1
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Jiang L, Tian Y, Zhang H, Liu S. Molecular-level insight into the effects of low moisture and trehalose on the thermostability of β-glucosidase. Food Chem 2024; 460:140607. [PMID: 39068804 DOI: 10.1016/j.foodchem.2024.140607] [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: 02/24/2024] [Revised: 07/12/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
The high temperature induces conformational changes in β-glucosidase, making it inactive and limiting its application field. In this paper, the effect of trehalose on the thermostability of β-glucosidase from low-moisture Hevea brasiliensis seeds was investigated. The results showed that the residual enzyme activities of β-glucosidase supplemented with trehalose after high-temperature treatment were significantly higher than that of the control group. The improvement of thermostability could be explained by low-field nuclear magnetic resonance (LF-NMR) and molecular dynamics (MD) simulations at the molecular level. Moreover, adding trehalose increased the water activity and water content of β-glucosidase, leading to a more stable conformation. Trehalose replaced some water and formed a stable network of hydrogen bonds with protein and surrounding water. The glass formed by trehalose also reduced molecular movement, thus providing good protection for enzymes.
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Affiliation(s)
- Lian Jiang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; Engineering Research Center of Utilization of Tropical Polysaccharide Resources, the Ministry of Education, Haikou 570228, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
| | - Yongli Tian
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; Engineering Research Center of Utilization of Tropical Polysaccharide Resources, the Ministry of Education, Haikou 570228, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
| | - Haide Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; Engineering Research Center of Utilization of Tropical Polysaccharide Resources, the Ministry of Education, Haikou 570228, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China
| | - Shisheng Liu
- School of Food Science and Engineering, Hainan University, Haikou 570228, China; Engineering Research Center of Utilization of Tropical Polysaccharide Resources, the Ministry of Education, Haikou 570228, China; Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou 570228, China.
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2
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Hernández-Sancho JM, Boudigou A, Alván-Vargas MVG, Freund D, Arnling Bååth J, Westh P, Jensen K, Noda-García L, Volke DC, Nikel PI. A versatile microbial platform as a tunable whole-cell chemical sensor. Nat Commun 2024; 15:8316. [PMID: 39333077 DOI: 10.1038/s41467-024-52755-y] [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: 05/08/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Biosensors are used to detect and quantify chemicals produced in industrial microbiology with high specificity, sensitivity, and portability. Most biosensors, however, are limited by the need for transcription factors engineered to recognize specific molecules. In this study, we overcome the limitations typically associated with traditional biosensors by engineering Pseudomonas putida for whole-cell sensing of a variety of chemicals. Our approach integrates fluorescent reporters with synthetic auxotrophies within central metabolism that can be complemented by target analytes in growth-coupled setups. This platform enables the detection of a wide array of structurally diverse chemicals under various conditions, including co-cultures of producer cell factories and sensor strains. We also demonstrate the applicability of this versatile biosensor platform for monitoring complex biochemical processes, including plastic degradation by either purified hydrolytic enzymes or engineered bacteria. This microbial system provides a rapid, sensitive, and readily adaptable tool for monitoring cell factory performance and for environmental analyzes.
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Affiliation(s)
- Javier M Hernández-Sancho
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Boudigou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maria V G Alván-Vargas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dekel Freund
- Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Jenny Arnling Bååth
- Department of Biotechnology and Biomedicine Interfacial Enzymology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine Interfacial Enzymology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Lianet Noda-García
- Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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3
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Retnadhas S, Ducat DC, Hegg EL. Nature-Inspired Strategies for Sustainable Degradation of Synthetic Plastics. JACS AU 2024; 4:3323-3339. [PMID: 39328769 PMCID: PMC11423324 DOI: 10.1021/jacsau.4c00388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 09/28/2024]
Abstract
Synthetic plastics have become integral to our daily lives, yet their escalating production, limited biodegradability, and inadequate waste management contribute to environmental contamination. Biological plastic degradation is one promising strategy to address this pollution. The inherent chemical and physical properties of synthetic plastics, however, pose challenges for microbial enzymes, hindering the effective degradation and the development of a sustainable biological recycling process. This Perspective explores alternative, nature-inspired strategies designed to overcome some key limitations in currently available plastic-degrading enzymes. Nature's refined degradation pathways for natural polymers, such as cellulose, present a compelling framework for the development of efficient technologies for enzymatic plastic degradation. By drawing insights from nature, we propose a general strategy of employing substrate binding domains to improve targeting and multienzyme scaffolds to overcome enzymatic efficiency limitations. As one potential application, we outline a multienzyme pathway to upcycle polyethylene into alkenes. Employing nature-inspired strategies can present a path toward sustainable solution to the environmental impact of synthetic plastics.
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Affiliation(s)
- Sreeahila Retnadhas
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Daniel C Ducat
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
| | - Eric L Hegg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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4
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Wang N, Li Y, Zheng M, Dong W, Zhang Q, Wang W. BhrPETase catalyzed polyethylene terephthalate depolymerization: A quantum mechanics/molecular mechanics approach. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135414. [PMID: 39102770 DOI: 10.1016/j.jhazmat.2024.135414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/20/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
Polyethylene terephthalate (PET) is a widely used material in our daily life, particularly in areas such as packaging, fibers, and engineering plastics. However, PET waste can accumulate in the environment and pose a great threat to our ecosystem. Recently enzymatic conversion has emerged as an efficient and green strategy to address the PET crisis. Here, using a theoretical approach combining molecular dynamics simulation and quantum mechanics/molecular mechanics calculations, the depolymerization mechanism of the thermophilic cutinase BhrPETase was fully deciphered. Surprisingly, unlike the previously studied cutinase LCCICCG, our results indicate that the first step, catalytic triad assisted nucleophilic attack, is the rate-determining step. The corresponding Boltzmann weighted average energy barrier is 18.2 kcal/mol. Through extensive comparison between BhrPETase and LCCICCG, we evidence that key features like charge CHis@N1 and angle APET@C1-Ser@O1-His@H1 significantly impact the depolymerization efficiency of BhrPETase. Non-covalent bond interaction and distortion/interaction analysis inform new insights on enzyme engineer and may aid the recycling of enzymatic PET waste. This study will aid the advancement of the plastic bio-recycling economy and promote resource conservation and reuse.
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Affiliation(s)
- Ningru Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Mingna Zheng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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5
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Xu S, Huo C, Chu X. Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases. J Chem Inf Model 2024. [PMID: 39269430 DOI: 10.1021/acs.jcim.4c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
The accumulation of polyethylene terephthalate (PET), a widely used polyester plastic in packaging and textiles, has led to a global environmental crisis. Biodegradation presents a promising strategy for PET recycling, with PET hydrolases (PETase) undertaking the task at the molecular level. Unfortunately, PETase operates only at ambient temperatures with low efficiency, limiting its industrial application. Current engineering efforts focus on enhancing the thermostability of PETase, but increased stability can reduce the structural dynamics needed for substrate binding, potentially slowing enzymatic activity. To elucidate the balance between stability and flexibility in optimizing PETase catalytic activity, we performed theoretical investigations on both wild-type PETase (WT-PETase) and a thermophilic variant (Thermo-PETase) using molecular dynamics simulations and frustration analysis. Despite being initially designed to stabilize the native structure of the enzyme, our findings reveal that Thermo-PETase exhibits an unprecedented increase in structural flexibility at the PET-binding and catalytic sites, beneficial for substrate recruitment and product release, compared to WT-PETase. Upon PET binding, we observed that the structural dynamics of Thermo-PETase is largely quenched, favoring the proximity between the catalytic residues and the carbonyl of the PET substrate. This may potentially contribute to a higher probability of a catalytic reaction occurring in Thermo-PETase compared to WT-PETase. We suggest that Thermo-PETase can exhibit higher PET-degradation performance than WT-PETase across a broad temperature range by leveraging stability and flexibility at high and low temperatures, respectively. Our findings provide valuable insights into how PETase optimizes its enzymatic performance by balancing stability and flexibility, which may contribute to future PETase design strategies.
