrow hydrophobic gas channel to selectively bind atmospheric H2 at the expense of O2, while three [3Fe-4S] clusters and their unusual ligation by a D-histidine modulate the electrochemical properties of the enzyme such that atmospheric H2 oxidation is energetically feasible. Huc forms an 833 kDa complex composed of an octamer of catalytic subunits around a membrane-associated central stalk, which extracts and transports menaquinone a remarkable 94 angstroms from the membrane, enabling its reduction. These findings provide a mechanistic basis for the biogeochemically and ecologically critical process of atmospheric H2 oxidation. Through the first characterisation of a group 2 [NiFe]-hydrogenase, we also uncover a novel mode of energy coupling dependent on long-range quinone transport and pave way for the development of biocatalysts that oxidize H2 in ambient air.

Atmospheric hydrogen oxidation extends to the domain archaea

“…This arrangement would thus enable these hydrogenases to provide electrons both to maintain the proton-motive force via quinone oxidation by either sulfur reductase or terminal oxidases, as well as drive carbon fixation during autotrophic growth. Modelling of Hys (group 2e) reveals an unexpected similarity to the recently characterized group 2a hydrogenase Huc from Mycobacterium smegmatis , which oxidizes H 2 at sub-atmospheric concentrations and forms a large oligomer around the central membrane-associated subunit HucM (60). Despite limited sequence identity (~45%), modelling reveals the HysSL subunit forms a dimer, which is highly similar to that of HucSL (RMSD = 1.55 Å; Fig.…”

“…4D ). In a similar manner, the modelled structure of HysM is a homologue to HucM (despite only sharing 18% sequence identity) and forms a characteristic tube-like structure, which in Huc scaffolds the enzyme and delivers quinone to the electron acceptor site of HucS (60). Based on these similarities, we generated a full model for Hys ( Fig.…”

“…Modelling of Hys (group 2e) reveals an unexpected similarity to the recently characterized group 2a hydrogenase Huc from Mycobacterium smegmatis, which oxidizes H 2 at subatmospheric concentrations and forms a large oligomer around the central membraneassociated subunit HucM (60). Despite limited sequence identity (~45%), modelling reveals the HysSL subunit forms a dimer, which is highly similar to that of HucSL (RMSD = 1.55 Å; Fig.…”

“…AlphaFold-derived models of the group 1g hydrogenase Hca ( B ), the novel group 1 clade SUL2 hydrogenase Hsu2 ( C ), the group 2e hydrogenase Hys ( D ) shown as a cartoon representation of the complex formed by the subunits identified in panel A ( left/top panel ) and the electron transport relay formed by modelled cofactors, with predicted electron donors and acceptors indicated ( right/bottom panel ). ( E ) A model of a higher order complex formed by Hys, incorporating the AlphaFold model of the HysM subunit, and based on the Cryo-EM structure of the group 2a hydrogenase Huc from Mycobacterium smegmatis (60).…”

Novel concepts and engineering strategies for heterologous expression of efficient hydrogenases in photosynthetic microorganisms

“…Most [NiFe] hydrogenases reported to-date are oxygensensitive tolerant enzymes, i.e., they display reversible oxygen-induced inhibition. A few [NiFe] hydrogenases even stand out as oxygeninsensitive as their function under atmospheric oxygen concentrations is not impaired (Buhrke et al, 2005;Leroux et al, 2008;Liebgott et al, 2010;Schäfer et al, 2013;Grinter et al, 2023). In contrast, the majority of [FeFe] hydrogenases are oxygen-sensitive intolerant enzymes as the active site is irreversibly damaged when exposed to trace amounts of oxygen.…”