Structural and functional characterization of an auxiliary domain-containing PET hydrolase from Burkholderiales bacterium

Discovery and characterization of two novel polyethylene terephthalate hydrolases: One from a bacterium identified in human feces and one from the Streptomyces genus

Polyethylene terephthalate (PET) is widely used for various industrial applications. However, owing to its extremely slow breakdown rate, PET accumulates as plastic trash, which negatively affects the environment and human health. Here, we report two novel PET hydrolases: PpPETase from Pseudomonas paralcaligenes MRCP1333, identified in human feces, and ScPETase from Streptomyces calvus DSM 41452. These two enzymes can decompose various PET materials, including semicrystalline PET powders (Cry-PET) and low-crystallinity PET films (gf-PET). By structure-guided engineering, two variants, PpPETaseY239R/F244G/Y250G and ScPETaseA212C/T249C/N195H/N243K were obtained that decompose Cry-PET 3.1- and 1.9-fold faster than their wild-type enzymes, respectively. The co-expression of ScPETase and mono-(2-hydroxyethyl) terephthalate hydrolase from Ideonella sakaiensis (IsMHETase) resulted in 1.4-fold more degradation than the single enzyme system. This engineered strain degraded Cry-PET and gf-PET by more than 40% and 6%, respectively, after 30 d. The concentrations of terephthalic acid (TPA) in the Cry-PET and gf-PET degradation products were 37.7% and 25.6%, respectively. The discovery of these two novel PET hydrolases provides opportunities to create more powerful biocatalysts for PET biodegradation.

Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan

Glycoside hydrolase (GH) 30 family xylanases are enzymes of biotechnological interest due to their capacity to degrade recalcitrant hemicelluloses, such as glucuronoxylan (GX). This study focuses on a subfamily 7 GH30, TtXyn30A from Thermothelomyces thermophilus, which acts on GX in an "endo" and "exo" mode, releasing methyl-glucuronic acid branched xylooligosaccharides (XOs) and xylobiose, respectively. The crystal structure of inactive TtXyn30A in complex with 23-(4-O-methyl-α-D-glucuronosyl)-xylotriose (UXX), along with biochemical analyses, corroborate the implication of E233, previously identified as alternative catalytic residue, in the hydrolysis of decorated xylan. At the -1 subsite, the xylose adopts a distorted conformation, indicative of the Michaelis complex of TtXyn30AEE with UXX trapped in the semi-functional active site. The most significant structural rearrangements upon substrate binding are observed at residues W127 and E233. The structures with neutral XOs, representing the "exo" function, clearly show the nonspecific binding at aglycon subsites, contrary to glycon sites, where the xylose molecules are accommodated via multiple interactions. Last, an unproductive ligand binding site is found at the interface between the catalytic and the secondary β-domain which is present in all GH30 enzymes. These findings improve current understanding of the mechanism of bifunctional GH30s, with potential applications in the field of enzyme engineering.

Biobased de novo synthesis, upcycling, and recycling - the heartbeat toward a green and sustainable polyethylene terephthalate industry

Polyethylene terephthalate (PET) has revolutionized the industrial sector because of its versatility, with its predominant uses in the textiles and packaging materials industries. Despite the various advantages of this polymer, its synthesis is, unfavorably, tightly intertwined with nonrenewable fossil resources. Additionally, given its widespread use, accumulating PET waste poses a significant environmental challenge. As a result, current research in the areas of biological recycling, upcycling, and de novo synthesis is intensifying. Biological recycling involves the use of micro-organisms or enzymes to breakdown PET into monomers, offering a sustainable alternative to traditional recycling. Upcycling transforms PET waste into value-added products, expanding its potential application range and promoting a circular economy. Moreover, studies of cascading biological and chemical processes driven by microbial cell factories have explored generating PET using renewable, biobased feedstocks such as lignin. These avenues of research promise to mitigate the environmental footprint of PET, underlining the importance of sustainable innovations in the industry.

