1
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Roman EKB, Ramos MA, Tomazetto G, Foltran BB, Galvão MH, Ciancaglini I, Tramontina R, de Almeida Rodrigues F, da Silva LS, Sandano ALH, Fernandes DGDS, Almeida DV, Baldo DA, de Oliveira Junior JM, Garcia W, Damasio A, Squina FM. Plastic-degrading microbial communities reveal novel microorganisms, pathways, and biocatalysts for polymer degradation and bioplastic production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174876. [PMID: 39067601 DOI: 10.1016/j.scitotenv.2024.174876] [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: 05/15/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
Plastics derived from fossil fuels are used ubiquitously owing to their exceptional physicochemical characteristics. However, the extensive and short-term use of plastics has caused environmental challenges. The biotechnological plastic conversion can help address the challenges related to plastic pollution, offering sustainable alternatives that can operate using bioeconomic concepts and promote socioeconomic benefits. In this context, using soil from a plastic-contaminated landfill, two consortia were established (ConsPlastic-A and -B) displaying versatility in developing and consuming polyethylene or polyethylene terephthalate as the carbon source of nutrition. The ConsPlastic-A and -B metagenomic sequencing, taxonomic profiling, and the reconstruction of 79 draft bacterial genomes significantly expanded the knowledge of plastic-degrading microorganisms and enzymes, disclosing novel taxonomic groups associated with polymer degradation. The microbial consortium was utilized to obtain a novel Pseudomonas putida strain (BR4), presenting a striking metabolic arsenal for aromatic compound degradation and assimilation, confirmed by genomic analyses. The BR4 displays the inherent capacity to degrade polyethylene terephthalate (PET) and produce polyhydroxybutyrate (PHB) containing hydroxyvalerate (HV) units that contribute to enhanced copolymer properties, such as increased flexibility and resistance to breakage, compared with pure PHB. Therefore, BR4 is a promising strain for developing a bioconsolidated plastic depolymerization and upcycling process. Collectively, our study provides insights that may extend beyond the artificial ecosystems established during our experiments and supports future strategies for effectively decomposing and valorizing plastic waste. Furthermore, the functional genomic analysis described herein serves as a valuable guide for elucidating the genetic potential of microbial communities and microorganisms in plastic deconstruction and upcycling.
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Affiliation(s)
- Ellen Karen Barreto Roman
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Murilo Antonio Ramos
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Geizecler Tomazetto
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Bruno Botega Foltran
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | | | - Iara Ciancaglini
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil; Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Robson Tramontina
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil; Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | | | | | | | - Diógenes G da S Fernandes
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Dnane Vieira Almeida
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Denicezar Angelo Baldo
- Laboratory of Applied Nuclear Physics, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | | | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, University of Sorocaba (UNISO), Sorocaba, SP, Brazil.
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2
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Almeida DV, Ciancaglini I, Sandano ALH, Roman EKB, Andrade VB, Nunes AB, Tramontina R, da Silva VM, Gabel F, Corrêa TLR, Damasio A, Muniz JRC, Squina FM, Garcia W. Unveiling the crystal structure of thermostable dienelactone hydrolase exhibiting activity on terephthalate esters. Enzyme Microb Technol 2024; 180:110498. [PMID: 39182429 DOI: 10.1016/j.enzmictec.2024.110498] [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: 05/03/2024] [Revised: 08/06/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Dienelactone hydrolase (DLH) is one of numerous hydrolytic enzymes with an α/β-hydrolase fold, which catalyze the hydrolysis of dienelactone to maleylacetate. The DLHs share remarkably similar tertiary structures and a conserved arrangement of catalytic residues. This study presents the crystal structure and comprehensive functional characterization of a novel thermostable DLH from the bacterium Hydrogenobacter thermophilus (HtDLH). The crystal structure of the HtDLH, solved at a resolution of about 1.67 Å, exhibits a canonical α/β-hydrolase fold formed by eight β-sheet strands in the core, with one buried α-helix and six others exposed to the solvent. The structure also confirmed the conserved catalytic triad of DHLs formed by Cys121, Asp170, and His202 residues. The HtDLH forms stable homodimers in solution. Functional studies showed that HtDLH has the expected esterase activity over esters with short carbon chains, such as p-nitrophenyl acetate, reaching optimal activity at pH 7.5 and 70 °C. Furthermore, HtDLH maintains more than 50 % of its activity even after incubation at 90 °C for 16 h. Interestingly, HtDLH exhibits catalytic activity towards polyethylene terephthalate (PET) monomers, including bis-1,2-hydroxyethyl terephthalate (BHET) and 1-(2-hydroxyethyl) 4-methyl terephthalate, as well as other aliphatic and aromatic esters. These findings associated with the lack of activity on amorphous PET indicate that HtDLH has characteristic of a BHET-degrading enzyme. This work expands our understanding of enzyme families involved in PET degradation, providing novel insights for plastic biorecycling through protein engineering, which could lead to eco-friendly solutions to reduce the accumulation of plastic in landfills and natural environments.
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Affiliation(s)
- Dnane Vieira Almeida
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil
| | - Iara Ciancaglini
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Ellen K B Roman
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Viviane Brito Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil
| | - Ana Bárbara Nunes
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Robson Tramontina
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Viviam Moura da Silva
- Institut de Biologie Structurale (IBS), CEA, CNRS, UGA, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Frank Gabel
- Institut de Biologie Structurale (IBS), CEA, CNRS, UGA, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Thamy L R Corrêa
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Fabio Marcio Squina
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil.
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC),Santo André, SP, Brazil.
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3
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Li C, Zheng Q, Liu W, Zhao Q, Jiang L. Enhancement of the degradation capacity of IsPETase by acidic amino acids insertion and carbohydrate-binding module fusion. 3 Biotech 2024; 14:195. [PMID: 39131175 PMCID: PMC11306670 DOI: 10.1007/s13205-024-04041-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
The biocatalytic degradation of poly(ethylene terephthalate) (PET) through enzymatic methods has garnered considerable attention due to its environmentally friendly and non-polluting nature, as well as its high specificity. While previous efforts in enhancing IsPETase performance have focused on amino acid substitutions in protein engineering, we introduced an amino acid insertion strategy in this work. By inserting a negatively charged acidic amino acid, Glu, at the right-angle bend of IsPETase, the binding capability between the enzyme's active pocket and PET was improved. The resulted mutant IsPETase9394insE exhibited enhanced hydrolytic activity towards PET at various temperatures ranging from 30 to 45 ℃ compared with the wild-type IsPETase. Notably, a 10.04-fold increase was observed at 45 ℃. To further enhance PET hydrolysis, different carbohydrate-binding modules (CBMs) were incorporated at the C-terminus of IsPETase9394insE. Among these, the fusion of CBM from Verrucosispora sioxanthis exhibited the highest enhancement, resulting in a 1.82-fold increase in PET hydrolytic activity at 37 ℃ compared with the IsPETase9394insE. Finally, the engineered variant was successfully employed for the degradation of polyester filter cloth, demonstrating its promising hydrolytic capacity. In conclusion, this research presents an alternative enzyme engineering strategy for modifying PETases and enriches the pool of potential candidates for industrial PET degradation.
