Study resolves how methane-producing microbes generate the important gas

In marshes and the guts of some animals, methane-producing bacteria, called methanogens, produce hundreds of millions of metric tons of methane each year. To design improved routes to methane for use as a chemical feedstock or fuel, researchers have long wanted to understand the molecular details of how these microbes generate the important gas.

A new study reports data that confirm a proposed mechanism used by a key bacterial enzyme in the methane-making process.

The enzyme, called methyl-coenzyme M reductase, catalyzes the final step in methane production, in which an H atom is added to a CH₃ group to yield the gas. Methane-oxidizing archaea use the same enzyme to catalyze the reverse process, methane oxidation—a process that uses up less than one-tenth the amount of methane methanogens produce annually.

Scientists have been studying the enzyme intensively for about two decades. Experimental studies beginning in the late 1990s favored the so-called mechanism I, in which a biomolecule called coenzyme M transfers an electron to a methyl-Ni(III) intermediate. In 2002, Per E. M. Siegbahn of Stockholm University and coworkers used density functional theory, a computational chemistry technique, to propose mechanism II, which involves a Ni(II) thiolate and a methyl radical. Other researchers have suggested mechanism III, which involves a methyl anion and a Ni(III) thiolate, but experts consider it less likely, so it has not been studied extensively.

Determining which mechanism is correct has been extremely difficult because the Ni intermediate reacts so fast that analytical techniques couldn’t characterize it.

In the new study, Stephen W. Ragsdale of the University of Michigan, Ann Arbor, and coworkers there and at Pacific Northwest National Laboratory used an analog of coenzyme B, a substrate in the reaction, to slow down the process (Science 2016, DOI: 10.1126/science.aaf0616). They then used electron paramagnetic resonance spectroscopy (EPR), magnetic circular dichroism (MCD), and computational and experimental transition-state energy measurements to study the process. EPR did not detect mechanism I’s methyl-Ni(III), and the MCD spectrum closely resembled that expected for mechanism II’s Ni(II) thiolate. The energy measurements further confirmed mechanism II.

“I am very happy to see that the crucial Ni(II) thiolate intermediate has been observed, giving direct support to mechanism II,” comments theoretician Shi-Lu Chen of Beijing Institute of Technology. The findings could aid “the design of biomimetic catalysts for methane formation and anaerobic methane oxidation,” he says.