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Qu Z, Chen K, Zhang L, Sun Y. Computation-Based Design of Salt Bridges in PETase for Enhanced Thermostability and Performance for PET Degradation. Chembiochem 2023; 24:e202300373. [PMID: 37639367 DOI: 10.1002/cbic.202300373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Polyethylene terephthalate (PET) is one of the most widely used plastics, and the accumulation of PET poses a great threat to the environment. IsPETase can degrade PET rapidly at moderate temperatures, but its application is greatly limited by the low stability. Herein, molecular dynamics (MD) simulations combined with a sequence alignment strategy were adopted to introduce salt bridges into the flexible region of IsPETase to improve its thermal stability. In the designed variants, the Tm values of IsPETaseI168R/S188D and IsPETaseI168R/S188E were 7.4 and 8.7 °C higher than that of the wild type, respectively. The release of products degraded by IsPETaseI168R/S188E was 4.3 times that of the wild type. Tertiary structure characterization demonstrated that the structure of the variants IsPETaseI168R/S188D and IsPETaseI168R/S188E became more compact. Extensive MD simulations verified that a stable salt bridge was formed between the residue R168 and D186 in IsPETaseI168R/S188D , while in IsPETaseI168R/S188E an R168-D186-E188 salt bridge network was observed. These results confirmed that the proposed computation-based salt bridge design strategy could efficiently generate variants with enhanced thermal stability for the long-term degradation of PET, which would be helpful for the design of enzymes with improved stability.
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Affiliation(s)
- Zhi Qu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Lin Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and, Key Laboratory of Systems Bioengineering and, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China
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Wang X, Meng F, Zhang B, Xia Y. Elimination of tetracyclines in seawater by laccase-mediator system. Chemosphere 2023; 333:138916. [PMID: 37172624 DOI: 10.1016/j.chemosphere.2023.138916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/21/2023] [Accepted: 05/10/2023] [Indexed: 05/15/2023]
Abstract
Long-term exposure of antibiotics at low level leads to the accumulation of antibiotics in environmental media and organisms, inducing the formation of antibiotic resistance genes. Seawater is an important sink for many contaminants. Here, laccase from Aspergillus sp. And mediators that follow different oxidation mechanisms were combined to degrade tetracyclines (TCs) at environmentally relevant levels (ng·L-1-μg·L-1) in coastal seawater. The high salinity and alkaline of seawater changed the enzymatic structure of laccase, resulting in a reduced affinity of laccase to the substrate in seawater (Km of 0.0556 mmol L-1) than that in buffer (Km of 0.0181 mmol L-1). Although the stability and activity of the laccase decreased in seawater, laccase at a concentration of 200 U·L-1 with a laccase/syringaldehyde (SA) ratio of 1 U: 1 μmol could completely degrade TCs in seawater at initial concentrations of less than 2 μg L-1 in 2 h. Molecular docking simulation showed that the interaction between TCs and laccase mainly includes hydrogen bond interaction and hydrophobic interaction. TCs were degraded into small molecular products through a series of reactions: demethylation, deamination, deamidation, dehydration, hydroxylation, oxidation, and ring-opening. Prediction of the toxicity of intermediates showed that the majority of TCs can be degraded into low-toxic or non-toxic, small-molecule products within 1 h, indicating that the degradation process of TCs by a laccase-SA system has good ecological safety. The successful removal of TCs by the laccase-SA system demonstrates its potential for the elimination of pollutants in marine environment.
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Affiliation(s)
- Xiaotong Wang
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Fanping Meng
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Bo Zhang
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Yufan Xia
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
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Shi L, Liu P, Tan Z, Zhao W, Gao J, Gu Q, Ma H, Liu H, Zhu L. Complete Depolymerization of PET Wastes by an Evolved PET Hydrolase from Directed Evolution. Angew Chem Int Ed Engl 2023; 62:e202218390. [PMID: 36751696 DOI: 10.1002/anie.202218390] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 02/09/2023]
Abstract
PETase displays great potential in PET depolymerization. Directed evolution has been limited to engineer PETase due to the lack of high-throughput screening assay. In this study, a novel fluorescence-based high-throughput screening assay employing a newly designed substrate, bis (2-hydroxyethyl) 2-hydroxyterephthalate (termed BHET-OH), was developed for PET hydrolases. The best variant DepoPETase produced 1407-fold more products towards amorphous PET film at 50 °C and showed a 23.3 °C higher Tm value than the PETase WT. DepoPETase enabled complete depolymerization of seven untreated PET wastes and 19.1 g PET waste (0.4 % Wenzyme /WPET ) in liter-scale reactor, suggesting that it is a potential candidate for industrial PET depolymerization processes. The molecular dynamic simulations revealed that the distal substitutions stabilized the loops around the active sites and transmitted the stabilization effect to the active sites through enhancing inter-loop interactions network.
