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Before this century is over, we will almost certainly have to emit massive amounts of carbon dioxide from the atmosphere. Although we already know how to capture and store carbon, it requires a fair amount of energy and equipment, and someone has to pay for it. It is much cheaper to draw CO2 from the air if we can turn it into a useful product, such as jet fuel. But such processes also require a lot of energy, plus raw materials like hydrogen that need energy to create.
Plants and a large variety of microbes successfully extract carbon dioxide from the air and use it to produce all kinds of complex (and valuable!) Chemicals. But the roads they use to absorb CO2 are not very efficient, so they can not fix enough of the greenhouse gas or incorporate it into enough products to be particularly useful. This has led many people to investigate an enzyme that is central to photosynthesis. But a team of European researchers has taken a completely different approach: a completely new biochemical orbit that contains the carbon of CO.2 in molecules that are critical for the basic metabolism of the cell.
Sounds good in theory
In the rare case that most biologists think about biochemical pathways, energy is an afterthought. Most cells have enough to save that they can afford to burn through their own energy supplies to force rather improbable ways forward to get the chemicals they want. But getting carbon out of the atmosphere is a whole other problem. You want it to take place as a central part of the cell’s metabolism, rather than as a pathway to the periphery so you can grab a lot of carbon. And you want it to happen in a more efficient way than the options that the cells already have.
Given the focus, energy really does matter. Thus, some biochemists have carefully gone through all the reaction cycles in and around those that usually contain carbon dioxide and looked into their energy and tried to find the one that uses the least amount of energy to break the strong bonds between carbon and oxygen. Surprisingly, one of the best that the researchers came up with does not seem to exist in any of the cells we looked at.
The chemical raw materials required are in the environment and are used by other roads. And there are enzymes that do related things. But as far as we can tell, evolution has never bothered to put the pieces together.
The researchers therefore decide that if evolution does not have the task, they should take over.
A path of your own
How then do you roll your own biochemical path? The previous identification of the road that does not exist has greatly facilitated the work contained in the new article. It has already identified initial chemicals that are common in the cell and every intermediate step. What the researchers had to do was identify the enzymes that could move the chemicals from one step to another. Emphasis on ‘could’ – remember that the path does not exist in nature, and therefore there are no enzymes that specialize in these reactions.
The road itself is quite short and requires only three steps. In the first, a two-carbon chemical commonly found 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 that is dissolved in water. The resulting three-carbon molecule must then have the co-factor cut off before it can be used elsewhere in cell metabolism. The researchers therefore had to find an enzyme for each step.
For the first step, there are already many enzymes that link the co-factor to something or transfer it from one molecule to another. The researchers tested 11 of them (some of course, others previously designed) to look for those that work well on glycolate. They found two that did an acceptable job – and oddly enough, the one that did less well was easier to solve, because we already knew something about how it was regulated.
Normally, one of the amino acids in the protein is chemically modified to stop the enzymatic activity. The researchers therefore changed this amino acid so that it could not change and produced it to a good extent in a bacterial strain that could not perform the modification. It increased the performance of the enzyme by a factor of 30. They also looked at a related enzyme that acts on a chemical similar to glycolate and made a change to the active site of the enzyme where the reactions take place, to open. This increased the enzyme by another 60 percent.
The researchers believed it was good enough and went shopping for another enzyme to catalyze the second step in the orbit, which connects the new carbon atom. They decided to test a set of enzymes that catalyze a similar reaction using a chemical slightly larger than glycolate. They found one with an activity they describe as ‘very low but measurable’.
To give it an initial boost, the researcher acquired the structure of the enzyme and made changes to increase the ability to communicate with glycolate. They then subjected it to random mutation and identified a form with three mutations that had 50 times the activity of the ‘very low but measurable’ version.
There are many enzymes that cut off the co-factor of other molecules, so it was easy to test it. The researchers found that one that worked without significant modification ended the way 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, it is absolutely wonderful. If we compare the natural path that plants use with this new one, it looks very good by some standards. The orbit is almost as energetically favorable as one of the major existing pathways for the extraction of carbon from carbon dioxide, and the vast majority of the reactions will proceed, producing the intended end product rather than digesting it. It grabs twice as much carbon for each cycle and consumes about 20 percent less energy to capture an equivalent amount of carbon. And unlike the enzyme used in plants, it will not shut down as oxygen levels rise.
As an added bonus, the researchers have shown that it can also be incorporated into an orbit that can eliminate an environmental contaminant used in the manufacture of PET plastic.
But the researchers did not test the new path in a living organism; all the tests were done in solutions using materials derived from bacteria, and according to the grand scheme it was not very effective. If you had one gram of the required enzymes (this is a very protein), it will eliminate only 1.3 mg of carbon dioxide per minute. This means that the grams of enzymes would take 13 hours to extract a whole gram of carbon dioxide from the atmosphere. And the road will have to be constantly fed with energy to continue the reaction.
In all these cases, the researchers tested the system outside the cells in a solution containing ingredients derived from bacteria. We have no idea how this route would work – or how it would work – if it were put back in a cell. But it is going to be a necessary step if we want it to be, as the authors suggest, ‘the key to sustainable biocatalysis and a carbon-neutral bioeconomy.’ Both because living things can take the glycerate and build it up in the larger chemicals we actually want, and because it’s the surest way to make evolution work to work with a much greater efficiency than to make an organism of it dependent on carbon. already has.
Of course, there is no reason to think that this will not be possible in the end. And it is important to recognize the importance of this work. While other groups determined how to optimize enzymes to perform entirely new functions, this group followed a whole path that existed only in calculations and made it a biological reality, bringing some enzymes into the process. has changed significantly. It points to a future where our biology can do much more than it probably would alone.
Earth Catalysis, 2021. DOI: 10.1038 / s41929-020-00557-y (About DOIs).