Microbes programmed to produce desired compounds autonomously.

It is known that the genes of bacteria can be manipulated to enable the production of large quantities of compounds such as insulin or human growth hormone. Currently, much work is being done to enable microbes to generate more complex products, including pharmaceuticals and biofuels. This usually requires adding several genes encoding the enzymes that catalyze each step of the overall synthesis and shutting down competing pathways within the cell. However, the timing of this shutdown is important because if the competing pathway is necessary for cell growth, turning it off greatly reduces the bacterial population size and amount of the desired compound. Now, a study from researchers at MIT programs bacteria to switch between different metabolic pathways, boosting their yield of desirable products autonomously. The team states their switches are programmed into the cells and are triggered by changes in population density, with no need for human intervention. The study is published in the journal Proceedings of the National Academy of Sciences.

Previous studies show that to make microbes synthesize useful compounds that they don’t normally produce, engineers insert genes for enzymes involved in the metabolic pathway. 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 overall yield of the end product. Recent studies from the group developed dynamic metabolic engineering to build switches that help cells maintain the balance between their own metabolic needs and the pathway that produces the desired product. The current study engineers multiple switching points into microbial cells, giving them a greater degree of control over the intermediates and the production process.

The current study utilizes two quorum sensing systems from two different species of bacteria that are then incorporated into E. coli. The E. coli is then engineered to produce a compound called naringenin, a flavonoid naturally found in citrus fruits, via the quorum-sensing systems engineered into two switching points in the cells. Results show that one switch prevents the bacteria from diverting a naringenin intermediate called malonyl-CoA into its’ own metabolic pathways. Data findings show the other switch delays production of an enzyme in the engineered pathway, to avoid accumulating an intermediate that normally inhibits the naringenin pathway if too much of the precursor accumulates.

The lab explains that as they took components from two different quorum-sensing systems, and the regulatory proteins are unique between the two systems, the switching time of each of the circuits can be changed independently. They go on to add they manufactured hundreds of E. coli variants to operate 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.

The team surmises they have programmed bacterial cells to autonomously switch between pathways to produce specific products, without the need for any human intervention. For the future, the researchers state their technique could also help improve yields for any other type of product where the cells have to balance between intermediates for compound formation or their own growth.

Source: Massachusetts Institute of Technology

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