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Winter 2019

Energy Is Encoded in the Genes

Scientists discover an enzyme that converts carbon dioxide into methane

Rubul Mout

An enzyme in certain species of bacteria can convert carbon dioxide to methane, which could feed your kitchen stove or car, if the produced methane is harvested properly. Credit: Rubul Mout, CSSAS EFRC, and Nathan Johnson, Pacific Northwest National Laboratory

Converting greenhouse gas into energy—a win-win solution

Two of the greatest problems facing humanity in the coming times are global warming and the need for an alternative energy source. Scientists in America and elsewhere are working hard to meet both problems. But one could hardly imagine a single solution to both. Researchers at the Center for Biological Electron Transfer and Catalysis (BETCy) Energy Frontier Research have found a protein molecule—an enzyme—in certain species of bacteria that can convert carbon dioxide, a greenhouse gas, to methane. In nature, methane itself is another potent greenhouse gas, but it could be an important source of energy to meet the world’s demand. The caveat is that the produced methane must be harvested to use as energy.

A tweak in an old story

The story began long ago—perhaps millions of years ago! It began when a set of enzymes evolved in bacteria to convert atmospheric nitrogen gas into products of ammonia, a process known as nitrogen fixation. These enzymes are now called nitrogenases, as the name reflects their functions. Nitrogenase was a boon for the plant kingdom, as plants greatly benefited from the benevolent work of these nitrogen-fixing bacteria—many plants needed fixed-nitrogen products as minerals to survive.

Over the years, scientists have discovered that a nitrogenase, which works like a tiny molecular machine, needs a pair of metal ions to function. This pair could be molybdenum-iron, vanadium-iron, or simply iron-iron. The enzyme that uses a pair of iron ions (iron-iron) is endearingly called an iron-only nitrogenase. Molybdenum-iron nitrogenase is, perhaps, the most prevalent among these three and, therefore, is responsible for most of the nitrogen fixation on Earth; iron-only is the least common. But gosh, who could have thought that there was another story of iron-only nitrogenase hiding in the darkness, waiting to be revealed!

The discovery

The secret story of iron-only nitrogenase is now revealed in a collaborative study at BETCy. Now, the fact is that this group of scientists did not set out to discover what they ended up discovering in iron-only nitrogenase. Instead, they took a cue from a previously reported research paper about the molybdenum-iron nitrogenase, where tiny tweaks to this enzyme could cause it to convert carbon dioxide to methane, instead of nitrogen to ammonia.

The BETCy team wanted to tweak the iron-only enzyme from Rhodopseudomonas palustris bacterium by making a few changes in the protein sequence to see if iron-only nitrogenase could also convert carbon dioxide to methane. They discovered that the tweaked one did not convert carbon dioxide to methane. To their great surprise, they found that the naturally existing iron-only nitrogenase can already convert carbon dioxide to methane in addition to its known function to convert nitrogen to ammonia. However, the production of methane was much lower. Each unit (nanomole) of the protein produced 296 units of ammonia and 1 unit of methane. That’s only 0.3 percent of methane as compared to ammonia. Nonetheless, it was enough to grow another bacterium (a Methylomonas strain) that feeds on methane gas.

Looking ahead

Tweaking enzymes to repurpose their function or to work better has been a popular project in biotechnology and medicine. In fact, the 2018 Nobel Prize in Chemistry went to scientists who pioneered exactly one such technology. Taking advantage of biotech, we may expect iron-only nitrogenase to be tweaked to elicit much more efficient carbon dioxide conversion into methane. Then, perhaps, we could envision a day when there will be a bioreactor or bioplant set up in our backyard that feeds on carbon dioxide to constantly supply energy to our kitchen or car.

More Information

Zheng Y, DF Harris, Z Yu, Y Fu, S Poudel, RN Ledbetter, KR Fixen, ZY Yang, ES Boyd, ME Lidstrom, LC Seefeldt, and CS Harwood. 2018. “A Pathway for Biological Methane Production Using Bacterial Iron-Only Nitrogenase.” Nature Microbiology 3(3):281. DOI: 10.1038/s41564-017-0091-5

Acknowledgments

This work was supported as part of the Center for Biological Electron Transfer and Catalysis (BETCy), an Energy Frontier Research Center, funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.

About the author(s):

  • Rubul Mout, Ph.D., is a Washington Research Foundation Innovation Fellow at David Baker’s laboratory at the Institute for Protein Design, University of Washington. He is a member of the Center for the Science of Synthesis Across Scales (CSSAS), an Energy Frontier Research Center. He received his Ph.D. from Vincent M. Rotello’s laboratory at the University of Massachusetts at Amherst, where he worked in the field of nanotechnology and gene editing. In his current research, he makes “brand new” proteins and protein machines, which were never built in the nature before, for a range of applications including in cell signaling, optogenetics, and bioelectronics. He is also the author of two books—a collection of short stories and a memoir—in his native language Assamese.

Scientists Reveal Nature's Double Agent

Protein that turns nitrogen to fertilizer also turns carbon dioxide to fuel

Researchers discovered how a natural catalyst turns carbon dioxide into methane, which is both a fuel and a building block for more energy-dense hydrocarbons. Credit: Nathan Johnson, Pacific Northwest National Laboratory

Known as a nitrogenase, an iron-based protein plays a bigger role than scientists thought. They knew it turned nitrogen gas into a needed nutrient, ammonia. But could it work with carbon dioxide? A team at the Center for Biological Electron Transfer and Catalysis (BETCy) found a nitrogenase that could do both. They made the discovery when they modified a nitrogenase; it didn’t work, but the natural protein they were using as a benchmark did. The unmodified protein turns the greenhouse gas carbon dioxide into a simple fuel—methane. The protein catalyzes both reactions at the same time. But it makes a lot more ammonia than methane, which may be why nobody noticed the methane before. This work is part of a broader effort to find ways to turn carbon dioxide into liquid fuels at the BETCy Energy Frontier Research Center, led by Washington State University.

More Information

Zheng Y, DF Harris, Z Yu, Y Fu, S Poudel, RN Ledbetter, KR Fixen, ZY Yang, ES Boyd, ME Lidstrom, LC Seefeldt, and CS Harwood. 2018. “A Pathway for Biological Methane Production Using Bacterial Iron-Only Nitrogenase.” Nature Microbiology 3(3):281. DOI: 10.1038/s41564-017-0091-5

Disclaimer: The opinions in this newsletter are those of the individual authors and do not represent the views or position of the Department of Energy.