Synthetic Biologists Transform Waste CO₂ Into Useful Chemicals

A groundbreaking new system paves the way for advances in synthetic biology and carbon recycling.

In brief

• A new system successfully transforms simple carbon molecules into acetyl-CoA, a building block of life that can be used to make a variety of materials.
• To build the system, scientists screened 66 enzymes and 3,000 enzyme variants.
• The work could lead to the development of sustainable, carbon-neutral fuels and materials.

In a breakthrough that defies nature, Stanford University and Northwestern University synthetic biologists have created a new artificial metabolism that transforms waste carbon dioxide (CO₂) into useful biological building blocks.

In the new study, the team engineered a biological system that can convert formate – a simple liquid molecule easily made from CO₂ in the atmosphere – 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.

The study was recently published in the journal Nature Chemical Engineering.

“We urgently need cost-effective, environmentally sustainable, and energy-efficient ways to deal with the abundance of CO₂ in our atmosphere,” said Michael Jewett, who is the senior author on the study. “Biology offers an exciting potential path, but so far remains inefficient in converting CO₂ into green chemicals. We set out to provide transformative new directions for a carbon- and energy-efficient future, and did so by creating the ReForm pathway.”

An expert in synthetic biology and biotechnology, Jewett is a professor of bioengineering at in the schools of Engineering and Medicine at Stanford, and Karim, who co-led the study, is an assistant professor of chemical and biological engineering at Northwestern’s McCormick School of Engineering and a member of the Center for Synthetic Biology (CSB).

Looking beyond nature
As researchers search for solutions to help fight the ever-warming atmosphere, many have sought to upcycle captured CO₂ 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.

We urgently need cost-effective, environmentally sustainable, and energy-efficient ways to deal with the abundance of CO₂ in our atmosphere. - Michael JewettProfessor of Bioengineering

But, 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.

“Cells naturally use metabolic reactions to convert one chemical into another,” Karim said. “For example, cells can take glucose, or sugar, and convert it into energy. But, in nature, nothing can turn formate into acetyl-CoA. There are some enzymes that can act on formate, but they cannot build it up into something useful. So, we started with a theoretical pathway design and the need for enzymes with functionalities that did not exist in nature.”

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 can then use this machinery – outside of a living organism – to make a product in a safe, inexpensive, and rapid manner.

“It’s like opening the hood of a car and removing the engine,” Jewett said. “Then, we can use that ‘engine’ for different purposes, free from the constraints of the car.”

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.

“Typically, people will test a handful of enzymes, and that takes months or more,” Karim said. “The cell-free environment enabled us to test thousands per week.”

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, the team used ReForm to convert acetyl-CoA into malate. The team also demonstrated ReForm can accept other carbon-based inputs, including formaldehyde and methanol.

“Looking forward, we are excited about the potential for synthetic biology to transform above ground carbon into the products that we use every day,” Jewett said. “We see the ReForm pathway as one key step in that direction.”