Methane is a greenhouse gas the contributes heavily to global warming. It’s a byproduct of many industrial and agricultural activities, as well as a byproduct of the metabolic processes of bacteria. But along with these known sources, there is the unknown phenomenon of methane release from the ocean, which has long puzzled scientists due to the fact that no known methane-producing organisms live near the ocean’s surface.
Several years ago, Wilfred van der Donk, a professor of chemistry at the University of Illinois and one of the paper’s senior authors, discovered a microbial enzyme that produces a compound called methylphosphonate. This molecule can become methane when a phosphate molecule is cleaved from it, and it is found in a microbe that lives near the ocean’s surface.
However, this enzyme was not identified in other ocean microbes, as it was expected to be. Van der Donk and his team searched for other versions of this enzyme by using its genetic sequence (MPnS), but they could never find an exact match in other microbes. What they did find instead was a closely related enzyme, hydrooxyethylphosphonate dioxygenase (HEPD), but this enzyme cannot be cleaved to produce methane.
Seemingly stuck, Van der Donk asked Catherine Drennan, an MIT professor of chemistry and biology and an expert in determining chemical structures of proteins, if she could determine the structure of MPnS. In doing so, it may help the researchers to find more variants of the enzyme in other bacteria. Drennan’s team used X-ray crystallography to find the enzyme’s structure and compared its structure to the HEPD enzyme, finding one small but crucial difference. On the active site of both enzymes, where chemical reactions are catalyzed, there is an amino acid called glutamine. In MPnS, glutamine binds to iron, which is a required cofactor for methylphosphonate production. The glutamine is fixed in an iron-binding orientation by the amino acid isoleucine. But in HEPD, the isoleucine is replaced by glycine, which isn’t as bulky and allows the glutamine more space to rearrange and not have to bind to iron.
“We were looking for differences that would lead to different products, and that was the only difference that we saw,” says David Born, a graduate student at MIT and one of the study’s lead authors. The researchers then determined that changing the glycine in HEPD to isoleucine was enough to allow conversion of the enzyme to MPnS.
Through searching databases of genetic sequences for thousands of microbes, the team found hundreds of enzymes with the same structural configuration seen in the original MPnS enzyme. In addition, all of these were microbes that are known to live in the ocean.
While this discovery could have significant implications, there is still a lot of work that needs to be done. “We know that methylphosphonate cleavage occurs when microbes are starved for phosphorus, but we need to figure out what nutrients are connected to this, and how is that connected to the pH of the ocean, and how is it connected to temperature of the ocean,” says Drennan. “We need all of that information to be able to think about what we’re doing, so we can make intelligent decisions about protecting the oceans.”