Microbes can be engineered to produce a variety of useful compounds, including plastics, biofuels, and pharmaceuticals. Now researchers are found the new way to control microbial metabolism.

But, often, these products compete with the metabolic pathways that the cells need to fuel themselves and grow.

To help optimize cells’ ability to produce desired compounds but also maintain their growth, MIT chemical engineers have devised a way to induce bacteria to switch between different metabolic pathways at different times.

These switches programmed into the cells and triggered by changes in population density, with no need for human intervention.

What we’re hoping is that this would allow more precise regulation of metabolism, to allow us to get higher productivity, but in a way where we the number of interventions, the Researcher said.

This kind of switching allowed the researchers to boost the microbial yields of two different products by up to tenfold.

To make microbes synthesize useful compounds that they don’t produce, engineers insert genes for enzymes involved in the metabolic pathway a chain of reactions that generate a specific product. This approach is now used to produce many complex products, such as pharmaceuticals and biofuels.

In some cases, intermediates produced during these reactions are also part of metabolic pathways that already exist in the cells. When cells divert these intermediates out of the engineered pathway, it lowers the yield of the end product.

Using a concept called dynamic metabolic engineering, Prather has before built switches that help cells maintain the balance between their own metabolic needs and the pathway that produces the desired product.

The researchers’ strategy based on quorum sensing, a phenomenon that bacterial cells use to communicate with each other. Each species of bacteria secretes particular molecules that help them sense nearby microbes and influence each other’s behavior.

This allows the cells to grow and divide until the population is large enough to start producing large quantities of the desired product.

That paper was the first to show that we could do autonomous control, the Researcher says. We could start the cultures going, and the cells would then sense when the time was right to make a change.

To achieve that, they used two quorum sensing systems from two different species of bacteria. They incorporated these systems into E. coli that engineered to produce a compound called naringenin, a flavonoid found in citrus fruits and has a variety of beneficial health effects.

Using these quorum-sensing systems, the researchers engineered two switching points into the cells. One switch designed to prevent bacteria from diverting a naringenin precursor called malonyl-CoA into the cells’ metabolic pathways.

At the other switching point, the researchers delayed the production of an enzyme in their engineered pathway, to avoid accumulating a precursor that inhibits the naringenin pathway if too much of the precursor accumulates.

The researchers created hundreds of E. coli variants that perform these two switches at different population densities, allowing them to identify which one was the most productive. The best-performing strain showed a tenfold increase in naringenin yield over strains that didn’t have these control switches built-in.

The researchers also demonstrated that the multiple-switch approach could be used to double E. coli production of salicylic acid, a building block of many drugs.

This process could also help improve yields for any other type of product where the cells have to balance between using intermediates for product formation or their growth, the Researcher said.

The researchers have not yet demonstrated that their method works on an industrial scale, but they are working on expanding the approach to more complex pathways and hope to test it at a larger scale in the future.

it has broader applicability, the Researcher says.

The process is very robust because it doesn’t need someone to be present at a particular point to add something or make any sort of change to the process, but rather allows the cells to be keeping track of when it’s time to make a shift.


The study was published in Massachusetts Institute of Technology