Machine learning-aided engineering of hydrolases for PET depolymerization

Current state and sustainable management of waste polyethylene terephthalate bio-disposal: enzymatic degradation to upcycling

Poly (ethylene terephthalate) (PET) is a widely used plastic that leads to significant environmental pollution due to its durability. Enzymatic degradation of PET presents an eco-friendly disposal approach, with potential scalability for industrial applications. This review examines key crucial factors influencing PET enzymatic degradation, including the catalytic efficiency of PET hydrolase, production scalability of PET hydrolase, and recyclability of degraded PET. We outline major advancements in PET hydrolase development, including discovery techniques, functional enhancement strategies, and degradation optimization. Additionally, it assesses the preparation methodologies for PET hydrolase, covering bacterial expression systems, high-density fermentation technologies, and approaches for sustainable catalytic use. The review also discusses upcycling processes for PET hydrolysates, focusing on repolymerization into new plastics or bioconversion into valuable chemicals. Successful achievement of waste PET bio-disposal in industrial-scale n hinges on balancing degradation costs with revenue from upcycling products. Aim at this target, the review further points out the critical challenges, and proposes targeted solutions and expectations.

Exploring biotechnology for plastic recycling, degradation and upcycling for a sustainable future

The persistent demand for plastic commodities, inadequate recycling infrastructure, and pervasive environmental contamination due to plastic waste present a formidable global challenge. Recycling, degradation and upcycling are the three most important ways to solve the problem of plastic pollution. Sequential enzymatic and microbial degradation of mechanically and chemically pre-treated plastic waste can be orchestrated, followed by microbial conversion into value-added chemicals and polymers through mixed culture systems. Furthermore, plastics-degrading enzymes can be optimized through protein engineering to enhance their specific binding capacities, stability, and catalytic efficiency across a broad spectrum of polymer substrates under challenging high salinity and temperature conditions. Also, the production and formulation of enzyme mixtures can be fine-tuned to suit specific waste compositions, facilitating their effective deployment both in vitro, in vivo and in combination with chemical technologies. Here, we emphasized the comprehensive strategy leveraging microbial processes to transform mixed plastics of fossil-derived polymers such as PP, PE, PU, PET, and PS, most notably polyesters, in conjunction with potential biodegradable alternatives such as PLA and PHA. Any residual material resistant to enzymatic degradation can be reintroduced into the process loop following appropriate physicochemical treatment.

Enhanced catalytic activity of polyethylene terephthalate hydrolase by structure-guided loop-focused iterative mutagenesis strategy

The accumulation of polyethylene terephthalate (PET) waste has caused significant environmental pollution. Although biological depolymerization offers a promising solution, its efficiency remains constrained by the limited activity of PET-degrading enzymes. In this study, we designed a Structure-guided Loop-focused Iterative Mutagenesis (SLIM) strategy and rationally engineered the PET degradation enzyme ICCG for higher activity. The strategy was designed by demonstrating the critical role of the β8-α6 loop in type Ⅰ enzymes, which has currently not been reported. The best variant obtained, YITA (H183Y/L202I/I208T/T153A), exhibited 4.46-fold higher hydrolytic activity on amorphous PET at 72 °C compared to ICCG, outperforming other PET hydrolases, and exhibited superior degradation activity on real substrates such as cake containers and PET fibers. Conformational analysis revealed the key role of the remodeled β8-α6 loop in substrate binding and overall stability. Collectively, this study explores a promising approach to modifying PET hydrolase and lays a theoretical foundation for advancing bio-circular economy.

Geography-guided industrial-level upcycling of polyethylene terephthalate plastics through alkaline seawater-based processes

The escalating plastic crisis can be mitigated by upgrading waste polyethylene terephthalate (PET). Leveraging the geographical advantages of offshores with established chlor-alkali industries, abundant renewable energy, and extensive seawater, we here present a technically and economically viable strategy of harnessing natural seawater as a medium to transform PET plastics into high-value chemicals. We report a nickel-molybdenum catalyst incorporating frustrated Lewis pairs for the efficient breakage of C─C bond and the oxidation of ethylene glycol, which sustains a current of 6 amperes at 1.74 volts over 350 hours, with a projected revenue of approximately $304 United States dollar (USD) per ton of processed PET plastics. In a customized electrolyzer, we successfully convert 301.0 grams of waste PET into 227.1 grams of p-phthalic acid (95.5% yield), 1486.2 grams of potassium diformate (67.2% yield), and approximately 214.9 liters of green hydrogen. This study paves the way for scalable PET upcycling, contributing to a circular economy and mitigating the plastic pollution crisis.

Engineered microbial platform confers resistance against heavy metals via phosphomelanin biosynthesis

Environmental concerns are increasingly fueling interest in engineered living materials derived from microbial sources. Melanin biosynthesis in microbes, particularly facilitated by recombinant tyrosinase expression, offers sustainable protection for the habitat of microorganisms against severe environmental stressors. However, there exists a vast urgency to optimize these engineered microbial platforms, which will amplify their protective capabilities, integrate multifaceted functions, and thereby expand their utility and effectiveness. Here, we genetically engineer microbial platforms capable of endogenously biosynthesizing phosphomelanin, a unique phosphorus-containing melanin. The ability to heterogeneously biosynthesize phosphomelanin endows the microbes with enhanced resistance to heavy metals, thus safeguarding their survival in adverse conditions. Furthermore, we upgrade these engineered microbes by integrating PET-degrading enzymes, thereby achieving effective integrated management of metallized plastic waste. This engineered microbial platform, with its phosphomelanin biosynthetic capabilities, presents significant opportunities for microbes to engage in bioengineering manufacturing, potentially serving as the next-generation guardians against global ecological challenges.

Further characterization and engineering of an 11-amino acid motif for enhancing recombinant soluble protein expression

BACKGROUND

Escherichia coli (E. coli) is a popular system for recombinant protein production, owing to its low cost and availability of genetic tools. However, the expression of soluble recombinant proteins remains an issue. As such, various solubility-enhancing and yield-improving methods such as the addition of fusion tags have been developed. This study focuses on a small solubility tag (NT11), derived from the N-terminal domain of a duplicated carbonic anhydrase from Dunaliella species. The small size of NT11 (< 10 kDa) lowers the chance of protein folding interference and post-translation removal requirement, which ultimately minimizes cost of production.

RESULTS

A comprehensive analysis was performed to improve the characteristics of the 11-amino acid tag. By investigating the alanine-scan library of NT11, we achieved at least a two-fold increase in protein yield for three different proteins and identified key residues for further development. We also demonstrated that the NT11 tag is not limited to the N-terminal position and can function at either the N- or C-terminal of the protein, providing flexibility in designing constructs. With these new insights, we have successfully doubled the recombinant soluble protein yields of valuable growth factors, such as fibroblast growth factor 2 (FGF2) and human epidermal growth factor (hEGF) in E. coli.

CONCLUSION

The further characterisation and development of the NT11 tag have provided valuable insights into the optimisation process for such small tags and expanded our understanding of its potential applications. The ability of the NT11 tag to be positioned at either the N- or C- termini within the protein construct without compromising its effectiveness to enhance soluble recombinant protein yields, makes it a valuable tool across a diverse range of proteins. Collectively, these findings demonstrate a promising approach to simplify and enhance the efficiency of soluble recombinant protein production.