Comparison of anaerobic digestion of starch- and petro-based bioplastic under hydrogen-rich conditions

To identify an economically viable waste management system for bioplastics, thermoplastic starch (TPS) and poly(butylene adipate-co-terephthalate) (PBAT) were anaerobically digested under hydrogen (H2)/carbon dioxide (CO2) and nitrogen (N2) gas-purged conditions to compare methane (CH4) production and biodegradation. Regardless of the type of bioplastics, CH4 production was consistently higher with H2/CO2 than with N2. The highest amount of CH4 was produced at 307.74 mL CH4/g volatile solids when TPS digested with H2/CO2. A stepwise increased in CH4 yield was observed, with a nominal initial increment followed by accelerated methanogenesis conversion as H2 was depleted. This may be attributed to a substantial shift in the microbial structure from hydrogenotrophic methanogen (Methanobacteriales and Methanomicrobiales) to heterotrophs (Spirochaetia). In contrast, no significant change was observed with PBAT, regardless of the type of purged gas. TPS was broken down into numerous derivatives, including volatile fatty acids. TPS produced more byproducts with H2/CO2 (i.e., 430) than with N2 (i.e., 320). In contrast, differential scanning calorimetry analysis on PBAT revealed an increase in crystallinity from 10.20 % to 12.31 % and 11.36 % in the H2/CO2- and N2-purged conditions, respectively, after 65 days of testing. PBAT surface modifications were characterized via Fourier transform infrared spectroscopy and scanning electron microscopy. The results suggest that the addition of H2/CO2 can enhance the CH4 yield and increase the breakdown rate of TPS more than that of PBAT. This study provides novel insights into the CH4 production potential of two bioplastics with different biodegradabilities in H2/CO2-mediated anaerobic digestion systems.

Recent Advances and Challenges in Enzymatic Depolymerization and Recycling of PET Wastes

Poly (ethylene terephthalate) (PET) is one of the most commonly used plastics in daily life and various industries. Enzymatic depolymerization and recycling of post-consumer PET (pc-PET) provides a promising strategy for the sustainable circular economy of polymers. Great protein engineering efforts have been devoted to improving the depolymerization performance of PET hydrolytic enzymes (PHEs). In this review, we first discuss the mechanisms and challenges of enzymatic PET depolymerization. Subsequently, we summarize the state-of-the-art engineering of PHEs including rational design, machine learning, and directed evolution for improved depolymerization performance, and highlight the advances in screening methods of PHEs. We further discuss several factors that affect the enzymatic depolymerization efficiency. We conclude with our perspective on the opportunities and challenges in bio-recycling and bio-upcycling of PET wastes.

A comprehensive review on enzymatic biodegradation of polyethylene terephthalate

Polyethylene terephthalate (PET) is a polymer synthesized via the dehydration and condensation reaction between ethylene glycol and terephthalic acid. PET has emerged as one of the most extensively employed plastic materials due to its exceptional plasticity and durability. Nevertheless, PET has a complex structure and is extremely difficult to degrade in nature, causing severe pollution to the global ecological environment and posing a threat to human health. Currently, the methods for PET processing mainly include physical, chemical, and biological methods. Biological enzyme degradation is considered the most promising PET degradation method. In recent years, an increasing number of enzymes that can degrade PET have been identified, and they primarily target the ester bond of PET. This review comprehensively introduced the latest research progress in PET enzymatic degradation from the aspects of PET-degrading enzymes, PET biodegradation pathways, the catalytic mechanism of PET-degrading enzymes, and biotechnological strategies for enhancing PET-degrading enzymes. On this basis, the current challenges within the enzymatic PET degradation process were summarized, and the directions that need to be worked on in the future were pointed out. This review provides a reference and basis for the subsequent effective research on PET biodegradation.

Recent advances in the biodegradation of polyethylene terephthalate with cutinase-like enzymes

Polyethylene terephthalate (PET) is a synthetic polymer in the polyester family. It is widely found in objects used daily, including packaging materials (such as bottles and containers), textiles (such as fibers), and even in the automotive and electronics industries. PET is known for its excellent mechanical properties, chemical resistance, and transparency. However, these features (e.g., high hydrophobicity and high molecular weight) also make PET highly resistant to degradation by wild-type microorganisms or physicochemical methods in nature, contributing to the accumulation of plastic waste in the environment. Therefore, accelerated PET recycling is becoming increasingly urgent to address the global environmental problem caused by plastic wastes and prevent plastic pollution. In addition to traditional physical cycling (e.g., pyrolysis, gasification) and chemical cycling (e.g., chemical depolymerization), biodegradation can be used, which involves breaking down organic materials into simpler compounds by microorganisms or PET-degrading enzymes. Lipases and cutinases are the two classes of enzymes that have been studied extensively for this purpose. Biodegradation of PET is an attractive approach for managing PET waste, as it can help reduce environmental pollution and promote a circular economy. During the past few years, great advances have been accomplished in PET biodegradation. In this review, current knowledge on cutinase-like PET hydrolases (such as TfCut2, Cut190, HiC, and LCC) was described in detail, including the structures, ligand-protein interactions, and rational protein engineering for improved PET-degrading performance. In particular, applications of the engineered catalysts were highlighted, such as improving the PET hydrolytic activity by constructing fusion proteins. The review is expected to provide novel insights for the biodegradation of complex polymers.