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Affiliation(s)
- Shiqinrui Xu
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China
| | - Chengze Huo
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China
| | - Xiakun Chu
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China
- Guangzhou Municipal Key Laboratory of Materials Informatics, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong 511400, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, China
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6
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Aer L, Jiang Q, Zhong L, Si Q, Liu X, Pan Y, Feng J, Zeng H, Tang L. Optimization of polyethylene terephthalate biodegradation using a self-assembled multi-enzyme cascade strategy. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134887. [PMID: 38901251 DOI: 10.1016/j.jhazmat.2024.134887] [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: 02/04/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
Although many efforts have been devoted to the modification of polyethylene terephthalate (PET) hydrolases for improving the efficiency of PET degradation, the catalytic performance of these enzymes at near-ambient temperatures remains a challenge. Herein, a multi-enzyme cascade system (PT-EC) was developed and validated by assembling three well-developed PETases, PETaseEHA, Fast-PETase, and Z1-PETase, respectively, together with carboxylesterase TfCa, and hydrophobic binding module CBM3a using scaffold proteins. The resulting PT-ECEHA, PT-ECFPE, PT-ECZPE all demonstrated outstanding PET degradation efficacy. Notably, PT-ECEHA exhibited a 16.5-fold increase in product release compared to PETaseEHA, and PT-ECZPE yielded the highest amount of product. Subsequently, PT-ECs were displayed on the surface of Escherichia coli, respectively, and their degradation efficiency toward three PET types was investigated. The displayed PT-ECEHA exhibited a 20-fold increase in degradation efficiency with PET film compared to the surface-displayed PETaseEHA. Remarkably, an almost linear increase in product release was observed for the displayed PT-ECZPE over a one-week degradation period, reaching 11.56 ± 0.64 mM after 7 days. TfCaI69W/L281Y evolved using a docking-based virtual screening strategy showed a further 2.5-fold increase in the product release of PET degradation. Collectively, these advantages of PT-EC demonstrated the potential of a multi-enzyme cascade system for PET bio-cycling.
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Affiliation(s)
- Lizhu Aer
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qifa Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Linling Zhong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qiuyue Si
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Xianghong Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yan Pan
- Medical School of University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Juan Feng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hongjuan Zeng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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7
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Ali SS, Elsamahy T, Al-Tohamy R, Sun J. A critical review of microplastics in aquatic ecosystems: Degradation mechanisms and removing strategies. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100427. [PMID: 38765892 PMCID: PMC11099331 DOI: 10.1016/j.ese.2024.100427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/21/2024] [Accepted: 04/21/2024] [Indexed: 05/22/2024]
Abstract
Plastic waste discarded into aquatic environments gradually degrades into smaller fragments, known as microplastics (MPs), which range in size from 0.05 to 5 mm. The ubiquity of MPs poses a significant threat to aquatic ecosystems and, by extension, human health, as these particles are ingested by various marine organisms including zooplankton, crustaceans, and fish, eventually entering the human food chain. This contamination threatens the entire ecological balance, encompassing food safety and the health of aquatic systems. Consequently, developing effective MP removal technologies has emerged as a critical area of research. Here, we summarize the mechanisms and recently reported strategies for removing MPs from aquatic ecosystems. Strategies combining physical and chemical pretreatments with microbial degradation have shown promise in decomposing MPs. Microorganisms such as bacteria, fungi, algae, and specific enzymes are being leveraged in MP remediation efforts. Recent advancements have focused on innovative methods such as membrane bioreactors, synthetic biology, organosilane-based techniques, biofilm-mediated remediation, and nanomaterial-enabled strategies, with nano-enabled technologies demonstrating substantial potential to enhance MP removal efficiency. This review aims to stimulate further innovation in effective MP removal methods, promoting environmental and social well-being.
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Affiliation(s)
- Sameh S. Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Tamer Elsamahy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Rania Al-Tohamy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
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8
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Ma HN, Hsiang CC, Ng IS. Tailored expression of ICCM cutinase in engineered Escherichia coli for efficient polyethylene terephthalate hydrolysis. Enzyme Microb Technol 2024; 179:110476. [PMID: 38944965 DOI: 10.1016/j.enzmictec.2024.110476] [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: 04/05/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Enzymatic depolymerization of PET waste emerges as a crucial and sustainable solution for combating environmental pollution. Over the past decade, PET hydrolytic enzymes, such as PETase from Ideonella sakaiensis (IsPETases), leaf compost cutinases (LCC), and lipases, have been subjected to rational mutation to enhance their enzymatic properties. ICCM, one of the best LCC mutants, was selected for overexpression in Escherichia coli BL21(DE3) for in vitro PET degradation. However, overexpressing ICCM presents challenges due to its low productivity. A new stress-inducible T7RNA polymerase-regulating E. coli strain, ASIAhsp, which significantly enhances ICCM production by 72.8 % and achieves higher enzyme solubility than other strains. The optimal cultural condition at 30 °C with high agitation, corresponding to high dissolved oxygen levels, has brought the maximum productivity of ICCM and high PET-hydrolytic activity. The most effective PET biodegradation using crude or pure ICCM occurred at pH 10 and 60 °C. Moreover, ICCM exhibited remarkable thermostability, retaining 60 % activity after a 5-day reaction at 60 °C. Notably, crude ICCM eliminates the need for purification and efficiently degrades PET films.
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Affiliation(s)
- Hsing-Ning Ma
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Chuan-Chieh Hsiang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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9
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Yip A, McArthur OD, Ho KC, Aucoin MG, Ingalls BP. Degradation of polyethylene terephthalate (PET) plastics by wastewater bacteria engineered via conjugation. Microb Biotechnol 2024; 17:e70015. [PMID: 39315602 PMCID: PMC11420662 DOI: 10.1111/1751-7915.70015] [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: 05/27/2024] [Accepted: 08/22/2024] [Indexed: 09/25/2024] Open
Abstract
Wastewater treatment plants are one of the major pathways for microplastics to enter the environment. In general, microplastics are contaminants of global concern that pose risks to ecosystems and human health. Here, we present a proof-of-concept for reduction of microplastic pollution emitted from wastewater treatment plants: delivery of recombinant DNA to bacteria in wastewater to enable degradation of polyethylene terephthalate (PET). Using a broad-host-range conjugative plasmid, we enabled various bacterial species from a municipal wastewater sample to express FAST-PETase, which was released into the extracellular environment. We found that FAST-PETase purified from some transconjugant isolates could degrade about 40% of a 0.25 mm thick commercial PET film within 4 days at 50°C. We then demonstrated partial degradation of a post-consumer PET product over 5-7 days by exposure to conditioned media from isolates. These results have broad implications for addressing the global plastic pollution problem by enabling environmental bacteria to degrade PET.
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Affiliation(s)
- Aaron Yip
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Owen D McArthur
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Kalista C Ho
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Marc G Aucoin
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Brian P Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada
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10
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Bergeson AR, Alper HS. Advancing sustainable biotechnology through protein engineering. Trends Biochem Sci 2024:S0968-0004(24)00185-3. [PMID: 39232879 DOI: 10.1016/j.tibs.2024.07.006] [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: 04/11/2024] [Revised: 07/20/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The push for industrial sustainability benefits from the use of enzymes as a replacement for traditional chemistry. Biological catalysts, especially those that have been engineered for increased activity, stability, or novel function, and are often greener than alternative chemical approaches. This Review highlights the role of engineered enzymes (and identifies directions for further engineering efforts) in the application areas of greenhouse gas sequestration, fuel production, bioremediation, and degradation of plastic wastes.
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Affiliation(s)
- Amelia R Bergeson
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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11
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dos Santos A, da Costa CHS, Silva PHA, Skaf MS, Lameira J. Exploring the Reaction Mechanism of Polyethylene Terephthalate Biodegradation through QM/MM Approach. J Phys Chem B 2024; 128:7486-7499. [PMID: 39072475 PMCID: PMC11317977 DOI: 10.1021/acs.jpcb.4c02207] [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: 04/03/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
The enzyme PETase fromIdeonella sakaiensis (IsPETase) strain 201-F6 can catalyze the hydrolysis of polyethylene terephthalate (PET), mainly converting it into mono(2-hydroxyethyl) terephthalic acid (MHET). In this study, we used quantum mechanics/molecular mechanics (QM/MM) simulations to explore the molecular details of the catalytic reaction mechanism of IsPETase in the formation of MHET. The QM region was described with AM1d/PhoT and M06-2X/6-31+G(d,p) potential. QM/MM simulations unveil the complete enzymatic PET hydrolysis mechanism and identify two possible reaction pathways for acylation and deacylation steps. The barrier obtained at M06-2X/6-31+G(d,p)/MM potential for the deacylation step corresponds to 20.4 kcal/mol, aligning with the experimental value of 18 kcal/mol. Our findings indicate that deacylation is the rate-limiting step of the process. Furthermore, per-residue interaction energy contributions revealed unfavorable contributions to the transition state of amino acids located at positions 200-230, suggesting potential sites for targeted mutations. These results can contribute to the development of more active and selective enzymes for PET depolymerization.
