Isocyanides as a Chemical Tool for Identifying [Fe]‐Hydrogenase‐Dependent Methanogenesis

Abstract

In the hydrogenotrophic methanogens cultivated under nickel‐sufficient standard medium (~5 µM Ni 2+ ), two cytosolic [NiFe]‐hydrogenases, F 420 ‐reducing hydrogenase (Frh) and heterodisulfide reductase (Hdr)‐associating hydrogenase (Mvh), mainly provide electrons to the methanogenic pathway. In Methanothermobacter marburgensis under strictly nickel‐limited conditions (< 50 nM Ni 2+ ), which are encountered in certain natural environments, Frh and Mvh are strongly downregulated. Under these conditions, a coupled reaction with [Fe]‐hydrogenase (Hmd) and F 420 ‐dependent methylene‐tetrahydromethanopterin dehydrogenase (Mtd) substitutes for the function of Frh, where F 420 ‐dependent electron‐donating protein (Elp) complexes with Hdr and donates electrons from the reduced form of F 420 to Hdr. Thus, Hmd mainly provides electrons to methanogenesis in nickel‐limited environments. In this study, to evaluate the potential of isocyanides as an Hmd‐specific chemical tool to probe this pathway, we determined their inhibitory effects on the H 2 ‐dependent F 420 ‐reducing activity in the cell extract and on the in vitro methanogenesis reaction in a cell extract and in a cell suspension. Isocyanides specifically inhibited the activities of the samples from nickel‐limited cells. The inhibitory effect on the cell suspension was strengthened by the use of a hydrophobic isocyanide. These results demonstrate their potential as a chemical tool for identifying in situ Hmd‐dependent methanogenesis activity in natural environmental samples.

The authors' abstract, as published at the source. ChemBioChem, 2026 · DOI ↗