Pickering Emulsion Biocatalysis with Engineered Living Cells for Degrading Polycarbonate Plastics

The efficient degradation of plastics remains a pressing environmental challenge due to their inherent resistance to breakdown. While biocatalysis offers a promising approach for sustainable and effective plastic degradation, the inherently low solubility of plastics in aqueous systems severely limits the efficiency of enzymatic reactions. To address this issue, we developed a biocompatible polymer coating strategy to engineer living cell surfaces, enabling the stabilization of Pickering emulsions for over 192 h and significantly enhancing plastic accessibility to biocatalysts. Leveraging this platform, Escherichia coli (E. coli) cells containing overexpressed Candida antarctica Lipase B performed well by dispersing at the emulsion interface of water and toluene, facilitating the efficient biodegradation of polycarbonate (PC) plastics. Under optimized reaction conditions (pH 9, 45 °C), this Pickering emulsion system achieved efficient PC degradation, producing up to 4.5 mm bisphenol A within 72 h-far exceeding the performance of biphasic systems using native E. coli cells. The findings highlight the transformative potential of surface-engineered whole-cell catalysts in addressing environmental challenges, particularly plastic waste remediation.

QM/MM-MD Studies on the Degradation Mechanism and Size Effect of PET by PETase

Polyethylene terephthalate (PET) has been widely used in our daily life, resulting in substantial accumulation of PET waste in the natural environment. PETase, in collaboration with MHETase, can effectively hydrolyze PET back into its constituent monomers, offering a promising solution for PET biorecycling. In this work, to address the controversial issues regarding the mechanism, the decomposition of PET oligomers by PETase was studied on the atomic level using M06-2X/MM-MD simulations. The reaction comprises two main stages: acylation and deacylation, each proceeding stepwise via a metastable intermediate. Deacylation is the rate-limiting step. The role of the third catalytic residue Asp177 was reinvestigated, which was found to take a combined charge-relay and low-energy hydrogen barrier mechanism to stabilize the tetrahedral transition states and intermediates. In addition, the influences of PET size on depolymerization activity were clarified, which enabled us to establish a relationship between structural features and the activation energy barrier. Ultimately, we have identified specific residues whose mutation could potentially enhance the enzyme's activity based on the electrostatic interaction. This work not only provides valuable insights into the PETase catalytic mechanism but also lays a foundation for rational enzyme engineering strategies of PETase.

Standardization guidelines and future trends for PET hydrolase research

Enzymatic depolymerization of polyethylene terephthalate (PET) towards monomer recycling offers a green route to a circular plastic economy, with scale-up currently underway. Yet, inconsistent assessment methods hinder clear comparisons between various PET hydrolases. This Perspective aims to identify critical gaps in this dynamic research field and outline key principles for selecting and tailoring novel enzymes, such as using uniform PET samples and standardizing reaction settings that mimic industrial conditions. Applying these guidelines will improve enzyme screening efficiency, increase data reproducibility, deepen the understanding of interfacial biocatalysis, and ultimately accelerate the development of more robust and cost-effective bio-based PET recycling methods.

On-demand, readily degradable Poly-2,3-dihydrofuran enabled by anion-binding catalytic copolymerization

Copolymerization with cleavable comonomers is a versatile approach to generate vinyl polymer with viable end-of-life options such as biodegradability. Nevertheless, such a strategy is ineffective in producing readily degradable 2, 3-dihydrofuran (DHF) copolymer with high-molecular-weight (>200 kDa). The latter is a strong and biorenewable thermoplastic that eluded efficient cationic copolymerization synthesis. Here, we show that an anion-binding catalyst seleno-cyclodiphosph(V)azanes enable the efficient cationic copolymerization with cyclic acetals by reversibly activating both different dormant species to achieve both high living chain-end retention and high-molecular-weight. This method leads to incorporating low density of individual in-chain acetal sequences in PDHF chains with high-molecular-weight (up to 314 kDa), imparting on-demand hydrolytic degradability while without sacrificing the thermomechanical, optical, and barrier properties of the native material. The proposed approach can be easily adapted to existing cationic polymerization to synthesize readily degradable polymers with tailored properties while addressing environmental sustainability requirements.

Breaking Symmetry of Active Sites in Metal-Organic Frameworks for Efficient Photocatalytic Valorization of Polyester Plastics

Chemical upcycling of waste plastics offers a promising way toward achieving a circular economy and alleviating environmental pollution but remains a huge challenge. Inspired by hydrolase enzymes and aiming to overcome their intrinsic limitations, we put forward a design principle for an innovative nanozyme featuring asymmetric metal sites. This nanozyme functions as photocatalyst, enabling sustainable valorization of polyester plastics. As a proof of concept, an asymmetric ligand substitution strategy is developed to construct metal-organic frameworks (MOFs) that are defective MIL-101(Fe) (D-MIL-101) with asymmetric Fe3-δ/Fe3+ (0< δ <1) sites. The differential electronic configurations inherent to adjacent Fe3-δ/Fe3+ sites endow a high photocatalytic activity for the valorization of polyester plastic. Accordingly, the ester bonds of polyesters can be preferentially cleaved, contributing to the low energy barrier of upcycling plastics. As a result, the D-MIL-101 achieves a high monomer yield with terephthalic acid (TPA) of ∼93.9% and ethylene glycol (EG) of ∼87.1% for photocatalytic valorization of poly (ethylene terephthalate) (PET), beyond the efficiency of natural enzymes and state-of-the-art photocatalysts. In addition, such a D-MIL-101 is demonstrated to be feasible for the valorization of various real-world polyester plastic wastes in a flow photocatalysis system.

Mild PET degradation by enzymes coupled with magnetic and optical manipulation

Regarding the issue of polyethylene terephthalate (PET) waste proliferation, various methods-including physical, chemical, and biological approaches-have been proposed for PET depolymerization, with bio-enzymatic degradation emerging as a sustainable solution. However, this process is hindered by slow kinetics and enzyme thermal instability, necessitating the development of more efficient and mild strategies. This study innovatively explored enhancing the efficiency of enzyme-catalyzed PET degradation by utilizing magnetic nanoparticle modulation and the photothermal effects of photo-responsive materials. Hydrophobic Fe3O4 nanoparticles (NPs) formed nanochains that exhibited whirlpool motion under a rotating magnetic field, enhancing hydrolytic enzyme activity through microreaction. It revealed that at a concentration of 1 mg/mL Fe3O4 NPs and a magnetic field strength of 2 mT, hydrolysis efficiency increased by 38 %. Furthermore, exposure to light radiation significantly altered the physicochemical properties of plastics, including crystallinity, hydrophobicity, surface functional groups, and morphology. Photo-responsive materials exhibited a photothermal effect, increasing the temperature of the enzyme-catalyzed system and thereby enhancing degradation efficiency. Light pretreatment of MXene followed by PET hydrolase improved degradation efficiency by 148 %. The successful implementation of this innovative strategy holds promise for further advancing the practical application of bio-enzyme degradation of PET and making a substantial contribution to environmental protection efforts.