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Affiliation(s)
- Alberto
M. dos Santos
- Institute
of Chemistry and Centre for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, Sao Paulo, Brazil
| | - Clauber H. S. da Costa
- Institute
of Chemistry and Centre for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, Sao Paulo, Brazil
| | - Pedro H. A. Silva
- Institute
of Biological Sciences, Federal University
of Para, 66075-110 Belem, Para, Brazil
| | - Munir S. Skaf
- Institute
of Chemistry and Centre for Computer in Engineering and Sciences, University of Campinas (UNICAMP), Campinas 13084-862, Sao Paulo, Brazil
| | - Jerônimo Lameira
- Institute
of Biological Sciences, Federal University
of Para, 66075-110 Belem, Para, Brazil
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12
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Safdar A, Ismail F, Safdar M, Imran M. Eco-friendly approaches for mitigating plastic pollution: advancements and implications for a greener future. Biodegradation 2024; 35:493-518. [PMID: 38310578 DOI: 10.1007/s10532-023-10062-1] [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: 03/14/2023] [Accepted: 12/13/2023] [Indexed: 02/06/2024]
Abstract
Plastic pollution has become a global problem since the extensive use of plastic in industries such as packaging, electronics, manufacturing and construction, healthcare, transportation, and others. This has resulted in an environmental burden that is continually growing, which has inspired many scientists as well as environmentalists to come up with creative solutions to deal with this problem. Numerous studies have been reviewed to determine practical, affordable, and environmentally friendly solutions to regulate plastic waste by leveraging microbes' innate abilities to naturally decompose polymers. Enzymatic breakdown of plastics has been proposed to serve this goal since the discovery of enzymes from microbial sources that truly interact with plastic in its naturalistic environment and because it is a much faster and more effective method than others. The scope of diverse microbes and associated enzymes in polymer breakdown is highlighted in the current review. The use of co-cultures or microbial consortium-based techniques for the improved breakdown of plastic products and the generation of high-value end products that may be utilized as prototypes of bioenergy sources is highlighted. The review also offers a thorough overview of the developments in the microbiological and enzymatic biological degradation of plastics, as well as several elements that impact this process for the survival of our planet.
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Affiliation(s)
- Ayesha Safdar
- Department of Biochemistry, The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan
- The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan
| | - Fatima Ismail
- Department of Biochemistry, The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan.
- The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan.
| | - Maryem Safdar
- University College of Conventional Medicine, The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan
- The Islamia University of Bahawalpur, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Imran
- Institute of Advanced Study, Shenzhen University, Shenzhen, 5180600, Guangdong Province, China.
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13
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Zheng Y, Zhang J, You S, Lin W, Su R, Qi W. Efficient thermophilic polyethylene terephthalate hydrolase enhanced by cross correlation-based accumulated mutagenesis strategy. BIORESOURCE TECHNOLOGY 2024; 406:130929. [PMID: 38838832 DOI: 10.1016/j.biortech.2024.130929] [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: 02/27/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 06/07/2024]
Abstract
Polyethylene terephthalate (PET) has caused significant pollution issues. Compared to chemical degradation with high energy consumption and cost, enzymatic degradation offers a sustainable solution for PET waste recycling. However, the hydrolytic activity of current PET hydrolases still requires improvement. In this study, a cross-correlation-based accumulated mutagenesis (CAM) strategy was developed to enhance the hydrolysis activity. By mitigating epistatic effect and combinational mutations, we achieved a highly active variant LCC-YGA (H183Y/L124G/S29A) with 2.1-fold hydrolytic activity on amorphous PET films of LCC-ICCG. Conformational analysis elucidated how the introduction of distal mutations enhanced activity. The dynamic correlation among different regions facilitated a synergistic effect, enhancing binding pocket flexibility through remote interactions. Totally, this work offers novel insights and methods for PET hydrolases engineering and provides an efficient enzyme for PET degradation and recycling.
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Affiliation(s)
- Yunxin Zheng
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Shengping You
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Wei Lin
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, PR China.
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14
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Ercolano C, Iacono R, Cafaro V, Pizzo E, Giovannelli D, Feuerriegel G, Streit WR, Strazzulli A, Moracci M. Biochemical Characterisation of Sis: A Distinct Thermophilic PETase with Enhanced NanoPET Substrate Hydrolysis and Thermal Stability. Int J Mol Sci 2024; 25:8120. [PMID: 39125688 PMCID: PMC11311821 DOI: 10.3390/ijms25158120] [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: 05/27/2024] [Revised: 07/12/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Polyethylene terephthalate (PET) degradation by enzymatic hydrolysis is significant for addressing plastic pollution and fostering sustainable waste management practices. Identifying thermophilic and thermostable PET hydrolases is particularly crucial for industrial bioprocesses, where elevated temperatures may enhance enzymatic efficiency and process kinetics. In this study, we present the discovery of a novel thermophilic and thermostable PETase enzyme named Sis, obtained through metagenomic sequence-based analysis. Sis exhibits robust activity on nanoPET substrates, demonstrating effectiveness at temperatures up to 70 °C and displaying exceptional thermal stability with a melting temperature (Tm) of 82 °C. Phylogenetically distinct from previously characterised PET hydrolases, Sis represents a valuable addition to the repertoire of enzymes suitable for PET degradation.
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Affiliation(s)
- Carmen Ercolano
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
| | - Roberta Iacono
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Valeria Cafaro
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), University of Naples Federico II, 80126 Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
- Institute for Marine Biological Resources and Biotechnologies, Italian National Research Council, CNR-IRBIM, 60125 Ancona, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ 08901, USA
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany; (G.F.); (W.R.S.)
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany; (G.F.); (W.R.S.)
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia 21, 80126 Naples, Italy; (C.E.); (R.I.); (V.C.); (E.P.); (D.G.); (M.M.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
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15
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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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16
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Wang T, Yang WT, Gong YM, Zhang YK, Fan XX, Wang GC, Lu ZH, Liu F, Liu XH, Zhu YS. Molecular engineering of PETase for efficient PET biodegradation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116540. [PMID: 38833982 DOI: 10.1016/j.ecoenv.2024.116540] [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: 02/23/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
The widespread utilization of polyethylene terephthalate (PET) has caused a variety of environmental and health problems. Compared with traditional thermomechanical or chemical PET cycling, the biodegradation of PET may offer a more feasible solution. Though the PETase from Ideonalla sakaiensis (IsPETase) displays interesting PET degrading performance under mild conditions; the relatively low thermal stability of IsPETase limits its practical application. In this study, enzyme-catalysed PET degradation was investigated with the promising IsPETase mutant HotPETase (HP). On this basis, a carbohydrate-binding module from Bacillus anthracis (BaCBM) was fused to the C-terminus of HP to construct the PETase mutant (HLCB) for increased PET degradation. Furthermore, to effectively improve PET accessibility and PET-degrading activity, the truncated outer membrane hybrid protein (FadL) was used to expose PETase and BaCBM on the surface of E. coli (BL21with) to develop regenerable whole-cell biocatalysts (D-HLCB). Results showed that, among the tested small-molecular weight ester compounds (p-nitrophenyl phosphate (pNPP), p-Nitrophenyl acetate (pNPA), 4-Nitrophenyl butyrate (pNPB)), PETase displayed the highest hydrolysing activity against pNPP. HP displayed the highest catalytic activity (1.94 μM(p-NP)/min) at 50 °C and increased longevity at 40 °C. The fused BaCBM could clearly improve the catalytic performance of PETase by increasing the optimal reaction temperature and improving the thermostability. When HLCB was used for PET degradation, the yield of monomeric products (255.7 μM) was ∼25.5 % greater than that obtained after 50 h of HP-catalysed PET degradation. Moreover, the highest yield of monomeric products from the D-HLCB-mediated system reached 1.03 mM. The whole-cell catalyst D-HLCB displayed good reusability and stability and could maintain more than 54.6 % of its initial activity for nine cycles. Finally, molecular docking simulations were utilized to investigate the binding mechanism and the reaction mechanism of HLCB, which may provide theoretical evidence to further increase the PET-degrading activities of PETases through rational design. The proposed strategy and developed variants show potential for achieving complete biodegradation of PET under mild conditions.
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Affiliation(s)
- Tao Wang
- School of Biological Science, Jining Medical University, Jining, China
| | - Wen-Tao Yang
- School of Biological Science, Jining Medical University, Jining, China
| | - Yu-Ming Gong
- School of Biological Science, Jining Medical University, Jining, China
| | - Ying-Kang Zhang
- School of Biological Science, Jining Medical University, Jining, China
| | - Xin-Xin Fan
- School of Biological Science, Jining Medical University, Jining, China
| | - Guo-Cheng Wang
- School of Biological Science, Jining Medical University, Jining, China
| | - Zhen-Hua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Xiao-Huan Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - You-Shuang Zhu
- School of Biological Science, Jining Medical University, Jining, China.