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Affiliation(s)
- Chuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Qingqing Zheng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Wei Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Quanyu Zhao
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Ling Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 People’s Republic of China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816 China
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4
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Chen J, Jia Y, Sun Y, Liu K, Zhou C, Liu C, Li D, Liu G, Zhang C, Yang T, Huang L, Zhuang Y, Wang D, Xu D, Zhong Q, Guo Y, Li A, Seim I, Jiang L, Wang L, Lee SMY, Liu Y, Wang D, Zhang G, Liu S, Wei X, Yue Z, Zheng S, Shen X, Wang S, Qi C, Chen J, Ye C, Zhao F, Wang J, Fan J, Li B, Sun J, Jia X, Xia Z, Zhang H, Liu J, Zheng Y, Liu X, Wang J, Yang H, Kristiansen K, Xu X, Mock T, Li S, Zhang W, Fan G. Global marine microbial diversity and its potential in bioprospecting. Nature 2024; 633:371-379. [PMID: 39232160 PMCID: PMC11390488 DOI: 10.1038/s41586-024-07891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ying Sun
- BGI Research, Qingdao, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Chuan Liu
- BGI Research, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Chengsong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | | | - Yang Guo
- BGI Research, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Simon Ming Yuen Lee
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yujing Liu
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | - Guoqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Sen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chen Qi
- BGI Research, Shenzhen, China
| | - Jing Chen
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | - Chen Ye
- BGI Research, Shenzhen, China
| | | | | | - Jie Fan
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | | | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, China
| | - Zhangyong Xia
- Department of Neurology, The Second People's Hospital of Liaocheng, Liaocheng, China
| | - He Zhang
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Xin Liu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Karsten Kristiansen
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Wenwei Zhang
- BGI Research, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
| | - Guangyi Fan
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
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5
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Fu X. How deep can we decipher protein evolution with deep learning models. PATTERNS (NEW YORK, N.Y.) 2024; 5:101043. [PMID: 39233697 PMCID: PMC11368669 DOI: 10.1016/j.patter.2024.101043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Evolutionary-based machine learning models have emerged as a fascinating approach to mapping the landscape for protein evolution. Lian et al. demonstrated that evolution-based deep generative models, specifically variational autoencoders, can organize SH3 homologs in a hierarchical latent space, effectively distinguishing the specific Sho1SH3 domains.
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Affiliation(s)
- Xiaozhi Fu
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden
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6
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Mubayi V, Ahern CB, Calusinska M, O’Malley MA. Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation. ACS Synth Biol 2024; 13:1978-1993. [PMID: 38918080 PMCID: PMC11264326 DOI: 10.1021/acssynbio.4c00077] [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: 02/02/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
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.
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Affiliation(s)
- Vikram Mubayi
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Colleen B. Ahern
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Magdalena Calusinska
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Environmental
Research and Innovation Department, Luxembourg
Institute of Science and Technology, L-4422 Belvaux, Luxembourg
| | - Michelle A. O’Malley
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Bioengineering, University of California, Santa Barbara, California 93106, United States
- Joint
BioEnergy Institute (JBEI), Emeryville, California 94608, United States
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7
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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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8
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Denton MR, Murphy NP, Norton-Baker B, Lua M, Steel H, Beckham GT. Integration of pH Control into Chi.Bio Reactors and Demonstration with Small-Scale Enzymatic Poly(ethylene terephthalate) Hydrolysis. Biochemistry 2024; 63:1599-1607. [PMID: 38907702 PMCID: PMC11223484 DOI: 10.1021/acs.biochem.4c00149] [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] [Received: 03/23/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/24/2024]
Abstract
Small-scale bioreactors that are affordable and accessible would be of major benefit to the research community. In previous work, an open-source, automated bioreactor system was designed to operate up to the 30 mL scale with online optical monitoring, stirring, and temperature control, and this system, dubbed Chi.Bio, is now commercially available at a cost that is typically 1-2 orders of magnitude less than commercial bioreactors. In this work, we further expand the capabilities of the Chi.Bio system by enabling continuous pH monitoring and control through hardware and software modifications. For hardware modifications, we sourced low-cost, commercial pH circuits and made straightforward modifications to the Chi.Bio head plate to enable continuous pH monitoring. For software integration, we introduced closed-loop feedback control of the pH measured inside the Chi.Bio reactors and integrated a pH-control module into the existing Chi.Bio user interface. We demonstrated the utility of pH control through the small-scale depolymerization of the synthetic polyester, poly(ethylene terephthalate) (PET), using a benchmark cutinase enzyme, and compared this to 250 mL bioreactor hydrolysis reactions. The results in terms of PET conversion and rate, measured both by base addition and product release profiles, are statistically equivalent, with the Chi.Bio system allowing for a 20-fold reduction of purified enzyme required relative to the 250 mL bioreactor setup. Through inexpensive modifications, the ability to conduct pH control in Chi.Bio reactors widens the potential slate of biochemical reactions and biological cultivations for study in this system, and may also be adapted for use in other bioreactor platforms.
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Affiliation(s)
- Mackenzie
C. R. Denton
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Natasha P. Murphy
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Brenna Norton-Baker
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Mauro Lua
- Catalytic
Carbon Transformation and Scale-up Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Harrison Steel
- Department
of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K.
| | - Gregg T. Beckham
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
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9
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Amanna R, Rakshit SK. Review of nomenclature and methods of analysis of polyethylene terephthalic acid hydrolyzing enzymes activity. Biodegradation 2024; 35:341-360. [PMID: 37688750 DOI: 10.1007/s10532-023-10048-z] [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: 03/07/2023] [Accepted: 08/15/2023] [Indexed: 09/11/2023]
Abstract
Enzymatic degradation of polyethylene terephthalic acid (PET) has been gaining increasing importance. This has resulted in a significant increase in the search for newer enzymes and the development of more efficient enzyme-based systems. Due to the lack of a standard screening process, screening new enzymes has relied on other assays to determine the presence of esterase activity. This, in turn, has led to various nomenclatures and methods used to describe them and measure their activity. Since all PET-hydrolyzing enzymes are α/β hydrolases, they catalyze a serine nucleophilic attack and cleave an ester bond. They are lipases, esterases, cutinases and hydrolases. This has been used interchangeably, leading to difficulties while comparing results and evaluating progress. This review discusses the varied enzyme nomenclature being adapted, the different assays and analysis methods reported, and the strategies used to increase PET-hydrolyzing enzyme efficiency. A section on the various ways to quantify PET hydrolysis is also covered.
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Affiliation(s)
- Ruth Amanna
- Department of Biotechnology, Lakehead University, Thunder Bay, ON, Canada
- Biorefining Research Institute (BRI), Lakehead University, Thunder Bay, ON, Canada
| | - Sudip K Rakshit
- Department of Biotechnology, Lakehead University, Thunder Bay, ON, Canada.
