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

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Before this century is over, we will almost certainly have to withdraw huge amounts of carbon dioxide from the atmosphere. We already know how to capture and store carbon, but it takes a lot of energy and equipment and someone has to pay for it. It would be far more economical to pull CO2 out of the air if we could turn it into a useful product like jet fuel. However, such processes also require a lot of energy and raw materials such as hydrogen, which require energy to be generated.

Plants and a host of microbes successfully pull carbon dioxide from the air, producing all sorts of complicated (and valuable!) Chemicals with it. However, the ways in which they incorporate CO2 are not very efficient, so they cannot capture enough greenhouse gas or incorporate into enough products to be particularly useful. This has led many people to revise an enzyme that is central to photosynthesis. However, a team of European researchers took a radically different approach: to develop a completely new biochemical way that binds the carbon from CO2 into molecules that are crucial for the basic metabolism of the cell.

Sounds good in theory

On the rare occasions when most biologists ponder biochemical pathways, energy is an afterthought. Most cells have enough of it to afford to burn their own stores of energy to force unlikely paths forward to obtain the chemicals they want. However, getting carbon out of the atmosphere is a completely different problem. You want this to happen as a central part of cell metabolism rather than a peripheral pathway so that you take in a lot of carbon. And you want this to happen more efficiently than the options the cells already have.

With these focuses, energy is really important. Some biochemists have therefore carefully gone through all of the reaction cycles in and around those that normally contain carbon dioxide, studying their energy in an attempt to find the one who uses the least amount of energy to break the strong bonds between carbon and oxygen. Amazingly, one of the best that researchers have found doesn't actually seem to exist in any of the cells we looked at.

The required chemical raw materials are available and are used in other ways. And there are enzymes that do related things. But as far as we can tell, evolution never bothered putting the pieces together.

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

Your own way

How do you roll your own biochemical path? The previous identification of the nonexistent path made work in the new paper much easier. This had already identified starting chemicals that were common in the cell and in each intermediate step. The researchers needed to identify the enzymes that could move the chemicals from one step to another on their way. The emphasis on "could" – remember that the path does not exist in nature, so there are no enzymes that specialize in these reactions.

The walk itself is pretty short and only takes three steps. In the first case, a two-carbon chemical (called glycolate) common in cells is linked to a cellular cofactor that makes them more reactive. In the second case, 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 split off the cofactor before it can be used elsewhere in the cell metabolism. So the researchers had to find an enzyme for each step.

For the first step, there are already many enzymes that combine the cofactor with something or transfer it from one molecule to another. The researchers tested 11 of them (some natural, others previously developed) to look for ones that work well with glycolate. They found two who did a passable job – and, oddly enough, the one that didn't do well turned out to be easier to fix since we already knew something about how it was regulated.

Usually one of the amino acids on the protein is chemically modified to turn off enzymatic activity. Therefore, the researchers changed this amino acid so that it could not be modified, and produced a large part of it in a bacterial strain that could not carry out 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 of similar size to glycolate and made a change that was supposed to open the active site of the enzyme where the reactions take place. This gave the enzyme another 60 percent boost.

Finding that this was good enough, the researchers looked for another enzyme to catalyze the second step on the way to linking the new carbon atom. They decided to test a number 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 it a first boost, the researcher got the structure of the enzyme and made some changes to increase its ability to interact with glycolate. They then randomly mutated it and identified a form with three mutations that had 50 times the activity of the "very low but measurable" version.

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There are many enzymes that cleave the cofactor from other molecules so these were easy to test. The researchers found one that worked without significant modification and ended the path with the production of glycerate, a three-carbon molecule closely related to glycerin. Glycerate can be used in the cell in a variety of ways, many of which result in larger and more complex molecules.

Good, but not great

From an energetic point of view, this is absolutely great. If we compare the natural path of the plants with this new one, it looks very good in some ways. The route is almost as energetic as one of the major routes in existence to extract carbon from carbon dioxide, and the vast majority of the reactions would run forward producing the intended end product rather than digesting it. It would absorb twice as much carbon for each cycle and use about 20 percent less energy to fix an equivalent amount of carbon. And unlike the enzyme used in plants, it doesn't turn off when the oxygen levels rise.

As an added bonus, the researchers showed that it can also be incorporated into a pathway that removes pollution used in making PET plastics.

But the researchers did not test the new pathway in a living organism. All tests were done in solutions using materials derived from bacteria and by and large it was not particularly efficient. If you had one gram of the enzymes you need (which is a lot of protein to produce), only 1.3 milligrams of carbon dioxide would be eliminated every minute. That is, it would take one gram of enzyme 13 hours to pull a whole gram of carbon dioxide out of the atmosphere. And the path would have to be constantly energized to continue the reaction.

In all of these cases, the researchers tested the system outside of cells in a solution with components derived from bacteria. We have no idea how this path would work – or if it would work – if it were put back into a cell. However, this is a necessary step if, as the authors suggest, "the key to sustainable biocatalysis and a climate-neutral bioeconomy" is to be. Both because living things can ingest the glycerate and incorporate it into the bigger chemicals we actually want, and because it's the safest way to force an organism to rely on carbon to make that pathway work far more efficiently than it has beautiful.

Of course, there is no reason to believe that this will ultimately not be possible. And it is important to recognize the importance of this work. While other groups have figured out how enzymes can be optimized to perform entirely new functions, this group has taken a whole path that had only existed in computation and made it a biological reality, with some enzymes significantly altered in the process . It points to a future where we can get biology to do a lot more than it would likely do on its own.

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