Ancestral Sequence Reconstruction and Comprehensive Computational Simulations Unmask an Efficient PET Hydrolase with the Wobbled Catalytic Triad

Beyond directed evolution, ancestral sequence reconstruction (ASR) has emerged as a powerful strategy for engineering proteins with superior functional properties. Herein, we harnessed ASR to uncover robust PET hydrolase variants, expanding the repertoire of PET-degrading enzymes and providing deeper insights into the underlying mechanisms of PET hydrolysis. As a result, ASR1-PETase, featuring a unique cysteine catalytic site, was discovered. Despite having only 19.3 % sequence identity with IsPETase, ASR1-PETase demonstrated improved PET degradation efficiency, with a finely-tuned substrate-binding cleft. Comprehensive experimental validation, including mutagenesis studies and comparisons with six state-of-the-art PET hydrolases, combined with microsecond-scale molecular dynamics (MD) simulations and QM-cluster calculations, revealed that ASR1-PETase's C161 catalytic residue assisted with the wobbled H242 can simultaneously cleave both ester bonds of BHET - a feature not commonly observed in other PET hydrolases. This mechanism may serve as the primary driving force for accelerating PET hydrolysis while minimizing the accumulation of the intermediate MHET, thereby enhancing the efficiency of TPA production.

Aliphatic Polyester Recognition and Reactivity at the Active Cleft of a Fungal Cutinase

Protein engineering of cutinases is a promising strategy for the biocatalytic degradation of non-natural polyesters. We report a mechanistic study addressing the hydrolysis of the aliphatic polyester poly(butylene succinate, or PBS) by the fungal Apergillus oryzae cutinase enzyme. Through atomistic molecular dynamics simulations and advanced alchemical transformations, we reveal how three units of a model PBS substrate fit the active site cleft of the enzyme, interacting with hydrophobic side chains. The substrate ester moiety approaches the Asp-His-Ser catalytic triad, displaying catalytically competent conformations. Acylation and deacylation hydrolytic reactions were modeled according to a canonical esterase mechanism using umbrella sampling simulations at the quantum mechanical/molecular mechanical DFT(B3LYP)/6-31G**/AMBERff level. The free energy profiles of both steps show a high-energy tetrahedral intermediate resulting from the nucleophilic attack on the ester's carboxylic carbon. The free energy barrier of the acylation step is higher (20.2 ± 0.6 kcal mol-1) than that of the deacylation step (13.6 ± 0.6 kcal mol-1). This is likely due to the interaction of the ester's carboxylic oxygen with the oxyanion hole in the reactive conformation of the deacylation step. In contrast, these interactions form as the reaction proceeds during the acylation step. The formation of an additional hydrogen bond interaction with the side chain of Ser48 is crucial to stabilizing the developing charge at the carboxylic oxygen, thus lowering the activation free energy barrier. These mechanistic insights will inform the design of enzyme variants with improved activity for plastic degradation.

Polyester-derived monomers as microbial feedstocks: Navigating the landscape of polyester upcycling

Since their large-scale adoption in the early 20th century, plastics have become indispensable to modern life. However, inadequate disposal and recycling methods have led to severe environmental consequences. While traditional end-of-life plastics management had predominantly relied on landfilling, a paradigm shift towards recycling and valorization emerged in the 1970s, leading to the development of various, mostly mechanochemical, recycling strategies, together with the more recent approach of biological depolymerization and upcycling. Plastic upcycling, which converts plastic waste into higher-value products, is gaining attention as a sustainable strategy to reduce environmental impact and reliance on virgin materials. Microbial plastic upcycling relies on efficient depolymerization methods to generate monomeric substrates, which are subsequently metabolized by native or engineered microbial systems yielding valuable bioproducts. This review focuses on the second phase of microbial polyester upcycling, examining the intracellular metabolic pathways that enable the assimilation and bioconversion of polyester-derived monomers into industrially relevant compounds. Both biodegradable and non-biodegradable polyesters with commercial significance are considered, with emphasis on pure monomeric feedstocks to elucidate intracellular carbon assimilation pathways. Understanding these metabolic processes provides a foundation for future metabolic engineering efforts, aiming to optimize microbial systems for efficient bioconversion of mixed plastic hydrolysates into valuable bioproducts.

Diluted alkaline pretreatment in hexafluoroisopropanol facilitates chemoenzymatic depolymerization of polyethylene terephthalate

Enzymatic PET degradation presents a sustainable and eco-friendly solution for recycling and upgrading PET materials. While various PET-degrading enzymes have proven effective in converting low-crystallinity PET into monomers, their efficiency decreases significantly for high-crystallinity PET. Given that most commercially available PET products are highly crystalline and have a limited specific surface area, conventional methods typically resort to heat treatment and ball milling to achieve decrystallization and micronization before enzymatic hydrolysis. However, these pretreatments often compromise environmental benefits due to their high energy consumption and dust pollution, and are difficult to scale up. In this study, we developed a chemoenzymatic strategy that efficiently depolymerizes waste PET materials into monomers in just 4 h. This process involves an alkaline treatment with diluted NaOH in 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), followed by enzymatic hydrolysis of the PET nanosuspensions generated from solvent exchange. The alkaline treatment partially breaks down the PET molecular chains and mitigates recrystallization during the precipitation process. Importantly, the complete hydrolysis of PET is attributed to reduced crystallinity rather than particle size. Notably, this method eliminates the need for PET micronization and minimizes the usage of NaOH. The effectiveness of this method was demonstrated through the hydrolysis of various commercially available PET products, showcasing its potential to advance enzymatic degradation processes for PET recycling.

Biodegradation of polyethylene with polyethylene-group-degrading enzyme delivered by the engineered Bacillus velezensis

Microplastics (MPs) pose an emerging threat to vegetable growing soils in Harbin, which have a relatively high abundance (11,065 n/kg) with 17.26 of potential ecological risk of single polymer hazard (EI) and 33.92 of potential ecological risk index (PERI). Polyethylene (PE) is the main type of microplastic pollution in vegetable growing soils in Harbin. In this study, the engineered Bacillus velezensis with polyethylene-group-degrading enzyme pathway (BCAv-PEase) was constructed to enhance the degradation of MPs of PE (PE-MPs). BCAv-PEase increased the biodegradation of PE-MPs, promoted weight loss of PE films, elevated surface tension, and decreased the surface hydrophobicity of PE through upregulating activities of depolymerases, dehydrogenase, and catalase. Mechanism analysis showed that BCAv-PEase degraded PE-MPs by promoting the secretion of PEase, thereby leading to the generation of new oxygenated functional groups within the PE-MPs substrate, which further accelerated the metabolic pathway of PE-MPs. The analysis of the microbial community during the PE-MPs degradation processes revealed that BCAv-PEase emerged as the principal bacterial player and stimulated the abundance of microbes and functional genes associated with the biodegradation of PE. In conclusion, this study provides a potential mechanism for biodegradation of PE-MPs mediated by BCAv-PEase via modulating substrate selectivity and optimizing biocatalytic pathways.

Optimized whole-cell depolymerization of polyethylene terephthalate to monomers using engineered Clostridium thermocellum

Polyethylene terephthalate (PET) is a widely produced thermoplastic derived from fossil fuels, and its accumulation and improper waste disposal pose significant environmental concerns. Innovative bio-based recycling technologies have evolved in recent years, offering viable solutions to PET waste-related challenges. While the enzyme-based PET recycling technology utilizing free thermophilic enzymes has already been commercialized, related whole-cell recycling approaches are still in the early stages of research. Here, we improve a Clostridium thermocellum-based whole-cell catalyst for PET depolymerization by integrating beneficial variants of leaf-branch compost cutinase (LCC) into the bacterial chromosome DNA, ensuring stable enzyme expression. We also implement a pH-controlled bioreactor to counteract the pH drop during PET depolymerization, enhancing enzyme stability and stable cell growth. Using this optimized system, we achieve 96.7 % conversion of pretreated waste PET into its monomer, terephthalic acid (TPA), in a 1-L reactor within 10 days. This work demonstrates the potential of whole-cell biocatalysts for efficient PET recycling.