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17
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Schneier A, Melaugh G, Sadler JC. Engineered plastic-associated bacteria for biodegradation and bioremediation. BIOTECHNOLOGY FOR THE ENVIRONMENT 2024; 1:7. [PMID: 39026535 PMCID: PMC11256910 DOI: 10.1186/s44314-024-00007-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/29/2024] [Indexed: 07/20/2024]
Abstract
The global plastic waste crisis has triggered the development of novel methods for removal of recalcitrant polymers from the environment. Biotechnological approaches have received particular attention due to their potential for enabling sustainable, low-intensity bioprocesses which could also be interfaced with microbial upcycling pathways to support the emerging circular bioeconomy. However, low biodegradation efficiency of solid plastic materials remains a bottleneck, especially at mesophilic conditions required for one-pot degradation and upcycling. A promising strategy used in nature to address this is localisation of plastic-degrading microbes to the plastic surface via biofilm-mediated surface association. This review highlights progress and opportunities in leveraging these naturally occurring mechanisms of biofilm formation and other cell-surface adhesion biotechnologies to co-localise engineered cells to plastic surfaces. We further discuss examples of combining these approaches with extracellular expression of plastic-degrading enzymes to accelerate plastic degradation. Additionally, we review this topic in the context of nano- and microplastics bioremediation and their removal from wastewater and finally propose future research directions for this nascent field.
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Affiliation(s)
- Arianna Schneier
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, King’s Buildings, Edinburgh, EH9 3FF UK
| | - Gavin Melaugh
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD UK
- School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL UK
| | - Joanna C. Sadler
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, King’s Buildings, Edinburgh, EH9 3FF UK
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18
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Li A, Wu L, Cui H, Song Y, Zhang X, Li X. Unlocking a Sustainable Future for Plastics: A Chemical-Enzymatic Pathway for Efficient Conversion of Mixed Waste to MHET and Energy-Saving PET Recycling. CHEMSUSCHEM 2024; 17:e202301612. [PMID: 38385577 DOI: 10.1002/cssc.202301612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
The heterogeneous monomers obtained from plastic waste degradation are unfavorable for PET recondensation and high-value derivative synthesis. Herein, we developed an efficient chemical-enzymatic approach to convert mixed plastic wastes into homogeneous mono-2-hydroxyethyl terephthalate (MHET) without downstream purification, benefiting from three discovered BHETases (KbEst, KbHyd, and BrevEst) in nature. Towards the mixed plastic waste, integrating the chemical K2CO3-driven glycolysis process with the BHETase depolymerization technique resulted in an MHET yield of up to 98.26 % in 40 h. Remarkably, BrevEst accomplished the highest BHET hydrolysis (~87 % efficiency in 12 h) for yielding analytical-grade MHET compared to seven state-of-the-art PET hydrolases (18 %-40 %). In an investigation combining quantum theoretical computations and experimental validations, we established a MHET-initiated PET repolymerization pathway. This shortcut approach with MHET promises to strengthen the valorization of mixed plastics, offering a substantially more efficient and energy-saving route for PET recycling.
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Affiliation(s)
- Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Luxuan Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yibo Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
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19
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Han Z, Nina MRH, Zhang X, Huang H, Fan D, Bai Y. Discovery and characterization of two novel polyethylene terephthalate hydrolases: One from a bacterium identified in human feces and one from the Streptomyces genus. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134532. [PMID: 38749251 DOI: 10.1016/j.jhazmat.2024.134532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Polyethylene terephthalate (PET) is widely used for various industrial applications. However, owing to its extremely slow breakdown rate, PET accumulates as plastic trash, which negatively affects the environment and human health. Here, we report two novel PET hydrolases: PpPETase from Pseudomonas paralcaligenes MRCP1333, identified in human feces, and ScPETase from Streptomyces calvus DSM 41452. These two enzymes can decompose various PET materials, including semicrystalline PET powders (Cry-PET) and low-crystallinity PET films (gf-PET). By structure-guided engineering, two variants, PpPETaseY239R/F244G/Y250G and ScPETaseA212C/T249C/N195H/N243K were obtained that decompose Cry-PET 3.1- and 1.9-fold faster than their wild-type enzymes, respectively. The co-expression of ScPETase and mono-(2-hydroxyethyl) terephthalate hydrolase from Ideonella sakaiensis (IsMHETase) resulted in 1.4-fold more degradation than the single enzyme system. This engineered strain degraded Cry-PET and gf-PET by more than 40% and 6%, respectively, after 30 d. The concentrations of terephthalic acid (TPA) in the Cry-PET and gf-PET degradation products were 37.7% and 25.6%, respectively. The discovery of these two novel PET hydrolases provides opportunities to create more powerful biocatalysts for PET biodegradation.
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Affiliation(s)
- Zhengyang Han
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Mario Roque Huanca Nina
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoyan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Hanyao Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Daidi Fan
- Shaanxi R&D Centre of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yunpeng Bai
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China.
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20
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Wang C, Long R, Lin X, Liu W, Zhu L, Jiang L. Development and characterization of a bacterial enzyme cascade reaction system for efficient and stable PET degradation. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134480. [PMID: 38703683 DOI: 10.1016/j.jhazmat.2024.134480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/15/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
The widespread use of polyethylene terephthalate (PET) in various industries has led to a surge in microplastics (MPs) pollution, posing a significant threat to ecosystems and human health. To address this, we have developed a bacterial enzyme cascade reaction system (BECRS) that focuses on the efficient degradation of PET. This system harnesses the Escherichia coli (E. coli) surface to display CsgA protein, which forms curli fibers, along with the carbohydrate-binding module 3 (CBM3) and PETases, to enhance the adsorption and degradation of PET. The study demonstrated that the BECRS achieved a notable PET film degradation rate of 3437 ± 148 μg/(d*cm²), with a degradation efficiency of 21.40% for crystalline PET MPs, and the degradation products were all converted to TPA. The stability of the system was evidenced by retaining over 80% of its original activity after multiple uses and during one month of storage. Molecular dynamics simulations confirmed that the presence of CsgA did not interfere with the enzymatic activity of PETases. This BECRS represents a significant step forward in the biodegradation of PET, particularly microplastics, offering a practical and sustainable solution for environmental pollution control.
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Affiliation(s)
- Chengyong Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Rui Long
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Xiran Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wei Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China; College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
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21
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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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22
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Saunders JW, Damry AM, Vongsouthi V, Spence MA, Frkic RL, Gomez C, Yates PA, Matthews DS, Tokuriki N, McLeod MD, Jackson CJ. Increasing the Soluble Expression and Whole-Cell Activity of the Plastic-Degrading Enzyme MHETase through Consensus Design. Biochemistry 2024; 63:1663-1673. [PMID: 38885634 DOI: 10.1021/acs.biochem.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The mono(2-hydroxyethyl) terephthalate hydrolase (MHETase) from Ideonella sakaiensis carries out the second step in the enzymatic depolymerization of poly(ethylene terephthalate) (PET) plastic into the monomers terephthalic acid (TPA) and ethylene glycol (EG). Despite its potential industrial and environmental applications, poor recombinant expression of MHETase has been an obstacle to its industrial application. To overcome this barrier, we developed an assay allowing for the medium-throughput quantification of MHETase activity in cell lysates and whole-cell suspensions, which allowed us to screen a library of engineered variants. Using consensus design, we generated several improved variants that exhibit over 10-fold greater whole-cell activity than wild-type (WT) MHETase. This is revealed to be largely due to increased soluble expression, which biochemical and structural analysis indicates is due to improved protein folding.