The structural and molecular mechanisms of type II PETases: a mini review

The advent of plastics has led to significant advances for humans, although the accompanying pollution has also been a source of concern for countries globally. Consequently, a biological method to effectively degrade polyethylene terephthalate (PET) has been an area of significant scientific interest. Following the report of the highly efficient PET hydrolase from the bacterium Ideonella sakaiensis strain 201-F6 (i.e., IsPETase) in 2016, its structure has been extensively studied, showing that it belongs to the type II PETase group. Unlike type I PETases that include most known cutinases, structural investigations of type II PETases have only been conducted since 2017. Type II PETases are further divided into type IIa and IIb enzymes. Moreover, even less research has been conducted on type IIa plastic-degrading enzymes. Here, we present a review of recent studies of the structure and mechanism of type II PETases, using the known structure of the type IIa PETase PE-H from the marine bacterium Pseudomonas aestusnigri in addition to the type IIb enzyme IsPETase as representatives. These studies have provided new insights into the structural features of type II PETases that exhibit PET catalytic activity. In addition, recent studies investigating the rational design of IsPETases are reviewed and summarized alongside a discussion of controversies surrounding PETase investigations.

Current advances in the structural biology and molecular engineering of PETase

Poly(ethylene terephthalate) (PET) is a highly useful synthetic polyester plastic that is widely used in daily life. However, the increase in postconsumer PET as plastic waste that is recalcitrant to biodegradation in landfills and the natural environment has raised worldwide concern. Currently, traditional PET recycling processes with thermomechanical or chemical methods also result in the deterioration of the mechanical properties of PET. Therefore, it is urgent to develop more efficient and green strategies to address this problem. Recently, a novel mesophilic PET-degrading enzyme (IsPETase) from Ideonella sakaiensis was found to streamline PET biodegradation at 30°C, albeit with a lower PET-degrading activity than chitinase or chitinase-like PET-degrading enzymes. Consequently, the molecular engineering of more efficient PETases is still required for further industrial applications. This review details current knowledge on IsPETase, MHETase, and IsPETase-like hydrolases, including the structures, ligand‒protein interactions, and rational protein engineering for improved PET-degrading performance. In particular, applications of the engineered catalysts are highlighted, including metabolic engineering of the cell factories, enzyme immobilization or cell surface display. The information is expected to provide novel insights for the biodegradation of complex polymers.

Rational Design of Disulfide Bridges in BbPETaseCD for Enhancing the Enzymatic Performance in PET Degradation

Polyethylene terephthalate (PET) is one of the most prevalent transparent thermoplastics. It is commonly utilized due to its low cost and high durability. With the massive accumulation of waste PET, however, serious environmental pollution has become a global problem. Compared to traditional chemical degradation, biodegradation of PET catalyzed by PET hydrolase (PETase) is more environmentally friendly and energy-efficient. BbPETase^CD from the Burkholderiales bacterium is a PETase that shows favorable properties for application in the biodegradation of PET. To enhance the enzymatic performance of this enzyme, this work focuses on the rational design of disulfide bridges in BbPETase^CD. We utilized two computational algorithms to predict the probable disulfide-bridge mutations in BbPETase^CD, and five variants were acquired from the computations. Among these, the N364C/D418C variant with one additional disulfide bond showed higher expression than the wild-type enzyme (WT) and the best enzymatic performance. The melting temperature (T_m) of the N364C/D418C variant presented an increase of 14.8 °C over that of WT (56.5 °C), indicating that the additional disulfide bond significantly raised the thermodynamic stability of the enzyme. Kinetic experiments at different temperatures also demonstrated the thermal stability increase of the variant. The variant also showed significantly increased activity over WT when using bis(hydroxyethyl) terephthalate (BHET) as the substrate. More remarkably, the N364C/D418C variant exhibited approximately an 11-fold increase over the WT enzyme in the long-term (14 days) degradation of PET films. The results prove that the rationally designed disulfide bond significantly improved the enzymatic performance of the enzyme for PET degradation.

