Enhanced Extracellular Production of IsPETase in Escherichia coli via Engineering of the pelB Signal Peptide

Enhanced production of extracellular triacylglycerol lipase for bioplastic degradation by replacing signal peptide

With the increase in plastic production, efficient and timely plastic degradation are urgently needed. In that point, biodegradable plastics have attracted attention as potential solutions for environmental pollution of plastics. However, finding of superior degrading strains and enzymes such as esterase, cutinase, and triacylglycerol lipase (TGL) of bioplastic are still needed together with the efficient secretion systems of degrading enzymes. As a result, we investigated methods to enhance protein expression and secretion of novel bioplastic degrading enzyme by using signal peptides. The genes encoding TGL from Bacillus sp. JY35 and various secretory (Sec) pathway signal peptides were cloned together by replacing the original signal sequence, and they were expressed under T7 promoters in Escherichia coli BL21 (DE3). Esterase activity with p-nitrophenol esters, a plate assay, and SDS-PAGE were performed to screen and evaluate signal peptide efficiency. As a result, the PhoA-TGL combination was the most effective against bioplastic degradation, achieving a Polycaprolactone (PCL) degradation efficiency of 77 %, which was approximately 3.3 times higher than that of TGL with the original signal peptide. Furthermore, Polybutylene succinate (PBS) degradation under similar conditions was 1.5 times higher. Overall, this study showed signal peptide engineering could enhance the extracellular secretion and degradation system of triacylglycerol lipase (TGL) and highlights the potential of PhoA signal peptides and E. coli host to enhance production and secretion of plastic-degrading enzyme and degrading system.

An all-in-one strategy for the simultaneous production of bioplastics and degrading enzymes in engineered Escherichia coli

Bioplastics are promising alternatives for traditional plastics, which contribute significantly to environmental pollution and have a detrimental impact on ecosystems. To advance their use, further research into bioplastic biodegradation is essential. In this study, we propose a novel approach for simultaneous polyhydroxybutyrate (PHB) and degrading enzyme production in a single-cell system using engineered Escherichia coli. Typically, PHB depolymerases, such as PhaZ, disrupt bioplastic synthesis in cells, leading to a self-defeating cycle of production and degradation. To counter this, we introduced synthetic PHB production genes and triacylglycerol lipase (TGL) from Bacillus sp. JY35, along with a native signal peptide for secretion. This enabled PHB accumulation inside the cells while TGL was secreted into the supernatant. The concentrations of PHB produced with and without TGL were similar (31.44 % PHB with TGL and 32.12 % PHB without TGL). TGL was efficiently secreted in E. coli, achieving specific esterase activities of 7.1 U/mg and 15.7 U/mg for p-Nitrophenyl butyrate and p-nitrophenyl octanoate, respectively, and degraded PHB film by 30.1 % over 14 d. Moreover, TGL retained 86 % and 91 % of its activities for the C4 and C8 substrates, respectively, after 30 d of storage at room temperature, suggesting potential use PHB degradation after use. Our study demonstrates a straightforward one-month circular cycle for bioplastic production and degradation by a single producer.

Establishing a novel pathway for the biosynthesis of nicotinamide mononucleotide

Nicotinamide mononucleotide (NMN) is a pivotal molecule within the realm of metabolic health, serving as a precursor to nicotinamide adenine dinucleotide (NAD+), a critical coenzyme in cellular energy metabolism. In recent years, the biological production of NMN has garnered significant interest. In this study, we developed the novel NRK-dependent synthesis routes for NMN production. Two strategies were designed to supply D-ribose-1-phosphate (R-1-P): (1) phosphorylation of exogenous D-ribose to ribose-5-phosphate (R-5-P) using engineered ribokinase (RK), followed by isomerization to R-1-P; (2) R-5-P synthesis from glucose through the pentose phosphate pathway. An optimized in vitro multi-enzyme cascade (XapA/PNP/NRK, PPM, NRK) identified NRK as the most efficient catalyst for NMN biosynthesis from D-ribose and niacinamide. In Escherichia coli, overexpression of this cascade, knockout of competing pathways, and secretion enhancement via a pelB signal peptide-fused PnuC transporter achieved an NMN titer of 62.0 mg L-¹ .This work provides a viable alternative for the biosynthesis of NMN.

A comprehensive review of recombinant technology in the food industry: Exploring expression systems, application, and future challenges

Biotechnology has significantly advanced the production of recombinant proteins (RPs). This review examines the latest advancements in protein production technologies, including CRISPR, genetic engineering, vector integration, and fermentation, and their implications for the food industry. This review delineates the merits and shortcomings of prevailing host systems for RP production, underscoring molecular and process strategies pivotal for amplifying yields and purity. It traverses the spectrum of RP applications, challenges, and burgeoning trends, highlighting the imperative of employing robust hosts and cutting-edge genetic engineering to secure high-quality, high-yield outputs while circumventing protein aggregation and ensuring correct folding for enhanced activity. Recombinant technology has paved the way for the food industry to produce alternative proteins like leghemoglobin and cytokines, along with enzyme preparations such as proteases and lipases, and to modify microbial pathways for synthesizing beneficial compounds, including pigments, terpenes, flavonoids, and functional sugars. However, scaling microbial production to industrial scales presents economic, efficiency, and environmental challenges that demand innovative solutions, including high-throughput screening and CRISPR/Cas9 systems, to bolster protein yield and quality. Although recombinant technology holds much promise, it must navigate high costs and scalability to satisfy the escalating global demand for RPs in therapeutics and food. The variability in ethical and regulatory hurdles across regions further complicates market acceptance, underscoring an urgent need for robust regulatory frameworks for genetically modified organisms. These frameworks are essential for safeguarding the production process, ensuring product safety, and upholding the efficacy of RPs in industrial applications.

Thermostability and Activity Improvements of PETase from Ideonella sakaiensis

Polyethylene terephthalate (PET), a widely used plastic, is a significant environmental pollutant due to its persistence. While the PET-degrading enzyme PETase from Ideonella sakaiensis offers promising solutions, its limited activity at higher temperatures hinders its practical application. This study aimed to enhance the PETase performance through protein engineering. We introduced multiple amino acid substitutions to the wild-type I. sakaiensis PETase to improve its thermostability, substrate binding, and catalytic activity. Several potential mutant IsPETases were generated using computational design and evaluated in silico. The selected mutant was then produced in E. coli BL21(DE3). Finally, the catalytic activity of the purified mutant IsPETase was examined in vitro using p-nitrophenyl butyrate and PET substrates. IsPETaseMT has been confirmed to be catalytically active and more thermostable with a maximum temperature reaching 60 °C and the T m value increasing up to 15.3 °C compared to the wild-type PETase, IsPETaseWT. IsPETaseMT also showed better degradation toward the PET plastic film in comparison to IsPETaseWT. Thus, these findings demonstrate successful protein engineering to create a more robust PETase for potential plastic waste management applications.

Analytical tools to assess polymer biodegradation: A critical review and recommendations

Many petroleum-derived plastic materials are highly recalcitrant and persistent in the environment, posing significant threats to human and ecological receptors due to their accumulation in ecosystems. In recent years, research efforts have focused on advancing biological methods for polymer degradation. Enzymatic depolymerization has emerged as particularly relevant for biobased plastic recycling, potentially scalable for industrial use. Biodegradation involves adsorption to the plastic solid surface, followed by an interfacial reaction, resulting in cleavage of bonds of polymer chains exposed on the surface. Here, widely varying substrate-specific kinetics are observed, with the polymer's properties possessing a significant impact on the rate of this interfacial catalysis. Thus, there is a critical need for sensitive and accurate characterization of the material surface during and after interfacial depolymerization to fully understand the reaction mechanisms. Here, we provide a critical review of a range of techniques used in the analysis of material surfaces to characterize the chemical, topological, and morphological features relevant to the study of enzymatic biocatalysis, including microscopy techniques, spectroscopic techniques (e.g., X-ray diffraction analysis, Fourier transform infrared attenuated total reflectance spectroscopy, and mass spectrometry detection of analytes associated with degradation). Techniques for evaluation of surface energy and topology in their relevancy for sensitive detection of biological surface modifications are also discussed. In addition, this paper provides an overview of the strengths of these techniques and compares their performance in both sensitivity and throughput, including emerging techniques, which can be useful, particularly for the rapid analysis of the surface properties of polymeric materials in high-throughput screening of candidate biocatalysts. This research serves as a starting point in selecting and applying appropriate methodologies that provide direct evidence to the ongoing biotic degradation of polymeric materials.