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Affiliation(s)
- Jake W Saunders
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Adam M Damry
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Patrick A Yates
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Dana S Matthews
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Malcolm D McLeod
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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23
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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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24
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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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25
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Orr G, Niv Y, Barakat M, Boginya A, Dessau M, Afriat-Jurnou L. Streamlined screening of extracellularly expressed PETase libraries for improved polyethylene terephthalate degradation. Biotechnol J 2024; 19:e2400021. [PMID: 38987219 DOI: 10.1002/biot.202400021] [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: 01/09/2024] [Revised: 05/26/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024]
Abstract
Enzyme-mediated polyethylene terephthalate (PET) depolymerization has recently emerged as a sustainable solution for PET recycling. Towards an industrial-scale implementation of this technology, various strategies are being explored to enhance PET depolymerization (PETase) activity and improve enzyme stability, expression, and purification processes. Recently, rational engineering of a known PET hydrolase (LCC-leaf compost cutinase) has resulted in the isolation of a variant harboring four-point mutations (LCC-ICCG), presenting increased PETase activity and thermal stability. Here, we revealed the enzyme's natural extracellular expression and used it to efficiently screen error-prone genetic libraries based on LCC-ICCG for enhanced activity toward consumer-grade PET. Following multiple rounds of mutagenesis and screening, we successfully isolated variants that exhibited up to a 60% increase in PETase activity. Among other mutations, the improved variants showed a histidine to tyrosine substitution at position 218, a residue known to be involved in substrate binding and stabilization. Introducing H218Y mutation on the background of LCC-ICCG (named here LCC-ICCG/H218Y) resulted in a similar level of activity improvement. Analysis of the solved structure of LCC-ICCG/H218Y compared to other known PETases featuring different amino acids at the equivalent position suggests that H218Y substitution promotes enhanced PETase activity. The expression and screening processes developed in this study can be further used to optimize additional enzymatic parameters crucial for efficient enzymatic degradation of consumer-grade PET.
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Affiliation(s)
- Guy Orr
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Yoav Niv
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
| | - Maya Barakat
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | - Moshe Dessau
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
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26
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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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27
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Charlier C, Gavalda S, Grga J, Perrot L, Gabrielli V, Löhr F, Schörghuber J, Lichtenecker R, Arnal G, Marty A, Tournier V, Lippens G. Exploring the pH dependence of an improved PETase. Biophys J 2024; 123:1542-1552. [PMID: 38664965 PMCID: PMC11213969 DOI: 10.1016/j.bpj.2024.04.026] [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: 02/06/2024] [Revised: 03/20/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Enzymatic recycling of plastic and especially of polyethylene terephthalate (PET) has shown great potential to reduce its negative impact on our society. PET hydrolases (PETases) have been optimized using rational design and machine learning, but the mechanistic details of the PET depolymerization process remain unclear. Belonging to the carboxylic-ester hydrolase family with a canonical Ser-His-Asp catalytic triad, their observed alkaline pH optimum is generally thought to be related to the protonation state of the catalytic His. Here, we explore this aspect in the context of LCCICCG, an optimized PETase, derived from the leaf-branch compost cutinase enzyme. We use NMR to identify the dominant tautomeric structure of the six histidines. Five show surprisingly low pKa values below 4.0, whereas the catalytic H242 in the active enzyme displays a pKa value that varies from 4.9 to 4.7 when temperatures increase from 30°C to 50°C. Whereas the hydrolytic activity of the enzyme toward a soluble substrate can be modeled by the corresponding protonation/deprotonation curve, an important discrepancy is found when the substrate is the solid plastic. This opens the way to further mechanistic understanding of the PETase activity and underscores the importance of studying the enzyme at the liquid-solid interface.
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Affiliation(s)
- Cyril Charlier
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Sabine Gavalda
- Carbios, Parc Cataroux - Bâtiment B80, Clermont-Ferrand, France
| | - Jelena Grga
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Laura Perrot
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Valeria Gabrielli
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe, University Frankfurt, Frankfurt am Main, Germany
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, Vienna, Austria
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstraße 38, Vienna, Austria; MAG-LAB, Vienna, Austria
| | - Grégory Arnal
- Carbios, Parc Cataroux - Bâtiment B80, Clermont-Ferrand, France
| | - Alain Marty
- Carbios, Parc Cataroux - Bâtiment B80, Clermont-Ferrand, France
| | | | - Guy Lippens
- Toulouse Biotechnology Institute (TBI), University of Toulouse, CNRS, INRAE, INSA Toulouse, Toulouse Cedex, France.
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28
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Taxeidis G, Nikolaivits E, Nikodinovic-Runic J, Topakas E. Mimicking the enzymatic plant cell wall hydrolysis mechanism for the degradation of polyethylene terephthalate. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124347. [PMID: 38857840 DOI: 10.1016/j.envpol.2024.124347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Plastic pollution presents a global challenge, impacting ecosystems, wildlife, and economies. Polyethylene terephthalate (PET), widely used in products like bottles, significantly contributes to this issue due to poor waste collection. In recent years, there has been increasing interest in plant biomass-degrading enzymes for plastic breakdown, due to the structural and physicochemical similarities between natural and synthetic polymers. Filamentous fungi involved in hemicellulose degradation have developed a complex mode of action that includes not only enzymes but also biosurfactants; surface-active molecules that facilitate enzyme-substrate interactions. For this reason, this study aimed to mimic the mechanism of biomass degradation by repurposing plant cell wall degrading enzymes including a cutinase and three esterases to cooperatively contribute to PET degradation. Surfactants of different charge were also introduced in the reactions, as their role is similar to biosurfactants, altering the surface tension of the polymers and thus improving enzymes' accessibility. Notably, Fusarium oxysporum cutinase combined with anionic surfactant exhibited a 2.3- and 1.6-fold higher efficacy in hydrolyzing amorphous and semi-crystalline PET, respectively. When cutinase was combined with either of two ferulic acid esterases, it resulted in complete conversion of PET intermediate products to TPA, increasing the overall product release up to 1.9- fold in presence of surfactant. The combination of cutinase with a glucuronoyl esterase demonstrated significant potential in plastic depolymerization, increasing degradation yields in semi-crystalline PET by up to 1.4-fold. The approach of incorporating enzyme cocktails and surfactants emerge as an efficient solution for PET degradation in mild reaction conditions, with potential applications in eco-friendly plastic waste management.
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Affiliation(s)
- George Taxeidis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772, Athens, Greece
| | - Jasmina Nikodinovic-Runic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000, Belgrade, Serbia
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772, Athens, Greece.
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29
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Bergeson AR, Silvera AJ, Alper HS. Bottlenecks in biobased approaches to plastic degradation. Nat Commun 2024; 15:4715. [PMID: 38830860 PMCID: PMC11148140 DOI: 10.1038/s41467-024-49146-8] [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: 07/29/2023] [Accepted: 05/23/2024] [Indexed: 06/05/2024] Open
Abstract
Plastic waste is an environmental challenge, but also presents a biotechnological opportunity as a unique carbon substrate. With modern biotechnological tools, it is possible to enable both recycling and upcycling. To realize a plastics bioeconomy, significant intrinsic barriers must be overcome using a combination of enzyme, strain, and process engineering. This article highlights advances, challenges, and opportunities for a variety of common plastics.
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Affiliation(s)
- Amelia R Bergeson
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ashli J Silvera
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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30
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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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31
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Çalbaş B, Keobounnam AN, Korban C, Doratan AJ, Jean T, Sharma AY, Wright TA. Protein-polymer bioconjugation, immobilization, and encapsulation: a comparative review towards applicability, functionality, activity, and stability. Biomater Sci 2024; 12:2841-2864. [PMID: 38683585 DOI: 10.1039/d3bm01861j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Polymer-based biomaterials have received a lot of attention due to their biomedical, agricultural, and industrial potential. Soluble protein-polymer bioconjugates, immobilized proteins, and encapsulated proteins have been shown to tune enzymatic activity, improved pharmacokinetic ability, increased chemical and thermal stability, stimuli responsiveness, and introduced protein recovery. Controlled polymerization techniques, increased protein-polymer attachment techniques, improved polymer surface grafting techniques, controlled polymersome self-assembly, and sophisticated characterization methods have been utilized for the development of well-defined polymer-based biomaterials. In this review we aim to provide a brief account of the field, compare these methods for engineering biomaterials, provide future directions for the field, and highlight impacts of these forms of bioconjugation.
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Affiliation(s)
- Berke Çalbaş
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Ashley N Keobounnam
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Christopher Korban
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ainsley Jade Doratan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Tiffany Jean
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Aryan Yashvardhan Sharma
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Thaiesha A Wright
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
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32
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Martín-González D, de la Fuente Tagarro C, De Lucas A, Bordel S, Santos-Beneit F. Genetic Modifications in Bacteria for the Degradation of Synthetic Polymers: A Review. Int J Mol Sci 2024; 25:5536. [PMID: 38791573 PMCID: PMC11121894 DOI: 10.3390/ijms25105536] [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: 03/28/2024] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Synthetic polymers, commonly known as plastics, are currently present in all aspects of our lives. Although they are useful, they present the problem of what to do with them after their lifespan. There are currently mechanical and chemical methods to treat plastics, but these are methods that, among other disadvantages, can be expensive in terms of energy or produce polluting gases. A more environmentally friendly alternative is recycling, although this practice is not widespread. Based on the practice of the so-called circular economy, many studies are focused on the biodegradation of these polymers by enzymes. Using enzymes is a harmless method that can also generate substances with high added value. Novel and enhanced plastic-degrading enzymes have been obtained by modifying the amino acid sequence of existing ones, especially on their active site, using a wide variety of genetic approaches. Currently, many studies focus on the common aim of achieving strains with greater hydrolytic activity toward a different range of plastic polymers. Although in most cases the depolymerization rate is improved, more research is required to develop effective biodegradation strategies for plastic recycling or upcycling. This review focuses on a compilation and discussion of the most important research outcomes carried out on microbial biotechnology to degrade and recycle plastics.