Floatable organic-inorganic hybrid-TiO2 unlocks superoxide radicals for plastic photoreforming in neutral solution

Plastic photoreforming offers a compelling technology to address the global issue of the large amount cumulative plastic waste by converting it into valuable fuels and chemical feedstocks. However, constrained by insufficient mass and energy transfers, the existing hydrophilic plastic photoreforming systems heavily rely on the unsustainable chemical pre-treatments in corrosive solutions. Herein, we demonstrate a conceptual plastic photoreforming system based on a floatable hydrophobic organic-inorganic hybrid-TiO2 photocatalyst, which unlocks superoxide radical as the major oxidizing species and forms a four-phase interface among photocatalyst, plastic substrate, water and air, thus greatly enhancing the mass and energy transfers. Consequently, the photoreforming yield rates in neutral aqueous solutions are increased by 1-2 orders of magnitude for typical plastic including polyethylene, polypropylene, and polyvinyl chloride without applying pre-treatments, whilst producing high-value C2H5OH with a selectivity of over 40%. We believe this work reveals a feasible route to sustainable plastic photoreforming.

Characterisation and Harnessing of 5-Hydroxymethylfurfural Metabolism in Pseudomonas umsongensis GO16 for the Production of 2,5-Furandicarboxylic Acid

In the search for biobased alternatives to traditional fossil plastics, 2,5-furandicarboxylic acid (FDCA) represents a potential substitute to terephthalic acid (TPA), a monomer of the ubiquitous polyester, polyethylene terephthalate (PET). Pseudomonas umsongensis GO16, which can metabolise TPA and ethylene glycol (EG), can also oxidise 5-hydroxymethylfurfural (HMF), a precursor to FDCA. The enzymes involved in the oxidation to FDCA, PsfA and PsfG, were identified and characterised. Deletion of FDCA decarboxylase HmfF involved in the conversion of FDCA to furoic acid, and subsequently to a central metabolic intermediate, 2-ketoglutarate, allowed for the accumulation of FDCA. GO16 ΔhmfF cells were grown on glycerol, TPA, EG or mock PET hydrolysate, and the catalyst was then used for the biotransformation of HMF to FDCA. When TPA was used as a growth substrate and to power the biotransformation, the transport of 5-hydroxymethyl-2-furancarboxylic acid (HMFCA) into the cytoplasm represented a rate-limiting step in HMF oxidation. De-bottlenecking transport limitations through in trans overexpression of the HMFCA transporter (HmfT) along with the PsfA aldehyde dehydrogenase and PsfG alcohol dehydrogenase allowed 100% conversion of 50 mM HMF to FDCA within 24 h when TPA, EG or mock PET hydrolysate were used to grow the biocatalyst and subsequently to power the biotransformation. This expands the repertoire of valuable products obtained from engineered P. umsongensis GO16 in the strategy to bio-upcycle post-consumer PET.

Replicating PET Hydrolytic Activity by Positioning Active Sites with Smaller Synthetic Protein Scaffolds

Evolutionary constraints significantly limit the diversity of naturally occurring enzymes, thereby reducing the sequence repertoire available for enzyme discovery and engineering. Recent breakthroughs in protein structure prediction and de novo design, powered by artificial intelligence, now enable to create enzymes with desired functions without solely relying on traditional genome mining. Here, a computational strategy is demonstrated for creating new-to-nature polyethylene terephthalate hydrolases (PET hydrolases) by leveraging the known catalytic mechanisms and implementing multiple deep learning algorithms and molecular computations. This strategy includes the extraction of functional motifs from a template enzyme (here leaf-branch compost cutinase, LCC, is used), regeneration of new protein sequences, computational screening, experimental validation, and sequence refinement. PET hydrolytic activity is successfully replicated with designer enzymes that are at least 30% shorter in sequence length than LCC. Among them, RsPETase1 stands out due to its robust expressibility. It exhibits comparable catalytic efficiency (kcat/Km) to LCC and considerable thermostability with a melting temperature of 56 °C, despite sharing only 34% sequence similarity with LCC. This work suggests that enzyme diversity can be expanded by recapitulating functional motifs with computationally built protein scaffolds, thus generating opportunities to acquire highly active and robust enzymes that do not exist in nature.

Synthesis of C-N bonds by nicotinamide-dependent oxidoreductase: an overview

Compounds containing chiral C-N bonds play a vital role in the composition of biologically active natural products and small pharmaceutical molecules. Therefore, the development of efficient and convenient methods for synthesizing compounds containing chiral C-N bonds is a crucial area of research. Nicotinamide-dependent oxidoreductases (NDOs) emerge as promising biocatalysts for asymmetric synthesis of chiral C-N bonds due to their mild reaction conditions, exceptional stereoselectivity, high atom economy, and environmentally friendly nature. This review aims to present the structural characteristics and catalytic mechanisms of various NDOs, including imine reductases/ketimine reductases, reductive aminases, EneIRED, and amino acid dehydrogenases. Additionally, the review highlights protein engineering strategies employed to modify the stereoselectivity, substrate specificity, and cofactor preference of NDOs. Furthermore, the applications of NDOs in synthesizing essential medicinal chemicals, such as noncanonical amino acids and chiral amine compounds, are extensively examined. Finally, the review outlines future perspectives by addressing challenges and discussing the potential of utilizing NDOs to establish efficient biosynthesis platforms for C-N bond synthesis. In conclusion, NDOs provide an economical, efficient, and environmentally friendly toolbox for asymmetric synthesis of C-N bonds, thus contributing significantly to the field of pharmaceutical chemical development.

Enzymatic recycling and microbial upcycling for a circular plastics bioeconomy

Since the 1950s, plastics have become commodity materials that are present in virtually every aspect of our daily lives. However, the current economic model of plastics is fundamentally linear, with less than 10% of plastics returning to the value chain at their end of life. In recent years, efforts have been dedicated to develop new technologies that can change this model to a circular economy for plastics, including enzymatic recycling and biological upcycling to value-added products. Here, we will review recent advances made in this rapidly evolving field and discuss how further development of these technologies could contribute to reduce the share of postconsumer plastic waste that is diverted toward landfilling and incineration.

Unraveling the complexity of organophosphorus pesticides: Ecological risks, biochemical pathways and the promise of machine learning

Organophosphorus pesticides (OPPs) are widely used in agriculture but pose significant ecological and human health risks due to their persistence and toxicity in the environment. While microbial degradation offers a promising solution, gaps remain in understanding the enzymatic mechanisms, degradation pathways, and ecological impacts of OPP transformation products. This review aims to bridge these gaps by integrating traditional microbial degradation research with emerging machine learning (ML) technologies. We hypothesize that ML can enhance OPP degradation studies by improving the efficiency of enzyme discovery, pathway prediction, and ecological risk assessment. Through a comprehensive analysis of microbial degradation mechanisms, environmental factors, and ML applications, we propose a novel framework that combines biochemical insights with data-driven approaches. Our review highlights the potential of ML to optimize microbial strain screening, predict degradation pathways, and identify key active sites, offering innovative strategies for sustainable pesticide management. By integrating traditional research with cutting-edge ML technologies, this work contributes to the journal's scope by promoting eco-friendly solutions for environmental protection and pesticide pollution control.

