January 17, 2021
biochemistry Biology carbon carbon dioxide catalysis Science synthetic biology Technology

Researchers make their own enzyme pathway to get CO₂ out of the air

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Researchers make their own enzyme pathway to get CO₂ out of the air

Olivier Le Moal | Getty Images

Before this century is over, we’re almost certainly going to need to pull massive amounts of carbon dioxide back out of the atmosphere. While we already know how to do carbon capture and storage, it takes a fair amount of energy and equipment, and someone has to pay for all that. It would be far more economical to pull CO2 out of the air if we could convert it to a useful product, like jet fuel. But processes like that also take a lot of energy, plus raw materials like hydrogen that take energy to create.

Plants and a huge range of microbes successfully pull carbon dioxide out of the air and use it to produce all sorts of complicated (and valuable!) chemicals. But the pathways they use to incorporate CO2 aren’t very efficient, so they can’t fix enough of the greenhouse gas or incorporate it into enough product to be especially useful. That has led a lot of people to look into re-engineering an enzyme that’s central to photosynthesis. But a team of European researchers has taken a radically different approach: engineering an entirely new biochemical pathway that incorporates the carbon of CO2 into molecules critical for the cell’s basic metabolism.

Sounds good in theory

On the rare occasions that most biologists think about biochemical pathways, energy is an afterthought. Most cells have enough of it to spare that they can afford to burn through their own energy supplies to force rather improbable pathways forward to get the chemicals they want. But grabbing carbon out of the atmosphere represents a very different sort of problem. You want it to happen as a central part of the cell’s metabolism rather than a pathway out on the periphery so that you grab a lot of carbon. And you want it to happen in a way that’s more efficient than the options the cells already have.

Given those focuses, energy really matters. So some biochemists have painstakingly gone through all the reaction cycles in and around the ones that normally incorporate carbon dioxide and looked into their energetics, trying to find the one that uses the least amount of energy to break the strong bonds between carbon and oxygen. Amazingly, one of the best the researchers came up with doesn’t seem to actually exist in any cells we’ve looked at.

The chemical raw materials needed are around, being used by other pathways. And there are enzymes that do related things. But as far as we can tell, evolution has never bothered to put the pieces together.

So the researchers decided that if evolution wasn’t up to the job, they would have to take over.

A pathway of one’s own

So how do you roll your own biochemical pathway? The previous identification of the non-existent pathway made the work that went into the new paper substantially easier. This had already identified starting chemicals that were common in the cell and each intermediate step. What the researchers had to do was identify the enzymes that could move the chemicals from one step to another in the pathway. Emphasis on “could”—remember that the pathway doesn’t exist in nature, so there aren’t any enzymes specialized in these reactions.

The pathway itself is rather short, needing only three steps. In the first, a two-carbon chemical that’s common in cells (called glycolate) is linked to a cellular co-factor that makes it more reactive. In the second, the activated glycolate reacts with carbonate, which is essentially a form of carbon dioxide dissolved in water. The resulting three-carbon molecule then has to have the co-factor cleaved off before it can be used elsewhere in the cell’s metabolism. So the researchers had to find an enzyme for each step.

For the first step, there are already a lot of enzymes that link the co-factor to something or transfer it from one molecule to another. The researchers tested 11 of them (some natural, some previously engineered) to look for ones that worked well on glycolate. They found two that did a passable job—and oddly, the one that did less well turned out to be easier to fix because we already knew something about how it was regulated.

Normally, one of the amino acids on the protein gets chemically modified in order to shut down the enzymatic activity. So the researchers changed this amino acid so it couldn’t be modified and, for good measure, produced it in a strain of bacteria that was unable to perform the modification. This boosted the enzyme’s performance by a factor of 30. They also looked at a related enzyme that acted on a chemical that was similar in size to glycolate and made a change that should open up the enzyme’s active site where the reactions take place. This gave the enzyme another 60 percent boost.

Figuring that was good enough, the researchers went shopping for another enzyme to catalyze the second step in the pathway, linking the new carbon atom. They decided to test a set of enzymes that catalyzed a similar reaction using a chemical that’s a bit larger than glycolate. They found one with an activity they describe as “very low but measurable.”

To give that an initial boost, the researcher obtained the structure of the enzyme and made some changes that should increase its ability to interact with glycolate. They then subjected it to random mutation, identifying a form with three mutations that had 50 times the activity of the “very low but measurable” version.

There are plenty of enzymes that cleave the co-factor off other molecules, so it was easy to test those. The researchers found one that worked without significant modification, ending the pathway with the production of glycerate, a three-carbon molecule that’s closely related to glycerol. Glycerate can be used by a wide variety of pathways in the cell, many of which lead to larger and more complex molecules.

Good, but not great

From an energetic perspective, this is absolutely great. If we compare the natural pathway used by plants with this new one, it looks very good by some measures. The pathway is nearly as energetically favorable as one of the major existing pathways for extracting carbon from carbon dioxide, and the vast majority of the reactions would be run forward, producing the intended end product rather than digesting it. It would grab twice as much carbon for every cycle and consume about 20 percent less energy for fixing an equivalent amount of carbon. And unlike the enzyme used in plants, it won’t be shut down when oxygen levels rise.

As an added bonus, the researchers showed that it could also be incorporated into a pathway that could eliminate an environmental contaminant that is used for the manufacture of PET plastics.

But the researchers haven’t tested the new pathway in a living organism; all the tests were done in solutions using materials derived from bacteria, and in the grand scheme of things, it wasn’t especially efficient. If you had a gram of the enzymes needed (which is a lot of protein to make), it would only eliminate 1.3 milligrams of carbon dioxide a minute. That means the gram of enzymes would take 13 hours to pull an entire gram of carbon dioxide out of the atmosphere. And the pathway would need to be constantly fed energy to continue the reaction.

In all these cases, the researchers tested the system outside of cells in a solution with components derived from bacteria. We have no idea how this pathway would operate—or if it would operate—if it were put back inside a cell. But that’s going to be a necessary step if we want this to be, as the authors propose, “key to sustainable biocatalysis and a carbon-neutral bio-economy.” Both because living things can take the glycerate and build it into the larger chemicals that we actually want and because forcing an organism to depend on it for carbon is the surest way to allow evolution to get this pathway to work with a far greater efficiency than it already has.

Of course, there’s no reason to think that won’t eventually be possible. And it’s important to acknowledge the significance of this work. While other groups have figured out how to optimize enzymes to perform completely new functions, this group took an entire pathway that had existed only in calculations and made it a biological reality, significantly altering a couple of enzymes in the process. It hints at a future where we can get biology to do a lot more than it was likely to end up doing on its own.

Nature Catalysis, 2021. DOI: 10.1038/s41929-020-00557-y  (About DOIs).