1
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Han H, Song P, Jiang Y, Fan J, Khan A, Liu P, Mašek O, Li X. Biochar immobilized hydrolase degrades PET microplastics and alleviates the disturbance of soil microbial function via modulating nitrogen and phosphorus cycles. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134838. [PMID: 38850944 DOI: 10.1016/j.jhazmat.2024.134838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/07/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
Microplastics (MPs) pose an emerging threat to soil ecological function, yet effective solutions remain limited. This study introduces a novel approach using magnetic biochar immobilized PET hydrolase (MB-LCC-FDS) to degrade soil polyethylene terephthalate microplastics (PET-MPs). MB-LCC-FDS exhibited a 1.68-fold increase in relative activity in aquatic solutions and maintained 58.5 % residual activity after five consecutive cycles. Soil microcosm experiment amended with MB-LCC-FDS observed a 29.6 % weight loss of PET-MPs, converting PET into mono(2-hydroxyethyl) terephthalate (MHET). The generated MHET can subsequently be metabolized by soil microbiota to release terephthalic acid. The introduction of MB-LCC-FDS shifted the functional composition of soil microbiota, increasing the relative abundances of Microbacteriaceae and Skermanella while reducing Arthobacter and Vicinamibacteraceae. Metagenomic analysis revealed that MB-LCC-FDS enhanced nitrogen fixation, P-uptake and transport, and organic-P mineralization in PET-MPs contaminated soil, while weakening the denitrification and nitrification. Structural equation model indicated that changes in soil total carbon and Simpson index, induced by MB-LCC-FDS, were the driving factors for soil carbon and nitrogen transformation. Overall, this study highlights the synergistic role of magnetic biochar-immobilized PET hydrolase and soil microbiota in degrading soil PET-MPs, and enhances our understanding of the microbiome and functional gene responses to PET-MPs and MB-LCC-FDS in soil systems.
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Affiliation(s)
- Huawen Han
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Peizhi Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu Province 730000, China; State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuchao Jiang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Jingwen Fan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu Province 730000, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Pu Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Ondřej Mašek
- UK Biochar Research Centre, School of GeoSciences, University of Edinburgh, Crew Building, King's Buildings, Edinburgh EH9 3FF, United Kingdom.
| | - Xiangkai Li
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu Province 730000, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu Province 730000, China.
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2
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Han Z, Nina MRH, Zhang X, Huang H, Fan D, Bai Y. Discovery and characterization of two novel polyethylene terephthalate hydrolases: One from a bacterium identified in human feces and one from the Streptomyces genus. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134532. [PMID: 38749251 DOI: 10.1016/j.jhazmat.2024.134532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Polyethylene terephthalate (PET) is widely used for various industrial applications. However, owing to its extremely slow breakdown rate, PET accumulates as plastic trash, which negatively affects the environment and human health. Here, we report two novel PET hydrolases: PpPETase from Pseudomonas paralcaligenes MRCP1333, identified in human feces, and ScPETase from Streptomyces calvus DSM 41452. These two enzymes can decompose various PET materials, including semicrystalline PET powders (Cry-PET) and low-crystallinity PET films (gf-PET). By structure-guided engineering, two variants, PpPETaseY239R/F244G/Y250G and ScPETaseA212C/T249C/N195H/N243K were obtained that decompose Cry-PET 3.1- and 1.9-fold faster than their wild-type enzymes, respectively. The co-expression of ScPETase and mono-(2-hydroxyethyl) terephthalate hydrolase from Ideonella sakaiensis (IsMHETase) resulted in 1.4-fold more degradation than the single enzyme system. This engineered strain degraded Cry-PET and gf-PET by more than 40% and 6%, respectively, after 30 d. The concentrations of terephthalic acid (TPA) in the Cry-PET and gf-PET degradation products were 37.7% and 25.6%, respectively. The discovery of these two novel PET hydrolases provides opportunities to create more powerful biocatalysts for PET biodegradation.
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Affiliation(s)
- Zhengyang Han
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Mario Roque Huanca Nina
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoyan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Hanyao Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Daidi Fan
- Shaanxi R&D Centre of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yunpeng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China.