Boosting extracellular FastPETase production in E. coli: A combined approach of cognate chaperones co-expression and vesicle nucleating peptide tag fusion

Enzymatic PET recycling has emerged as a promising green solution in addition to mechanical recycling, but low soluble expression levels of the inherently hydrophobic PET hydrolases hinder large-scale applications. Here, we propose a novel strategy for enhanced production of FastPETase in Escherichia coli using co-expression of molecular chaperones from Ideonella sakaiensis. Co-expression of cognate DnaK and DnaJ chaperones significantly increased soluble FastPETase expression (up to 2.5-fold), surpassing commercial chaperone plasmids. Furthermore, a combinatorial approach employing co-expression of DnaK/DnaJ chaperones and fusion of FastPETase with the VNp6-tag significantly boosted FastPETase secretion, yielding over 2 g/L of target protein in a 5-l bioreactor. Notably, the crude FastPETase in fermentation broth displayed comparable PET hydrolysis effects to the purified enzyme. This work not only provides new insights into the process of chaperones in protein folding but also suggests a novel and efficient strategy for producing recombinant proteins.

Cutting-edge developments in plastic biodegradation and upcycling via engineering approaches

The increasing use of plastics has resulted in the production of high quantities of plastic waste that pose a serious risk to the environment. The upcycling of plastics into value-added products offers a potential solution for resolving the plastics environmental crisis. Recently, various microorganisms and their enzymes have been identified for their ability to degrade plastics effectively. Furthermore, many investigations have revealed the application of plastic monomers as carbon sources for bio-upcycling to generate valuable materials such as biosurfactants, bioplastics, and biochemicals. With the advancement in the fields of synthetic biology and metabolic engineering, the construction of high-performance microbes and enzymes for plastic removal and bio-upcycling can be achieved. Plastic valorization can be optimized by improving uptake and conversion efficiency, engineering transporters and enzymes, metabolic pathway reconstruction, and also using a chemo-biological hybrid approach. This review focuses on engineering approaches for enhancing plastic removal and the methods of depolymerization and upcycling processes of various microplastics. Additionally, the major challenges and future perspectives for facilitating the development of a sustainable circular plastic economy are highlighted.

Comparative Secretory Efficiency of Two Chitosanase Signal Peptides from Bacillus subtilis in Escherichia coli

The production of recombinant proteins in Escherichia coli is often challenged by cytoplasmic expression due to proteolytic degradation and inclusion body formation. Extracellular expression can overcome these problems by simplifying downstream processing and improving protein yields. This study aims to compare the efficiency of two Bacillus subtilis chitosanase signal peptides in mediating extracellular secretion in E. coli. We identified a naturally occurring mutant signal peptide (mCsn2-SP) from B. subtilis CH2 chitosanase (CH2CSN), which is characterized by a deletion of six amino acids in the N-region relative to the signal peptide (Csn1-SP) from B. subtilis CH1 chitosanase (CH1CSN). The CH1CSN and CH2CSN genes were cloned into the pET-11a vector and protein secretion was evaluated in E. coli BL21(DE3) host cells. Expression was induced with 0.1 mM and 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) at 30 °C for one and three days. CH2CSN showed higher secretion levels compared to CH1CSN under all experimental conditions, especially with 0.1 mM IPTG induction for 3 days, which resulted in a 2.37-fold increase in secretion. Furthermore, it was demonstrated that mCsn2-SP is capable of secreting human Cu,Zn-superoxide dismutase (hSOD) in E. coli BL21(DE3) and successfully translocating it to the periplasmic region. This study represents the inaugural investigation into the utilisation of a naturally modified signal peptide, thereby corroborating the assertion that signal peptide deletion variants can influence protein secretion efficiency. Furthermore, the findings substantiate the proposition that such variants can serve as a viable alternative for the secretion of heterologous proteins in E. coli.

Unravelling biochemical and molecular mechanism of a carboxylesterase from Dietzia kunjamensis IITR165 reveal novel activities against polyethylene terephthalate

Plastics and plasticizers accumulate in the ecological niches affecting biodiversity, and human and environmental health. Bacteria degrading polyethylene terephthalate (PET) were screened and PETases involved in PET degradation were characterized. Here, we identified a carboxylesterase Dkca1 of 48.44 kDa molecular mass from Dietzia kunjamensis IITR165 shown to degrade amorphous PET film into bis(2-hydroxyethyl) terephthalate (BHET) and terephthalic acid (TPA) formed 64.35 μM and 35.26 μM, respectively within 96 h at 37 °C as revealed by LC-MS analysis showed significant PET hydrolase activity similar to reported PETases. SEM analysis confirms the surface erosion as cavities and holes. Dkca1 also hydrolysed BHET and dibutyl phthalate (DBP) at a concentration of 1 mM within 3 h indicating its versatility. Fluorescence quenching shows Dkca1 protein has a maximum affinity (Kd) towards BHET (86.55 μM) than DBP (134.2 μM). The protein demonstrated high stability under temperatures above 40 °C and at the pH range of 6.0-9.0. Moreover, Amino acid composition showed that the Dkca1 enzyme belongs to family VII carboxylesterase containing conserved catalytic triad of Ser183-Glu289-His378 with pentapeptide motif GXSAG and an oxyanion hole H103GGG106, sharing 37.47 % and 32.44 % similarity with a PET hydrolase TfCa from Thermobifida fusca and PAE hydrolase CarEW from Bacillus sp. K91, respectively. A docking study revealed that ligand PET, BHET, and DBP showed favourable binding in the catalytic pocket of the Dkca1 protein.

Increased cytoplasmic expression of PETase enzymes in E. coli

BACKGROUND

Depolymerizing polyethylene terephthalate (PET) plastics using enzymes, such as PETase, offers a sustainable chemical recycling route. To enhance degradation, many groups have sought to engineer PETase for faster catalysis on PET and elevated stability. Considerably less effort has been focused toward expressing large quantities of the enzyme, which is necessary for large-scale application and widespread use. In this work, we evaluated several E. coli strains for their potential to produce soluble, folded, and active IsPETase, and moved the production to a benchtop bioreactor. As PETase is known to require disulfide bonds to be functional, we screened several disulfide-bond promoting strains of E. coli to produce IsPETase, FAST-PETase and Hot-PETase.

RESULTS

We found expression in SHuffle T7 Express results in higher active expression of IsPETase compared to standard E. coli production strains such as BL21(DE3), reaching a purified titer of 20 mg enzyme per L of culture from shake flasks using 2xLB medium. We characterized purified IsPETase on 4-nitrophenyl acetate and PET microplastics, showing the enzyme produced in the disulfide-bond promoting host has high activity. Using a complex medium with glycerol and a controlled bioreactor, IsPETase titer reached 104 mg per L for a 46-h culture. FAST-PETase was found to be produced at similar levels in BL21(DE3) or SHuffle T7 Express, with purified production reaching 65 mg per L culture when made in BL21(DE3). Hot-PETase titers were greatest in BL21(DE3) reaching 77 mg per L culture.

CONCLUSIONS

We provide protein expression methods to produce three important PETase variants. Importantly, for IsPETase, changing expression host, medium optimization and movement to a bioreactor resulted in a 50-fold improvement in production amount with a per cell dry weight productivity of 0.45 mgPETase gCDW-1 h-1, which is tenfold greater than that for K. pastoris. We show that the benefit of using SHuffle T7 Express for expression only extends to IsPETase, with FAST-PETase and Hot-PETase better produced and purified from BL21(DE3), which is unexpected given the number of cysteines present. This work represents a systematic evaluation of protein expression and purification conditions for PETase variants to permit further study of these important enzymes.