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Affiliation(s)
- Diego Martín-González
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; (D.M.-G.); (A.D.L.); (S.B.)
| | - Carlos de la Fuente Tagarro
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; (D.M.-G.); (A.D.L.); (S.B.)
| | - Andrea De Lucas
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; (D.M.-G.); (A.D.L.); (S.B.)
| | - Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; (D.M.-G.); (A.D.L.); (S.B.)
- Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
| | - Fernando Santos-Beneit
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; (D.M.-G.); (A.D.L.); (S.B.)
- Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
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33
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Joho Y, Royan S, Caputo AT, Newton S, Peat TS, Newman J, Jackson C, Ardevol A. Enhancing PET Degrading Enzymes: A Combinatory Approach. Chembiochem 2024; 25:e202400084. [PMID: 38584134 DOI: 10.1002/cbic.202400084] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Plastic waste has become a substantial environmental issue. A potential strategy to mitigate this problem is to use enzymatic hydrolysis of plastics to depolymerize post-consumer waste and allow it to be reused. Over the last few decades, the use of enzymatic PET-degrading enzymes has shown promise as a great solution for creating a circular plastic waste economy. PsPETase from Piscinibacter sakaiensis has been identified as an enzyme with tremendous potential for such applications. But to improve its efficiency, enzyme engineering has been applied aiming at enhancing its thermal stability, enzymatic activity, and ease of production. Here, we combine different strategies such as structure-based rational design, ancestral sequence reconstruction and machine learning to engineer a more highly active Combi-PETase variant with a melting temperature of 70 °C and optimal performance at 60 °C. Furthermore, this study demonstrates that these approaches, commonly used in other works of enzyme engineering, are most effective when utilized in combination, enabling the improvement of enzymes for industrial applications.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Santana Royan
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Alessandro T Caputo
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Sophia Newton
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Thomas S Peat
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Janet Newman
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
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34
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Rahmati F, Sethi D, Shu W, Asgari Lajayer B, Mosaferi M, Thomson A, Price GW. Advances in microbial exoenzymes bioengineering for improvement of bioplastics degradation. CHEMOSPHERE 2024; 355:141749. [PMID: 38521099 DOI: 10.1016/j.chemosphere.2024.141749] [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: 09/06/2023] [Revised: 03/06/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Plastic pollution has become a major global concern, posing numerous challenges for the environment and wildlife. Most conventional ways of plastics degradation are inefficient and cause great damage to ecosystems. The development of biodegradable plastics offers a promising solution for waste management. These plastics are designed to break down under various conditions, opening up new possibilities to mitigate the negative impact of traditional plastics. Microbes, including bacteria and fungi, play a crucial role in the degradation of bioplastics by producing and secreting extracellular enzymes, such as cutinase, lipases, and proteases. However, these microbial enzymes are sensitive to extreme environmental conditions, such as temperature and acidity, affecting their functions and stability. To address these challenges, scientists have employed protein engineering and immobilization techniques to enhance enzyme stability and predict protein structures. Strategies such as improving enzyme and substrate interaction, increasing enzyme thermostability, reinforcing the bonding between the active site of the enzyme and substrate, and refining enzyme activity are being utilized to boost enzyme immobilization and functionality. Recently, bioengineering through gene cloning and expression in potential microorganisms, has revolutionized the biodegradation of bioplastics. This review aimed to discuss the most recent protein engineering strategies for modifying bioplastic-degrading enzymes in terms of stability and functionality, including enzyme thermostability enhancement, reinforcing the substrate binding to the enzyme active site, refining with other enzymes, and improvement of enzyme surface and substrate action. Additionally, discovered bioplastic-degrading exoenzymes by metagenomics techniques were emphasized.
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Affiliation(s)
- Farzad Rahmati
- Department of Microbiology, Faculty of Science, Qom Branch, Islamic Azad University (IAU), Qom 37185364, Iran
| | - Debadatta Sethi
- Sugarcane Research Station, Odisha University of Agriculture and Technology, Nayagarh, India
| | - Weixi Shu
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | | | - Mohammad Mosaferi
- Health and Environment Research Center, Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Allan Thomson
- Perennia Food and Agriculture Corporation., 173 Dr. Bernie MacDonald Dr., Bible Hill, Truro, NS, B6L 2H5, Canada
| | - G W Price
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
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35
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Shi C, Quinn EC, Diment WT, Chen EYX. Recyclable and (Bio)degradable Polyesters in a Circular Plastics Economy. Chem Rev 2024; 124:4393-4478. [PMID: 38518259 DOI: 10.1021/acs.chemrev.3c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Polyesters carrying polar main-chain ester linkages exhibit distinct material properties for diverse applications and thus play an important role in today's plastics economy. It is anticipated that they will play an even greater role in tomorrow's circular plastics economy that focuses on sustainability, thanks to the abundant availability of their biosourced building blocks and the presence of the main-chain ester bonds that can be chemically or biologically cleaved on demand by multiple methods and thus bring about more desired end-of-life plastic waste management options. Because of this potential and promise, there have been intense research activities directed at addressing recycling, upcycling or biodegradation of existing legacy polyesters, designing their biorenewable alternatives, and redesigning future polyesters with intrinsic chemical recyclability and tailored performance that can rival today's commodity plastics that are either petroleum based and/or hard to recycle. This review captures these exciting recent developments and outlines future challenges and opportunities. Case studies on the legacy polyesters, poly(lactic acid), poly(3-hydroxyalkanoate)s, poly(ethylene terephthalate), poly(butylene succinate), and poly(butylene-adipate terephthalate), are presented, and emerging chemically recyclable polyesters are comprehensively reviewed.
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Affiliation(s)
- Changxia Shi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Ethan C Quinn
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Wilfred T Diment
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Eugene Y-X Chen
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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36
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Gao L, Xu Z, Zhou J. Simulation Study of Polyethylene Terephthalate Hydrolase Adsorption on Self-Assembled Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7225-7233. [PMID: 38501967 DOI: 10.1021/acs.langmuir.4c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Polyethylene terephthalate (PET) hydrolase, discovered in Ideonella sakaiensis (IsPETase), is a promising agent for the biodegradation of PET under mild reaction conditions, yet the thermal stability is poor. The efficient immobilization and orientation of IsPETase on different solid substrates are essential for its application. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of IsPETase adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (SCDs). The results show that the protein adsorption orientation was determined not only by attraction interactions but also by repulsion interactions. IsPETase is adsorbed on the COOH-SAM surface with an "end-on" orientation, which favors the exposure of the catalyzed triplet to the solution. In addition, the entrance to the catalytic active center is larger on the COOH-SAM surface with a low SCD. This work reveals the controlled orientation and conformational information on IsPETase on charged surfaces at the atomistic level. This study would certainly promote our understanding of the mechanism of IsPETase adsorption and provide theoretical support for the design of substrates for IsPETase immobilization.
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Affiliation(s)
- Lijian Gao
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Zhiyong Xu
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China
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37
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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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38
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Choi J, Kim H, Ahn YR, Kim M, Yu S, Kim N, Lim SY, Park JA, Ha SJ, Lim KS, Kim HO. Recent advances in microbial and enzymatic engineering for the biodegradation of micro- and nanoplastics. RSC Adv 2024; 14:9943-9966. [PMID: 38528920 PMCID: PMC10961967 DOI: 10.1039/d4ra00844h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024] Open
Abstract
This review examines the escalating issue of plastic pollution, specifically highlighting the detrimental effects on the environment and human health caused by microplastics and nanoplastics. The extensive use of synthetic polymers such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS) has raised significant environmental concerns because of their long-lasting and non-degradable characteristics. This review delves into the role of enzymatic and microbial strategies in breaking down these polymers, showcasing recent advancements in the field. The intricacies of enzymatic degradation are thoroughly examined, including the effectiveness of enzymes such as PETase and MHETase, as well as the contribution of microbial pathways in breaking down resilient polymers into more benign substances. The paper also discusses the impact of chemical composition on plastic degradation kinetics and emphasizes the need for an approach to managing the environmental impact of synthetic polymers. The review highlights the significance of comprehending the physical characteristics and long-term impacts of micro- and nanoplastics in different ecosystems. Furthermore, it points out the environmental and health consequences of these contaminants, such as their ability to cause cancer and interfere with the endocrine system. The paper emphasizes the need for advanced analytical methods and effective strategies for enzymatic degradation, as well as continued research and development in this area. This review highlights the crucial role of enzymatic and microbial strategies in addressing plastic pollution and proposes methods to create effective and environmentally friendly solutions.