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3
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Wang C, Long R, Lin X, Liu W, Zhu L, Jiang L. Development and characterization of a bacterial enzyme cascade reaction system for efficient and stable PET degradation. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134480. [PMID: 38703683 DOI: 10.1016/j.jhazmat.2024.134480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/15/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
The widespread use of polyethylene terephthalate (PET) in various industries has led to a surge in microplastics (MPs) pollution, posing a significant threat to ecosystems and human health. To address this, we have developed a bacterial enzyme cascade reaction system (BECRS) that focuses on the efficient degradation of PET. This system harnesses the Escherichia coli (E. coli) surface to display CsgA protein, which forms curli fibers, along with the carbohydrate-binding module 3 (CBM3) and PETases, to enhance the adsorption and degradation of PET. The study demonstrated that the BECRS achieved a notable PET film degradation rate of 3437 ± 148 μg/(d*cm²), with a degradation efficiency of 21.40% for crystalline PET MPs, and the degradation products were all converted to TPA. The stability of the system was evidenced by retaining over 80% of its original activity after multiple uses and during one month of storage. Molecular dynamics simulations confirmed that the presence of CsgA did not interfere with the enzymatic activity of PETases. This BECRS represents a significant step forward in the biodegradation of PET, particularly microplastics, offering a practical and sustainable solution for environmental pollution control.
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Affiliation(s)
- Chengyong Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Rui Long
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Xiran Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wei Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
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4
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Kawai F, Iizuka R, Kawabata T. Engineered polyethylene terephthalate hydrolases: perspectives and limits. Appl Microbiol Biotechnol 2024; 108:404. [PMID: 38953996 PMCID: PMC11219463 DOI: 10.1007/s00253-024-13222-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024]
Abstract
Polyethylene terephthalate (PET) is a major component of plastic waste. Enzymatic PET hydrolysis is the most ecofriendly recycling technology. The biorecycling of PET waste requires the complete depolymerization of PET to terephthalate and ethylene glycol. The history of enzymatic PET depolymerization has revealed two critical issues for the industrial depolymerization of PET: industrially available PET hydrolases and pretreatment of PET waste to make it susceptible to full enzymatic hydrolysis. As none of the wild-type enzymes can satisfy the requirements for industrialization, various mutational improvements have been performed, through classical technology to state-of-the-art computational/machine-learning technology. Recent engineering studies on PET hydrolases have brought a new insight that flexibility of the substrate-binding groove may improve the efficiency of PET hydrolysis while maintaining sufficient thermostability, although the previous studies focused only on enzymatic thermostability above the glass transition temperature of PET. Industrial biorecycling of PET waste is scheduled to be implemented, using micronized amorphous PET. Next stage must be the development of PET hydrolases that can efficiently degrade crystalline parts of PET and expansion of target PET materials, not only bottles but also textiles, packages, and microplastics. This review discusses the current status of PET hydrolases, their potential applications, and their profespectal goals. KEY POINTS: • PET hydrolases must be thermophilic, but their operation must be below 70 °C • Classical and state-of-the-art engineering approaches are useful for PET hydrolases • Enzyme activity on crystalline PET is most expected for future PET biorecycling.
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Affiliation(s)
- Fusako Kawai
- Graduate School of Environmental and Life Sciences, Okayama University, 1-1-1 Tsushima-Naka, Kita-Ku, Okayama, 700-8530, Japan.
| | - Ryo Iizuka
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Takeshi Kawabata
- Graduate School of Information Sciences, Tohoku University, Aoba 6-3-09, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
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5
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Norton-Baker B, Denton MCR, Murphy NP, Fram B, Lim S, Erickson E, Gauthier NP, Beckham GT. Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline. Sci Rep 2024; 14:14449. [PMID: 38914665 PMCID: PMC11196671 DOI: 10.1038/s41598-024-64938-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
As genomic databases expand and artificial intelligence tools advance, there is a growing demand for efficient characterization of large numbers of proteins. To this end, here we describe a generalizable pipeline for high-throughput protein purification using small-scale expression in E. coli and an affordable liquid-handling robot. This low-cost platform enables the purification of 96 proteins in parallel with minimal waste and is scalable for processing hundreds of proteins weekly per user. We demonstrate the performance of this method with the expression and purification of the leading poly(ethylene terephthalate) hydrolases reported in the literature. Replicate experiments demonstrated reproducibility and enzyme purity and yields (up to 400 µg) sufficient for comprehensive analyses of both thermostability and activity, generating a standardized benchmark dataset for comparing these plastic-degrading enzymes. The cost-effectiveness and ease of implementation of this platform render it broadly applicable to diverse protein characterization challenges in the biological sciences.