Heterologous protein exposure and secretion optimization in Mycoplasma pneumoniae

The non-pathogenic Mycoplasma pneumoniae engineered chassis (Mycochassis) has demonstrated the ability to express therapeutic molecules in vitro and to be effective for treatment of lung infectious diseases in in vivo mouse models. However, the expression of heterologous molecules, whether secreted or exposed on the bacterial membrane has not been optimized to ensure sufficient secretion and/or exposure levels to exert a maximum in vivo biological effect. Here, we have improved the currently used secretion signal from MPN142 protein. We found that mutations at P1' position of the signal peptide cleavage site do not abrogate secretion but affect it. Increasing hydrophobicity and mutations at the C-terminal of the signal peptide increases secretion. We tested different lipoprotein signal peptides as possible N-terminal protein anchoring motifs on the Mpn cell surface. Unexpectedly we found that these peptides exhibit variable retention and secretion rates of the protein, with some sequences behaving as full secretion motifs. This raises the question of the biological role of the lipobox motif traditionally thought to anchor membrane proteins without a helical transmembrane domain. These results altogether represent a step forward in chassis optimization, offering different sequences for secretion or membrane retention, which could be used to improve Mycochassis as a delivery vector, and broadening its therapeutic possibilities.

Screening, identification, engineering, and characterization of Bacillus-derived α-amylase for effective tobacco starch degradation

In this study, two high-performing α-amylase-producing strains, CK3-5 and A8-1 were successfully isolated and characterized, which were taxonomically confirmed as Bacillus velezensis through whole-genome sequencing and bioinformatics. Bioinformatic sequence analysis and molecular docking revealed the catalytic triad (Asp173-Glu208-Asp274) essential for α-amylase function. Through metabolic engineering, the recombinant strain BAX-5/PT17amy(A8-1)SP002 was developed, which exhibited the highest α-amylase activity of 1440 U/mL upon fermentation optimization, marking a 9.2-fold enhancement over the wild-type strain A8-1, and it successfully degraded 6 % of the starch in the tobacco leaves within 48 h, while the content of 13 harmful substances, including acetamide, pyridine, and acetonitrile, was reduced by 8.6 % to 25.2 %. This study reveals a novel α-amylase gene from B. velezensis and establishes an efficient expression system in B. amyloliquefaciens, offering valuable insights for industrial α-amylase production.

Bridging the Gap in the Structure-Function Paradigm of Enzymatic PET Degradation-Aromatic Residue Driven Balanced Interactions with Catalytic and Anchoring Subsite

Understanding all parameters contributing to enzyme activity is crucial in enzyme catalysis. For enzymatic PET degradation, this involves examining the formation of the enzyme-PET complex. In IsPETase (WT), a PET-degrading enzyme from Ideonella sakaiensis, mutating two non-catalytic residues (DM) significantly enhances activity. Such mutations, depending on their position in the tertiary structure, fine-tune enzyme function. However, detailed molecular insights into these mutations' structure-function relationship for PET degradation are lacking. This study characterizes IsPETase's catalytic ability compared to WT TfCut2 using molecular dynamics simulations and quantum mechanical methods. We explore the conformational landscape of the enzyme-PET complex and quantify residue-wise interaction energy. Notably, aromatic and hydrophobic residues Tyr, Trp, and Ile in the catalytic subsite S1, and aromatic Phe and polar Asn in the anchoring subsite S3, crucially optimize PET binding. These residues enhance PET specificity over non-aromatic plastics. Our findings suggest that the balance between binding at subsite S1 and subsite S3, which is influenced by cooperative mutations, underlies catalytic activity. This balance shows a positive correlation with experimentally obtained kcat/Km values: WT TfCut2 Collapse

Key Words

• Cooperative effect
• Enzyme catalysis
• IsPETase
• Molecular dynamics
• Mutation

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MESH Headings

• Molecular Dynamics Simulation
• Polyethylene Terephthalates/chemistry
• Polyethylene Terephthalates/metabolism
• Catalytic Domain
• Structure-Activity Relationship
• Burkholderiales/enzymology
• Biocatalysis
• Mutation
• Bacterial Proteins/chemistry
• Bacterial Proteins/metabolism
• Bacterial Proteins/genetics

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Grants

• CRG/2019/002891 DST
• SPG/2022/001350 DST
• SIR/2022/000924 DST
• University of Calicut

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Affiliation(s)

Anjima James Department of Applied Chemistry, Cochin University of Science and Technology, Thrikakkara, Kochi, Kerala, 682 022, India
Anjitha Bhasi Department of Applied Chemistry, Cochin University of Science and Technology, Thrikakkara, Kochi, Kerala, 682 022, India
Susmita De Department of Chemistry, University of Calicut, Calicut University P.O., Malappuram, Kerala, 673 635, India

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A bacteriocin expression platform for targeting pathogenic bacterial species

Bacteriocins are antimicrobial peptides that are naturally produced by many bacteria. They hold great potential in the fight against antibiotic resistant bacteria, including ESKAPE pathogens. Engineered live biotherapeutic products (eLBPs) that secrete bacteriocins can be created to deliver targeted bacteriocin production. Here we develop a modular bacteriocin secretion platform that can be used to express and secrete multiple bacteriocins from non-pathogenic Escherichia coli host strains. As a proof of concept we create Enterocin A (EntA) and Enterocin B (EntB) secreting strains that show strong antimicrobial activity against Enterococcus faecalis and Enterococcus faecium in vitro, and characterise this activity in both solid culture and liquid co-culture. We then develop a Lotka-Volterra model that can be used to capture the interactions of these competitor strains. We show that simultaneous exposure to EntA and EntB can delay Enterococcus growth. Our system has the potential to be used as an eLBP to secrete additional bacteriocins for the targeted killing of pathogenic bacteria.

Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation

Polymer production is rapidly increasing, but there are no large-scale technologies available to effectively mitigate the massive accumulation of these recalcitrant materials. One potential solution is the development of a carbon-neutral polymer life cycle, where microorganisms convert plant biomass to chemicals, which are used to synthesize biodegradable materials that ultimately contribute to the growth of new plants. Realizing a circular carbon life cycle requires the integration of knowledge across microbiology, bioengineering, materials science, and organic chemistry, which itself has hindered large-scale industrial advances. This review addresses the biodegradation status of common synthetic polymers, identifying novel microbes and enzymes capable of metabolizing these recalcitrant materials and engineering approaches to enhance their biodegradation pathways. Design considerations for the next generation of biodegradable polymers are also reviewed, and finally, opportunities to apply findings from lignocellulosic biodegradation to the design and biodegradation of similarly recalcitrant synthetic polymers are discussed.

High-Efficiency Degradation of PET Plastics by Glutathione S-Transferase under Mild Conditions

Plastic pollution is a significant environmental concern globally. Plastics are normally considered chemically inert and resistant to biodegradation. Although many papers have reported enzyme-induced biodegradation of plastics, these studies are primarily limited to enzymes of microbial origin or engineered enzymes. This study reveals that poly(ethylene terephthalate) (PET, ∼6000 Da and 100 kDa) particles and plastic bottle debris (PBD, 24.9 kDa) can be efficiently degraded by a mammal-origin natural phase II metabolic isozyme, glutathione S-transferase (GST), under mild conditions. The degradation efficiency of PET plastics reached 98.9%, with a degradation rate of 2.6 g·L-1·h-1 under ambient or physiological conditions at 1 atm. PET plastics can be degraded by GST with varying environmental or biological factors (i.e., temperature, light irradiation, pH, and presence of humic acid or protein). We suggest a novel mechanism for PET degradation other than hydrolysis, i.e., the mechanism of cleavage and release of PET plastic monomers via nitridation and oxidation. This finding also reveals a novel function of GST, previously thought to only degrade small molecules (<1000 Da). This method has been successfully applied in real human serum samples. Additionally, we have tested and confirmed the ability to degrade PET of a mammal-origin natural digestive enzyme (trypsin) and a human-derived natural metabolic enzyme (CYP450). Overall, our findings provide a potential new route to plastic pollution control and contribute to our understanding of the metabolism and fate of plastics in organisms.

