Methane mystery: Marine microbes X-rayed

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  • Published: Dec 15, 2017
  • Author: David Bradley
  • Channels: X-ray Spectrometry
thumbnail image: Methane mystery: Marine microbes X-rayed

Making methane

MIT scientists have determined the structure of an enzyme that is found in ocean microbes and can produce a precursor to methane. Credit: David Born

Industry and agriculture generate vast quantities of methane, a potent greenhouse gas. However, marine microbes also represent an important source although exactly how is entangled in the “ocean methane paradox.” Now, US researchers have used X-ray crystallography to explain it.

Scientists from Massachusetts Institute of Technology and the University of Illinois at Urbana-Champaign have determined the structure of an enzyme that generates a precursor to methane. This enzyme, the team has now demonstrated, is present in some of the most abundant marine microbes. It could thus explain the source of marine methane. It is estimated that methane from the oceans accounts for about 4 percent of the total volume of gas released into the Earth's atmosphere. An improved understanding of its oceanic source could improve models of climate change.

“Understanding the global carbon cycle is really important, especially when talking about climate change,” explains MIT's Catherine Drennan. “Where is methane really coming from? How is it being used? Understanding nature’s flux is important information to have in all of those discussions.” Drennan has worked with Illinois' Wilfred van der Donk, and graduate students David Born and Emily Ulrich.

Bacterial source

It was already known that some bacteria produce methane as a metabolic byproduct, but these microbes exist in oxygen-poor environments such as the deep ocean or in the digestive tract of animals, not near the ocean’s surface from where their gaseous emissions might easily enter the atmosphere. van der Donk and colleague William Metcalf had previously identified a microbial enzyme that generates methylphosphonate, from which methane is released when it loses a phosphate group. The enzyme in question was present in Nitrosopumilus maritimus, which lives near the ocean surface, but they did not see it in other surface microbes as they had expected.

The team did have the genetic sequence for this enzyme, methylphosphonate synthase (MPnS), so they could search for related enzymes in the genomes of other microbes. Oddly, every potential match revealed itself as the related enzyme hydroxyethylphosphonate dioxygenase (HEPD). The enzyme makes a chemical cousin of methylphosphonate but the methane molecule cannot be cleaved from it. So, van der Donk approached Drennan, to determine the structure of MPnS, in the hope that this would make the search for variants of the enzyme in other bacteria easier.

Intelligent decisions

The MIT team carried out the requisite X-ray crystallography in the absence of oxygen so they could obtain a structure with the enzyme bound to putative substrates but without it being able to carry out any transformation on them. The data from MPnS was compared with the related HEPD enzyme and this revealed a small but critical difference. Glutamine is present in the active site of both enzymes, but in MPnS, the glutamine is bound to iron as a cofactor for methylphosphonate production. The orientation of this iron-bound glutamine is fixed by the bulky amino acid isoleucine. In contrast, HEPD, has a glycine instead of this isoleucine residue, so its glutamine can move freely.

“We were looking for differences that would lead to different products, and that was the only difference that we saw,” Born explains. Furthermore, the researchers found that changing the glycine in HEPD to isoleucine was sufficient to convert the enzyme to an MPnS type enzyme.

The researchers are yet to work out what the function of the MPnS enzyme and its product is in ocean bacteria. However, what is known is that methylphosphonates can be incorporated into phosphonolipids, which are similar to the phospholipids that make up cell membranes. That said, the team now knows that they are produced in large amounts but is still unsure as to why.

The next obvious question, given methane's important role in climate, is how these microbes are influenced by environmental conditions in the ocean, such as temperature, pH, pollution, and the presence of fertilizer runoff. Methylphosphonate cleavage occurs when the microbes are starved of phosphorus. Drennan suggests that we now need to find out how that chemistry is affected by the changing ocean. “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," Drennan says.

Related Links

Science 2017,  358 (6368) 1336-1339: "Structural basis for methylphosphonate biosynthesis"

Article by David Bradley

The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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