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Grants
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-SC0022024 U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER), Genomic Science Program
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- DE-AC36-08GO28308 Advanced Materials and Manufacturing Technologies Office (AMMTO)
- U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Bioenergy Technologies Office (BETO)
- Bio-Optimized Technologies to keep Thermoplastics out of Landfills and the Environment (BOTTLE) Consortium
- Dana-Farber Cancer Institute
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Affiliation(s)
- Brenna Norton-Baker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
- Agile BioFoundry, Emeryville, CA, USA
| | - Mackenzie C R Denton
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
| | - Natasha P Murphy
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
| | - Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Erika Erickson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- BOTTLE Consortium, Golden, CO, USA
| | - Nicholas P Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA.
- BOTTLE Consortium, Golden, CO, USA.
- Agile BioFoundry, Emeryville, CA, USA.
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6
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Wu Y, Hu Q, Che Y, Niu Z. Opportunities and challenges for plastic depolymerization by biomimetic catalysis. Chem Sci 2024; 15:6200-6217. [PMID: 38699266 PMCID: PMC11062090 DOI: 10.1039/d4sc00070f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/20/2024] [Indexed: 05/05/2024] Open
Abstract
Plastic waste has imposed significant burdens on the environment. Chemical recycling allows for repeated regeneration of plastics without deterioration in quality, but often requires harsh reaction conditions, thus being environmentally unfriendly. Enzymatic catalysis offers a promising solution for recycling under mild conditions, but it faces inherent limitations such as poor stability, high cost, and narrow substrate applicability. Biomimetic catalysis may provide a new avenue by combining high enzyme-like activity with the stability of inorganic materials. Biomimetic catalysis has demonstrated great potential in biomass conversion and has recently shown promising progress in plastic degradation. This perspective discusses biomimetic catalysis for plastic degradation from two perspectives: the imitation of the active centers and the imitation of the substrate-binding clefts. Given the chemical similarity between biomass and plastics, relevant work is also included in the discussion to draw inspiration. We conclude this perspective by highlighting the challenges and opportunities in achieving sustainable plastic recycling via a biomimetic approach.
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Affiliation(s)
- Yanfen Wu
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Qikun Hu
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Yizhen Che
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Zhiqiang Niu
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University Beijing 100084 China
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7
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Qi X, Wu Y, Zhang ST, Yin CF, Ji M, Liu Y, Xu Y, Zhou NY. The unique salt bridge network in GlacPETase: a key to its stability. Appl Environ Microbiol 2024; 90:e0224223. [PMID: 38358247 PMCID: PMC10952487 DOI: 10.1128/aem.02242-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
The extensive accumulation of polyethylene terephthalate (PET) has become a critical environmental issue. PET hydrolases can break down PET into its building blocks. Recently, we identified a glacial PET hydrolase GlacPETase sharing less than 31% amino acid identity with any known PET hydrolases. In this study, the crystal structure of GlacPETase was determined at 1.8 Å resolution, revealing unique structural features including a distinctive N-terminal disulfide bond and a specific salt bridge network. Site-directed mutagenesis demonstrated that the disruption of the N-terminal disulfide bond did not reduce GlacPETase's thermostability or its catalytic activity on PET. However, mutations in the salt bridges resulted in changes in melting temperature ranging from -8°C to +2°C and the activity on PET ranging from 17.5% to 145.5% compared to the wild type. Molecular dynamics simulations revealed that these salt bridges stabilized the GlacPETase's structure by maintaining their surrounding structure. Phylogenetic analysis indicated that GlacPETase represented a distinct branch within PET hydrolases-like proteins, with the salt bridges and disulfide bonds in this branch being relatively conserved. This research contributed to the improvement of our comprehension of the structural mechanisms that dictate the thermostability of PET hydrolases, highlighting the diverse characteristics and adaptability observed within PET hydrolases.IMPORTANCEThe pervasive problem of polyethylene terephthalate (PET) pollution in various terrestrial and marine environments is widely acknowledged and continues to escalate. PET hydrolases, such as GlacPETase in this study, offered a solution for breaking down PET. Its unique origin and less than 31% identity with any known PET hydrolases have driven us to resolve its structure. Here, we report the correlation between its unique structure and biochemical properties, focusing on an N-terminal disulfide bond and specific salt bridges. Through site-directed mutagenesis experiments and molecular dynamics simulations, the roles of the N-terminal disulfide bond and salt bridges were elucidated in GlacPETase. This research enhanced our understanding of the role of salt bridges in the thermostability of PET hydrolases, providing a valuable reference for the future engineering of PET hydrolases.