Molecular engineering of PETase for efficient PET biodegradation

The widespread utilization of polyethylene terephthalate (PET) has caused a variety of environmental and health problems. Compared with traditional thermomechanical or chemical PET cycling, the biodegradation of PET may offer a more feasible solution. Though the PETase from Ideonalla sakaiensis (IsPETase) displays interesting PET degrading performance under mild conditions; the relatively low thermal stability of IsPETase limits its practical application. In this study, enzyme-catalysed PET degradation was investigated with the promising IsPETase mutant HotPETase (HP). On this basis, a carbohydrate-binding module from Bacillus anthracis (BaCBM) was fused to the C-terminus of HP to construct the PETase mutant (HLCB) for increased PET degradation. Furthermore, to effectively improve PET accessibility and PET-degrading activity, the truncated outer membrane hybrid protein (FadL) was used to expose PETase and BaCBM on the surface of E. coli (BL21with) to develop regenerable whole-cell biocatalysts (D-HLCB). Results showed that, among the tested small-molecular weight ester compounds (p-nitrophenyl phosphate (pNPP), p-Nitrophenyl acetate (pNPA), 4-Nitrophenyl butyrate (pNPB)), PETase displayed the highest hydrolysing activity against pNPP. HP displayed the highest catalytic activity (1.94 μM(p-NP)/min) at 50 °C and increased longevity at 40 °C. The fused BaCBM could clearly improve the catalytic performance of PETase by increasing the optimal reaction temperature and improving the thermostability. When HLCB was used for PET degradation, the yield of monomeric products (255.7 μM) was ∼25.5 % greater than that obtained after 50 h of HP-catalysed PET degradation. Moreover, the highest yield of monomeric products from the D-HLCB-mediated system reached 1.03 mM. The whole-cell catalyst D-HLCB displayed good reusability and stability and could maintain more than 54.6 % of its initial activity for nine cycles. Finally, molecular docking simulations were utilized to investigate the binding mechanism and the reaction mechanism of HLCB, which may provide theoretical evidence to further increase the PET-degrading activities of PETases through rational design. The proposed strategy and developed variants show potential for achieving complete biodegradation of PET under mild conditions.

Engineered plastic-associated bacteria for biodegradation and bioremediation

The global plastic waste crisis has triggered the development of novel methods for removal of recalcitrant polymers from the environment. Biotechnological approaches have received particular attention due to their potential for enabling sustainable, low-intensity bioprocesses which could also be interfaced with microbial upcycling pathways to support the emerging circular bioeconomy. However, low biodegradation efficiency of solid plastic materials remains a bottleneck, especially at mesophilic conditions required for one-pot degradation and upcycling. A promising strategy used in nature to address this is localisation of plastic-degrading microbes to the plastic surface via biofilm-mediated surface association. This review highlights progress and opportunities in leveraging these naturally occurring mechanisms of biofilm formation and other cell-surface adhesion biotechnologies to co-localise engineered cells to plastic surfaces. We further discuss examples of combining these approaches with extracellular expression of plastic-degrading enzymes to accelerate plastic degradation. Additionally, we review this topic in the context of nano- and microplastics bioremediation and their removal from wastewater and finally propose future research directions for this nascent field.

Towards consolidated bioprocessing of biomass and plastic substrates for semi-synthetic production of bio-poly(ethylene furanoate) (PEF) polymer using omics-guided construction of artificial microbial consortia

Poly(ethylene furanoate) (PEF) plastic is a 100% renewable polyester that is currently being pursued for commercialization as the next-generation bio-based plastic. This is in line with growing demand for circular bioeconomy and new plastics economy that is aimed at minimizing plastic waste mismanagement and lowering carbon footprint of plastics. However, the current catalytic route for the synthesis of PEF is impeded with technical challenges including high cost of pretreatment and catalyst refurbishment. On the other hand, the semi-biosynthetic route of PEF plastic production is of increased biotechnological interest. In particular, the PEF monomers (Furan dicarboxylic acid and ethylene glycol) can be synthesized via microbial-based biorefinery and purified for subsequent catalyst-mediated polycondensation into PEF. Several bioengineering and bioprocessing issues such as efficient substrate utilization and pathway optimization need to be addressed prior to establishing industrial-scale production of the monomers. This review highlights current advances in semi-biosynthetic production of PEF monomers using consolidated waste biorefinery strategies, with an emphasis on the employment of omics-driven systems biology approaches in enzyme discovery and pathway construction. The roles of microbial protein transporters will be discussed, especially in terms of improving substrate uptake and utilization from lignocellulosic biomass, as well as from depolymerized plastic waste as potential bio-feedstock. The employment of artificial bioengineered microbial consortia will also be highlighted to provide streamlined systems and synthetic biology strategies for bio-based PEF monomer production using both plant biomass and plastic-derived substrates, which are important for circular and new plastics economy advances.

Sonogenetics-controlled synthetic designer cells for cancer therapy in tumor mouse models

Bacteria-based therapies are powerful strategies for cancer therapy, yet their clinical application is limited by a lack of tunable genetic switches to safely regulate the local expression and release of therapeutic cargoes. Rapid advances in remote-control technologies have enabled precise control of biological processes in time and space. We developed therapeutically active engineered bacteria mediated by a sono-activatable integrated gene circuit based on the thermosensitive transcriptional repressor TlpA39. Through promoter engineering and ribosome binding site screening, we achieved ultrasound (US)-induced protein expression and secretion in engineered bacteria with minimal noise and high induction efficiency. Specifically, delivered either intratumorally or intravenously, engineered bacteria colonizing tumors suppressed tumor growth through US-irradiation-induced release of the apoptotic protein azurin and an immune checkpoint inhibitor, a nanobody targeting programmed death-ligand 1, in different tumor mouse models. Beyond developing safe and high-performance designer bacteria for tumor therapy, our study illustrates a sonogenetics-controlled therapeutic platform that can be harnessed for bacteria-based precision medicine.

Synthesis of Mesoporous Silica Using the Sol-Gel Approach: Adjusting Architecture and Composition for Novel Applications

The sol-gel chemistry of silica has long been used for manipulating the size, shape, and microstructure of mesoporous silica particles. This manipulation is performed in mild conditions through controlling the hydrolysis and condensation of silicon alkoxide. Compared to amorphous silica particles, the preparation of mesoporous silica, such as MCM-41, using the sol-gel approach offers several unique advantages in the fields of catalysis, medicament, and environment, due to its ordered mesoporous structure, high specific surface area, large pore volume, and easily functionalized surface. In this review, our primary focus is on the latest research related to the manipulation of mesoporous silica architectures using the sol-gel approach. We summarize various structures, including hollow, yolk-shell, multi-shelled hollow, Janus, nanotubular, and 2D membrane structures. Additionally, we survey sol-gel strategies involving the introduction of various functional elements onto the surface of mesoporous silica to enhance its performance. Furthermore, we outline the prospects and challenges associated with mesoporous silica featuring different structures and functions in promising applications, such as high-performance catalysis, biomedicine, wastewater treatment, and CO2 capture.

Recent advances in nanotechnology-based modifications of micro/nano PET plastics for green energy applications

Poly(ethylene terephthalate) (PET) plastic is an omnipresent synthetic polymer in our lives, which causes negative impacts on the ecosystem. It is crucial to take mandatory action to control the usage and sustainable disposal of PET plastics. Recycling plastics using nanotechnology offers potential solutions to the challenges associated with traditional plastic recycling methods. Nano-based degradation techniques improve the degradation process through the influence of catalysts. It also plays a crucial role in enhancing the efficiency and effectiveness of recycling processes and modifying them into value-added products. The modified PET waste plastics can be utilized to manufacture batteries, supercapacitors, sensors, and so on. The waste PET modification methods have massive potential for research, which can play major role in removing post-consumer plastic waste. The present review discusses the effects of micro/nano plastics in terrestrial and marine ecosystems and its impacts on plants and animals. Briefly, the degradation and bio-degradation methods in recent research were explored. The depolymerization methods used for the production of monomers from PET waste plastics were discussed in detail. Carbon nanotubes, fullerene, and graphene nanosheets synthesized from PET waste plastics were delineated. The reuse of nanotechnologically modified PET waste plastics for potential green energy storage products, such as batteries, supercapacitors, and sensors were presented in this review.