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Affiliation(s)
- Lixia Shi
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Zijian Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- Jiangsu Collaborative Innovation Centre of Chinese Medicinal Resources Industrialization, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wei Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Junfei Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Qun Gu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
| | - Haifeng Liu
- Jiangsu Collaborative Innovation Centre of Chinese Medicinal Resources Industrialization, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
- National Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, P. R. China
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Giraldo-Narcizo S, Guenani N, Sánchez-Pérez AM, Guerrero A. Accelerated Polyethylene Terephthalate (PET) Enzymatic Degradation by Room Temperature Alkali Pre-treatment for Reduced Polymer Crystallinity. Chembiochem 2023; 24:e202200503. [PMID: 36341520 DOI: 10.1002/cbic.202200503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Polyethylene terephthalate (PET) is the most widely employed plastic for single-use applications. The use of enzymes isolated from microorganisms, such as PETase with the capacity to hydrolyze PET into its monomers, represents a promising method for its sustainable recycling. However, the accessibility of the enzyme to the hydrolysable bonds is an important challenge that needs to be addressed for effective biodegradation of postconsumer PET. Here, we combined an alkali pre-treatment (25 °C) with PETase incubation (30 °C) with post-consumed PET bottles. The pre-treatment modifies the surface of the plastic and decreases its crystallinity enabling the access of the enzyme to the hydrolysable chemical bonds. When the alkali pre-treatment is incorporated into the enzymatic process the degradation yields increase more than one order of magnitude reaching values comparable to those obtained during heating/cooling cycles. Our results show energetic advantages over other reported pre-treatments and open new avenues for sustainable PET recycling.
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Affiliation(s)
| | - Nihal Guenani
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12006, Castelló, Spain
| | - Ana María Sánchez-Pérez
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12006, Castelló, Spain.,Faculty of Health Sciences, Universitat Jaume I, 12006, Castelló, Spain
| | - Antonio Guerrero
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12006, Castelló, Spain
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Kosiorowska KE, Moreno AD, Iglesias R, Leluk K, Mirończuk AM. Production of PETase by engineered Yarrowia lipolytica for efficient poly(ethylene terephthalate) biodegradation. Sci Total Environ 2022; 846:157358. [PMID: 35850328 DOI: 10.1016/j.scitotenv.2022.157358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
There has been a growing interest in poly(ethylene terephthalate) PET degradation studies in the last few years due to its widespread use and large-scale plastic waste accumulation in the environment. One of the most promising enzymatic methods in the context of PET degradation is the use of PETase from Ideonella sakaiensis, which has been reported to be an efficient enzyme for hydrolysing ester bonds in PET. In our study, we expressed a codon-optimized PETase gene in the yeast Yarrowia lipolytica. The obtained strain was tested for its ability to degrade PET directly in culture, and a screening of different supplements that might raise the level of PET hydrolysis was performed. We also carried out long-term cultures with PET film, the surface of which was examined by scanning electron microscopy. The efficiency of PET degradation was tested based on the concentration of degradation products released, and the results showed that supplementation of the culture with olive oil resulted in 66 % higher release of terephthalic acid into the medium compared to the mutant culture without supplementation. The results indicate the possibility of ethylene glycol uptake by both strains, and, additionally, the PETase produced by the newly engineered strain hydrolyses MHET. The structure of the PET film after culture with the modified strain, meanwhile, had numerous surface defects, cracks, and deformations.
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Affiliation(s)
- Katarzyna E Kosiorowska
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland.
| | - Antonio D Moreno
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Centre for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, 28040 Madrid, Spain.
| | - Raquel Iglesias
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Centre for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, 28040 Madrid, Spain.
| | - Karol Leluk
- Wroclaw University of Science and Technology, Faculty of Environmental Engineering, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Aleksandra M Mirończuk
- Wrocław University of Environmental and Life Sciences, Department of Biotechnology and Food Microbiology, Chełmońskiego 37, 51-630 Wrocław, Poland.
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Su L, Chen K, Bai S, Yu L, Sun Y. Cutinase fused with C-terminal residues of α-synuclein improves polyethylene terephthalate degradation by enhancing the substrate binding. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Zurier HS, Goddard JM. Directed Immobilization of PETase on Mesoporous Silica Enables Sustained Depolymerase Activity in Synthetic Wastewater Conditions. ACS Appl Bio Mater 2022; 5:4981-4992. [PMID: 36194455 DOI: 10.1021/acsabm.2c00700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microplastic accumulation in terrestrial and aquatic environments is a growing environmental challenge. Biodegradation has shown promise as an intervention strategy for reducing the spread of microplastics. The wastewater treatment system is a key intervention point in microplastic biodegradation due to its pivotal role in the water cycle at the interface between human activity and the environmental. However, the best characterized microplastic degradation enzyme, PETase, lacks the stability to perform at scale in wastewater treatment. In this work, we show that genetic fusion of PETase to a silica binding peptide enables directed immobilization of the enzyme onto silica nanoparticles. PETase activity in simulated wastewater conditions is quantified by linear regression from time zero to the time of maximum fluorescence of a fluorescent oxidized product of PETase degradation of PET microfibers. Mesoporous silica is shown to be a superior support material to nonporous silica. The resulting biocatalytic nanomaterial has up to 2.5-fold enhanced stability and 6.2-fold increased activity compared to free enzyme in unbuffered, 40 °C simulated influent (ionic strength ∼15 mM). In unbuffered, 40 °C simulated effluent (ionic strength ∼700 μM), reaction velocity and overall catalytic activity were increased by the biocatalytic material 2.1-fold relative to free PETase. All reactions were performed in 0.2 mL volumes, and enzyme concentrations were normalized across both free and immobilized samples to 9 μg/mL. Site-directed mutagenesis is shown to be a complementary technique to directed immobilization, which may aid in optimization of the biomaterial for wastewater applications. PETase stabilization in application-relevant environments as shown here enables progress toward application of PETase for microplastic biodegradation in wastewater treatment.
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Affiliation(s)
- Hannah S Zurier
- Department of Food Science and Technology, Cornell University, Ithaca, New York14853, United States
| | - Julie M Goddard
- Department of Food Science and Technology, Cornell University, Ithaca, New York14853, United States
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