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Affiliation(s)
- Xiaoyan Qi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanfei Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shu-Ting Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao-Fan Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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8
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Cui Y, Chen Y, Sun J, Zhu T, Pang H, Li C, Geng WC, Wu B. Computational redesign of a hydrolase for nearly complete PET depolymerization at industrially relevant high-solids loading. Nat Commun 2024; 15:1417. [PMID: 38360963 PMCID: PMC10869840 DOI: 10.1038/s41467-024-45662-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Biotechnological plastic recycling has emerged as a suitable option for addressing the pollution crisis. A major breakthrough in the biodegradation of poly(ethylene terephthalate) (PET) is achieved by using a LCC variant, which permits 90% conversion at an industrial level. Despite the achievements, its applications have been hampered by the remaining 10% of nonbiodegradable PET. Herein, we address current challenges by employing a computational strategy to engineer a hydrolase from the bacterium HR29. The redesigned variant, TurboPETase, outperforms other well-known PET hydrolases. Nearly complete depolymerization is accomplished in 8 h at a solids loading of 200 g kg-1. Kinetic and structural analysis suggest that the improved performance may be attributed to a more flexible PET-binding groove that facilitates the targeting of more specific attack sites. Collectively, our results constitute a significant advance in understanding and engineering of industrially applicable polyester hydrolases, and provide guidance for further efforts on other polymer types.
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Affiliation(s)
- Yinglu Cui
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yanchun Chen
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jinyuan Sun
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tong Zhu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hua Pang
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chunli Li
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Chao Geng
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Chemistry, Nankai University, Tianjin, China
| | - Bian Wu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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9
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Bell EL, Rosetto G, Ingraham MA, Ramirez KJ, Lincoln C, Clarke RW, Gado JE, Lilly JL, Kucharzyk KH, Erickson E, Beckham GT. Natural diversity screening, assay development, and characterization of nylon-6 enzymatic depolymerization. Nat Commun 2024; 15:1217. [PMID: 38336849 PMCID: PMC10858056 DOI: 10.1038/s41467-024-45523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Successes in biocatalytic polyester recycling have raised the possibility of deconstructing alternative polymers enzymatically, with polyamide (PA) being a logical target due to the array of amide-cleaving enzymes present in nature. Here, we screen 40 potential natural and engineered nylon-hydrolyzing enzymes (nylonases), using mass spectrometry to quantify eight compounds resulting from enzymatic nylon-6 (PA6) hydrolysis. Comparative time-course reactions incubated at 40-70 °C showcase enzyme-dependent variations in product distributions and extent of PA6 film depolymerization, with significant nylon deconstruction activity appearing rare. The most active nylonase, a NylCK variant we rationally thermostabilized (an N-terminal nucleophile (Ntn) hydrolase, NylCK-TS, Tm = 87.4 °C, 16.4 °C higher than the wild-type), hydrolyzes 0.67 wt% of a PA6 film. Reactions fail to restart after fresh enzyme addition, indicating that substrate-based limitations, such as restricted enzyme access to hydrolysable bonds, prohibit more extensive deconstruction. Overall, this study expands our understanding of nylonase activity distribution, indicates that Ntn hydrolases may have the greatest potential for further development, and identifies key targets for progressing PA6 enzymatic depolymerization, including improving enzyme activity, product selectivity, and enhancing polymer accessibility.
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Affiliation(s)
- Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Gloria Rosetto
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Morgan A Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Clarissa Lincoln
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Ryan W Clarke
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Japheth E Gado
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Jacob L Lilly
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | | | - Erika Erickson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
- BOTTLE Consortium, Golden, CO, 80401, USA.