- Biorefining Research Institute (BRI), Lakehead University, Thunder Bay, ON, Canada.
- Department of Chemical Engineering, Lakehead University, Thunder Bay, ON, Canada.
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10
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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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11
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Yang J, Li Z, Xu Q, Liu W, Gao S, Qin P, Chen Z, Wang A. Towards carbon neutrality: Sustainable recycling and upcycling strategies and mechanisms for polyethylene terephthalate via biotic/abiotic pathways. ECO-ENVIRONMENT & HEALTH 2024; 3:117-130. [PMID: 38638172 PMCID: PMC11021832 DOI: 10.1016/j.eehl.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 04/20/2024]
Abstract
Polyethylene terephthalate (PET), one of the most ubiquitous engineering plastics, presents both environmental challenges and opportunities for carbon neutrality and a circular economy. This review comprehensively addressed the latest developments in biotic and abiotic approaches for PET recycling/upcycling. Biotically, microbial depolymerization of PET, along with the biosynthesis of reclaimed monomers [terephthalic acid (TPA), ethylene glycol (EG)] to value-added products, presents an alternative for managing PET waste and enables CO2 reduction. Abiotically, thermal treatments (i.e., hydrolysis, glycolysis, methanolysis, etc.) and photo/electrocatalysis, enabled by catalysis advances, can depolymerize or convert PET/PET monomers in a more flexible, simple, fast, and controllable manner. Tandem abiotic/biotic catalysis offers great potential for PET upcycling to generate commodity chemicals and alternative materials, ideally at lower energy inputs, greenhouse gas emissions, and costs, compared to virgin polymer fabrication. Remarkably, over 25 types of upgraded PET products (e.g., adipic acid, muconic acid, catechol, vanillin, and glycolic acid, etc.) have been identified, underscoring the potential of PET upcycling in diverse applications. Efforts can be made to develop chemo-catalytic depolymerization of PET, improve microbial depolymerization of PET (e.g., hydrolysis efficiency, enzymatic activity, thermal and pH level stability, etc.), as well as identify new microorganisms or hydrolases capable of degrading PET through computational and machine learning algorithms. Consequently, this review provides a roadmap for advancing PET recycling and upcycling technologies, which hold the potential to shape the future of PET waste management and contribute to the preservation of our ecosystems.
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Affiliation(s)
- Jiaqi Yang
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qiongying Xu
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Wenzong Liu
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Shuhong Gao
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zhenglin Chen
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Aijie Wang
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Plakys G, Urbelienė N, Urbelis G, Vaitekūnas J, Labanauskas L, Mažonienė E, Meškys R. Conversion of β-1,6-Glucans to Gentiobiose using an endo-β-1,6-Glucanase PsGly30A from Paenibacillus sp. GKG. Chembiochem 2024; 25:e202400010. [PMID: 38439711 DOI: 10.1002/cbic.202400010] [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: 01/04/2024] [Revised: 02/20/2024] [Accepted: 03/04/2024] [Indexed: 03/06/2024]
Abstract
A plethora of di- and oligosaccharides isolated from the natural sources are used in food and pharmaceutical industry. An enzymatic hydrolysis of fungal cell wall β-glucans is a good alternative to produce the desired oligosaccharides with different functionalities, such as the flavour enhancer gentiobiose. We have previously identified PsGly30A as a potential yeast cell wall degrading β-1,6-glycosidase. The aim of this study is to characterise the PsGly30A enzyme, a member of the GH30 family, and to evaluate its suitability for the production of gentiobiose from β-1,6-glucans. An endo-β-1,6-glucanase PsGly30A encoding gene from Paenibacillus sp. GKG has been cloned and overexpressed in Escherichia coli. The recombinant enzyme has been active towards pustulan and yeast β-glucan, but not on laminarin from the Laminaria digitata, confirming the endo-β-1,6-glucanase mode of action. The PsGly30A shows the highest activity at pH 5.5 and 50 °C. The specific activity of PsGly30A on pustulan (1262±82 U/mg) is among the highest reported for GH30 β-1,6-glycosidases. Moreover, gentiobiose is the major reaction product when pustulan, yeast β-glucan or yeast cell walls have been used as a substrate. Therefore, PsGly30A is a promising catalyst for valorisation of the yeast-related by-products.
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Affiliation(s)
- Gediminas Plakys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257, Vilnius, Lithuania
- Department of Research and Development Roquette Amilina, AB, J. Janonio 12, LT, 35101 Panevezys, Lithuania
| | - Nina Urbelienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257, Vilnius, Lithuania
| | - Gintaras Urbelis
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Akademijos 7, LT-08412, Vilnius, Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257, Vilnius, Lithuania
| | - Linas Labanauskas
- Department of Organic Chemistry, Center for Physical Sciences and Technology, Akademijos 7, LT-08412, Vilnius, Lithuania
| | - Edita Mažonienė
- Department of Research and Development Roquette Amilina, AB, J. Janonio 12, LT, 35101 Panevezys, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio 7, LT-10257, Vilnius, Lithuania
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13
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Ridley RS, Conrad RE, Lindner BG, Woo S, Konstantinidis KT. Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes. Sci Rep 2024; 14:8798. [PMID: 38627476 PMCID: PMC11021508 DOI: 10.1038/s41598-024-59279-x] [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: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.
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Affiliation(s)
- Rodney S Ridley
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Seongwook Woo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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14
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Weiland F, Kohlstedt M, Wittmann C. Biobased de novo synthesis, upcycling, and recycling - the heartbeat toward a green and sustainable polyethylene terephthalate industry. Curr Opin Biotechnol 2024; 86:103079. [PMID: 38422776 DOI: 10.1016/j.copbio.2024.103079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Polyethylene terephthalate (PET) has revolutionized the industrial sector because of its versatility, with its predominant uses in the textiles and packaging materials industries. Despite the various advantages of this polymer, its synthesis is, unfavorably, tightly intertwined with nonrenewable fossil resources. Additionally, given its widespread use, accumulating PET waste poses a significant environmental challenge. As a result, current research in the areas of biological recycling, upcycling, and de novo synthesis is intensifying. Biological recycling involves the use of micro-organisms or enzymes to breakdown PET into monomers, offering a sustainable alternative to traditional recycling. Upcycling transforms PET waste into value-added products, expanding its potential application range and promoting a circular economy. Moreover, studies of cascading biological and chemical processes driven by microbial cell factories have explored generating PET using renewable, biobased feedstocks such as lignin. These avenues of research promise to mitigate the environmental footprint of PET, underlining the importance of sustainable innovations in the industry.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Germany
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15
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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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16
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Jiménez DJ, Sanchez A, Dini-Andreote F. Engineering microbiomes to transform plastics. Trends Biotechnol 2024; 42:265-268. [PMID: 37845169 DOI: 10.1016/j.tibtech.2023.09.011] [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: 08/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/18/2023]
Abstract
The design and study of active microbial consortia able to degrade plastics represent an exciting area of research toward the development of bio-based alternatives to efficiently transform plastic waste. This forum article discusses concepts and mechanisms to inform emerging strategies for engineering microbiomes to transform plastics under controlled settings.