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.

Metal Synergistic Dual Activation Enables Efficient Transesterification by Multinuclear Titanium Catalyst: Recycling and Upcycling of Polyester Waste

Developing highly efficient and selective catalysts for chemical recycling and upcycling of plastic waste is essential for establishing a sustainable plastics economy and reducing environmental impact. Here, we report a novel tetranuclear titanium catalyst that enables highly efficient transesterification reactions of esters and polyesters. Detailed experimental and computational studies have revealed that a bi-titanium framework facilitates a dual activation mechanism, activating both alcohol and ester simultaneously, thereby significantly enhancing the transesterification process. This catalyst demonstrated exceptionally high activity in the methanolysis of poly(ethylene terephthalate) (PET) with an activity up to 1.9 × 107 gPET molTi -1 h-1 at 0.005 mol% catalyst loading, producing polymerizable dimethyl ester and glycol monomers. Additionally, it effectively catalyzed the re-polymerization of the recovered monomers, yielding the original polyester with high molecular weight and thereby achieving an ideal circular economy for commodity polyesters. Furthermore, this catalyst can also be utilized for the efficient upgrading of PET waste via transesterification with 1,4-butanediol, polybutylene adipate, and poly(tetramethyene ether glycol), yielding engineering plastic, biodegradable polyester, and thermoplastic elastomer, respectively.

Biocatalytic recycling of plastics: facts and fiction

Due to the lack of efficient end-of-life management, the mass production of plastics has resulted in serious environmental problems. Sustainable biological approaches using enzymes to degrade and recycle plastic waste are emerging as a complement to conventional methods to promote a circular economy of plastics. Only a fraction of the plastic waste generated is currently suitable for biocatalytic deconstruction and the development of economically and environmentally competitive processes is still pending. Inconsistent claims about new plastic-degrading enzymes reveal a need for robust and standardized analysis methods to ensure reproducible results and a realistic evaluation of their potential. This paper critically reviews enzymatic synthetic polymer degradation and its recycling challenges.

An Update: Enzymatic Synthesis for Industrial Applications

Supported by rapid technological advancements, biocatalytic applications have matured into sustainable, scalable, and cost-competitive alternatives to established chemical catalysis. This review presents the most recent examples of enzyme-based solutions for the manufacturing of molecules with extended carbon-carbon frameworks and multiple stereogenic centers at commercial scale, including peptide building blocks, (rare) sugars, synthetic (oligo)nucleotides, and terpenoids, such as (-)-Ambrox®. Novel enzyme classes are highlighted along with their potential applications-the synthesis of DNA/RNA, the depolymerization of synthetic plastics, or fully enzymatic protection/deprotection schemes-pointing toward the diversification and broader industrial utilization of biocatalysis-based processes.

Discovery and solution for microplastics: New risk carriers in food

Microplastics (MPs), as a kind of plastic particles with an equal volume size of less than 5 mm, similar to PM2.5 in the air, are causing severe contamination issues in food. Along with the food chain accumulation, they have been confirmed to appear in daily foods and cause serious health risks to the organisms. However, there were no unifying national and local policies on separating, extracting, and detecting MPs in food, which is an essential and imperative early-warning strategy. This review carefully and comprehensively summarized the validated contaminated food, physical and chemical characteristics, extraction methods, traditional and rapid detection techniques, as well as degradation methods of MPs. We thoroughly analyzed the differences among these traditional strategies, and innovatively generalized the existing rapid detection techniques for MPs. Finally, the shortcomings of existing research were discussed, and the possibility of novel rapid and intelligent detection techniques for MPs in food was proposed.

An informatics-based analysis platform identifies diverse microbial species with plastic-degrading potential

Plastic waste has accumulated rapidly in the past century and is now found throughout every ecosystem on Earth. Its ubiquitous presence means that plastic is routinely ingested by countless organisms, with potential negative consequences for organismal health. New solutions are urgently needed to combat plastic pollution. Among the many strategies required to curb the plastic pollution crisis, the bioremediation of plastic via enzymatic activity of microbial species represents a promising approach. Diverse microbes harbor enzymes capable of degrading plastic polymers and utilizing the polymers as a carbon source. Herein, we characterize the landscape of microbial protein-coding sequences with potential plastic degrading capability. Using the two enzyme systems of PETase and MHETase as a guide, we combined sequence motif analysis, phylogenetic inference, and machine learning-guided 3D protein structure prediction to pinpoint potential plastic-degrading enzymes. Our analysis platform identified hundreds of enzymes from diverse microbial taxa with similarity to known PETases, and far fewer enzymes with similarity to known MHETases. Phylogenetic reconstruction revealed that the plastic degrading enzymes formed distinct clades from the sequences of ancestral enzymes. Among the potential candidate sequences, we pinpointed both a PETase-like and MHETase-like enzyme within the bacterium Pseudomonas stutzeri. Using plate clearing assays, we demonstrated that P. stutzeri is capable of degrading both polyurethane (Impranil®) and polycaprolactone (PCL). Pseudomonas stutzeri also grew on carbon-free agar supplemented with polystyrene, suggesting this organism can utilize synthetic polymers as a carbon source. Overall, our integrated bioinformatics and experimental approach provides a rapid and low-cost solution to identify and test novel polymer-degrading enzymes for use in the development of plastic bioremediation technologies.

Pulsed electrosynthesis of glycolic acid through polyethylene terephthalate upcycling over a mesoporous PdCu catalyst

Electrocatalytic upcycling of polyethylene terephthalate (PET) plastics offers a promising and sustainable route that not only addresses serious waste pollution but also produces high value-added chemicals. Despite some important achievements, their activity and selectivity have been slower than needed. In this work, pulsed electrocatalysis is employed to engineer chemisorption properties on a lamellar mesoporous PdCu (LM-PdCu) catalyst, which delivers high activity and stability for selective electrosynthesis of high value-added glycolic acid (GA) from PET upcycling under ambient conditions. LM-PdCu is synthesized by in situ nucleation and attachment strategy along assembled lamellar templates, whose stacked morphology and lamellar mesoporous structure kinetically accelerate selective desorption of GA and expose fresh active sites of metal catalysts for continuous electrocatalysis at pulsed mode. This strategy thus delivers GA Faraday efficiency of >92% in wide potential windows, yield rate of reaching 0.475 mmol cm-2 h-1, and cycling stability of exceeding 20 cycles for electrocatalytic PET upcycling. Moreover, pulsed electrocatalysis discloses good electrocatalytic performance for scaled-up GA electrosynthesis from real bottle waste plastics. This work presents a sustainable route for selective electrosynthesis of value-added chemicals through upcycling of various waste feedstocks.

Complete Enzymatic Depolymerization of Polyethylene Terephthalate (PET) Plastic Using a Saccharomyces cerevisiae-Based Whole-Cell Biocatalyst

Management of polyethylene terephthalate (PET) plastic waste remains a challenge. PET-hydrolyzing enzymes (PHEs) such as IsPETase and variants like FAST-PETase demonstrate promising PET depolymerization capabilities at ambient temperatures and can be utilized to recycle and upcycle plastic waste. Whole-cell biocatalysts displaying PHEs on their surface offer high efficiency, reusability, and stability for PET depolymerization. However, their efficacy in fully breaking down PET is hindered by the necessity of two enzymes: PETase and MHETase. Current whole-cell systems either display only one enzyme or struggle with performance when displaying larger enzymes such as the MHETase-PETase chimera. We developed a Saccharomyces cerevisiae-based whole-cell biocatalyst for complete depolymerization of PET into its constituent monomers with no accumulation of intermediate products. Leveraging a cellulosome-inspired trifunctional protein scaffoldin displayed on the yeast surface, we co-immobilized FAST-PETase and MHETase, forming a multi-enzyme cluster. This whole-cell biocatalyst achieved complete PET depolymerization at 30 °C, yielding 4.95 mM terephthalic acid (TPA) when tested on a PET film. Furthermore, we showed improved PET depolymerization ability by binding FAST-PETase at multiple sites on the scaffoldin. The whole cells had the added advantage of retained activity over multiple reusability cycles. This breakthrough in complete PET depolymerization marks a step toward a circular plastic economy.

