A team of scientists from LanzaTech, Northwestern University and the Department of Energy’s Oak Ridge National Laboratory have engineered a microbe to convert molecules of industrial waste gases, such as carbon dioxide and carbon monoxide, into acetone and isopropanol (IPA). These widely used chemicals serve as the basis of thousands of products, from fuels and solvents to acrylic glass and fabrics.

Researchers built on LanzaTech technology to develop an efficient new process that converts waste gases, such as emissions from heavy industry or syngas generated from biomass, into either acetone or IPA, using an engineered bacterium called Clostridium autoethanogenum, or C. auto. Their methods, including a pilot-scale demonstration and life cycle analysis showing the economic viability, are published in an open-access paper in the journal Nature Biotechnology.

This bioprocess provides a sustainable alternative to today's production routes to these essential chemicals, which currently rely on fresh fossil feedstocks and result in significant toxic waste. We can reduce greenhouse gases by more than 160%, achieve carbon-negative production and lock up carbon that would have ended up in the atmosphere.

—Jennifer Holmgren, CEO of LanzaTech

LanzaTech is currently scaling up this technology, which can be inserted into their existing systems and deployed for use around the world.

The research began at LanzaTech, where scientists previously commercialized a process using C. auto strains that can produce ethanol, a common biofuel, from carbon emissions. Identifying the best enzymes for acetone and IPA production and engineering microbial strains to achieve efficient, high-yielding carbon-to-chemical conversion presented a complex scientific challenge.

The scientists used a three-pronged approach comprising innovations in pathway screening, strain optimization and process development.

Overview of three-pronged approach for pathway, strain and process optimization. Liew et al.

As a first step, LanzaTech screened nearly 300 strains for enzymes that could be useful in the acetone and IPA-producing pathways. After identifying useful strains, the scientists built a combinatorial DNA library—the largest ever for this class of microbe—to find enzyme variants that optimized acetone production.

Further optimization relied on synthetic biology tools, including cell-free prototyping by Northwestern University, advanced modeling by LanzaTech and molecular analyses by ORNL.

Oak Ridge has very unique capabilities in terms of DNA sequencing, systems biology and various metabolomics and proteomics. Oak Ridge’s expertise helped us troubleshoot the process to find out which steps may be limiting.

—Michael Köpke, LanzaTech’s vice president for synthetic biology

Proteomics, the study of proteins, and metabolomics, the study of small molecules called metabolites, provide a molecular-level view of which specific chemicals are being used and produced by a microbe. Like any organism, when microbes consume or metabolize the substances they need to survive, they produce byproducts. For scientists engineering microbes to produce certain substances, these byproducts represent bottlenecks.

The protein and metabolite profiles show where a production bottleneck is occurring inside the C. auto cell. We can see what needs to be modified next in the pathways to flow more of the carbon to the product.

—Tim Tschaplinski, head of ORNL’s Biodesign and Systems Biology Section

In this case of C. auto, ORNL scientists determined that the microbe was producing a significant amount of the compound 3-hydroxybutyrate that would require downstream treatment and increase process costs. This compound sits in the middle of a key metabolic pathway where it can move carbon in different directions.

We look at the enzyme pathways and say, ‘Here’s the block, and there may be a dozen different enzymes within the original collection that may do a better job. Then our partners at Northwestern University express those enzymes in cell-free systems, and we look at what accumulates, which feeds into LanzaTech’s advanced computational models.

—Tim Tschaplinski

This collaboration is the latest in a longstanding relationship between ORNL and LanzaTech. In 2015, a team of ORNL and LanzaTech scientists sequenced the entire C. auto genome, laying the groundwork for the current research.

The acetone strain and process development, genome-scale modeling, life cycle analysis and initial pilot runs were supported by LanzaTech and the Bioenergy Technologies Office in DOE’s Office of Energy Efficiency and Renewable Energy. The cell-free prototyping and ‘omics analyses were funded by the Biological and Environmental Research program in DOE’s Office of Science. DNA sequencing was supported by the Joint Genome Institute, a DOE Office of Science user facility.

Resources

• Liew, F.E., Nogle, R., Abdalla, T. et al. (2022) “Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale.” Nat Biotechnol doi: 10.1038/s41587-021-01195-w