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Affiliation(s)
- Diego Javier Jiménez
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| | - Alvaro Sanchez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología - CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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17
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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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18
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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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19
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Joho Y, Vongsouthi V, Gomez C, Larsen JS, Ardevol A, Jackson CJ. Improving plastic degrading enzymes via directed evolution. Protein Eng Des Sel 2024; 37:gzae009. [PMID: 38713696 PMCID: PMC11091475 DOI: 10.1093/protein/gzae009] [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: 12/15/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/09/2024] Open
Abstract
Plastic degrading enzymes have immense potential for use in industrial applications. Protein engineering efforts over the last decade have resulted in considerable enhancement of many properties of these enzymes. Directed evolution, a protein engineering approach that mimics the natural process of evolution in a laboratory, has been particularly useful in overcoming some of the challenges of structure-based protein engineering. For example, directed evolution has been used to improve the catalytic activity and thermostability of polyethylene terephthalate (PET)-degrading enzymes, although its use for the improvement of other desirable properties, such as solvent tolerance, has been less studied. In this review, we aim to identify some of the knowledge gaps and current challenges, and highlight recent studies related to the directed evolution of plastic-degrading enzymes.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Research Way, Clayton, Victoria 3168, Australia
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Joachim S Larsen
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Synthetic Biology, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Research Way, Clayton, Victoria 3168, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Synthetic Biology, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
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20
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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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21
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Shi L, Zhu L. Recent Advances and Challenges in Enzymatic Depolymerization and Recycling of PET Wastes. Chembiochem 2024; 25:e202300578. [PMID: 37960968 DOI: 10.1002/cbic.202300578] [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: 08/16/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/15/2023]
Abstract
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.
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Affiliation(s)
- Lixia Shi
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Leilei Zhu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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22
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Zhou H, Shi S, You Q, Zhang K, Chen Y, Zheng D, Sun J. Polyethylene Terephthalate Hydrolases in Human Gut Microbiota and Their Implications for Human Health. Microorganisms 2024; 12:138. [PMID: 38257965 PMCID: PMC10820491 DOI: 10.3390/microorganisms12010138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Polyethylene terephthalate (PET), primarily utilized for food and beverage packaging, consistently finds its way into the human gut, thereby exerting adverse effects on human health. PET hydrolases, critical for the degradation of PET, have been predominantly sourced from environmental microbial communities. Given the fact that the human gut harbors a vast and intricate consortium of microorganisms, inquiry into the presence of potential PET hydrolases within the human gut microbiota becomes imperative. In this investigation, we meticulously screened 22,156 homologous sequences that could potentially encode PET hydrolases using the hidden Markov model (HMM) paradigm, drawing from 4984 cultivated genomes of healthy human gut bacteria. Subsequently, we methodically validated the hydrolytic efficacy of five selected candidate PET hydrolases on both PET films and powders composed of micro-plastics (MPs). Notably, our study also unveiled the influence of both diverse PET MP powders and their resultant hydrolysates on the modulation of cytokine expression in macrophages. In summary, our research underscores the ubiquitous prevalence and considerable potential of the human gut microbiota in PET hydrolysis. Furthermore, our study significantly contributes to the holistic evaluation of the potential health hazards posed by PET MPs to human well-being.
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Affiliation(s)
- Heqi Zhou
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Songbiao Shi
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China;
| | - Qiuhong You
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Kaikai Zhang
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Yuchuan Chen
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Dekai Zheng
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
| | - Jian Sun
- State Key Laboratory of Organ Failure Research, Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Guangdong Provincial Clinical Research Center for Viral Hepatitis, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; (H.Z.); (Q.Y.); (K.Z.); (Y.C.); (D.Z.)
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23
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309305. [PMID: 38516574 PMCID: PMC10952289 DOI: 10.1002/ange.202309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 03/23/2024]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - John Davidson
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center National Renewable Energy Laboratory Golden CO USA
- BOTTLE Consortium Golden CO USA
| | - Anthony P Green
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
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24
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. Angew Chem Int Ed Engl 2023; 62:e202309305. [PMID: 37651344 PMCID: PMC10952156 DOI: 10.1002/anie.202309305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2 ) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - John Davidson
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Elizabeth L. Bell
- Renewable Resources and Enabling Sciences CenterNational Renewable Energy LaboratoryGoldenCOUSA
- BOTTLE ConsortiumGoldenCOUSA
| | - Anthony P. Green
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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25
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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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26
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Qi X, Ji M, Yin CF, Zhou NY, Liu Y. Glacier as a source of novel polyethylene terephthalate hydrolases. Environ Microbiol 2023; 25:2822-2833. [PMID: 37775503 DOI: 10.1111/1462-2920.16516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Polyethylene terephthalate (PET) is a major component of microplastic contamination globally, which is now detected in pristine environments including Polar and mountain glaciers. As a carbon-rich molecule, PET could be a carbon source for microorganisms dwelling in glacier habitats. Thus, glacial microorganisms may be potential PET degraders with novel PET hydrolases. Here, we obtained 414 putative PET hydrolase sequences by searching a global glacier metagenome dataset. Metagenomes from the Alps and Tibetan glaciers exhibited a higher relative abundance of putative PET hydrolases than those from the Arctic and Antarctic. Twelve putative PET hydrolase sequences were cloned and expressed, with one sequence (designated as GlacPETase) proven to degrade amorphous PET film with a similar performance as IsPETase, but with a higher thermostability. GlacPETase exhibited only 30% sequence identity to known active PET hydrolases with a novel disulphide bridge location and, therefore may represent a novel PET hydrolases class. The present work suggests that extreme carbon-poor environments may harbour a diverse range of known and novel PET hydrolases for carbon acquisition as an environmental adaptation mechanism.
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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
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, 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
| | - 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
| | - Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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27
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Tiong E, Koo YS, Bi J, Koduru L, Koh W, Lim YH, Wong FT. Expression and engineering of PET-degrading enzymes from Microbispora, Nonomuraea, and Micromonospora. Appl Environ Microbiol 2023; 89:e0063223. [PMID: 37943056 PMCID: PMC10686063 DOI: 10.1128/aem.00632-23] [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: 04/16/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Mismanagement of PET plastic waste significantly threatens human and environmental health. Together with the relentless increase in plastic production, plastic pollution is an issue of rising concern. In response to this challenge, scientists are investigating eco-friendly approaches, such as bioprocessing and microbial factories, to sustainably manage the growing quantity of plastic waste in our ecosystem. Industrial applicability of enzymes capable of degrading PET is limited by numerous factors, including their scarcity in nature. The objective of this study is to enhance our understanding of this group of enzymes by identifying and characterizing novel enzymes that can facilitate the breakdown of PET waste. This data will expand the enzymatic repertoire and provide valuable insights into the prerequisites for successful PET degradation.