In vivo degradation of polyethylene terephthalate using microbial isolates from plastic polluted environment

Accumulation of plastics alarms a risk to the environment worldwide. As polyethylene pterephthalate (PET) degrades slowly and produces hazardous substances, therefore, it is now essential to eliminate plastic wastes from the environment. Given that, the current study is concerned with PET degradation potential of naturally occurring microbial strains isolated from plastic waste dumping sites, Sarcina aurantiaca (TB3), Bacillus subtilis (TB8), Aspergillus flavus (STF1), Aspergillus niger (STF2). To test the biodegradability of PET films, the films were incubated for 60 days at 37 °C with the microorganisms designated as TB3, TB8, STF1, STF2 and the microbial consortium (TB3+TB8+STF1+STF2) in Minimal Salt Medium and Bushnell Hass Broth. Hydrophobicity, viability, and total protein content of isolates were investigated. Using Field Emission Scanning Electron Microscopy and Fourier Transform Infrared Spectrophotometry to measure variations in functional groups and carbonyl index on PET surface, biodegradation process was affirmed by fissures and modified surfaces. Results revealed that the microbial consortium (S. aurantiaca + B. subtilis + A. flavus + A. niger) that the weight loss of PET films was 28.78%. The microbial consortium could be used to treat PET waste, posing no health or environmental risks. The developed microbial consortium has the potential to degrade PET, hence can be employed for eliminating PET in plastic contaminated sites.

Mechanoenzymatic reactions for the hydrolysis of PET†

Recent advances in the enzymatic degradation of poly(ethylene terphthalate) (PET) have led to a number of PET hydrolytic enzymes and mutants being developed. With the amount of PET building up in the natural world, there is a pressing need to develop scalable methods of breaking down the polymer into its monomers for recycling or other uses. Mechanoenzymatic reactions have gained traction recently as a green and efficient alternative to traditional biocatalytic reactions. For the first time we report increased yields of PET degradation by whole cell PETase enzymes by up to 27-fold by utilising ball milling cycles of reactive aging, when compared with typical solution-based reactions. This methodology leads to up to a 2600-fold decrease in the solvent required when compared with other leading degradation reactions in the field and a 30-fold decrease in comparison to reported industrial scale PET hydrolysis reactions.

Mechanoenzymatic reactions are described for the degradation of different PET materials using whole cell PETases.

Sequentially co-immobilized PET and MHET hydrolases via Spy chemistry in calcium phosphate nanocrystals present high-performance PET degradation

Accumulation of polyethylene terephthalate (PET) has brought an enormous threat to the ecosystem. The recently reported PET hydrolase (DuraPETase) and MHET hydrolase (MHETase) can synergistically catalyze the complete PET degradation. Hence, this work was designed to develop a bienzymatic cascade catalysis by co-immobilizing the two enzymes for PET biodegradation. DuraPETase and MHETase were sequentially co-immobilized in calcium phosphate nanocrystals (CaP) through SpyTag/SpyCatcher system. MHETase-SpyCatcher was first embedded inside the nanocrystals via biomimetic mineralization, and DuraPETase-SpyTag was then conjugated on the outlayer (~1.5 µm). The bienzyme compartmentalization facilitated DuraPETase interaction with the solid substrate, and the layered structures of the nanocrystals protected the enzymes, thus enhancing their stability. The high specific surface area of the nanocrystals and the proximity effects from the bienzymatic cascade were beneficial to the improved enzyme activity. Experimental data and molecular dynamics simulations revealed the activation effect of Ca²⁺ on DuraPETase. Taken together, the final results indicate that the PET degradation efficiency of DuraPETase-MHETase@CaP increased by 6.1 and 1.5 times over the free bienzyme system within 10 d at 40 °C and 50 °C, with weight losses at 32.2% and 50.3%, respectively. The bienzymatic cascade with DuraPETase-MHETase@CaP can completely degrade PET, contributing to the recycling of PET.

In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations

The accumulation of polyethylene terephthalate (PET) seriously harms the environment because of its high resistance to degradation. The recent discovery of the bacteria-secreted biodegradation enzyme, PETase, sheds light on PET recycling; however, the degradation efficiency is far from practical use. Here, in silico alanine scanning mutagenesis (ASM) and site-saturation mutagenesis (SSM) were employed to construct the protein sequence space from binding energy of the PETase–PET interaction to identify the number and position of mutation sites and their appropriate side-chain properties that could improve the PETase–PET interaction. The binding mechanisms of the potential PETase variant were investigated through atomistic molecular dynamics simulations. The results show that up to two mutation sites of PETase are preferable for use in protein engineering to enhance the PETase activity, and the proper side chain property depends on the mutation sites. The predicted variants agree well with prior experimental studies. Particularly, the PETase variants with S238C or Q119F could be a potential candidate for improving PETase. Our combination of in silico ASM and SSM could serve as an alternative protocol for protein engineering because of its simplicity and reliability. In addition, our findings could lead to PETase improvement, offering an important contribution towards a sustainable future.