Synthetic Condensates Turbocharge Protein Production in Bacteria

Biomedical engineers at Duke University have developed a novel synthetic method that enhances bacteria's ability to produce higher quantities of specific proteins, including those that would typically harm them, such as antibiotics.

This approach directs bacteria to generate synthetic disordered proteins that cluster together to form structures known as biological condensates. These condensates trap mRNA, which carries instructions for specific proteins, along with the cellular machinery required to produce them, significantly boosting the rate of protein production.

The technique holds promise for industries that rely on bacteria to manufacture a variety of products, including pharmaceuticals, industrial chemicals, and biofuels.

The findings were published in the journal Nature Chemistry.

Biological condensates are naturally occurring tools that are already prevalent in cells. Cells use these condensates to group or separate biomolecular machinery, allowing them to regulate activity levels. Since their discovery in 2009, their roles and applications have been the focus of extensive research.

Condensates are useful for cells to temporarily control gene expression in response to new conditions or challenges because, by quickly controlling gene expression at the protein production level, rather than at the DNA level, they can make changes in which proteins are produced in minutes instead of hours or even days."

Daniel Shapiro, PhD Student and Distinguished Professor, Duke University

Daniel Shapiro said, “But naturally occurring condensates are extremely complicated and difficult to engineer. Our lab is one of the few directing cells to make synthetic versions that can be specifically tailored to fit our purposes.”

The Chilkoti Laboratory specializes in elastin-like polypeptides (ELPs), which are long, disordered proteins resembling tangled noodles. These proteins can be engineered to clump together or dissolve based on various factors such as temperature or acidity.

In 2023, the lab became the first to demonstrate that bacteria could be programmed to produce these synthetic disordered proteins, which then form condensates that influence biological processes.

That work showed that we, as biomedical engineers, could design new molecular parts from the ground up, convince cells to make them, and assemble these parts inside the cell to make a new machine. It was the beginnings of an emerging field that is now allowing us to reprogram life in new and exciting ways."

Daniel Shapiro, PhD Student and Distinguished Professor, Duke University

Earlier research demonstrated that synthetic biological condensates could group biomolecular machinery to enhance their efficiency. However, it did not specifically direct the cell on which processes to accelerate or which proteins to produce.

This new study builds on that foundation to achieve precisely that. The researchers programmed bacterial cells to produce ELPs that form condensates and bind to specific RNA sequences, which carry the instructions for protein synthesis from DNA to the rest of the cell. By concentrating these RNA sequences within the condensates, the researchers believe they made them more accessible to the cell’s protein-making machinery.

Our work has shown that we, as biomedical engineers, could design new molecular parts from the ground up, convince cells to make them, and assemble these parts inside the cell to make a new machine."

Ashutosh Chilkoti, Alan L. Kaganov Distinguished Professor, Duke University

Shapiro said, “Rather than hiding the RNA from the cell’s machinery, it seems to bring it all together at a higher concentration into a sort of reaction crucible that increases the rate of protein production. You can make a cell express more RNA and make more of its protein, but once the RNA is made, there are very few ways of enhancing the rate at which proteins are translated from it. That is what we did here, which is very exciting.”

The researchers are now working to expand their platform. For instance, experiments suggest that condensates designed to be more viscous produce fewer proteins. Insights like this provide the team with tools to fine-tune production rates. Shapiro is also investigating how the structure of the targeted mRNA influences its production rate.

This research could benefit at least two major industrial sectors. Many biological therapeutics, such as antibodies, vaccines, and immune proteins, are currently produced in mammalian cells because bacteria lack the necessary chemical machinery.

By leveraging synthetic condensates, Shapiro envisions a way to assemble the required components to enable bacteria to efficiently produce these therapeutics.

Another potential application is using condensates to isolate the proteins being produced, preventing them from harming the host bacterium, a common challenge in the efficient production of antibiotics and other antimicrobial proteins.