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Grants
- C211917006 Agency for Science, Technology, and Research (A*STAR)
- C211917006 Agency for Science, Technology, and Research (A*STAR)
- C211917003 Agency for Science, Technology, and Research (A*STAR)
- A*STAR Graduate Academy Agency for Science, Technology, and Research (A*STAR)
- C233017006 Agency for Science, Technology, and Research (A*STAR)
- C233017004 Agency for Science, Technology, and Research (A*STAR)
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Affiliation(s)
- Elaine Tiong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Ying Sin Koo
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Jiawu Bi
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Winston Koh
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Yee Hwee Lim
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
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28
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Buller R, Lutz S, Kazlauskas RJ, Snajdrova R, Moore JC, Bornscheuer UT. From nature to industry: Harnessing enzymes for biocatalysis. Science 2023; 382:eadh8615. [PMID: 37995253 DOI: 10.1126/science.adh8615] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/17/2023] [Indexed: 11/25/2023]
Abstract
Biocatalysis harnesses enzymes to make valuable products. This green technology is used in countless applications from bench scale to industrial production and allows practitioners to access complex organic molecules, often with fewer synthetic steps and reduced waste. The last decade has seen an explosion in the development of experimental and computational tools to tailor enzymatic properties, equipping enzyme engineers with the ability to create biocatalysts that perform reactions not present in nature. By using (chemo)-enzymatic synthesis routes or orchestrating intricate enzyme cascades, scientists can synthesize elaborate targets ranging from DNA and complex pharmaceuticals to starch made in vitro from CO2-derived methanol. In addition, new chemistries have emerged through the combination of biocatalysis with transition metal catalysis, photocatalysis, and electrocatalysis. This review highlights recent key developments, identifies current limitations, and provides a future prospect for this rapidly developing technology.
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Affiliation(s)
- R Buller
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - S Lutz
- Codexis Incorporated, Redwood City, CA 94063, USA
| | - R J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
| | - R Snajdrova
- Novartis Institutes for BioMedical Research, Global Discovery Chemistry, 4056 Basel, Switzerland
| | - J C Moore
- MRL, Merck & Co., Rahway, NJ 07065, USA
| | - U T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology and Enzyme Catalysis, Greifswald University, Greifswald, Germany
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29
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Zeng C, Ding F, Zhou J, Dong W, Cui Z, Yan X. Biodegradation of Poly(ethylene terephthalate) by Bacillus safensis YX8. Int J Mol Sci 2023; 24:16434. [PMID: 38003625 PMCID: PMC10671283 DOI: 10.3390/ijms242216434] [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: 10/17/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Due to the extensive utilization of poly (ethylene terephthalate) (PET), a significant amount of PET waste has been discharged into the environment, endangering both human health and the ecology. As an eco-friendly approach to PET waste treatment, biodegradation is dependent on efficient strains and enzymes. In this study, a screening method was first established using polycaprolactone (PCL) and PET nanoparticles as substrates. A PET-degrading strain YX8 was isolated from the surface of PET waste. Based on the phylogenetic analysis of 16S rRNA and gyrA genes, this strain was identified as Bacillus safensis. Strain YX8 demonstrated the capability to degrade PET nanoparticles, resulting in the production of terephthalic acid (TPA), mono (2-hydroxyethyl) terephthalic acid (MHET), and bis (2-hydroxyethyl) terephthalic acid (BHET). Erosion spots on the PET film were observed after incubation with strain YX8. Furthermore, the extracellular enzymes produced by strain YX8 exhibited the ability to form a clear zone on the PCL plate and to hydrolyze PET nanoparticles to generate TPA, MHET, and BHET. This work developed a method for the isolation of PET-degrading microorganisms and provides new strain resources for PET degradation and for the mining of functional enzymes.
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Affiliation(s)
- Caiting Zeng
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
| | - Fanghui Ding
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
| | - Jie Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (J.Z.); (W.D.)
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; (J.Z.); (W.D.)
| | - Zhongli Cui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
| | - Xin Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (F.D.); (Z.C.)
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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30
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Li M, Wang H, Yang Z, Zhang L, Zhu Y. DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences. Comput Struct Biotechnol J 2023; 21:5544-5560. [PMID: 38034401 PMCID: PMC10681957 DOI: 10.1016/j.csbj.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Thermally stable proteins find extensive applications in industrial production, pharmaceutical development, and serve as a highly evolved starting point in protein engineering. The thermal stability of proteins is commonly characterized by their melting temperature (Tm). However, due to the limited availability of experimentally determined Tm data and the insufficient accuracy of existing computational methods in predicting Tm, there is an urgent need for a computational approach to accurately forecast the Tm values of thermophilic proteins. Here, we present a deep learning-based model, called DeepTM, which exclusively utilizes protein sequences as input and accurately predicts the Tm values of target thermophilic proteins on a dataset consisting of 7790 thermophilic protein entries. On a test set of 1550 samples, DeepTM demonstrates excellent performance with a coefficient of determination (R2) of 0.75, Pearson correlation coefficient (P) of 0.87, and root mean square error (RMSE) of 6.24 ℃. We further analyzed the sequence features that determine the thermal stability of thermophilic proteins and found that dipeptide frequency, optimal growth temperature (OGT) of the host organisms, and the evolutionary information of the protein significantly affect its melting temperature. We compared the performance of DeepTM with recently reported methods, ProTstab2 and DeepSTABp, in predicting the Tm values on two blind test datasets. One dataset comprised 22 PET plastic-degrading enzymes, while the other included 29 thermally stable proteins of broader classification. In the PET plastic-degrading enzyme dataset, DeepTM achieved RMSE of 8.25 ℃. Compared to ProTstab2 (20.05 ℃) and DeepSTABp (20.97 ℃), DeepTM demonstrated a reduction in RMSE of 58.85% and 60.66%, respectively. In the dataset of thermally stable proteins, DeepTM (RMSE=7.66 ℃) demonstrated a 51.73% reduction in RMSE compared to ProTstab2 (RMSE=15.87 ℃). DeepTM, with the sole requirement of protein sequence information, accurately predicts the melting temperature and achieves a fully end-to-end prediction process, thus providing enhanced convenience and expediency for further protein engineering.
