Sun. Oct 2nd, 2022
Researchers create their own enzyme pathway to remove CO₂ from the air

Olivier Le Moal | Getty Images

Before this century is over, we will almost certainly have to remove massive amounts of carbon dioxide from the atmosphere. While we already know how to do carbon capture and storage, it takes quite a bit of energy and equipment, and someone has to pay for that. It would be much more economical to use CO . to pull2 from the air if we could convert it into a usable product, such as jet fuel. But such processes also cost a lot of energy, plus raw materials such as hydrogen that cost energy to create.

Plants and a vast array of microbes successfully extract carbon dioxide from the air and use it to produce a variety of complicated (and valuable!) chemicals. But the pathways they use to transfer CO. to include2 are not very efficient, so they cannot absorb enough of the greenhouse gas or incorporate it in enough product to be particularly useful. That has led many people to look at the re-engineering of an enzyme that is central to photosynthesis. But a team of European researchers has taken a radically different approach: developing an entirely new biochemical pathway containing the carbon of CO.2 in molecules that are crucial for the basic metabolism of the cell.

Sounds good in theory

On the rare occasions when most biologists think about biochemical pathways, energy is an afterthought. Most cells are fed up with enough to afford to burn their own energy supply to force rather improbable avenues forward to get the chemicals they want. But getting carbon out of the atmosphere represents a very different kind of problem. You want it to happen as a central part of the cell’s metabolism rather than a pathway to the periphery so that you take in a lot of carbon. And you want it to be done in a way that is 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 those that normally take in carbon dioxide and looked at their energies, 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 actually seem to exist in the cells we looked at.

The necessary chemical raw materials are nearby and are used by other roads. And there are enzymes that do related things. But as far as we can tell, evolution never bothered to put the pieces together.

So the researchers decided that if evolution couldn’t handle the work, they should take it over.

A path of your own

So how do you roll your own biochemical pathway? The earlier identification of the non-existent path made the work going into the new paper considerably easier. This had already identified starting chemicals that are common in the cell and at every 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 does not exist in nature, so there are no enzymes that specialize in these reactions.

The path itself is quite short and only needs three steps. In the first, a two-carbon chemical commonly found in cells (called glycolate) is linked to a cellular cofactor 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 must then have split off the cofactor 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 many enzymes that link the cofactor to something or transfer it from one molecule to another. The researchers tested 11 of them (some natural, some developed earlier) to look for the ones that worked well on glycolate. They found two that did a decent job – and oddly enough, 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 is chemically modified to stop the enzymatic activity. So the researchers changed this amino acid so that it couldn’t be modified and, for good measure, produced it in a strain of bacteria that couldn’t make the modification. This increased the enzyme’s performance by a factor of 30. They also looked at a related enzyme that acted on a chemical similar in size to glycolate and altered the active site of the enzyme, where the reactions take place. should open. This gave the enzyme another 60 percent boost.

Thinking that was good enough, the researchers set out to find another enzyme to catalyze the second step in the pathway, which involves linking the new carbon atom. They decided to test a series of enzymes that catalyzed a similar reaction with a chemical slightly larger than glycolate. They found one with an activity they describe as “very low but measurable.”

To give that a first boost, the researcher obtained the structure of the enzyme and made some changes that should increase the interaction 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 many enzymes that cleave the cofactor from 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 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 amazing. If we compare the natural path of plants with this new one, it looks very good according to some measures. The pathway is nearly as energetically favorable as any of the major existing pathways for extracting carbon from carbon dioxide, and the vast majority of reactions would run forward, producing the intended end product rather than digesting it. It would take up twice as much carbon for each cycle and use about 20 percent less energy to capture an equivalent amount of carbon. And unlike the enzyme used in plants, it doesn’t turn off when oxygen levels rise.

As an added bonus, the researchers showed that it can also be incorporated into a pathway that can eliminate an environmental pollutant used to manufacture PET plastics.

But the researchers have not tested the new pathway in a living organism; all tests were done in solutions containing materials derived from bacteria, and overall it was not particularly efficient. If you had a gram of the necessary enzymes (what a lot protein), it would eliminate only 1.3 milligrams of carbon dioxide per minute. That means the gram of enzymes would take 13 hours to remove a whole gram of carbon dioxide from the atmosphere. And the pathway should be constantly energized to continue the reaction.

In all these cases, the researchers tested the system outside the cells in a solution containing components derived from bacteria. We have no idea how this path would work – or would work – if put back into a cell. But that will be a necessary step if we want this to be, as the authors propose, “the key to sustainable biocatalysis and a carbon neutral bioeconomy.” Both because living things can take the glycerate and incorporate it into the bigger chemicals we actually want, and because forcing an organism to depend on it for carbon is the surest way to enable evolution to follow this path with a much greater efficiency than it is. has already.

Of course, there’s no reason to believe that this won’t be possible in the end. And it is important to recognize the significance of this work. While other groups have discovered how to optimize enzymes to perform completely new functions, this group took an entire route that existed only in calculations and made it a biological reality, significantly altering a number of enzymes in the process. It hints at a future where we can make biology do much more than it probably would on its own.

Nature Catalysis2021. DOI: 10.1038/s41929-020-00557-y (About DOIs).

By akfire1

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