The Amazing Microbe Secretly Devouring Our Plastic Waste

The plastic water bottle you drank from so many years ago will exist in some form, long after you, your children, and your grandchildren are gone. These plastic bottles are made from PET (polyethylene terephthalate), which take an awfully long time to decompose. At first, breaking down PET with microbes didn’t seem practical because scientists thought only a few fungi species could do it. Then, a team set out to find a microbe that could. By screening natural microbial communities exposed to PET environments, they discovered Ideonella sakaiensis. I. sakaiensis was almost able to completely break down a thin film of PET after six weeks at 30°C, with nutrients provided every two weeks. It does this through two enzymes: PETase and MHETase. PETase hydrolyzes PET into smaller molecules, including MHET. MHETase then breaks MHET into terephthalic acid and ethylene glycol. (Yoshida et al. 2016). The process of breaking down PET can be seen in Figure 1.

Figure 1. PETase breaks PET down into BHET, MHET, and TPA, and MHETase then breaks MHET into the building blocks TPA and EG (Austin et al. 2018).

To understand how PETase breaks down PET, scientists built a detailed model of the enzyme and found that it shares features with cutinases and lipases. They then tested whether PETase evolved specifically to break down PET by mutating two parts of the active site to make it more like cutinase. Unexpectedly, the mutated enzyme broke down PET better than the natural one, suggesting that PETase isn’t fully optimized and can still be engineered to improve its efficiency. PETase can also break down PEF, which is a newer plant-based plastic designed to replace PET, so even if PEF replaces PET, PETase could still help (Austin et al. 2018).

But PETase is only half of the story. MHETase, the second enzyme, is like PETase but has an extra lid, which is essential for breaking down MHET. It likely evolved from ferulic acid esterases, which break down compounds found in cell walls. Researchers physically linked PETase and MHETase into a chimeric protein, which showed an improved breakdown of PET and MHET compared to when the enzymes were separated (Knott et al. 2020).

Other researchers took a different route. Instead of pairing PETase with a partner, they redesigned the enzyme itself. They found that PETase works well under mild conditions but is naturally unstable, which limits its practical use. The challenge in improving an enzyme is finding a correct pathway through countless possible mutations. The researchers devised a computational strategy called GRAPE (greedy accumulated strategy for protein engineering), which groups predicted mutations into clusters and then stacks beneficial ones step by step. The redesigned enzyme, DuraPETase, raised the melting temperature by 31°C and was able to break down semicrystalline PET film 300 times faster at mild temperatures. Crystallinity measures how tightly packed a plastic’s molecular chains are. The natural enzyme handles low-crystallinity PET well, but commercial containers are 30–50% crystalline and far more resistant to enzymes, which is why DuraPETase’s improvement on semicrystalline film matters (Cui et al., 2021).

The bottle you drank from years ago was supposed to outlast your grandchildren, but thanks to I. sakaiensis and its enzyme, it might not even outlast you.

References:

Austin, Harry P., Mark D. Allen, Bryon S. Donohoe, Nicholas A. Rorrer, Fiona L. Kearns, Rodrigo L. Silveira, Benjamin C. Pollard, et al. 2018. “Characterization and Engineering of a Plastic-degrading Aromatic Polyesterase.” Proceedings of the National Academy of Sciences 115 (19): E4350–57. https://doi.org/10.1073/pnas.1718804115.

Cui, Yinglu, Yanchun Chen, Xinyue Liu, Saijun Dong, Yu’e Tian, Yuxin Qiao, Ruchira Mitra, et al. 2021. “Computational Redesign of a PETase for Plastic Biodegradation Under Ambient Condition by the GRAPE Strategy.” ACS Catalysis 11 (3): 1340–50. https://doi.org/10.1021/acscatal.0c05126.

Knott, Brandon C., Erika Erickson, Mark D. Allen, Japheth E. Gado, Rosie Graham, Fiona L. Kearns, Isabel Pardo, et al. 2020. “Characterization and Engineering of a Two-enzyme System for Plastics Depolymerization.” Proceedings of the National Academy of Sciences 117 (41): 25476–85. https://doi.org/10.1073/pnas.2006753117.

Yoshida, Shosuke, Kazumi Hiraga, Toshihiko Takehana, Ikuo Taniguchi, Hironao Yamaji, Yasuhito Maeda, Kiyotsuna Toyohara, Kenji Miyamoto, Yoshiharu Kimura, and Kohei Oda. 2016. “A Bacterium That Degrades and Assimilates Poly(Ethylene Terephthalate).” Science 351 (6278): 1196–99. https://doi.org/10.1126/science.aad6359.