Scalable nanoplastic degradation in water with enzyme-functionalized porous hydrogels

The prevalence of nanoplastics in water has led to significant environmental and health concerns, yet effective and scalable strategies for mitigating this contamination remain limited. Here, we report a straightforward, efficient, and scalable approach to degrade nanoplastics in water using enzyme-loaded hydrogel granules with an interconnected porous structure and adjustable properties. These porous hydrogels were synthesized via a polymerization-induced phase separation method, allowing easy scaling-up. Our results show that enzyme-functionalized porous hydrogels slightly outperform free cutinase in nanoplastic degradation. Furthermore, immobilized enzymes exhibited enhanced stability under harsh conditions, achieving a 104.1 % higher PET removal rate at pH 5 than free cutinase. Notably, the immobilized enzyme retained 39.9 % of its initial degradation activity after five cycles, demonstrating good reuse stability. This method offers a promising and practical solution for using enzymes to address nanoplastic pollution in aquatic environments.

Customization of Ethylene Glycol (EG)-Induced BmoR-Based Biosensor for the Directed Evolution of PET Degrading Enzymes

The immense volume of plastic waste poses continuous threats to the ecosystem and human health. Despite substantial efforts to enhance the catalytic activity, robustness, expression, and tolerance of plastic-degrading enzymes, the lack of high-throughput screening (HTS) tools hinders efficient enzyme engineering for industrial applications. Herein, we develop a novel fluorescence-based HTS tool for evolving polyethylene terephthalate (PET) degrading enzymes by constructing an engineered BmoR-based biosensor targeting the PET breakdown product, ethylene glycol (EG). The EG-responsive biosensors, with notably enhanced dynamic range and operation range, are customized by fluorescence-activated cell sorting (FACS)-assisted transcription factor engineering. The ingeniously designed SUMO-MHETase-FastPETase (SMF) chimera successfully addresses the functional soluble expression of MHETase in Escherichia coli and mitigates the inhibitory effect of mono-(2-hydroxyethyl) terephthalic acid (MHET) intermediate commonly observed with PETase alone. The obtained SMM3F mutant demonstrates 1.59-fold higher terephthalic acid (TPA) production, with a 1.18-fold decrease in Km, a 1.29-fold increase in Vmax, and a 1.52-fold increase in kcat/Km, indicating stronger affinity and catalytic activity toward MHET. Furthermore, the SMM3F crude extract depolymerizes 5 g L-1 bis-(2-hydroxyethyl) terephthalic acid (BHET) into TPA completely at 37 °C within 10 h, which is then directedly converted into value-added protocatechuic acid (PCA) (997.16 mg L-1) and gallic acid (GA) (411.69 mg L-1) at 30 °C, establishing an eco-friendly 'PET-BHET-MHET-TPA-PCA-GA' upcycling route. This study provides a valuable HTS tool for screening large-scale PET and MHET hydrolases candidates or metagenomic libraries, and propels the complete biodegradation and upcycling of PET waste.

Bio-contaminated plastic micropipette tip sterilization stations: Environmentally, economically, and energetically viable solution

Bioscientific research laboratories significantly contribute to global plastic waste production through their use of plastic products, such as single-use micropipette tips. Biologically contaminated pipette tips must undergo several washing and sterilization steps before being reused or recycled. There is a dearth of available research studying the feasibility of pipette tip washing and sterilization in research laboratories. While automated tip-washing systems are available commercially for tip decontamination and reuse, the high initial purchasing cost of these washing stations and concerns related to washing efficiency deter many research laboratories from incorporating them. To mitigate these concerns, considering the University of Texas at Austin as an example, we performed a cost-benefit analysis of employing a university-wide pipette tip washing station. We estimated that only a single-time reuse of pipette tips could result in a 100% return on investment from the equipment. Additionally, preliminary analysis shows that pipette tip recycling can result in significant energy and water savings. With pilot experiments, we replicated UV-based decontamination steps employed by the commercial equipment and found the washing to be 100% efficient in sterilizing pipette tips contaminated with bacteriophage, DNA, and RNA. Decontaminated pipette tips were used to conduct phage quantification to demonstrate the feasibility of reuse for biological assays. Finally, we proposed an alternative autoclave-based sterilization method that can be used in individual research labs to decontaminate pipette tips. We found autoclave-based washing to be 100% efficient in sterilizing pipette tips contaminated with bacteriophage, whereas it is not efficient enough to decontaminate DNA and RNA.

Engineering carbon assimilation in plants

Carbon assimilation is a crucial part of the photosynthetic process, wherein inorganic carbon, typically in the form of CO2, is converted into organic compounds by living organisms, including plants, algae, and a subset of bacteria. Although several carbon fixation pathways have been elucidated, the Calvin-Benson-Bassham (CBB) cycle remains fundamental to carbon metabolism, playing a pivotal role in the biosynthesis of starch and sucrose in plants, algae, and cyanobacteria. However, Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the key carboxylase enzyme of the CBB cycle, exhibits low kinetic efficiency, low substrate specificity, and high temperature sensitivity, all of which have the potential to limit flux through this pathway. Consequently, RuBisCO needs to be present at very high concentrations, which is one of the factors contributing to its status as the most prevalent protein on Earth. Numerous attempts have been made to optimize the catalytic efficiency of RuBisCO and thereby promote plant growth. Furthermore, the limitations of this process highlight the potential benefits of engineering or discovering more efficient carbon fixation mechanisms, either by improving RuBisCO itself or by introducing alternative pathways. Here, we review advances in artificial carbon assimilation engineering, including the integration of synthetic biology, genetic engineering, metabolic pathway optimization, and artificial intelligence in order to create plants capable of performing more efficient photosynthesis. We additionally provide a perspective of current challenges and potential solutions alongside a personal opinion of the most promising future directions of this emerging field.

Structural Stabilization and Activity Enhancement of Glucoamylase via the Machine-Learning Technique and Immobilization

Glucoamylases (GLL) hydrolyze starch to glucose syrup without yielding intermediate oligosaccharides, but their lack of stability under industrial conditions poses a major limiting factor. Using consensus- and ancestral-based machine-learning tools, a functional GLL with six mutations (GLLI73l/T130V/N212V/D238G/N327M/S332P) was constructed that exhibited superior hydrolytic activity relative to the wild-type (WT-GLL). An oxidized multi-walled carbon nanotube (oMW-CNT) was used as a solid support to immobilize the WT-GLL with an immobilization capacity of 211.28 mg/g. The specific activity of mutant GLL-6M and GLL@oMW-CNTII was improved by 2.5-fold and 3.9-fold respectively, with both retaining 64.5% residual activity after incubation at 50 °C for 2 h compared to the WT-GLL with 42.6% activity. GLL and GLL-6M were however completely inactivated at 55 °C in 30 min while oMW-CNTII retained ∼43.1% activity. Our results demonstrate that employing a machine-learning approach for enzyme redesign and immobilization is a practicable alternative for improving enzyme performance and stability for industrial applications.