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10
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Oda K, Wlodawer A. Development of Enzyme-Based Approaches for Recycling PET on an Industrial Scale. Biochemistry 2024. [PMID: 38285602 DOI: 10.1021/acs.biochem.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Pollution by plastics such as polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), polyurethane (PUR), polyamide (PA), polystyrene (PS), and poly(ethylene terephthalate) (PET) is now gaining worldwide attention as a critical environmental issue, closely linked to climate change. Among them, PET is particularly prone to hydrolysis, breaking down into its constituents, ethylene glycol (EG) and terephthalate (TPA). Biorecycling or bioupcycling stands out as one of the most promising methods for addressing PET pollution. For dealing with pollution by the macrosize PET, a French company Carbios has developed a pilot-scale plant for biorecycling waste PET beverage bottles into new bottles using derivatives of thermophilic leaf compost cutinase (LCC). However, this system still provides significant challenges in its practical implementation. For the micro- or nanosize PET pollution that poses significant human health risks, including cancer, no industrial-scale approach has been established so far, despite the need to develop such technologies. In this Perspective, we explore the enhancement of the low activity and thermostability of the enzyme PETase to match that of LCC, along with the potential application of microbes and enzymes for the treatment of waste PET as microplastics. Additionally, we discuss the shortcomings of the current biorecycling protocols from a life cycle assessment perspective, covering aspects such as the diversity of PET-hydrolyzing enzymes in nature, the catalytic mechanism for crystallized PET, and more. We also provide an overview of the Ideonella sakaiensis system, highlighting its ability to operate and grow at moderate temperatures, in contrast to high-temperature processes.
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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Cribari MA, Unger MJ, Unarta IC, Ogorek AN, Huang X, Martell JD. Ultrahigh-Throughput Directed Evolution of Polymer-Degrading Enzymes Using Yeast Display. J Am Chem Soc 2023; 145:27380-27389. [PMID: 38051911 PMCID: PMC11058326 DOI: 10.1021/jacs.3c08291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Enzymes that degrade synthetic polymers have attracted intense interest for eco-friendly plastic recycling. However, because enzymes did not evolve for the cleavage of abiotic polymers, directed evolution strategies are needed to enhance activity for plastic degradation. Previous directed evolution efforts relied on polymer degradation assays that were limited to screening ∼104 mutants. Here, we report a high-throughput yeast surface display platform to rapidly evaluate >107 enzyme mutants for increased activity in cleaving synthetic polymers. In this platform, individual yeast cells display distinct mutants, and enzyme activity is detected by a change in fluorescence upon the cleavage of a synthetic probe resembling a polymer of interest. Highly active mutants are isolated by fluorescence activated cell sorting and identified through DNA sequencing. To demonstrate this platform, we performed directed evolution of a polyethylene terephthalate (PET)-depolymerizing enzyme, leaf and branch compost cutinase (LCC). We identified activity-boosting mutations that substantially increased the kinetics of degradation of solid PET films. Biochemical assays and molecular dynamics (MD) simulations of the most active variants suggest that the H218Y mutation improves the binding of the enzyme to PET. Overall, this evolution platform increases the screening throughput of polymer-degrading enzymes by 3 orders of magnitude and identifies mutations that enhance kinetics for depolymerizing solid substrates.
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Affiliation(s)
- Mario A. Cribari
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Maxwell J. Unger
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ilona C. Unarta
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ashley N. Ogorek
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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12
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Guo W, Duan J, Shi Z, Yu X, Shao Z. Biodegradation of PET by the membrane-anchored PET esterase from the marine bacterium Rhodococcus pyridinivorans P23. Commun Biol 2023; 6:1090. [PMID: 37891241 PMCID: PMC10611731 DOI: 10.1038/s42003-023-05470-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Evidence for microbial biodegradation of polyethylene terephthalate (PET) has been reported, but little is known about the PET biodegradation process and molecular mechanism by marine microorganisms. Here, we show the biodegradation of PET by the membrane-anchored PET esterase from the marine bacterium Rhodococcus pyridinivorans P23, elucidate the properties of this enzyme, and propose the PET biodegradation by this strain in biofilm. We identify the PET-degrading enzyme dubbed PET esterase through activity tracking. In addition to depolymerizing PET, it hydrolyzes MHET into TPA under acid conditions. We prove that it is a low and constitutively transcribed, membrane-anchored protein displayed on the cell surface. Furthermore, we also investigate the microbial groups possessing PET esterase coupled with the TPA degradation pathway, mainly in the phyla Proteobacteria and Actinobacteriota. Clarification of the microbial PET biodegradation in the marine environment will contribute to the understanding of bioremediation of marine PET pollution.
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Affiliation(s)
- Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China.
| | - Jingjing Duan
- College of Environment and Ecology, Xiamen University, 361005, Xiamen, Fujian, China.
| | - Zhengguang Shi
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China
- School of Advanced Manufacturing, Fuzhou University, 362251, Jinjiang, China
| | - Xue Yu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China
- School of Advanced Manufacturing, Fuzhou University, 362251, Jinjiang, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China
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