Methane-eating bacteria help convert greenhouse gas to fuel

Methanotrophic bacteria consume 30 megatonnes of methane per year and researchers have paid attention to their natural ability to convert the potent greenhouse gas into usable fuel. But scientists know very little about how the complex reaction occurs, limiting the ability to use this double benefit in different applications.

By studying the enzyme, the bacteria use to catalyse the reaction, a team at Northwestern University has now discovered key structures that may drive this process, which ultimately could lead to the development of human-made biological catalysts that convert methane gas into methanol.

“Methane has a powerful [chemical] bond, so it’s pretty remarkable there’s an enzyme that can do this,” said Northwestern’s Amy Rosenzweig. “If we don’t understand exactly how the enzyme performs this difficult chemistry, we cannot engineer and optimise it for biotechnological applications.”

According to the researchers, the enzyme, called particulate methane monooxygenase (pMMO), is a difficult protein to study because it’s embedded in the cell membrane of the bacteria.

Typically, when researchers study these methanotrophic bacteria, they use a harsh process in which they rip the proteins out of the cell membranes using a detergent solution. While this procedure effectively isolates the enzyme, it also kills all enzyme activity and limits how much information researchers can gather.

In this study, the team used a new technique entirely. Christopher Koo, a PhD candidate in Rosenzweig’s lab, wondered if by putting the enzyme back into a membrane that resembles its native environment, they could learn something new. Koo used lipids from the bacteria to form a membrane within a protective particle called a nanodisc, and then embedded the enzyme into that membrane.

“By recreating the enzyme’s native environment within the nanodisc, we could restore activity to the enzyme,” Koo said. “Then, we could use structural techniques to determine at the atomic level how the lipid bilayer restored activity. In doing so, we discovered the full arrangement of the copper site in the enzyme where methane oxidation likely occurs.”

The researchers used cryo-electron microscopy (cryo-EM); a technique well-suited to membrane proteins because the lipid membrane environment is undisturbed throughout the experiment. This allowed the team to visualise the atomic structure of the active enzyme at high resolution for the first time.

“Because of the recent ‘resolution revolution’ in cryo-EM, we could see the structure in atomic detail,” Rosenzweig explained. “What we saw completely changed the way we were thinking about the active site of this enzyme.”

Next, the team plans to study the enzyme directly within the bacterial cell using a forefront imaging technique called cryo-electron tomography (cryo-ET). If successful, the researchers will see exactly how the enzyme is arranged in the cell membrane, determine how it operates in its truly native environment, and learn whether other proteins around the enzyme interact with it. These discoveries would provide a key missing link to engineers.

“If you want to optimise the enzyme to plug it into bio-manufacturing pathways or to consume pollutants other than methane, then we need to know what it looks like in its native environment and where the methane binds,” Rosenzweig said. “You could use bacteria with an engineered enzyme to harvest methane from fracking sites or to clean up oil spills.”