New combined absorption/1H NMR method for qualitative and quantitative analysis of PET degradation products

Poly(ethylene terephthalate) (PET) is a very valuable and beneficial material for industrial purposes, with various different applications. Due to the high annual production volume of over 50 million tons worldwide and the indiscriminate disposal by consumers, the polymers accumulate in the environment, causing negative effects on various ecosystems. Biodegradation via suitable enzymes represents a promising approach to combat the plastic waste issue so validated methods are required to measure the efficiency and efficacy of these enzymes. PETase and MHETase from Ideonella sakaiensis are suitable enzymes needed in combination to completely degrade PET into its environmentally friendly monomers. In this project, we compare and combine a previously described bulk absorbance measurement method with a newly established 1H NMR analysis method of the PET degradation products mono(2-hydroxyethyl) terephthalic acid, bis(2-hydroxyethyl) terephthalic acid and terephthalic acid. Both were optimized regarding different solvents, pH values and drying processes. The accuracy of the measurements can be confirmed with sensitivity limits of 2.5-5 µM for the absorption method and 5-10 µM for the 1H NMR analysis. The combination of the described methods therefore allows a quantitative analysis by using bulk absorption coupled with a qualitative analysis through 1H NMR. The methods established in our work can potentially contribute to the development of suitable recycling strategies of PET using recombinant enzymes.

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.

Insight on recently discovered PET polyester-degrading enzymes, thermostability and activity analyses

The flexibility and the low production costs offered by plastics have made them crucial to society. Unfortunately, due to their resistance to biological degradation, plastics remain in the environment for an extended period of time, posing a growing risk to life on earth. Synthetic treatments of plastic waste damage the environment and may cause damage to human health. Bacterial and fungal isolates have been reported to degrade plastic polymers in a logistic safe approach with the help of their microbial cell enzymes. Recently, the bacterial strain Ideonella sakaiensis (201-F6) was discovered to break down and assimilate polyethylene terephthalate (PET) plastic via metabolic processes at 30 °C to 37 °C. PETase and MHETase enzymes help the bacterium to accomplish such tremendous action at lower temperatures than previously discovered enzymes. In addition to functioning at low temperatures, the noble bacterium's enzymes have amazing qualities over pH and PET plastic degradation, including a shorter period of degradation. It has been proven that using the enzyme PETase, this bacterium hydrolyzes the ester linkages of PET plastic, resulting in production of terephthalic acid (TPA), nontoxic compound and mono-2-hydroxyethyl (MHET), along with further depolymerization of MHET to release ethylene glycogen (EG) and terephthalic acid (TPA) by the second enzyme MHETase. Enzymatic plastic degradation has been proposed as an environmentally friendly and long-term solution to plastic waste in the environment. As a result, this review focuses on the enzymes involved in hydrolyzing PET plastic polymers, as well as some of the other microorganisms involved in plastic degradation.

Signal peptide independent secretion of bifunctional dual-hydrolase to enhance the bio-depolymerization of polyethylene terephthalate

The use of polyethylene terephthalate (PET) results in a significant amount of plastic waste, which poses a threat to the environment and human health. Dual-enzyme system is promising candidate for PET depolymerization. However, its production in Escherichia coli is challenging, especially for secretory expression. Herein, a novel bifunctional dual-enzyme, TfH-FPE, was constructed through fusion of FAST-PETase and TfH. TfH modifies cell membrane permeability via phospholipid degradation, thus facilitating the secretion of TfH-FPE into the medium. After systematic optimization, purified secreted TfH-FPE reached 104 ± 5.2 mg/L, which is 32.5-fold higher than that of the secreted enzyme using a signal peptide. TfH-FPE exhibits remarkable PET depolymerization capacity compared to FAST-PETase, releasing 6-fold more product than FAST-PETase and 2-fold more product than an equimolar enzyme mixture. Collectively, this study explores a novel secretory approach for efficient production of TfH-FPE and provides a valuable tool to promote PET bio-depolymerization via multi-enzyme cascades.

Production of Optically Pure (S)-3-Hydroxy-γ-butyrolactone from d-Xylose Using Engineered Escherichia coli

Biocatalysis has advantages in asymmetric synthesis due to the excellent stereoselectivity of enzymes. The present study established an efficient biosynthesis pathway for optically pure (S)-3-hydroxy-γ-butyrolactone [(S)-3HγBL] production using engineered Escherichia coli. We mimicked the 1,2,4-butanetriol biosynthesis route and constructed a five-step pathway consisting of d-xylose dehydrogenase, d-xylonolactonase, d-xylonate dehydratase, 2-keto acid decarboxylase, and aldehyde dehydrogenase. The engineered strain harboring the five enzymes could convert d-xylose to 3HγBL with glycerol as the carbon source. Stereochemical analysis by chiral GC proved that the microbially synthesized product was a single isomer, and the enantiomeric excess (ee) value reached 99.3%. (S)-3HγBL production was further enhanced by disrupting the branched pathways responsible for d-xylose uptake and intermediate reduction. Fed-batch fermentation of the best engineered strain showed the highest (S)-3HγBL titer of 3.5 g/L. The volumetric productivity and molar yield of (S)-3HγBL on d-xylose reached 50.6 mg/(L·h) and 52.1%, respectively. The final fermentation product was extracted, purified, and confirmed by NMR. This process utilized renewable d-xylose as the feedstock and offered an alternative approach for the production of the valuable chemical.

Membrane vesicle engineering with "à la carte" bacterial-immunogenic molecules for organism-free plant vaccination

The United Nations heralds a world population exponential increase exceeding 9.7 billion by 2050. This poses the challenge of covering the nutritional needs of an overpopulated world by the hand of preserving the environment. Extensive agriculture practices harnessed the employment of fertilizers and pesticides to boost crop productivity and prevent economic and harvest yield losses attributed to plagues and diseases. Unfortunately, the concomitant hazardous effects stemmed from such agriculture techniques are cumbersome, that is, biodiversity loss, soils and waters contaminations, and human and animal poisoning. Hence, the so-called 'green agriculture' research revolves around designing novel biopesticides and plant growth-promoting bio-agents to the end of curbing the detrimental effects. In this field, microbe-plant interactions studies offer multiple possibilities for reshaping the plant holobiont physiology to its benefit. Along these lines, bacterial extracellular membrane vesicles emerge as an appealing molecular tool to capitalize on. These nanoparticles convey a manifold of molecules that mediate intricate bacteria-plant interactions including plant immunomodulation. Herein, we bring into the spotlight bacterial extracellular membrane vesicle engineering to encase immunomodulatory effectors into their cargo for their application as biocontrol agents. The overarching goal is achieving plant priming by deploying its innate immune responses thereby preventing upcoming infections.

Enzyme selection, optimization, and production toward biodegradation of post-consumer poly(ethylene terephthalate) at scale

Poly(ethylene terephthalate) (PET) is one of the world's most widely used polyester plastics. Due to its chemical stability, PET is extremely difficult to hydrolyze in a natural environment. Recent discoveries in new polyester hydrolases and breakthroughs in enzyme engineering strategies have inspired enormous research on biorecycling of PET. This study summarizes our research efforts toward large-scale, efficient, and economical biodegradation of post-consumer waste PET, including PET hydrolase selection and optimization, high-yield enzyme production, and high-capacity enzymatic degradation of post-consumer waste PET. First, genes encoding PETase and MHETase from Ideonella sakaiensis and the ICCG variant of leaf-branch compost cutinase (LCCICCG ) were codon-optimized and expressed in Escherichia coli BL21(DE3) for high-yield production. To further lower the enzyme production cost, a pelB leader sequence was fused to LCCICCG so that the enzyme can be secreted into the medium to facilitate recovery. To help bind the enzyme on the hydrophobic surface of PET, a substrate-binding module in a polyhydroxyalkanoate depolymerase from Alcaligenes faecalis (PBM) was fused to the C-terminus of LCCICCG . The resulting four different LCCICCG variants (LCC, PelB-LCC, LCC-PBM, and PelB-LCC-PBM), together with PETase and MHETase, were compared for PET degradation efficiency. A fed-batch fermentation process was developed to produce the target enzymes up to 1.2 g L-1 . Finally, the best enzyme, PelB-LCC, was selected and used for the efficient degradation of 200 g L-1 recycled PET in a well-controlled, stirred-tank reactor. The results will help develop an economical and scalable biorecycling process toward a circular PET economy.

