Enzymes from nine organisms combined to create a new route to use CO2 | Techilink

There is no question that humans are causing long-lasting changes in the amount of carbon in the atmosphere. But the human impact is taking place against a background of natural carbon fluxes that are staggering. For example, the amount of CO₂ in the atmosphere cycles up and down by more than one percent purely due to seasonal differences in plant growth.

The effectiveness of biological activity offers hope that we can use it to help us recover some of our carbon from the atmosphere at an accelerated rate. But the incredible scale of biology hides a bit of an ugly secret: the individual enzymes and pathways used to take up CO₂ in living organisms are not as efficient. These pathways are also linked to a complex biochemistry within the cell that is not always suitable for our purposes.

Tired of waiting for life to develop a solution to our industrialization problem, a German-Swiss team of researchers has decided to go its own way. In an astonishing amount of work, they have taken enzymes from nine different organisms in all three domains of life and used them to build and optimize a synthetic cycle that can utilize carbon dioxide at an efficiency 20 times higher than that of the system used by plants.

break up CO₂

The problem with carbon dioxide is that it is a very stable molecule. It takes quite a bit of energy to break it down, but unless we know how to break it down efficiently, we can’t use CO from the atmosphere₂ for one of the many things we use carbon for, such as the polymers in our plastics or the graphite in our electrodes. While several ideas have been put forward for capturing atmospheric CO₂ to useful chemicals, none of which have yet managed to scale up economically.

However, living organisms do this trick all the time. More than 90 percent of the carbon removed from the atmosphere is ultimately converted to sugars by photosynthetic organisms, and there are at least five other minor pathways by which organisms build complex molecules, starting with CO₂. All of these processes have problems when it comes to how we would like to use them. Many of them are relatively inefficient; others work only in adverse environmental conditions; all are wired into a complex cellular biochemistry that often results in many by-products or an end product that is not easy to turn into something useful.

All those annoying traits are what you’d expect from evolution, which is to tailor the carbon responses to the environments and needs of specific organisms. So the team behind the new work decided to do what evolution hasn’t: bring together enzymes from organisms that would never come into contact and build a pathway designed for efficient use of CO₂.

To do this, they first targeted the limiting enzyme in most of the known pathways: the one that breaks down CO₂ in the first place. The team searched the databases for all enzymes belonging to this class and identified those that had the properties they were looking for. They settled on a group of enzymes called enoyl-CoA carboxylases/reductases, or ECRs.

ECRs have only been discovered quite recently and are usually not even the main route of obtaining carbon in the organisms that have them. But for the purposes here, ECRs have many good properties: they are very efficient, don’t undergo side reactions with oxygen, and don’t need unusual chemicals to make the reaction work.

Build a trajectory

But the reaction that ECRs catalyze is only the first step, and a constant supply of chemicals would be required to get the CO to react₂ of. Most organisms obtain carbon dioxide as part of a cycle. They react it with a larger chemical, then break down a smaller carbonaceous molecule, then use a few further reactions to reform the original chemical. (You can see an example of this in a Calvin Cycle diagram.) So the team decided to build a full cycle that incorporates the ECR enzyme.

Rather than modify an existing cycle, the researchers started from scratch, building hypothetical pathways that use biologically plausible molecules and then evaluating them for energy efficiency. Only once a cycle had been identified did they search databases to find out if any enzymes existed that could catalyze the reaction. They ended up with a 13-step cycle that included CO₂ in two different steps and ended by combining the two resulting carbons with acetic acid to form a four-carbon molecule called malic acid. Along the way, some chemical cofactors and energy in the form of ATP would have to be added, but on paper it all worked out.

And then the real work began.

In total, 12 of those 13 steps required a separate enzyme to work, so the authors had to obtain the genes for all of these steps, make proteins, and then purify them. Once they got that, the team showed that adding the enzymes for each step eventually yielded the expected products. After all enzymes were added, the expected final product (malic acid) was produced.

This process allows researchers to identify any inefficiencies in the process. For example, things stalled at step 10 of the cycle, leading to the accumulation of the chemical produced at step nine. So they looked at the enzyme involved and determined that the reaction would be more efficient if it used oxygen instead of the chemical normally required. The team looked at the structure of the enzyme and redesigned to use oxygen. It worked.

They kept adjusting the path. The overall design was replaced with one that used a slightly different response path. Some enzymes ended up spewing out a bunch of by-products that were useless dead ends; that are designed to stop this. In other cases, new enzymes were added to do what the researchers call “proofreading” — when a dead-end byproduct was created, they converted it back into a usable product.

By the time the team was done, the system used 17 different enzymes from nine different organisms, including bacteria, archaea, plants and humans. The final system was really impressive, using carbon dioxide at an efficiency 20 times higher than that of the system used in photosynthesis.

The big picture

Take a moment to appreciate the magnitude of this achievement. In four billion years of evolution, life has only managed to evolve six known pathways that start with carbon dioxide and build more complex molecules. In just a few years, a bunch of graduate students in Zurich added a seventh.

There are some pretty obvious limitations to this system as it stands. A variety of biochemical cofactors must be added to the reaction for it to work, and the output – malic acid – is currently only used as a food additive. But malic acid undergoes several reactions in cells, and there’s no reason to believe that some of them couldn’t convert it into a useful industrial chemical. Or there’s no reason to believe we couldn’t find other ways to use malic acid if there was a sudden surplus of it.

The other thing is that the entire pathway can now be placed in cells, like normal bacteria E coli or the synthetic cells with a minimal genome that researchers are working on. If so, the need to supply all the chemical cofactors should disappear, because the cells would have to produce them anyway. More importantly, if the cell were made dependent on this pathway as its sole source of carbon, evolution would have a chance to optimize it even further.

The newspaper also comes at an interesting time. International climate negotiations are taking place as countries begin to grapple with the fact that the Paris Agreement is not enough to keep the planet below the 2 degrees Celsius warming target. The US has submitted its mid-century plans, which include extensive use of carbon capture and storage to make its energy system carbon neutral. But even then, it’s likely we’ll need to pull carbon directly from the atmosphere before this century to limit warming.

Something like this, which could turn atmospheric carbon into an industrial resource, could be essential to making that future possible. The same applies to a separate article in the same issue of Science that describes redesigning trees to make them photosynthesize more efficiently under varying lighting conditions. We’re probably going to need some kind of technology like this, so it’s nice to see that basic science can get this done.

Science2016. DOI: 10.1126/science.aah5237 (About DOIs).

Updated to clarify the need for external energy supply.