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Affiliation(s)
- Mengyu Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hongzhao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhenwu Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Longgui Zhang
- SINOPEC Beijing Research Institute of Chemical Industry, Beijing 100013, China
| | - Yushan Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing 100029, China
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31
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Arnal G, Anglade J, Gavalda S, Tournier V, Chabot N, Bornscheuer UT, Weber G, Marty A. Assessment of Four Engineered PET Degrading Enzymes Considering Large-Scale Industrial Applications. ACS Catal 2023; 13:13156-13166. [PMID: 37881793 PMCID: PMC10594578 DOI: 10.1021/acscatal.3c02922] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/13/2023] [Indexed: 10/27/2023]
Abstract
In recent years, enzymatic recycling of the widely used polyester polyethylene terephthalate (PET) has become a complementary solution to current thermomechanical recycling for colored, opaque, and mixed PET. A large set of promising hydrolases that depolymerize PET have been found and enhanced by worldwide initiatives using various methods of protein engineering. Despite the achievements made in these works, it remains difficult to compare enzymes' performance and their applicability to large-scale reactions due to a lack of homogeneity between the experimental protocols used. Here, we pave the way for a standardized enzymatic PET hydrolysis protocol using reaction conditions relevant for larger scale hydrolysis and apply these parameters to four recently reported PET hydrolases (LCCICCG, FAST-PETase, HotPETase, and PES-H1L92F/Q94Y). We show that FAST-PETase and HotPETase have intrinsic limitations that may not permit their application on larger reaction scales, mainly due to their relatively low depolymerization rates. With 80% PET depolymerization, PES-H1L92F/Q94Y may be a suitable candidate for industrial reaction scales upon further rounds of enzyme evolution. LCCICCG outperforms the other enzymes, converting 98% of PET into the monomeric products terephthalic acid (TPA) and ethylene glycol (EG) in 24 h. In addition, we optimized the reaction conditions of LCCICCG toward economic viability, reducing the required amount of enzyme by a factor of 3 and the temperature of the reaction from 72 to 68 °C. We anticipate our findings to advance enzymatic PET hydrolysis toward a coherent assessment of the enzymes and materialize feasibility at larger reaction scales.
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Affiliation(s)
- Grégory Arnal
- Carbios, Parc Cataroux—Bâtiment
B80, 8 Rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Julien Anglade
- Toulouse
Biotechnology Institute, TBI, Université
de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, 31077 Toulouse Cedex 4, France
| | - Sabine Gavalda
- Carbios, Parc Cataroux—Bâtiment
B80, 8 Rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Vincent Tournier
- Carbios, Parc Cataroux—Bâtiment
B80, 8 Rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Nicolas Chabot
- Carbios, Parc Cataroux—Bâtiment
B80, 8 Rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Uwe T. Bornscheuer
- Institute
of Biochemistry, Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Gert Weber
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin
für Materialien und Energie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Alain Marty
- Carbios, Parc Cataroux—Bâtiment
B80, 8 Rue de la Grolière, 63100 Clermont-Ferrand, France
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32
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Sui B, Wang T, Fang J, Hou Z, Shu T, Lu Z, Liu F, Zhu Y. Recent advances in the biodegradation of polyethylene terephthalate with cutinase-like enzymes. Front Microbiol 2023; 14:1265139. [PMID: 37849919 PMCID: PMC10577388 DOI: 10.3389/fmicb.2023.1265139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Polyethylene terephthalate (PET) is a synthetic polymer in the polyester family. It is widely found in objects used daily, including packaging materials (such as bottles and containers), textiles (such as fibers), and even in the automotive and electronics industries. PET is known for its excellent mechanical properties, chemical resistance, and transparency. However, these features (e.g., high hydrophobicity and high molecular weight) also make PET highly resistant to degradation by wild-type microorganisms or physicochemical methods in nature, contributing to the accumulation of plastic waste in the environment. Therefore, accelerated PET recycling is becoming increasingly urgent to address the global environmental problem caused by plastic wastes and prevent plastic pollution. In addition to traditional physical cycling (e.g., pyrolysis, gasification) and chemical cycling (e.g., chemical depolymerization), biodegradation can be used, which involves breaking down organic materials into simpler compounds by microorganisms or PET-degrading enzymes. Lipases and cutinases are the two classes of enzymes that have been studied extensively for this purpose. Biodegradation of PET is an attractive approach for managing PET waste, as it can help reduce environmental pollution and promote a circular economy. During the past few years, great advances have been accomplished in PET biodegradation. In this review, current knowledge on cutinase-like PET hydrolases (such as TfCut2, Cut190, HiC, and LCC) was described in detail, including the structures, ligand-protein interactions, and rational protein engineering for improved PET-degrading performance. In particular, applications of the engineered catalysts were highlighted, such as improving the PET hydrolytic activity by constructing fusion proteins. The review is expected to provide novel insights for the biodegradation of complex polymers.
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Affiliation(s)
- Beibei Sui
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Jingxiang Fang
- Rizhao Administration for Market Regulation, Rizhao, Shandong, China
| | - Zuoxuan Hou
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Ting Shu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Zhenhua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Youshuang Zhu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
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Chatonnet A, Perochon M, Velluet E, Marchot P. The ESTHER database on alpha/beta hydrolase fold proteins - An overview of recent developments. Chem Biol Interact 2023; 383:110671. [PMID: 37582413 DOI: 10.1016/j.cbi.2023.110671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/01/2023] [Accepted: 08/12/2023] [Indexed: 08/17/2023]
Abstract
The ESTHER database, dedicated to ESTerases and alpha/beta-Hydrolase Enzymes and Relatives (https://bioweb.supagro.inra.fr/ESTHER/general?what=index), offers online access to a continuously updated, sequence-based classification of proteins harboring the alpha/beta hydrolase fold into families and subfamilies. In particular, the database proposes links to the sequences, structures, ligands and huge diversity of functions of these proteins, and to the related literature and other databases. Taking advantage of the promiscuity of enzymatic function, many engineered esterases, lipases, epoxide-hydrolases, haloalkane dehalogenases are used for biotechnological applications. Finding means for detoxifying those protein members that are targeted by insecticides, herbicides, antibiotics, or for reactivating human cholinesterases when inhibited by nerve gas, are still active areas of research. Using or improving the capacity of some enzymes to breakdown plastics with the aim to recycle valuable material and reduce waste is an emerging challenge. Most hydrolases in the superfamily are water-soluble and act on or are inhibited by small organic compounds, yet in a few subfamilies some members interact with other, unrelated proteins to modulate activity or trigger functional partnerships. Recent development in 3D structure prediction brought by AI-based programs now permits analysis of enzymatic mechanisms for a variety of hydrolases with no experimental 3D structure available. Finally, mutations in as many as 34 of the 120 human genes compiled in the database are now linked to genetic diseases, a feature fueling research on early detection, metabolic pathways, pharmacological treatment or enzyme replacement therapy. Here we review those developments in the database that took place over the latest decade and discuss potential new applications and recent and future expected research in the field.