Selective Hydrolysis by Engineered Cutinases: Characterization of Aliphatic-Aromatic Homo and Co-Polyesters by LC and LC-MS Methods

The performance, biodegradability, and recyclability of polymers can be tuned during synthesis by adopting monomers with different chemical characteristics. Recent research has shown the aptness of some hydrolases to depolymerize polyesters under mild conditions compared to chemical approaches. Herein, we engineered a cutinase from Thermobifida cellulosilytica (Tc_Cut2NVWCCG) for improved thermostability (up to 91 °C) and compared it with previously reported leaf-branch compost cutinase (LCCWCCG) for the hydrolysis of low molar mass substrates, as well as aliphatic and aromatic homo- and co-polyesters. For both enzymes, higher hydrolysis rates were observed for aliphatic compared to aromatic homo-polyesters. SEC-MS analysis revealed that the hydrolysis of aliphatic/aromatic co-polyesters occurred at the aliphatic monomers, significantly reducing the molecular weight and changing the end-group composition. These results underline the importance of co-polymer composition in the biodegradation of co-polymer systems and demonstrate the applicability of enzymes for the analytical characterization of synthetic polymers by selectively reducing their molecular weight. Finally, the discovery and engineering of highly active enzymes that can efficiently hydrolyze a wide variety of synthetic polyesters create new opportunities for their efficient recycling under mild conditions.

Towards polyethylene terephthalate valorisation into PHB using an engineered Comamonas testosteroni strain

The abundant production of plastic materials, coupled with their recalcitrant nature, makes plastic waste a major challenge as a pollutant. Polyethylene terephthalate (PET) is a polyester formed by polycondensation of terephthalic acid (TPA) and ethylene glycol (EG). This plastic polymer can be completely depolymerized to its monomers using microbial enzymes. In this study, we verified in silico and in vivo that the bacterium Comamonas testosteroni RW31 is able to assimilate TPA and to produce the bioplastic polyhydroxybutyrate (PHB). This bacterium was engineered to heterologously express a fusion of the PET-degrading enzymes FAST-PETase and IsMHETase. We verified that our strain successfully secretes the enzymes and depolymerize PET both in vitro and in vivo, achieving a weight loss of 37.1 % and 0.83 %, respectively. We also studied its capacity to form biofilm. Furthermore, our strain can employ bis(2-hydroxyethyl) terephthalate (BHET), an intermediate of PET degradation, as feedstock to accumulate PHB up to 12.03 % of its dry weight in 14 h. Our findings highlight C. testosteroni RW31 as a promising chassis for synthetic biology strategies aimed at upcycling PET waste.

Engineering highly active nuclease enzymes with machine learning and high-throughput screening

Optimizing enzymes to function in novel chemical environments is a central goal of synthetic biology, but optimization is often hindered by a rugged fitness landscape and costly experiments. In this work, we present TeleProt, a machine learning (ML) framework that blends evolutionary and experimental data to design diverse protein libraries, and employ it to improve the catalytic activity of a nuclease enzyme that degrades biofilms that accumulate on chronic wounds. After multiple rounds of high-throughput experiments, TeleProt found a significantly better top-performing enzyme than directed evolution (DE), had a better hit rate at finding diverse, high-activity variants, and was even able to design a high-performance initial library using no prior experimental data. We have released a dataset of 55,000 nuclease variants, one of the most extensive genotype-phenotype enzyme activity landscapes to date, to drive further progress in ML-guided design. A record of this paper's transparent peer review process is included in the supplemental information.

Eco-microbiology: discovering biochemical enhancers of PET biodegradation by Piscinibacter sakaiensis

The scale of plastic pollution boggles the mind. Nearly 400 megatons of virgin plastics are produced annually, with an environmental release rate of 80%, and plastic waste, including microplastics and nanoplastics, is associated with a plethora of problems. The naturally evolved abilities of plastic-degrading microbes offer a starting point for generating sustainable and eco-centric solutions to plastic pollution-a field of endeavor we term eco-microbiology. Here, we developed an iterative discovery procedure coupling faster polyethylene terephthalate (PET)-dependent bioactivity screens with longer-term PET biodegradation assays to find biochemical boosters of PET consumption by the bacterium Piscinibacter sakaiensis. We discovered multiple hits supporting the enhancement of PET biodegradation, with a 0.39% dilution of growth medium #802, a rich medium similar to Luria-Bertani broth, on average more than doubling the rate of PET biodegradation both alone and in combination with 0.125% ethylene glycol. In addition, we identified other chemical species (sodium phosphate, L-serine, GABA) worth further exploring, especially in combination with growth medium #802, for enhanced PET biodegradation by P. sakaiensis. This work represents an important step toward the creation of a low-cost PET fermentation process needed to help solve PET plastic pollution.

IMPORTANCE

Plastic pollution is an urgent issue. Adding to the well-known problems of bulk plastic litter, shed microplastics and nanoplastics are globally distributed, found in diverse organisms including human foodstuffs and tissues, and increasingly associated with chronic disease. Solutions are needed and the microbial world offers abundant help via naturally evolved consumers of plastic waste. We are working to accelerate polyethylene terephthalate (PET) plastic biodegradation by Piscinibacter sakaiensis, a recently described bacterium that evolved to slowly but completely consume PET, one of the most common types of plastic pollution. We used a combination of PET-dependent bioactivity screens and biodegradation tests to find stimulators of PET biodegradation. Out of hundreds, we found a small number of biochemical conditions that more than double the PET biodegradation rate. Our work provides a foundation for further studies to realize a fermentation process needed to help solve PET plastic pollution.

Selective Modification of the Product Profile of Biocatalytic Hydrolyzed PET via Product-Specific Medium Engineering

Over the past years, enzymatic depolymerization of PET, one of the most widely used plastics worldwide, has become very efficient leading to the end products terephthalic acid (TPA) and ethylene glycol (EG) used for PET re-synthesis. Potent alternatives to these monomers are the intermediates BHET and MHET, the mono- and di-esters of TPA and EG which avoid total hydrolysis and can serve as single starting materials for direct re-polymerization. This study therefore aimed to selectively prepare those intermediates through reaction medium engineering during the biocatalytic hydrolysis of PET. After a comparative pre-screening of 12 PET-hydrolyzing enzymes, two of them (LCCICCG, IsPETasewt) were chosen for detailed investigations. Depending on the reaction conditions, MHET and BHET are predominantly obtainable: (i) MHET was produced in a better ratio and high concentrations at the beginning of the reaction when IsPETasewt and 10 % EG was used; (ii) BHET was produced as predominant product when LCCICCG and 25 % EG was used. TPA itself was nearly the single product at pH 9.0 after 24 h due to the self-hydrolysis of MHET and BHET under basic conditions. Using medium engineering in biocatalytic PET-hydrolysis, the product profile can be adjusted so that TPA, MHET or BHET is predominantly produced.

Can the insects Galleria mellonella and Tenebrio molitor be the future of plastic biodegradation?

