IGI Scientists Make E. coli That Can Take Carbon Dioxide From the Air — And Use It

New study shows that re-engineered E. coli can absorb and concentrate carbon dioxide from the air, taking a step towards carbon sequestration.

Rising levels of carbon dioxide (CO₂) in the atmosphere are causing climate change and environmental destruction. But what if we could draw more CO₂ out of the atmosphere using living organisms? Better yet, what if we could use the carbon in CO₂ to feed more people or fuel a new, green chemical industry? In a paper published today in eLife, a team from IGI researcher Dave Savage’s lab at UC Berkeley reports a major advance in this direction.

Carbon: the real MVP

All life forms on Earth use carbon. Carbon is an essential building block of the cell and of compounds cells use for fuel. Some life forms, notably plants and microorganisms that use photosynthesis, get all of their carbon from CO₂ in the atmosphere. But because CO₂ makes up just 0.04% of Earth’s atmosphere, it isn’t easy for organisms that rely on atmospheric CO₂ to get the carbon they need. Pumping CO₂ into a cellular compartment called a carboxysome is a common way many microorganisms concentrate CO₂, giving the cell a readily available pool.

Most other organisms, including humans, get carbon from their food. E. coli — bacteria that live in the guts of humans and other animals and are used extensively in scientific research — usually get carbon by eating simple sugars from the foods we consume. Being able to put carboxysomes, and their ability to capture CO₂, into new organisms could have huge implications for the environment, agriculture, chemical engineering, and more.

A carbon roadblock

Carboxysomes aren’t simply empty compartments, but complex structures made of more than 10,000 distinct protein pieces that spontaneously self-assemble. In previous work, researchers from the Savage lab identified what they hoped was the full complement of genes needed to make a functioning carboxysome in a microorganism they were studying, as well as crucial transporters, which bring CO₂ into the cell. In the work published today, they tested whether they had actually uncovered all of the crucial carboxysome and transporter genes by adding them to E. coli bacteria. Their goal was to recreate a functioning CO₂ concentrating system in a foreign host cell that never had one to begin with.

The Savage team was confident they could create something that looked like a carboxysome by inserting the right genes, but they wanted to see if it actually worked like a carboxysome, too. But, normal E. coli get carbon from their diet. They don’t need to concentrate CO₂, and will grow happily without it. So, they needed to engineer E. coli that had no option but to use their new carboxysomes and transporters to get the carbon they craved.

“For many years, I’ve been interested in reconstituting the carboxysome to study its structure and remarkable ability to self-assemble. But it wasn’t clear how we could do the home run experiment of functionally reconstituting the entire CO₂-concentrating system,” says Savage. “The critical event was Avi Flamholz joining the lab!”

Flamholz, who had previous experience with studying photosynthesis in Ron Milo’s lab at the Weizmann Institute of Science, realized the key was to force the bacteria to look elsewhere.

“We made a roadblock in their metabolism by deleting an important gene,” explains Flamholz. “And then we gave them the opportunity to take a detour around the roadblock by using CO₂.”

In other words, the research team removed genes that E. coli usually uses to process sugars. This change meant the E. coli needed another source of carbon — like CO₂. But they can only get enough carbon if the transporter and carboxysome work together effectively to concentrate ambient CO₂ from the air. It worked.

“Actually productively concentrating CO₂ out of ambient air is bananas!” says Savage. “Although atmospheric CO₂ levels are rising in a way that is hugely significant for climate, most organisms that use ambient CO₂ for their carbon source are practically starving for CO₂! To see the system work as hypothesized was very satisfying.”

Feeding a growing planet with CO₂

Microorganisms invented CO₂-concentrating technology, and this research brings us a step closer to being able to borrow and harness it. There has long been excitement about the possibility of adding engineered CO₂ concentrating systems to plants so they can pull more CO₂ from the air, potentially slowing climate change.

“We’re very excited about the potential applications, which is one reason it’s so great to be a part of the collaborative research going on at the IGI,” says Savage. “Moving forward we have a large interest in the chloroplast, which is the powerhouse of the plant cell. We think that some of the principles learned here could be used to improve photosynthesis in plants.”

Adding additional CO₂-concentrating power to crops could give them more fuel to grow bigger, faster, while reducing water and fertilizer usage. In other words, the aim is to both capture CO₂ from the air and create more food to help feed our growing global population with fewer farm inputs.

Greening chemistry out of thin air

In addition to reducing chemical use, this advance could affect how chemicals and chemical reactions are made in the first place. Traditional chemical manufacturing produces heavy metals, petroleum, toxic waste, and releases CO₂ into the atmosphere. “Green chemistry” uses engineered organisms to perform chemical reactions, cutting back on these environmental hazards. Transplanting this CO₂-concentrating system into E. coli or other microbes used in green chemistry could become one way to actually take CO₂ out of the atmosphere, instead of adding more.

The Savage lab and their collaborators are now working on adding carboxysomes and CO₂ transporters into industrially relevant microorganisms to see if they can concentrate CO₂ and make it into useful products.

“Think about all the things you might possibly make out of microbes, like chemicals, biofuels, additives for food or even bulk edible protein, like imitation meats,” says Flamholz. “For all of those things, why shouldn’t the carbon source be CO₂? Why shouldn’t we pull it out of the air?”

By Hope Henderson

Hope Henderson holds a B.A. in Biology from Brown University and a Ph.D. in Molecular & Cell Biology from the University of California, Berkeley. She joined the IGI in 2019 to work in science communication. In addition to serving as IGI’s main writer, she plans content strategy and manages IGI’s social media, illustration, and translation.