Engineering the catalytic activity of an Antarctic PET-degrading enzyme by loop exchange

Discovery of two novel cutinases from a gut yeast of plastic-eating mealworm for polyester depolymerization

Identification of novel plastic-degrading enzymes is crucial for developing enzymatic degradation and recycling strategies for plastic waste. Here, we report the discovery of two novel cutinases, SiCut1 and SiCut2, from a yeast strain Sakaguchia sp. BIT-D3 was isolated from the gut of plastic-eating mealworms. Their amino acid sequences share less than 25% identity with all previously described cutinases and reveal a conserved S-D-H catalytic triad with a unique GYSKG motif. Their recombinant proteins were successfully overexpressed in Pichia pastoris. The pH range for both enzymes was 4.0 to 11.0 and the temperature range for SiCut1 and SiCut2 was 10°C to 50°C and 10°C to 70°C, respectively. Both enzymes showed strong activity against apple cutin and short-chain fatty acid esters of p-nitrophenol and glycerol, substantiating their classification as true cutinases. SiCut1 and SiCut2 have been demonstrated to exhibit efficient degradation of polycaprolactone (PCL) film, polybutylene succinate (PBS) film, and polyester-polyurethane (PUR) foam. Molecular docking and molecular dynamics simulations were used to elucidate the underlying mechanisms of the observed catalytic activity and thermal stability. This study shows that SiCut1 and SiCut2 are novel yeast-derived cutinases with the potential for depolymerization and recycling of plastic waste.IMPORTANCEThe identification of novel plastic-degrading enzymes is critical in addressing the pervasive problem of plastic pollution. This study presents two unique cutinases, SiCut1 and SiCut2, derived from the yeast Sakaguchia sp. BIT-D3 isolated from the gut of plastic-feeding mealworms. Despite sharing less than 25% sequence identity with known cutinases, both enzymes exhibit remarkable degradation capabilities against various polyester plastics, including polycaprolactone (PCL) film, polybutylene succinate (PBS) film, and polyester-polyurethane (PUR) foam. Our results elucidate the catalytic mechanisms of SiCut1 and SiCut2 and provide insights into their potential applications in enzymatic degradation and recycling strategies. By harnessing the gut microbiota of plastic-degrading organisms, this research lays the foundation for innovative enzyme-based solutions to reduce plastic waste and promote sustainable practices in waste management.

Landscape profiling of PET depolymerases using a natural sequence cluster framework

Enzymes capable of breaking down polymers have been identified from natural sources and developed for industrial use in plastic recycling. However, there are many potential starting points for enzyme optimization that remain unexplored. We generated a landscape of 170 lineages of 1894 polyethylene terephthalate depolymerase (PETase) candidates and performed profiling using sampling approaches with features associated with PET-degrading capabilities. We identified three promising yet unexplored PETase lineages and two potent PETases, Mipa-P and Kubu-P. An engineered variant of Kubu-P outperformed benchmarks in terms of PET depolymerization in harsh environments, such as those with high substrate load and ethylene glycol as the solvent.

Plastic-Degrading Enzymes from Marine Microorganisms and Their Potential Value in Recycling Technologies

Since the 2005 discovery of the first enzyme capable of depolymerizing polyethylene terephthalate (PET), an aromatic polyester once thought to be enzymatically inert, extensive research has been undertaken to identify and engineer new biocatalysts for plastic degradation. This effort was directed toward developing efficient enzymatic recycling technologies that could overcome the limitations of mechanical and chemical methods. These enzymes are versatile molecules obtained from microorganisms living in various environments, including soil, compost, surface seawater, and extreme habitats such as hot springs, hydrothermal vents, deep-sea regions, and Antarctic seawater. Among various plastics, PET and polylactic acid (PLA) have been the primary focus of enzymatic depolymerization research, greatly enhancing our knowledge of enzymes that degrade these specific polymers. They often display unique catalytic properties that reflect their particular ecological niches. This review explores recent advancements in marine-derived enzymes that can depolymerize synthetic plastic polymers, emphasizing their structural and functional features that influence the efficiency of these catalysts in biorecycling processes. Current status and future perspectives of enzymatic plastic depolymerization are also discussed, with a focus on the underexplored marine enzymatic resources.

Engineering the next-generation synthetic cell factory driven by protein engineering

Synthetic cell factory offers substantial advantages in economically efficient production of biofuels, chemicals, and pharmaceutical compounds. However, to create a high-performance synthetic cell factory, precise regulation of cellular material and energy flux is essential. In this context, protein components including enzymes, transcription factor-based biosensors and transporters play pivotal roles. Protein engineering aims to create novel protein variants with desired properties by modifying or designing protein sequences. This review focuses on summarizing the latest advancements of protein engineering in optimizing various aspects of synthetic cell factory, including: enhancing enzyme activity to eliminate production bottlenecks, altering enzyme selectivity to steer metabolic pathways towards desired products, modifying enzyme promiscuity to explore innovative routes, and improving the efficiency of transporters. Furthermore, the utilization of protein engineering to modify protein-based biosensors accelerates evolutionary process and optimizes the regulation of metabolic pathways. The remaining challenges and future opportunities in this field are also discussed.

Streamlined screening of extracellularly expressed PETase libraries for improved polyethylene terephthalate degradation

Enzyme-mediated polyethylene terephthalate (PET) depolymerization has recently emerged as a sustainable solution for PET recycling. Towards an industrial-scale implementation of this technology, various strategies are being explored to enhance PET depolymerization (PETase) activity and improve enzyme stability, expression, and purification processes. Recently, rational engineering of a known PET hydrolase (LCC-leaf compost cutinase) has resulted in the isolation of a variant harboring four-point mutations (LCC-ICCG), presenting increased PETase activity and thermal stability. Here, we revealed the enzyme's natural extracellular expression and used it to efficiently screen error-prone genetic libraries based on LCC-ICCG for enhanced activity toward consumer-grade PET. Following multiple rounds of mutagenesis and screening, we successfully isolated variants that exhibited up to a 60% increase in PETase activity. Among other mutations, the improved variants showed a histidine to tyrosine substitution at position 218, a residue known to be involved in substrate binding and stabilization. Introducing H218Y mutation on the background of LCC-ICCG (named here LCC-ICCG/H218Y) resulted in a similar level of activity improvement. Analysis of the solved structure of LCC-ICCG/H218Y compared to other known PETases featuring different amino acids at the equivalent position suggests that H218Y substitution promotes enhanced PETase activity. The expression and screening processes developed in this study can be further used to optimize additional enzymatic parameters crucial for efficient enzymatic degradation of consumer-grade PET.

Characterization and engineering of plastic-degrading polyesterases jmPE13 and jmPE14 from Pseudomonas bacterium

Polyester plastics are widely used in daily life, but also cause a large amount of waste. Degradation by microbial enzymes is the most promising way for the biobased upcycling of the wastes. However, there is still a shortage of high-performance enzymes, and more efficient polyester hydrolases need to be developed. Here we identified two polyester hydrolases, jmPE13 and jmPE14, from a previously isolated strain Pseudomonas sp. JM16B3. The proteins were recombinantly expressed and purified in E. coli, and their enzymatic properties were characterized. JmPE13 and jmPE14 showed hydrolytic activity towards polyethylene terephthalate (PET) and Poly (butylene adipate-co-terephthalate) (PBAT) at medium temperatures. The enzyme activity and stability of jmPE13 were further improved to 3- and 1.5-fold, respectively, by rational design. The results of our research can be helpful for further engineering of more efficient polyester plastic hydrolases and their industrial applications.