Plastics have been an integral part of human lives, enhancing the functionality and safety of many everyday products, contributing significantly to our overall well-being. However, petroleum-based plastics can take hundreds or even thousands of years to decompose, resulting in an unprecedented plastic waste accumulation in the environment. Widely used conventional plastic disposal methods as landfilling and incineration are also environmentally harmful, frequently leading to soil/water contamination and the release of microplastics. To overcome these limitations, researchers have been investigating novel sustainable alternatives for plastic waste management, such as the use of microorganisms, microbial-based enzymes, and, more recently, some insect larvae, being Galleria mellonella and Tenebrio molitor the most promising ones. In this review, we explore different methods of plastic waste disposal focusing on recent discoveries regarding biological plastic degradation using insects as alternative methods. We also discuss the plastic degradation mechanisms employed by G. mellonella and T. molitor larvae known so far, as salivary enzymes and the pool of microorganisms in their gut. Finally, this review highlights key challenges in plastic biodegradation, such as standardization and experimental comparability, while proposing innovative perspectives like using insects as bioreactors and exploring unexplored research directions.

Efficient Bioprocess for Mixed PET Waste Depolymerization Using Crude Cutinase

In recent years, several plastic-degrading enzymes with efficient depolymerization abilities for PET have been reported. Here, we report a bioprocess for mixed PET waste depolymerization using crude extracellularly expressed enzymes in E. coli. The enzymes, namely FastPETase, LCC, and LCCICCG, were screened to depolymerize amorphous PET powder and films of different sizes and crystallinity. FastPETase, LCC, and LCCICCG achieved approximately 25, 34, and 70% depolymerization, respectively, when applied to 13 g L-1 of PET film, powder, or mixed waste in optimized enzyme conditions without any pH control. The yield of terephthalic acid in the hydrolytic process was maximum for LCCICCG followed by LCC and FastPETase. Finally, extracellular LCCICCG-producing E. coli cells were cultivated using minimal media supplemented with 0.1% ammonium chloride and 1% glycerol as nitrogen and carbon sources in a bioreactor with a final protein content and specific activity of 119 ± 5 mg L-1 and 1232 ± 18 U mg-1, respectively. Nearly complete depolymerization of 13 g L-1 PET and 23.8 g L-1 post-consumer PET was achieved in 50 h using crude LCCICCG supernatant, without enzyme purification, at 62 °C. A bioprocess was thus developed to depolymerize 100 g L-1 mixed PET trays and bottle waste (MW1 and MW2), reaching 78% and 50% yield at 62 °C with a crude enzyme loading of 2.32 mg g-1 PET in 60 h. The results demonstrate an easy PET depolymerization strategy that could be exploited in large-scale facilities for efficient plastic waste treatment.

Rational multienzyme architecture design with iMARS

Biocatalytic cascades with spatial proximity can orchestrate multistep pathways to form metabolic highways, which enhance the overall catalytic efficiency. However, the effect of spatial organization on catalytic activity is poorly understood, and multienzyme architectural engineering with predictable performance remains unrealized. Here, we developed a standardized framework, called iMARS, to rapidly design the optimal multienzyme architecture by integrating high-throughput activity tests and structural analysis. The approach showed potential for industrial-scale applications, with artificial fusion enzymes designed by iMARS significantly improving the production of resveratrol by 45.1-fold and raspberry ketone by 11.3-fold in vivo, as well as enhancing ergothioneine synthesis in fed-batch fermentation. In addition, iMARS greatly enhanced the in vitro catalytic efficiency of the multienzyme complexes for PET plastic depolymerization and vanillin biosynthesis. As a generalizable and flexible strategy at molecular level, iMARS could greatly facilitate green chemistry, synthetic biology, and biomanufacturing.

Computational analysis reveals temperature-induced stabilization of FAST-PETase

More than 10 % of global solid waste consists of poly(ethyleneterephthalate) (PET). Among other techniques, PET hydrolases (PETases) can be used to depolymerize this plastic. However, wildtype PETases exhibit poor specific activities and insufficient thermostability, limiting their use in depolymerization processes which require high temperatures. In 2022, machine learning-aided enzyme engineering of a PETase stemming from the bacterium Ideonella sakaiensis (IsPETase) resulted in a more functional, active, stable, and tolerant variant (FAST-PETase). To rationalize the molecular basis of FAST-PETase's improved thermal stability, we performed comparative Constraint Network Analysis (CNAnalysis) and Molecular Dynamics (MD) simulations of wildtype IsPETase (WT-PETase) and FAST-PETase at 30°C and 50°C identifying thermolabile sequence stretches in the wildtype enzyme. Further analysis of the backbone flexibility revealed that all mutations of FAST-PETase affected these critical regions. Counterintuitively, the in-silico analyses additionally highlighted that the flexibility of these regions decreased at 50°C in FAST-PETase, instead of exhibiting increased flexibility at higher temperature as would be expected from thermodynamic considerations. This effect was confirmed by physical energy calculations, which suggest that temperature-dependent conformational changes of FAST-PETase decrease the free energy of unfolding (ΔG(stability)) and rigidify the enzyme at elevated temperatures enhancing stability. Looking forward, these findings might help guide the rational engineering of protein thermostability and contribute to our understanding of the thermal adaptation of thermophilic enzymes.

FGeneBERT: function-driven pre-trained gene language model for metagenomics

Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.

Intelligent design and synthesis of energy catalytic materials

Efficient energy conversion and storage are crucial for the sustainable development and growth of renewable energy sources. However, the limited varieties of traditional energy catalytic materials cannot match the fast-expansion requirement of raising various clean energy for industrial applications. Thus, accelerating the design and synthesis of high-performance catalysts is necessary for the application of energy equipment. Recently, with artificial intelligence (AI) technology being advanced by leaps and bounds, it is feasible to efficiently and precisely screen materials and optimize synthesis conditions in a huge unknown space. Here, we introduce and review AI techniques used in the development of catalytic materials in detail. We describe the workflow for designing and synthesizing new materials using machine learning (ML) and robotics. We summarize the sources of data collection, the intelligent algorithms commonly used to build ML models, and the laboratory modules for the intelligent synthesis of materials. We provide the illustrations of predicting the properties of catalytic materials with ML assistance in different material types. In addition, we present the potential strategies for finding material synthesis pathways, and advances in robotics to accelerate high-performance catalytic materials synthesis in the review. Finally, the summary, challenges, and potential directions in the development of AI-assisted catalytic materials are presented and discussed.

Unusual depolymerization mechanism of Poly(ethylene terephthalate) by hydrolase 202

Polyethylene terephthalate (PET) waste significantly contributes to the global plastic crisis, but enzymatic conversion has become an efficient and environmentally friendly strategy to combat it. Therefore, this study explored the Re-face selective depolymerization mechanisms of a novel PET-degradation peptidase, hydrolase 202. Theoretical calculations revealed that the first step, a catalytic triad-assisted nucleophilic attack, is the rate-determining step. The corresponding Boltzmann-weighted average barrier was 21.6 kcal/mol. Furthermore, hydrolase 202 degraded Re-face PET more effectively than FAST-PETase, whereas other reported PET hydrolases (e.g., FAST-PETase) degraded Si-face PET more effectively. The hydrogen bond network significantly influenced the depolymerization efficiency. We also identified correlations between 24 important structural and charge features and energy barriers. Key charge, distance, and angle features were responsible for the superiority of the Re-face depolymerization. Finally, we identified residues that may affect the depolymerization efficiency of hydrolase 202, such as Glu215. These findings offer new insights into the potential engineering of PETases and may enhance enzymatic PET waste recycling.