Researchers at Oak Ridge National Laboratory (ORNL) have discovered a microbial enzyme that degrades tough-to-break bonds in lignin, a waste product of biorefineries. When inserted into a bioengineered bacterium, the enzyme helps efficiently convert lignin compounds into a common component of plastics—muconic acid—opening a pathway to transform waste into a commercially valuable biochemical.

A paper on the work is published in the journal Metabolic Engineering.

Researchers discovered the enzyme, named LsdE, in the bacterium Novosphingobium aromaticivorans, pictured, a microbe of interest in lignin valorization. Credit: Delyana Vasileva and Andy Sproles, ORNL/US Dept. of Energy; John Dunlap, University of Tennessee

The lignin polymer, which contributes to the structural rigidity of plants, consists of useful monomer units held together by weak and strong bonds. With lignin comprising 20% to 30% of plant biomass by weight, breaking the polymer’s strong bonds and converting the chemicals they link together into value-added products is necessary to make the production of plant-based biofuels and products economically viable.

Diverse communities of bacteria and fungi perform these processes in nature, but maintaining a mix of so many different microbes in one bioreactor can be tricky. To solve this problem, ORNL scientists in the Center for Bioenergy Innovation (CBI) want to identify the enzymes that microbes use to degrade specific bonds in lignin and engineer the genes that code for those enzymes into a single organism.

Working toward this goal, ORNL researchers targeted a particularly stubborn bond linking two carbon molecules in a lignin dimer—a unit of two joined monomers—called 1,2-diguaiacylpropane-1,3-diol, or DGPD.

The team used the bacterium Novosphingobium aromaticivorans, a microbe of interest in lignin valorization. After identifying and cultivating a mutant N. aromaticivorans strain that efficiently degraded the desired linkage in DGPD, the researchers used bacterial genetics and gene disruption techniques to find which enzyme was responsible.

To their surprise, the enzyme they identified—which they named LsdE—had been labeled as a hypothetical protein, meaning its function was unknown.

No one had seen this kind of chemistry before. There weren’t any examples in the literature of a single enzyme that could do this particular transformation.

—Josh Michener, who led ORNL’s research

After identifying LsdE, the ORNL team tested to see if they could further validate its function. Their test confirmed the role of LsdE and revealed that a better-known enzyme, LsdA, played a complementary role in further breaking down DGPD into useful compounds.

Presley et al.

At the National Renewable Energy Laboratory, a project partner in CBI, scientists inserted both enzymes into a strain of the bacterium Pseudomonas putida that had already been engineered to produce muconic acid, a value-added precursor for plastics. They found that adding the enzymes enabled P. putida to convert DGPD into muconic acid at a nearly 100% yield.

With many products, you’re losing carbon along the way. But in this case, we have a very efficient pathway.

—Allison Werner, NREL postdoc and co-author

This work is part of a larger effort to convert lignin into value-added products. Future research will aim to discover new enzymes that break down other tough linkages and to better understand the chemical structure of LsdE.

Resources

• Gerald N. Presley, Allison Z. Werner, Rui Katahira, David C. Garcia, Stefan J. Haugen, Kelsey J. Ramirez, Richard J. Giannone, Gregg T. Beckham, Joshua K. Michener (2021) “Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound,” Metabolic Engineering, Volume 65, Pages 1-10 doi: 10.1016/j.ymben.2021.02.003