Computation-Based Design of Salt Bridges in PETase for Enhanced Thermostability and Performance for PET Degradation

Polyethylene terephthalate (PET) is one of the most widely used plastics, and the accumulation of PET poses a great threat to the environment. IsPETase can degrade PET rapidly at moderate temperatures, but its application is greatly limited by the low stability. Herein, molecular dynamics (MD) simulations combined with a sequence alignment strategy were adopted to introduce salt bridges into the flexible region of IsPETase to improve its thermal stability. In the designed variants, the Tm values of IsPETaseI168R/S188D and IsPETaseI168R/S188E were 7.4 and 8.7 °C higher than that of the wild type, respectively. The release of products degraded by IsPETaseI168R/S188E was 4.3 times that of the wild type. Tertiary structure characterization demonstrated that the structure of the variants IsPETaseI168R/S188D and IsPETaseI168R/S188E became more compact. Extensive MD simulations verified that a stable salt bridge was formed between the residue R168 and D186 in IsPETaseI168R/S188D , while in IsPETaseI168R/S188E an R168-D186-E188 salt bridge network was observed. These results confirmed that the proposed computation-based salt bridge design strategy could efficiently generate variants with enhanced thermal stability for the long-term degradation of PET, which would be helpful for the design of enzymes with improved stability.

Identification and characterisation of a major outer membrane protein from Methylacidiphilum fumariolicum SolV

The outer membrane (OM) protects Gram-negative bacteria against a hostile environment. The proteins embedded in the OM fulfil a number of tasks that are crucial to the bacterial cell. In this study, we identified and characterised a major outer membrane protein (WP_009059494) from Methylacidiphilum fumariolicum SolV. PRED-TMBB and AlphaFold2 predicted this protein to form a porin with a β-barrel structure consisting of ten antiparallel β-sheets and with a small amphipathic N-terminal α-helix in the periplasm. We purified soluble recombinant protein WP_009059494 from E. coli using Tris-HCl buffer with SDS. Antibodies were raised against two peptides in the two large extracellular loops of protein WP_009059494 and immunogold localisation showed this protein to be mainly present in the OM of strain SolV. In addition, this protein is tightly associated with the OM, and is resistant to extraction. Only a small amount can be isolated from the cell envelope using harsh conditions (SDS and boiling). Despite this resistance to extraction, WP_009059494 most likely is an outer membrane protein. A regular lattice could not be detected by negative staining TEM of strain SolV and isolated protein WP_009059494. Considering the specific ecological niche of strain SolV living in a geothermal environment with low pH and high temperatures, this major protein WP_009059494 may act as barrier to resist the extreme conditions found in its natural environment. In addition, we found an absence of the BamB, BamC and BamE proteins of the canonical BAM complex, in Methylacidiphilum and Methylacidimicrobium species. This suggests that these bacteria use a simple BAM complex for folding and transport of OM proteins.

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.

Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology

In microbial biotechnology, there is a constant demand for functional peptides to give new functionality to engineered proteins to address problems such as direct delivery of functional proteins into bacterial cells, enhanced protein solubility during the expression of recombinant proteins, and efficient protein secretion from bacteria. To tackle these critical issues, we selected three types of functional small peptides: cell-penetrating peptides (CPPs) enable the delivery of diverse cargoes into bacterial cytoplasm for a variety of purposes, protein-solubilizing peptide tags demonstrate remarkable efficiency in solubilizing recombinant proteins without folding interference, and signal peptides play a key role in enabling the secretion of recombinant proteins from bacterial cells. In this review, we introduced these three functional small peptides that offer effective solutions to address emerging problems in microbial biotechnology. Additionally, we summarized various engineering efforts aimed at enhancing the activity and performance of these peptides, thereby providing valuable insights into their potential for further applications.

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.

Harnessing extremophilic carboxylesterases for applications in polyester depolymerisation and plastic waste recycling

The steady growth in industrial production of synthetic plastics and their limited recycling have resulted in severe environmental pollution and contribute to global warming and oil depletion. Currently, there is an urgent need to develop efficient plastic recycling technologies to prevent further environmental pollution and recover chemical feedstocks for polymer re-synthesis and upcycling in a circular economy. Enzymatic depolymerization of synthetic polyesters by microbial carboxylesterases provides an attractive addition to existing mechanical and chemical recycling technologies due to enzyme specificity, low energy consumption, and mild reaction conditions. Carboxylesterases constitute a diverse group of serine-dependent hydrolases catalysing the cleavage and formation of ester bonds. However, the stability and hydrolytic activity of identified natural esterases towards synthetic polyesters are usually insufficient for applications in industrial polyester recycling. This necessitates further efforts on the discovery of robust enzymes, as well as protein engineering of natural enzymes for enhanced activity and stability. In this essay, we discuss the current knowledge of microbial carboxylesterases that degrade polyesters (polyesterases) with focus on polyethylene terephthalate (PET), which is one of the five major synthetic polymers. Then, we briefly review the recent progress in the discovery and protein engineering of microbial polyesterases, as well as developing enzyme cocktails and secreted protein expression for applications in the depolymerisation of polyester blends and mixed plastics. Future research aimed at the discovery of novel polyesterases from extreme environments and protein engineering for improved performance will aid developing efficient polyester recycling technologies for the circular plastics economy.

Revealing the key gene involved in bioplastic degradation from superior bioplastic degrader Bacillus sp. JY35

The use of bioplastics, which can alleviate environmental pollution caused by non-degradable bioplastics, has received attention. As there are many types of bioplastics, method that can treat them simultaneously is important. Therefore, Bacillus sp. JY35 which can degrade different types of bioplastics, was screened in previous study. Most types of bioplastics, such as polyhydroxybutyrate (PHB), (P(3HB-co-4HB)), poly(butylene adipate-co-terephthalate) (PBAT), polybutylene succinate (PBS), and polycaprolactone (PCL), can be degraded by esterase family enzymes. To identify the genes that are involved in bioplastic degradation, analysis with whole-genome sequencing was performed. Among the many esterase enzymes, three carboxylesterase and one triacylglycerol lipase were identified and selected based on previous studies. Esterase activity using p-nitrophenyl substrates was measured, and the supernatant of JY35_02679 showed strong emulsion clarification activity compared with others. In addition, when recombinant E. coli was applied to the clear zone test, only the JY35_02679 gene showed activity in the clear zone test with bioplastic containing solid cultures. Further quantitative analysis showed 100 % PCL degradation at 7 days and 45.7 % PBS degradation at 10 days. We identified a gene encoding a bioplastic-degrading enzyme in Bacillus sp. JY35 and successfully expressed the gene in heterologous E. coli, which secreted esterases with broad specificity.

Functional tailoring of a PET hydrolytic enzyme expressed in Pichia pastoris

Using enzymes to hydrolyze and recycle poly(ethylene terephthalate) (PET) is an attractive eco-friendly approach to manage the ever-increasing PET wastes, while one major challenge to realize the commercial application of enzyme-based PET degradation is to establish large-scale production methods to produce PET hydrolytic enzyme. To achieve this goal, we exploited the industrial strain Pichia pastoris to express a PET hydrolytic enzyme from Caldimonas taiwanensis termed CtPL-DM. In contrast to the protein expressed in Escherichia coli, CtPL-DM expressed in P. pastoris is inactive in PET degradation. Structural analysis indicates that a putative N-glycosylation site N181 could restrain the conformational change of a substrate-binding Trp and hamper the enzyme action. We thus constructed N181A to remove the N-glycosylation and found that the PET hydrolytic activity of this variant was restored. The performance of N181A was further enhanced via molecular engineering. These results are of valuable in terms of PET hydrolytic enzyme production in industrial strains in the future.