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Affiliation(s)
- Arnaud Chatonnet
- DMEM, Université de Montpellier, INRAE, 34000 Montpellier, France.
| | - Michel Perochon
- DMEM, Université de Montpellier, INRAE, 34000 Montpellier, France
| | - Eric Velluet
- INRAE-AgroM / UIC, Place Viala, 34060, Montpellier, France
| | - Pascale Marchot
- CNRS / Aix-Marseille Univ, lab Architecture et Fonction des Macromolécules Biologiques, Marseille, France
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Barclay A, Acharya KR. Engineering Plastic Eating Enzymes Using Structural Biology. Biomolecules 2023; 13:1407. [PMID: 37759807 PMCID: PMC10526444 DOI: 10.3390/biom13091407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Plastic pollution has emerged as a significant environmental concern in recent years and has prompted the exploration of innovative biotechnological solutions to mitigate plastic's negative impact. The discovery of enzymes capable of degrading specific types of plastics holds promise as a potential solution. However, challenges with efficiency, industrial scalability, and the diverse range of the plastic waste in question, have hindered their widespread application. Structural biology provides valuable insights into the intricate interactions between enzymes and plastic materials at an atomic level, and a deeper understanding of their underlying mechanisms is essential to harness their potential to address the mounting plastic waste crisis. This review article examines the current biochemical and biophysical methods that may facilitate the development of enzymes capable of degrading polyethylene terephthalate (PET), one of the most extensively used plastics. It also discusses the challenges that must be addressed before substantial advancements can be achieved in using these enzymes as a solution to the plastic pollution problem.
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Affiliation(s)
| | - K. Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK;
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35
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Liu F, Wang T, Yang W, Zhang Y, Gong Y, Fan X, Wang G, Lu Z, Wang J. Current advances in the structural biology and molecular engineering of PETase. Front Bioeng Biotechnol 2023; 11:1263996. [PMID: 37795175 PMCID: PMC10546322 DOI: 10.3389/fbioe.2023.1263996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023] Open
Abstract
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.
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Affiliation(s)
- Fei Liu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Wentao Yang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yingkang Zhang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yuming Gong
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Xinxin Fan
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Guocheng Wang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Zhenhua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianmin Wang
- School of Pharmacy, Jining Medical University, Rizhao, China
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36
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Perez-Garcia P, Chow J, Costanzi E, Gurschke M, Dittrich J, Dierkes RF, Molitor R, Applegate V, Feuerriegel G, Tete P, Danso D, Thies S, Schumacher J, Pfleger C, Jaeger KE, Gohlke H, Smits SHJ, Schmitz RA, Streit WR. An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate. Commun Chem 2023; 6:193. [PMID: 37697032 PMCID: PMC10495362 DOI: 10.1038/s42004-023-00998-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 80 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme had been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46 (RLI42440.1), an archaeal promiscuous feruloyl esterase exhibiting degradation activity on semi-crystalline PET powder comparable to IsPETase and LCC (wildtypes), and higher activity on bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, is derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 Å. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a plant cell wall-degrading esterase.
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Affiliation(s)
- Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Elisa Costanzi
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marno Gurschke
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Robert F Dierkes
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Rebecka Molitor
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Violetta Applegate
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Prince Tete
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Dominik Danso
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Julia Schumacher
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.
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37
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James-Pearson LF, Dudley KJ, Te'o VSJ, Patel BKC. A hot topic: thermophilic plastic biodegradation. Trends Biotechnol 2023; 41:1117-1126. [PMID: 37121828 DOI: 10.1016/j.tibtech.2023.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023]
Abstract
Biological degradation of plastic waste is an environmentally and economically friendlier alternative to current recycling practices and enables the cycling of plastic monomers back into virgin-quality plastics. However, due to slow reaction rates, there is a lack of an industrially viable biodegradation strategy for most plastics. Here, we highlight the applicability of a thermophilic biodegradation strategy over a mesophilic approach, to enhance enzyme accessibility and catalyze plastic biodegradation. Thus, at reactions closer to the melting temperature or glass transition temperature of plastics, thermophilic reactions can offer an alternative direction to conventional plastic biodegradation strategies.
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Affiliation(s)
- Louisa F James-Pearson
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Valentino Setoa Junior Te'o
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Bharat K C Patel
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia.
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38
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Williams GB, Ma H, Khusnutdinova AN, Yakunin AF, Golyshin PN. Harnessing extremophilic carboxylesterases for applications in polyester depolymerisation and plastic waste recycling. Essays Biochem 2023; 67:715-729. [PMID: 37334661 PMCID: PMC10423841 DOI: 10.1042/ebc20220255] [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: 03/19/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
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.
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Affiliation(s)
- Gwion B Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Hairong Ma
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Anna N Khusnutdinova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Alexander F Yakunin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
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39
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Hong H, Ki D, Seo H, Park J, Jang J, Kim KJ. Discovery and rational engineering of PET hydrolase with both mesophilic and thermophilic PET hydrolase properties. Nat Commun 2023; 14:4556. [PMID: 37507390 PMCID: PMC10382486 DOI: 10.1038/s41467-023-40233-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Excessive polyethylene terephthalate (PET) waste causes a variety of problems. Extensive research focused on the development of superior PET hydrolases for PET biorecycling has been conducted. However, template enzymes employed in enzyme engineering mainly focused on IsPETase and leaf-branch compost cutinase, which exhibit mesophilic and thermophilic hydrolytic properties, respectively. Herein, we report a PET hydrolase from Cryptosporangium aurantiacum (CaPETase) that exhibits high thermostability and remarkable PET degradation activity at ambient temperatures. We uncover the crystal structure of CaPETase, which displays a distinct backbone conformation at the active site and residues forming the substrate binding cleft, compared with other PET hydrolases. We further develop a CaPETaseM9 variant that exhibits robust thermostability with a Tm of 83.2 °C and 41.7-fold enhanced PET hydrolytic activity at 60 °C compared with CaPETaseWT. CaPETaseM9 almost completely decompose both transparent and colored post-consumer PET powder at 55 °C within half a day in a pH-stat bioreactor.
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Affiliation(s)
- Hwaseok Hong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dongwoo Ki
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jiyoung Park
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jaewon Jang
- Institute of Biotechnology, CJ CheilJedang Co., Suwon-si, Gyeonggi-do, 16495, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Zyen Co, Daegu, 41566, Republic of Korea.
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40
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Avilan L, Lichtenstein BR, König G, Zahn M, Allen MD, Oliveira L, Clark M, Bemmer V, Graham R, Austin HP, Dominick G, Johnson CW, Beckham GT, McGeehan JE, Pickford AR. Concentration-Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering. CHEMSUSCHEM 2023; 16:e202202277. [PMID: 36811288 DOI: 10.1002/cssc.202202277] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Enzyme-based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis (IsPETase) is capable of PET hydrolysis under mild conditions but suffers from concentration-dependent inhibition. In this study, this inhibition is found to be dependent on incubation time, the solution conditions, and PET surface area. Furthermore, this inhibition is evident in other mesophilic PET-degrading enzymes to varying degrees, independent of the level of PET depolymerization activity. The inhibition has no clear structural basis, but moderately thermostable IsPETase variants exhibit reduced inhibition, and the property is completely absent in the highly thermostable HotPETase, previously engineered by directed evolution, which simulations suggest results from reduced flexibility around the active site. This work highlights a limitation in applying natural mesophilic hydrolases for PET hydrolysis and reveals an unexpected positive outcome of engineering these enzymes for enhanced thermostability.