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Affiliation(s)
- Jaewon Choi
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Hongbin Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Yu-Rim Ahn
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Minse Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Seona Yu
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Nanhyeon Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Su Yeon Lim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Jeong-Ann Park
- Department of Environmental Engineering, Kangwon National University Chuncheon 24341 Republic of Korea
| | - Suk-Jin Ha
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Kwang Suk Lim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Hyun-Ouk Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
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Clark R, Shaver MP. Depolymerization within a Circular Plastics System. Chem Rev 2024; 124:2617-2650. [PMID: 38386877 PMCID: PMC10941197 DOI: 10.1021/acs.chemrev.3c00739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/18/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
The societal importance of plastics contrasts with the carelessness with which they are disposed. Their superlative properties lead to economic and environmental efficiency, but the linearity of plastics puts the climate, human health, and global ecosystems at risk. Recycling is fundamental to transitioning this linear model into a more sustainable, circular economy. Among recycling technologies, chemical depolymerization offers a route to virgin quality recycled plastics, especially when valorizing complex waste streams poorly served by mechanical methods. However, chemical depolymerization exists in a complex and interlinked system of end-of-life fates, with the complementarity of each approach key to environmental, economic, and societal sustainability. This review explores the recent progress made into the depolymerization of five commercial polymers: poly(ethylene terephthalate), polycarbonates, polyamides, aliphatic polyesters, and polyurethanes. Attention is paid not only to the catalytic technologies used to enhance depolymerization efficiencies but also to the interrelationship with other recycling technologies and to the systemic constraints imposed by a global economy. Novel polymers, designed for chemical depolymerization, are also concisely reviewed in terms of their underlying chemistry and potential for integration with current plastic systems.
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Affiliation(s)
- Robbie
A. Clark
- Department
of Materials, School of Natural Sciences, University of Manchester, Manchester M13 9PL, United
Kingdom
- Sustainable
Materials Innovation Hub, Henry Royce Institute, University of Manchester, Manchester M13 9PL, United
Kingdom
| | - Michael P. Shaver
- Department
of Materials, School of Natural Sciences, University of Manchester, Manchester M13 9PL, United
Kingdom
- Sustainable
Materials Innovation Hub, Henry Royce Institute, University of Manchester, Manchester M13 9PL, United
Kingdom
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40
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Zhong-Johnson EZL, Dong Z, Canova CT, Destro F, Cañellas M, Hoffman MC, Maréchal J, Johnson TM, Zheng M, Schlau-Cohen GS, Lucas MF, Braatz RD, Sprenger KG, Voigt CA, Sinskey AJ. Analysis of Poly(ethylene terephthalate) degradation kinetics of evolved IsPETase variants using a surface crowding model. J Biol Chem 2024; 300:105783. [PMID: 38395309 PMCID: PMC10963241 DOI: 10.1016/j.jbc.2024.105783] [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: 12/31/2023] [Revised: 02/10/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Poly(ethylene terephthalate) (PET) is a major plastic polymer utilized in the single-use and textile industries. The discovery of PET-degrading enzymes (PETases) has led to an increased interest in the biological recycling of PET in addition to mechanical recycling. IsPETase from Ideonella sakaiensis is a candidate catalyst, but little is understood about its structure-function relationships with regards to PET degradation. To understand the effects of mutations on IsPETase productivity, we develop a directed evolution assay to identify mutations beneficial to PET film degradation at 30 °C. IsPETase also displays enzyme concentration-dependent inhibition effects, and surface crowding has been proposed as a causal phenomenon. Based on total internal reflectance fluorescence microscopy and adsorption experiments, IsPETase is likely experiencing crowded conditions on PET films. Molecular dynamics simulations of IsPETase variants reveal a decrease in active site flexibility in free enzymes and reduced probability of productive active site formation in substrate-bound enzymes under crowding. Hence, we develop a surface crowding model to analyze the biochemical effects of three hit mutations (T116P, S238N, S290P) that enhanced ambient temperature activity and/or thermostability. We find that T116P decreases susceptibility to crowding, resulting in higher PET degradation product accumulation despite no change in intrinsic catalytic rate. In conclusion, we show that a macromolecular crowding-based biochemical model can be used to analyze the effects of mutations on properties of PETases and that crowding behavior is a major property to be targeted for enzyme engineering for improved PET degradation.
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Affiliation(s)
| | - Ziyue Dong
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher T Canova
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Francesco Destro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Mikaila C Hoffman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jeanne Maréchal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; AgroParisTech, Palaiseau, France
| | - Timothy M Johnson
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Maya Zheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kayla G Sprenger
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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41
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Zhang H, Ye YH, Wang Y, Liu JZ, Jiao QC. A Bibliometric Analysis: Current Perspectives and Potential Trends of Enzyme Thermostability from 1991-2022. Appl Biochem Biotechnol 2024; 196:1211-1240. [PMID: 37382790 DOI: 10.1007/s12010-023-04615-6] [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] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
Thermostability is considered a crucial parameter to evaluate the viability of enzymes in industrial applications. Over the past 31 years, many studies have been reported on the thermostability of enzymes. However, there is no systematic bibliometric analysis of publications on the thermostability of enzymes. In this study, 16,035 publications related to the thermostability of enzymes were searched and collected, showing an increasing annual trend. China contributed the most publications, while the United States had the highest citation count. International Journal of Biological Macromolecules is the most productive journal in the research field. Moreover, Chinese acad sci and Khosro Khajeh are the most active institutions and prolific authors in the field, respectively. Analysis of references with the strongest citation bursts and keyword co-occurrences, magnetic nanoparticles, metal-organic frameworks, molecular dynamics, and rational design are current hot spots and significant future research directions. This study is the first comprehensive bibliometric analysis summarizing trends and developments in enzyme thermostability research. Our findings could provide scholars with an understanding of the fundamental knowledge framework of the field and identify recent potential hotspots and research trends that could facilitate the discovery of collaboration opportunities.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yun-Hui Ye
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yu Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jun-Zhong Liu
- Nanjing Institute for Comprehensive Utilization of Wild Plants, CHINA CO-OP, Nanjing, 211111, China.
| | - Qing-Cai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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42
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Kornberger D, Paatsch T, Schmidt M, Salat U. New combined absorption/ 1H NMR method for qualitative and quantitative analysis of PET degradation products. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20689-20697. [PMID: 38393574 PMCID: PMC10927764 DOI: 10.1007/s11356-024-32481-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/10/2024] [Indexed: 02/25/2024]
Abstract
Poly(ethylene terephthalate) (PET) is a very valuable and beneficial material for industrial purposes, with various different applications. Due to the high annual production volume of over 50 million tons worldwide and the indiscriminate disposal by consumers, the polymers accumulate in the environment, causing negative effects on various ecosystems. Biodegradation via suitable enzymes represents a promising approach to combat the plastic waste issue so validated methods are required to measure the efficiency and efficacy of these enzymes. PETase and MHETase from Ideonella sakaiensis are suitable enzymes needed in combination to completely degrade PET into its environmentally friendly monomers. In this project, we compare and combine a previously described bulk absorbance measurement method with a newly established 1H NMR analysis method of the PET degradation products mono(2-hydroxyethyl) terephthalic acid, bis(2-hydroxyethyl) terephthalic acid and terephthalic acid. Both were optimized regarding different solvents, pH values and drying processes. The accuracy of the measurements can be confirmed with sensitivity limits of 2.5-5 µM for the absorption method and 5-10 µM for the 1H NMR analysis. The combination of the described methods therefore allows a quantitative analysis by using bulk absorption coupled with a qualitative analysis through 1H NMR. The methods established in our work can potentially contribute to the development of suitable recycling strategies of PET using recombinant enzymes.