A high-throughput expression and screening platform for applications-driven PETase engineering

The environmental consequences of plastic waste have impacted all kingdoms of life in terrestrial and aquatic ecosystems. However, as the burden of plastic pollution has increased, microbes have evolved to utilize anthropogenic polymers as nutrient sources. Of depolymerase enzymes, the best characterized is PETase, which hydrolyzes aromatic polyesters. PETase engineering has made impressive progress in recent years; however, further optimization of engineered PETase toward industrial application has been limited by lower throughput techniques used in protein purification and activity detection. Here, we address these deficiencies through development of a higher-throughput PETase engineering platform. Secretory expression via YebF tagging eliminates lysis and purification steps, facilitating production of large mutant libraries. Fluorescent detection of degradation products permits rapid screening of depolymerase activity in microplates as opposed to serial chromatographic methods. This approach enabled development of more stable PETase, semi-rational (SR) PETase variant containing previously unpublished mutations. SR-PETase releases 1.9-fold more degradation products and has up to 7.4-fold higher activity than wild-type PETase over 10 days at 40°C. These methods can be adapted to a variety of chemical environments, enabling screening of PETase mutants in applications-relevant conditions. Overall, this work promises to facilitate advancements in PETase engineering toward industrial depolymerization of plastic waste.

Complete Depolymerization of PET Wastes by an Evolved PET Hydrolase from Directed Evolution

PETase displays great potential in PET depolymerization. Directed evolution has been limited to engineer PETase due to the lack of high-throughput screening assay. In this study, a novel fluorescence-based high-throughput screening assay employing a newly designed substrate, bis (2-hydroxyethyl) 2-hydroxyterephthalate (termed BHET-OH), was developed for PET hydrolases. The best variant DepoPETase produced 1407-fold more products towards amorphous PET film at 50 °C and showed a 23.3 °C higher T_m value than the PETase WT. DepoPETase enabled complete depolymerization of seven untreated PET wastes and 19.1 g PET waste (0.4 % W_enzyme /W_PET ) in liter-scale reactor, suggesting that it is a potential candidate for industrial PET depolymerization processes. The molecular dynamic simulations revealed that the distal substitutions stabilized the loops around the active sites and transmitted the stabilization effect to the active sites through enhancing inter-loop interactions network.

Repurposing of waste PET by microbial biotransformation to functionalized materials for additive manufacturing

Plastic waste is an outstanding environmental thread. Poly(ethylene terephthalate) (PET) is one of the most abundantly produced single-use plastics worldwide, but its recycling rates are low. In parallel, additive manufacturing is a rapidly evolving technology with wide-ranging applications. Thus, there is a need for a broad spectrum of polymers to meet the demands of this growing industry and address post-use waste materials. This perspective article highlights the potential of designing microbial cell factories to upcycle PET into functionalized chemical building blocks for additive manufacturing. We present the leveraging of PET hydrolyzing enzymes and rewiring the bacterial C2 and aromatic catabolic pathways to obtain high-value chemicals and polymers. Since PET mechanical recycling back to original materials is cost-prohibitive, the biochemical technology is a viable alternative to upcycle PET into novel 3D printing materials, such as replacements for acrylonitrile butadiene styrene. The presented hybrid chemo-bio approaches potentially enable the manufacturing of environmentally friendly degradable or higher-value high-performance polymers and composites and their reuse for a circular economy.

ONE-SENTENCE SUMMARY

Biotransformation of waste PET to high-value platform chemicals for additive manufacturing.

Recent Advances in the Chemobiological Upcycling of Polyethylene Terephthalate (PET) into Value-Added Chemicals

Polyethylene terephthalate (PET) is a plastic material commonly applied to beverage packaging used in everyday life. Owing to PET's versatility and ease of use, its consumption has continuously increased, resulting in considerable waste generation. Several physical and chemical recycling processes have been developed to address this problem. Recently, biological upcycling is being actively studied and has come to be regarded as a powerful technology for overcoming the economic issues associated with conventional recycling methods. For upcycling, PET should be degraded into small molecules, such as terephthalic acid and ethylene glycol, which are utilized as substrates for bioconversion, through various degradation processes, including gasification, pyrolysis, and chemical/biological depolymerization. Furthermore, biological upcycling methods have been applied to biosynthesize value-added chemicals, such as adipic acid, muconic acid, catechol, vanillin, and glycolic acid. In this review, we introduce and discuss various degradation methods that yield substrates for bioconversion and biological upcycling processes to produce value-added biochemicals. These technologies encourage a circular economy, which reduces the amount of waste released into the environment.

Can wood-feeding termites solve the environmental bottleneck caused by plastics? A critical state-of-the-art review

The abundance of synthetic polymers has become an ever-increasing environmental threat in the world. The excessive utilization of plastics leads to the accumulation of such recalcitrant pollutants in the environment. For example, during the COVID-19 pandemic, unprecedented demand for personal protective equipment (PPE) kits, face masks, and gloves made up of single-use items has resulted in the massive generation of plastic biomedical waste. As secondary pollutants, microplastic particles (<5 mm) are derived from pellet loss and degradation of macroplastics. Therefore, urgent intervention is required for the management of these hazardous materials. Physicochemical approaches have been employed to degrade synthetic polymers, but these approaches have limited efficiency and cause the release of hazardous metabolites or by-products into the environment. Therefore, bioremediation is a proper option as it is both cost-efficient and environmentally friendly. On the other hand, plants evolved lignocellulose to be resistant to destruction, whereas insects, such as wood-feeding termites, possess diverse microorganisms in their guts, which confer physiological and ecological benefits to their host. Plastic and lignocellulose polymers share a number of physical and chemical properties, despite their structural and recalcitrance differences. Among these similarities are a hydrophobic nature, a carbon skeleton, and amorphous/crystalline regions. Compared with herbivorous mammals, lignocellulose digestion in termites is accomplished at ordinary temperatures. This unique characteristic has been of great interest for the development of a plastic biodegradation approach by termites and their gut symbionts. Therefore, transferring knowledge from research on lignocellulosic degradation by termites and their gut symbionts to that on synthetic polymers has become a new research hotspot and technological development direction to solve the environmental bottleneck caused by synthetic plastic polymers.

Biodegradation of different PET variants from food containers by Ideonella sakaiensis

The accumulation of macro-, micro- and nano-plastic wastes in the environment is a major global concern, as these materials are resilient to degradation processes. However, microorganisms have evolved their own biological means to metabolize these petroleum-derived polymers, e.g., Ideonella sakaiensis has recently been found to be capable of utilizing polyethylene terephthalate (PET) as its sole carbon source. This study aims to prove its potential capacity to biodegrade two commercial PET materials, obtained from food packaging containers. Plastic pieces of different crystallinity were simultaneously introduced to Ideonella sakaiensis during a seven-week lasting investigation. Loss in weight, appearance of plastics, as well as growth of Ideonella sakaiensis—through quantitative real-time PCR—were determined. Both plastics were found enzymatically attacked in a two-stage degradation process, reaching biodegradation capacities of up to 96%. Interestingly, the transparent, high crystallinity PET was almost fully degraded first, followed by the colored low-crystallinity PET. Results of quantitative real-time PCR-based gene copy numbers were found in line with experimental results, thus underlining its potential of this method to be applied in future studies with Ideonella sakaiensis.

