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Werner AZ, Avina YSC, Johnsen J, Bratti F, Alt HM, Mohamed ET, Clare R, Mand TD, Guss AM, Feist AM, Beckham GT. Adaptive laboratory evolution and genetic engineering improved terephthalate utilization in Pseudomonas putida KT2440. Metab Eng 2025; 88:196-205. [PMID: 39701409 DOI: 10.1016/j.ymben.2024.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 12/06/2024] [Accepted: 12/16/2024] [Indexed: 12/21/2024]
Abstract
Poly (ethylene terephthalate) (PET) is one of the most ubiquitous plastics and can be depolymerized through biological and chemo-catalytic routes to its constituent monomers, terephthalic acid (TPA) and ethylene glycol (EG). TPA and EG can be re-synthesized into PET for closed-loop recycling or microbially converted into higher-value products for open-loop recycling. Here, we expand on our previous efforts engineering and applying Pseudomonas putida KT2440 for PET conversion by employing adaptive laboratory evolution (ALE) to improve TPA catabolism. Three P. putida strains with varying degrees of metabolic engineering for EG catabolism underwent an automation-enabled ALE campaign on TPA, a TPA and EG mixture, and glucose as a control. ALE increased the growth rate on TPA and TPA-EG mixtures by 4.1- and 3.5-fold, respectively, in approximately 350 generations. Evolved isolates were collected at the midpoints and endpoints of 39 independent ALE experiments, and growth rates were increased by 0.15 and 0.20 h-1 on TPA and a TPA-EG, respectively, in the best performing isolates. Whole-genome re-sequencing identified multiple converged mutations, including loss-of-function mutations to global regulators gacS, gacA, and turA along with large duplication and intergenic deletion events that impacted the heterologously-expressed tphABII catabolic genes. Reverse engineering of these targets confirmed causality, and a strain with all three regulators deleted and second copies of tphABII and tpaK displayed improved TPA utilization compared to the base strain. Taken together, an iterative strain engineering process involving heterologous pathway engineering, ALE, whole genome sequencing, and genome editing identified five genetic interventions that improve P. putida growth on TPA, aimed at developing enhanced whole-cell biocatalysts for PET upcycling.
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Affiliation(s)
- Allison Z Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; BOTTLE Consortium, Golden, CO, USA
| | - Young-Saeng C Avina
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; BOTTLE Consortium, Golden, CO, USA
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Felicia Bratti
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; BOTTLE Consortium, Golden, CO, USA
| | - Hannah M Alt
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Elsayed T Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Rita Clare
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; BOTTLE Consortium, Golden, CO, USA
| | - Thomas D Mand
- BOTTLE Consortium, Golden, CO, USA; Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, USA
| | - Adam M Guss
- BOTTLE Consortium, Golden, CO, USA; Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, USA
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark; Department of Bioengineering, University of California, San Diego, CA, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; BOTTLE Consortium, Golden, CO, USA.
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Hu Y, Tian Y, Zou C, Moon TS. The current progress of tandem chemical and biological plastic upcycling. Biotechnol Adv 2024; 77:108462. [PMID: 39395608 DOI: 10.1016/j.biotechadv.2024.108462] [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: 02/26/2024] [Revised: 08/31/2024] [Accepted: 10/03/2024] [Indexed: 10/14/2024]
Abstract
Each year, millions of tons of plastics are produced for use in such applications as packaging, construction, and textiles. While plastic is undeniably useful and convenient, its environmental fate and transport have raised growing concerns about waste and pollution. However, the ease and low cost of producing virgin plastic have so far made conventional plastic recycling economically unattractive. Common contaminants in plastic waste and shortcomings of the recycling processes themselves typically mean that recycled plastic products are of relatively low quality in some cases. The high cost and high energy requirements of typical recycling operations also reduce their economic benefits. In recent years, the bio-upcycling of chemically treated plastic waste has emerged as a promising alternative to conventional plastic recycling. Unlike recycling, bio-upcycling uses relatively mild process conditions to economically transform pretreated plastic waste into value-added products. In this review, we first provide a précis of the general methodology and limits of conventional plastic recycling. Then, we review recent advances in hybrid chemical/biological upcycling methods for different plastics, including polyethylene terephthalate, polyurethane, polyamide, polycarbonate, polyethylene, polypropylene, polystyrene, and polyvinyl chloride. For each kind of plastic, we summarize both the pretreatment methods for making the plastic bio-available and the microbial chassis for degrading or converting the treated plastic waste to value-added products. We also discuss both the limitations of upcycling processes for major plastics and their potential for bio-upcycling.
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Affiliation(s)
- Yifeng Hu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Yuxin Tian
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Chenghao Zou
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, United States; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States; Synthetic Biology Group, J. Craig Venter Institute, La Jolla, CA, United States.
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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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Du M, Xue R, Yuan W, Cheng Y, Cui Z, Dong W, Qiu B. Tandem Integration of Biological and Electrochemical Catalysis for Efficient Polyester Upcycling under Ambient Conditions. NANO LETTERS 2024; 24:9768-9775. [PMID: 39057181 DOI: 10.1021/acs.nanolett.4c02966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Excessive production of waste polyethylene terephthalate (PET) poses an ecological challenge, which necessitates developing technologies to extract the values from end-of-life PET. Upcycling has proven effective in addressing the low profitability of current recycling strategies, yet existing upcycling technologies operate under energy-intensive conditions. Here we report a cascade strategy to steer the transformation of PET waste into glycolate in an overall yield of 92.6% under ambient conditions. The cascade approach involves setting up a robust hydrolase with 95.6% PET depolymerization into ethylene glycol (EG) monomer within 12 h, followed by an electrochemical process initiated by a CO-tolerant Pd/Ni(OH)2 catalyst to convert the EG intermediate into glycolate with high Faradaic efficiency of 97.5%. Techno-economic analysis and life cycle assessment indicate that, compared with the widely adopted electrochemical technology that heavily relies on alkaline pretreatment for PET depolymerization, our designed enzymatic-electrochemical approach offers a cost-effective and low-carbon pathway to upgrade PET.
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Affiliation(s)
- Mengmeng Du
- Jiangsu Key Laboratory of Pesticide Sciences, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Rui Xue
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Wenfang Yuan
- Jiangsu Key Laboratory of Pesticide Sciences, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yun Cheng
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Bocheng Qiu
- Jiangsu Key Laboratory of Pesticide Sciences, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
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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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