Artificial metabolism turns waste carbon dioxide into useful chemicals

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Engineered enzymes have been shown to perform metabolic reactions that do not exist in nature, successfully transforming simple carbon molecules into acetyl-CoA. A building block of life, acetyl-CoA can be used to make a variety of materials.

To build the system, Northwestern University and Stanford University scientists screened 66 enzymes and 3,000 enzyme variants. This required the use of molecular machinery outside of living cells.

With the new study, the researchers engineered a biological system that can convert formate — a simple liquid molecule easily made from carbon dioxide — into acetyl-CoA, a universal metabolite used by all living cells. As a proof of concept, the engineers then used the same system to convert acetyl-CoA into malate, a commercially valuable chemical used in foods, cosmetics and biodegradable plastics.

Unlike natural metabolic routes, the new system is entirely synthetic and operates outside of living cells. The engineers built the system, called the Reductive Formate Pathway (ReForm), from engineered enzymes that performed metabolic reactions never before seen in nature.

The work marks a major advance for synthetic biology and carbon recycling, opening the door for developing sustainable, carbon-neutral fuels and materials.

Looking beyond nature

As researchers search for solutions to help fight the ever-warming atmosphere, many have sought to upcycle captured carbon dioxide into valuable chemicals. Because it’s easy to make from electricity and water, formate has emerged as a promising starting point. Then, biological systems could perform the work needed to convert formate into useful materials.

Unfortunately, living cells struggle to use formate efficiently. Only a few rare microbes can digest formate naturally, and those microbes are difficult to engineer for large-scale production.

Testing thousands of enzymes per week

Before building the metabolic pathway, the research team needed enzymes that could perform these non-natural reactions. To rapidly express and test large numbers of enzyme variants, the team turned to cell-free synthetic biology. In this approach, scientists essentially remove a cell’s wall, collect its molecular machinery (enzymes, cofactors and small molecules) and put it all into a test tube. Scientists then can use this machinery — outside of a living organism — to make a product in a safe, inexpensive and rapid manner.

Using a cell-free system enabled the team to rapidly screen 66 enzymes and more than 3,000 enzyme variants to find the ones that worked best. This process was much faster and more flexible than using live cells, which would have been slow and laborious.

How it works

With this process, the researchers engineered five distinct enzymes. The final pathway design comprises six total reaction steps, in which each enzyme performs one step. Together, the series of reactions successfully transformed formate into acetyl-CoA.

Much like the enzyme testing, the entire system is run outside of living cells. That means the team could precisely control enzyme concentrations, cofactors and conditions — something that’s nearly impossible to accomplish inside a living organism.

After establishing the system, Karim, Jewett and their teams used ReForm to convert acetyl-CoA into malate. The team also demonstrated ReForm can accept other carbon-based inputs, including formaldehyde and methanol.

The research appears in the journal Nature Chemical Engineering, titled “A synthetic cell-free pathway for biocatalytic upgrading of formate from electrochemically reduced CO₂”.