Researchers at Northwestern University have discovered how the soil bacterium Pseudomonas putida reorganizes its metabolism to break down lignin, a tough plant material. The study provides a detailed look at how the bacteria balance energy use and production while digesting complex carbons from lignin.
Lignin is one of the most abundant biopolymers on Earth after cellulose. When it breaks down, it creates chemical compounds that could be used as renewable feedstocks for making valuable chemicals. However, few organisms can efficiently process these compounds because they require significant energy to digest.
“Lignin is an abundant, renewable and sustainable source of carbon that could potentially provide an alternative to petroleum in the production plastics and valuable chemicals,” said Ludmilla Aristilde of Northwestern University, who led the research. “Certain microbes naturally have an ability to make precursors to valuable chemicals that are lignin-based rather than petroleum-based. But if we want to take advantage of that natural ability to develop new biological platforms, we first need to know how it works. Now, we finally have a roadmap.”
Aristilde is a professor at Northwestern’s McCormick School of Engineering and is affiliated with several research institutes within the university.
The team grew Pseudomonas putida on four common lignin-derived compounds and used advanced techniques such as proteomics and metabolomics to track how carbon moved through the bacteria’s metabolic pathways. They found that when digesting lignin, the bacteria increased certain enzyme levels dramatically and rerouted metabolic pathways away from their usual routes. This allowed them to avoid bottlenecks and produce six times more ATP—the molecule cells use for energy—than when consuming simpler compounds.
“We wanted to see what happens on every street at very high resolution,” Aristilde said about mapping bacterial metabolism. “We wanted to know where every ‘stoplight’ and ‘traffic jam’ might occur. That allowed us to determine which pathways are important to balance the energy in a way that is optimal for the cell.”
However, attempts by researchers to further boost efficiency by overexpressing some enzymes resulted in negative effects; disrupting this delicate balance caused problems for bacterial metabolism.
“Engineering strategies can often result in negative effects on the metabolism in a completely unexpected way,” Aristilde said. “By speeding up the flow of one pathway, it can introduce an imbalance in energy that is detrimental to the operation of the cell.”
These findings are relevant for industries looking for ways to convert plant waste into biofuels or other products using microbial factories.
“Before this study, we could not explain exactly the coordination of carbon metabolism and energy fluxes important in the rational design of bacterial platforms for lignin carbon processing,” Aristilde said. “We just had to figure it out as we went along. Now that we have an actual roadmap, we know how to navigate the network.”
The study was published August 29 in Communications Biology with support from the U.S. Department of Energy (award number DE-SC0022181).