Critical Review on the Progress of Plastic Bioupcycling Technology as a Potential Solution for Sustainable Plastic Waste Management

Plastic production worldwide has doubled in the last two decades and is expected to reach a four-fold increase by 2050. The durability of plastic makes them a perfect material for many applications, but it is also a key limitation to their end-of-life management. The current plastic lifecycle is far from circular, with only 13% being collected for recycling and 9% being successfully recycled, indicating the failure of current recycling technology. The remaining plastic waste streams are thus incinerated, landfilled, or worse, mismanaged, leading to them leaking into the environment. To promote plastic circularity, keeping material in the loop is a priority and represents a more sustainable solution. This can be achieved through the reuse of plastic items, or by using plastic waste as a resource for new materials, instead of discarding them as waste. As the discovery of plastic-degrading/utilizing microorganisms and enzymes has been extensively reported recently, the possibility of developing biological plastic upcycling processes is opening up. An increasing amount of studies have investigated the use of plastic as a carbon source for biotechnological processes to produce high-value compounds such as bioplastics, biochemicals, and biosurfactants. In the current review, the advancements in fossil-based plastic bio- and thermochemical upcycling technologies are presented and critically discussed. In particular, we highlight the developed (bio)depolymerization coupled with bioconversion/fermentation processes to obtain industrially valuable products. This review is expected to contribute to the future development and scale-up of effective plastic bioupcycling processes that can act as a drive to increase waste removal from the environment and valorize post-consumer plastic streams, thus accelerating the implementation of a circular (plastic) economy.

Production of PETase by engineered Yarrowia lipolytica for efficient poly(ethylene terephthalate) biodegradation

There has been a growing interest in poly(ethylene terephthalate) PET degradation studies in the last few years due to its widespread use and large-scale plastic waste accumulation in the environment. One of the most promising enzymatic methods in the context of PET degradation is the use of PETase from Ideonella sakaiensis, which has been reported to be an efficient enzyme for hydrolysing ester bonds in PET. In our study, we expressed a codon-optimized PETase gene in the yeast Yarrowia lipolytica. The obtained strain was tested for its ability to degrade PET directly in culture, and a screening of different supplements that might raise the level of PET hydrolysis was performed. We also carried out long-term cultures with PET film, the surface of which was examined by scanning electron microscopy. The efficiency of PET degradation was tested based on the concentration of degradation products released, and the results showed that supplementation of the culture with olive oil resulted in 66 % higher release of terephthalic acid into the medium compared to the mutant culture without supplementation. The results indicate the possibility of ethylene glycol uptake by both strains, and, additionally, the PETase produced by the newly engineered strain hydrolyses MHET. The structure of the PET film after culture with the modified strain, meanwhile, had numerous surface defects, cracks, and deformations.

An Overview into Polyethylene Terephthalate (PET) Hydrolases and Efforts in Tailoring Enzymes for Improved Plastic Degradation

Plastic or microplastic pollution is a global threat affecting ecosystems, with the current generation reaching as much as 400 metric tons per/year. Soil ecosystems comprising agricultural lands act as microplastics sinks, though the impact could be unexpectedly more far-reaching. This is troubling as most plastic forms, such as polyethylene terephthalate (PET), formed from polymerized terephthalic acid (TPA) and ethylene glycol (EG) monomers, are non-biodegradable environmental pollutants. The current approach to use mechanical, thermal, and chemical-based treatments to reduce PET waste remains cost-prohibitive and could potentially produce toxic secondary pollutants. Thus, better remediation methods must be developed to deal with plastic pollutants in marine and terrestrial environments. Enzymatic treatments could be a plausible avenue to overcome plastic pollutants, given the near-ambient conditions under which enzymes function without the need for chemicals. The discovery of several PET hydrolases, along with further modification of the enzymes, has considerably aided efforts to improve their ability to degrade the ester bond of PET. Hence, this review emphasizes PET-degrading microbial hydrolases and their contribution to alleviating environmental microplastics. Information on the molecular and degradation mechanisms of PET is also highlighted in this review, which might be useful in the future rational engineering of PET-hydrolyzing enzymes.

Directed Immobilization of PETase on Mesoporous Silica Enables Sustained Depolymerase Activity in Synthetic Wastewater Conditions

Microplastic accumulation in terrestrial and aquatic environments is a growing environmental challenge. Biodegradation has shown promise as an intervention strategy for reducing the spread of microplastics. The wastewater treatment system is a key intervention point in microplastic biodegradation due to its pivotal role in the water cycle at the interface between human activity and the environmental. However, the best characterized microplastic degradation enzyme, PETase, lacks the stability to perform at scale in wastewater treatment. In this work, we show that genetic fusion of PETase to a silica binding peptide enables directed immobilization of the enzyme onto silica nanoparticles. PETase activity in simulated wastewater conditions is quantified by linear regression from time zero to the time of maximum fluorescence of a fluorescent oxidized product of PETase degradation of PET microfibers. Mesoporous silica is shown to be a superior support material to nonporous silica. The resulting biocatalytic nanomaterial has up to 2.5-fold enhanced stability and 6.2-fold increased activity compared to free enzyme in unbuffered, 40 °C simulated influent (ionic strength ∼15 mM). In unbuffered, 40 °C simulated effluent (ionic strength ∼700 μM), reaction velocity and overall catalytic activity were increased by the biocatalytic material 2.1-fold relative to free PETase. All reactions were performed in 0.2 mL volumes, and enzyme concentrations were normalized across both free and immobilized samples to 9 μg/mL. Site-directed mutagenesis is shown to be a complementary technique to directed immobilization, which may aid in optimization of the biomaterial for wastewater applications. PETase stabilization in application-relevant environments as shown here enables progress toward application of PETase for microplastic biodegradation in wastewater treatment.

Overexpression and kinetic analysis of Ideonella sakaiensis PETase for polyethylene terephthalate (PET) degradation

Ideonella sakaiensis PET hydrolase (IsPETase) is a well-characterized enzyme for effective PET biodegradation. However, the low soluble expression level of the enzyme hampers its practical implementation in the biodegradation of PET. Herein, the expression of IsPETase^Mut, one of the most active mutants of IsPETase obtained so far, was systematically explored in E. coli by adopting a series of strategies. A notable improvement of soluble IsPETase^Mut was observed by using chaperon co-expression and fusion expression systems. Under the optimized conditions, GroEL/ES co-expression system yielded 75 ± 3.4 mg·L^-1 purified soluble IsPETase^Mut (GroEL/ES), and NusA fusion expression system yielded 80 ± 3.7 mg·L^-1 purified soluble NusA-IsPETase^Mut, which are 12.5- and 4.6-fold, respectively, higher than its commonly expression in E. coli. The two purified enzymes were further characterized. The results showed that IsPETase^Mut (GroEL/ES) displayed the same catalytic behavior as IsPETase^Mut, while the fusion of NusA conferred new enzymatic properties to IsPETase^Mut. Although NusA-IsPETase^Mut displayed a lower initial hydrolysis capacity than IsPETase^Mut, it showed a 1.4-fold higher adsorption constant toward PET. Moreover, the product inhibition effect of terephthalic acid (TPA) on IsPETase was reduced with NusA-IsPETase^Mut. Taken together, the latter two catalytic properties of NusA-IsPETase^Mut are more likely to contribute to the enhanced product release by NusA-IsPETase^Mut PET degradation for two weeks.

Integration of Multiple Phage Attachment Sites System to Create the Chromosomal T7 System for Protein Production in Escherichia coli Nissle 1917

Escherichia coli Nissle 1917 (EcN) is a probiotic used to treat gastrointestinal diseases. The probiotic and endotoxin-free characteristics of EcN support its potential to be developed into a microbial expression system. With this aim, in this study, the powerful T7 expression system was constructed in the cryptic plasmid-free EcN (EcNP) to generate the T7 expression host ENL6P. The concept of multiple copies of gene expression cassettes regulated by the chromosomal T7 promoter was promoted due to plasmid instability issues with protein production in ENL6P. The integration of multiple phage attachment sites (IMPACT) system, which combined Cre-lox72, CRIM, and lambda red recombinase systems, was designed to simplify the manipulation and achieve the multiple φ80 bacterial attachment sites (attB) in ENL6P to generate the new strain ENL6PP4 with four φ80 attB sites. The strain can simultaneously integrate four copies of gene expression cassettes in the chromosome to produce recombinant proteins. The IMPACT systems incorporated several tools in gene editing to rapidly achieve more robust and stable microbial strains for research and various industrial applications.