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Affiliation(s)
- Luisana Avilan
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Bruce R Lichtenstein
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Gerhard König
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Mark D Allen
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Liliana Oliveira
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Matilda Clark
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Victoria Bemmer
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Rosie Graham
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Harry P Austin
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, D-17487, Greifswald, Germany
| | - Graham Dominick
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, United States
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, United States
| | - Gregg T Beckham
- BOTTLE Consortium, Golden, CO 80401, United States
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, United States
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
| | - Andrew R Pickford
- Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, United Kingdom
- BOTTLE Consortium, Golden, CO 80401, United States
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Pellis A, Guebitz GM, Ribitsch D. Bio-upcycling of multilayer materials and blends: closing the plastics loop. Curr Opin Biotechnol 2023; 81:102938. [PMID: 37058877 DOI: 10.1016/j.copbio.2023.102938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 04/16/2023]
Abstract
The urge to discover and develop new technologies for closing the plastic carbon cycle is motivating industries, governments, and academia to work closely together to find suitable solutions in a timely manner. In this review article, a combination of uprising breakthrough technologies is presented highlighting their potential and complementarity to be integrated one with the other, therefore providing a potential solution to efficiently solve the plastics problem. First, modern approaches for bio-exploration and engineering of polymer-active enzymes are presented to degrade polymers into valuable building blocks. Special focus is placed on the recovery of components from multilayered materials since these complex materials can only be recycled insufficiently or not at all by existing technologies. Then, the potential of microbes and enzymes for resynthesis of polymers and reuse of building blocks is summarized and discussed. Finally, examples for improvement of the bio-based content and enzymatic degradability and future perspectives are given.
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Affiliation(s)
- Alessandro Pellis
- Department of Chemistry and Industrial Chemistry, University of Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Georg M Guebitz
- ACIB - Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria; Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria
| | - Doris Ribitsch
- ACIB - Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria; Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria.
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42
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Determinants for an Efficient Enzymatic Catalysis in Poly(Ethylene Terephthalate) Degradation. Catalysts 2023. [DOI: 10.3390/catal13030591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
The enzymatic degradation of the recalcitrant poly(ethylene terephthalate) (PET) has been an important biotechnological goal. The present review focuses on the state of the art in enzymatic degradation of PET, and the challenges ahead. This review covers (i) enzymes acting on PET, (ii) protein improvements through selection or engineering, (iii) strategies to improve biocatalyst–polymer interaction and monomer yields. Finally, this review discusses critical points on PET degradation, and their related experimental aspects, that include the control of physicochemical parameters. The search for, and engineering of, PET hydrolases, have been widely studied to achieve this, and several examples are discussed here. Many enzymes, from various microbial sources, have been studied and engineered, but recently true PET hydrolases (PETases), active at moderate temperatures, were reported. For a circular economy process, terephtalic acid (TPA) production is critical. Some thermophilic cutinases and engineered PETases have been reported to release terephthalic acid in significant amounts. Some bottlenecks in enzyme performance are discussed, including enzyme activity, thermal stability, substrate accessibility, PET microstructures, high crystallinity, molecular mass, mass transfer, and efficient conversion into reusable fragments.
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43
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Orlando M, Molla G, Castellani P, Pirillo V, Torretta V, Ferronato N. Microbial Enzyme Biotechnology to Reach Plastic Waste Circularity: Current Status, Problems and Perspectives. Int J Mol Sci 2023; 24:3877. [PMID: 36835289 PMCID: PMC9967032 DOI: 10.3390/ijms24043877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The accumulation of synthetic plastic waste in the environment has become a global concern. Microbial enzymes (purified or as whole-cell biocatalysts) represent emerging biotechnological tools for waste circularity; they can depolymerize materials into reusable building blocks, but their contribution must be considered within the context of present waste management practices. This review reports on the prospective of biotechnological tools for plastic bio-recycling within the framework of plastic waste management in Europe. Available biotechnology tools can support polyethylene terephthalate (PET) recycling. However, PET represents only ≈7% of unrecycled plastic waste. Polyurethanes, the principal unrecycled waste fraction, together with other thermosets and more recalcitrant thermoplastics (e.g., polyolefins) are the next plausible target for enzyme-based depolymerization, even if this process is currently effective only on ideal polyester-based polymers. To extend the contribution of biotechnology to plastic circularity, optimization of collection and sorting systems should be considered to feed chemoenzymatic technologies for the treatment of more recalcitrant and mixed polymers. In addition, new bio-based technologies with a lower environmental impact in comparison with the present approaches should be developed to depolymerize (available or new) plastic materials, that should be designed for the required durability and for being susceptible to the action of enzymes.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 21100 Varese, Italy
| | - Gianluca Molla
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 21100 Varese, Italy
| | - Pietro Castellani
- Department of Theoretical and Applied Sciences (DiSTA), University of Insubria, Via G.B. Vico 46, 21100 Varese, Italy
| | - Valentina Pirillo
- Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant, 21100 Varese, Italy
| | - Vincenzo Torretta
- Department of Theoretical and Applied Sciences (DiSTA), University of Insubria, Via G.B. Vico 46, 21100 Varese, Italy
| | - Navarro Ferronato
- Department of Theoretical and Applied Sciences (DiSTA), University of Insubria, Via G.B. Vico 46, 21100 Varese, Italy
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44
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Holst LH, Madsen NG, Toftgård FT, Rønne F, Moise IM, Petersen EI, Fojan P. De novo design of a polycarbonate hydrolase. Protein Eng Des Sel 2023; 36:gzad022. [PMID: 38035789 DOI: 10.1093/protein/gzad022] [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: 03/08/2023] [Revised: 10/31/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023] Open
Abstract
Enzymatic degradation of plastics is currently limited to the use of engineered natural enzymes. As of yet, all engineering approaches applied to plastic degrading enzymes retain the natural $\alpha /\beta $-fold. While mutations can be used to increase thermostability, an inherent maximum likely exists for the $\alpha /\beta $-fold. It is thus of interest to introduce catalytic activity toward plastics in a different protein fold to escape the sequence space of plastic degrading enzymes. Here, a method for designing highly thermostable enzymes that can degrade plastics is described. With the help of Rosetta an active site catalysing the hydrolysis of polycarbonate is introduced into a set of thermostable scaffolds. Through computational evaluation, a potential PCase was selected and produced recombinantly in Escherichia coli. Thermal analysis suggests that the design has a melting temperature of >95$^{\circ }$C. Activity toward polycarbonate was confirmed using atomic force spectroscopy (AFM), proving the successful design of a PCase.
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Affiliation(s)
- Laura H Holst
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Niklas G Madsen
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Freja T Toftgård
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Freja Rønne
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Ioana-Malina Moise
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Evamaria I Petersen
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Peter Fojan
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
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