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Affiliation(s)
- David Kornberger
- Faculty Medical and Life Sciences, Institute of Applied Biology, Molecular Biology Lab, Furtwangen University, Jakob-Kienzle-Str. 17, 78054, Villingen-Schwenningen, Germany
| | - Tanja Paatsch
- Faculty Medical and Life Sciences, Institute of Applied Biology, Molecular Biology Lab, Furtwangen University, Jakob-Kienzle-Str. 17, 78054, Villingen-Schwenningen, Germany
| | - Magnus Schmidt
- Faculty Medical and Life Sciences, Institute of Precision Medicine, Organic and Bioorganic Chemistry Labs, Furtwangen University, Jakob-Kienzle-Str. 17, 78054, Villingen-Schwenningen, Germany
| | - Ulrike Salat
- Faculty Medical and Life Sciences, Institute of Applied Biology, Molecular Biology Lab, Furtwangen University, Jakob-Kienzle-Str. 17, 78054, Villingen-Schwenningen, Germany.
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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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Pinto ESM, Mangini AT, Novo LCC, Cavatao FG, Krause MJ, Dorn M. Assessment of Kaistella jeonii esterase conformational dynamics in response to poly(ethylene terephthalate) binding. Curr Res Struct Biol 2024; 7:100130. [PMID: 38406590 PMCID: PMC10885555 DOI: 10.1016/j.crstbi.2024.100130] [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: 12/11/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 02/27/2024] Open
Abstract
The pervasive presence of plastic in the environment has reached a concerning scale, being identified in many ecosystems. Bioremediation is the cheapest and most eco-friendly alternative to remove this polymer from affected areas. Recent work described that a novel cold-active esterase enzyme extracted from the bacteria Kaistella jeonii could promiscuously degrade PET. Compared to the well-known PETase from Ideonella sakaiensis, this novel esterase presents a low sequence identity yet has a remarkably similar folding. However, enzymatic assays demonstrated a lower catalytic efficiency. In this work, we employed a strict computational approach to investigate the binding mechanism between the esterase and PET. Understanding the underlying mechanism of binding can shed light on the evolutive mechanism of how enzymes have been evolving to degrade these artificial molecules and help develop rational engineering approaches to improve PETase-like enzymes. Our results indicate that this esterase misses a disulfide bridge, keeping the catalytic residues closer and possibly influencing its catalytic efficiency. Moreover, we describe the structural response to the interaction between enzyme and PET, indicating local and global effects. Our results aid in deepening the knowledge behind the mechanism of biological catalysis of PET degradation and as a base for the engineering of novel PETases.
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Affiliation(s)
- Ederson Sales Moreira Pinto
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Arthur Tonietto Mangini
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Lorenzo Chaves Costa Novo
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Fernando Guimaraes Cavatao
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
| | - Mathias J. Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Englerstraße 2, D-76131, Karlsruhe, BW, Germany
| | - Marcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Buildings 43421, Porto Alegre, RS, Brazil
- Institute of Informatics, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, Building 43424, Porto Alegre, RS, Brazil
- National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
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45
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Naidu G, Nagar N, Poluri KM. Mechanistic Insights into Cellular and Molecular Basis of Protein-Nanoplastic Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305094. [PMID: 37786309 DOI: 10.1002/smll.202305094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Plastic waste is ubiquitously present across the world, and its nano/sub-micron analogues (plastic nanoparticles, PNPs), raise severe environmental concerns affecting organisms' health. Considering the direct and indirect toxic implications of PNPs, their biological impacts are actively being studied; lately, with special emphasis on cellular and molecular mechanistic intricacies. Combinatorial OMICS studies identified proteins as major regulators of PNP mediated cellular toxicity via activation of oxidative enzymes and generation of ROS. Alteration of protein function by PNPs results in DNA damage, organellar dysfunction, and autophagy, thus resulting in inflammation/cell death. The molecular mechanistic basis of these cellular toxic endeavors is fine-tuned at the level of structural alterations in proteins of physiological relevance. Detailed biophysical studies on such protein-PNP interactions evidenced prominent modifications in their structural architecture and conformational energy landscape. Another essential aspect of the protein-PNP interactions includes bioenzymatic plastic degradation perspective, as the interactive units of plastics are essentially nano-sized. Combining all these attributes of protein-PNP interactions, the current review comprehensively documented the contemporary understanding of the concerned interactions in the light of cellular, molecular, kinetic/thermodynamic details. Additionally, the applicatory, economical facet of these interactions, PNP biogeochemical cycle and enzymatic advances pertaining to plastic degradation has also been discussed.
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Affiliation(s)
- Goutami Naidu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Nupur Nagar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
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46
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Amalia L, Chang CY, Wang SSS, Yeh YC, Tsai SL. Recent advances in the biological depolymerization and upcycling of polyethylene terephthalate. Curr Opin Biotechnol 2024; 85:103053. [PMID: 38128200 DOI: 10.1016/j.copbio.2023.103053] [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: 10/01/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Polyethylene terephthalate (PET) is favored for its exceptional properties and widespread daily use. This review highlights recent advancements that enable the development of biological tools for PET decomposition, transforming PET into valuable platform chemicals and materials in upcycling processes. Enhancing PET hydrolases' catalytic activity and efficiency through protein engineering strategies is a priority, facilitating more effective PET waste management. Efforts to create novel PET hydrolases for large-scale PET depolymerization continue, but cost-effectiveness remains challenging. Hydrolyzed monomers must add additional value to make PET recycling economically attractive. Valorization of hydrolysis products through the upcycling process is expected to produce new compounds with different values and qualities from the initial polymer, making the decomposed monomers more appealing. Advances in synthetic biology and enzyme engineering hold promise for PET upcycling. While biological depolymerization offers environmental benefits, further research is needed to make PET upcycling sustainable and economically feasible.
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Affiliation(s)
- Lita Amalia
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Chia-Yu Chang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Steven S-S Wang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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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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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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49
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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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50
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Greene AF, Abbel R, Vaidya AA, Tanjay Q, Chen Y, Risani R, Saggese T, Barbier M, Petcu M, West M, Theobald B, Gaugler E, Parker K. Environmentally Benign Fast-Degrading Conductive Composites. Biomacromolecules 2024; 25:455-465. [PMID: 38147683 DOI: 10.1021/acs.biomac.3c01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
An environmentally benign conductive composite that rapidly degrades in the presence of warm water via enzyme-mediated hydrolysis is described. This represents the first time that hydrolytic enzymes have been immobilized onto eco-friendly conductive carbon sources with the express purpose of degrading the encapsulating biodegradable plastic. Amano Lipase (AL)-functionalized carbon nanofibers (CNF) were compounded with polycaprolactone (PCL) to produce the composite film CNFAL-PCL (thickness ∼ 600 μm; CNFAL = 20.0 wt %). To serve as controls, films of the same thickness were also produced, including CNF-AL5-PCL (CNF mixed with AL and PCL; CNF = 19.2 wt % and AL = 5.00 wt %), CNF-PCL (CNF = 19.2 wt %), ALx-PCL (AL = x = 1.00 or 5.00 wt %), and PCL. The electrical performance of the CNF-containing composites was measured, and conductivities of 14.0 ± 2, 22.0 ± 5, and 31.0 ± 6 S/m were observed for CNFAL-PCL, CNF-AL5-PCL, and CNF-PCL, respectively. CNFAL-PCL and control films were degraded in phosphate buffer (2.00 mg/mL film/buffer) at 50 °C, and their average percent weight loss (Wtavg%) was recorded over time. After 3 h CNFAL-PCL degraded to a Wtavg% of 90.0% and had completely degraded after 8 h. This was considerably faster than CNF-AL5-PCL, which achieved a total Wtavg% of 34.0% after 16 days, and CNF-PCL, which was with a Wtavg% of 7.00% after 16 days. Scanning electron microscopy experiments (SEM) found that CNFAL-PCL has more open pores on its surface and that it fractures faster during degradation experiments which exposes the interior enzyme to water. An electrode made from CNFAL-PCL was fabricated and attached to an AL5-PCL support to form a fast-degrading thermal sensor. The resistance was measured over five cycles where the temperature was varied between 15.0-50.0 °C. The sensor was then degraded fully in buffer at 50 °C over a 48 h period.
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Affiliation(s)
- Angelique F Greene
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Robert Abbel
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Alankar A Vaidya
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Queenie Tanjay
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Yi Chen
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Regis Risani
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Taryn Saggese
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Maxime Barbier
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Miruna Petcu
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Mark West
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Beatrix Theobald
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Eva Gaugler
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
| | - Kate Parker
- Te Papa Tipu Innovation Park, Ti̅tokorangi Drive, Rotorua, New Zealand 3010
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