1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Li C, Zheng Q, Liu W, Zhao Q, Jiang L. Enhancement of the degradation capacity of IsPETase by acidic amino acids insertion and carbohydrate-binding module fusion. 3 Biotech 2024; 14:195. [PMID: 39131175 PMCID: PMC11306670 DOI: 10.1007/s13205-024-04041-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
The biocatalytic degradation of poly(ethylene terephthalate) (PET) through enzymatic methods has garnered considerable attention due to its environmentally friendly and non-polluting nature, as well as its high specificity. While previous efforts in enhancing IsPETase performance have focused on amino acid substitutions in protein engineering, we introduced an amino acid insertion strategy in this work. By inserting a negatively charged acidic amino acid, Glu, at the right-angle bend of IsPETase, the binding capability between the enzyme's active pocket and PET was improved. The resulted mutant IsPETase9394insE exhibited enhanced hydrolytic activity towards PET at various temperatures ranging from 30 to 45 ℃ compared with the wild-type IsPETase. Notably, a 10.04-fold increase was observed at 45 ℃. To further enhance PET hydrolysis, different carbohydrate-binding modules (CBMs) were incorporated at the C-terminus of IsPETase9394insE. Among these, the fusion of CBM from Verrucosispora sioxanthis exhibited the highest enhancement, resulting in a 1.82-fold increase in PET hydrolytic activity at 37 ℃ compared with the IsPETase9394insE. Finally, the engineered variant was successfully employed for the degradation of polyester filter cloth, demonstrating its promising hydrolytic capacity. In conclusion, this research presents an alternative enzyme engineering strategy for modifying PETases and enriches the pool of potential candidates for industrial PET degradation.
Collapse
Affiliation(s)
- Chuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Qingqing Zheng
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Wei Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
| | - Quanyu Zhao
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816 People’s Republic of China
| | - Ling Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 People’s Republic of China
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816 China
| |
Collapse
|
3
|
Lu D, Chen Y, Jin S, Wu Q, Wu J, Liu J, Wang F, Deng L, Nie K. The evolution of cutinase Est1 based on the clustering strategy and its application for commercial PET bottles degradation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122217. [PMID: 39146645 DOI: 10.1016/j.jenvman.2024.122217] [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: 02/08/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
The rapid increase in global plastic consumption, especially the worldwide use of polyethylene terephthalate (PET), has caused serious pollution problems. Due to the low recycling rate of PET, a substantial amount of waste accumulates in the environment, which prompts a growing focus on enzymatic degradation for its efficiency and environmentally friendliness. This study systematically designed and modified a cutinase, Est1 from Thermobifida alba AHK119, known for its potential of plastic-degradation at high temperatures. Additionally, the introduction of clustering algorithms provided the ability to understand and modify biomolecules, to accelerate the process of finding the optimal mutations. K-means was further proceeded based on the positive mutations. After comprehensive screening for thermostability and activity mutation sites, the dominant mutation Est1_5M (Est1 with the mutations of N213M, T215P, S115P, Q93A, and L91W) exhibited satisfying degradation ability for commercial PET bottles. The results showed that Est1_5M achieved a degradation rate of 90.84% in 72 h, 65-fold higher than the wild type. This study offers reliable theoretical and practical support for the development of efficient PET-degrading enzymes, providing a reference for plastic pollution management.
Collapse
Affiliation(s)
- Dong Lu
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ying Chen
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuming Jin
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qiuyang Wu
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jinglong Wu
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Junfeng Liu
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fang Wang
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Li Deng
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Kaili Nie
- National Energy R&D Center for Biorefinery, Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Yan ZF, Feng CQ, Chen XQ, Jin CX, Xia W, Chen S, Wu J. Design and construction of chemical-biological module clusters for degradation and assimilation of poly(ethylene terephthalate) waste. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 361:121258. [PMID: 38815428 DOI: 10.1016/j.jenvman.2024.121258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/11/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
The rising accumulation of poly(ethylene terephthalate) (PET) waste presents an urgent ecological challenge, necessitating an efficient and economical treatment technology. Here, we developed chemical-biological module clusters that perform chemical pretreatment, enzymatic degradation, and microbial assimilation for the large-scale treatment of PET waste. This module cluster included (i) a chemical pretreatment that involves incorporating polycaprolactone (PCL) at a weight ratio of 2% (PET:PCL = 98:2) into PET via mechanical blending, which effectively reduces the crystallinity and enhances degradation; (ii) enzymatic degradation using Thermobifida fusca cutinase variant (4Mz), that achieves complete degradation of pretreated PET at 300 g/L PET, with an enzymatic loading of 1 mg protein per gram of PET; and (iii) microbial assimilation, where Rhodococcus jostii RHA1 metabolizes the degradation products, assimilating each monomer at a rate above 90%. A comparative life cycle assessment demonstrated that the carbon emissions from our module clusters (0.25 kg CO2-eq/kg PET) are lower than those from other established approaches. This study pioneers a closed-loop system that seamlessly incorporates pretreatment, degradation, and assimilation processes, thus mitigating the environmental impacts of PET waste and propelling the development of a circular PET economy.
Collapse
Affiliation(s)
- Zheng-Fei Yan
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
| | - Chu-Qi Feng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Xiao-Qian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Chang-Xu Jin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Wei Xia
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Sheng Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Jing Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
| |
Collapse
|
6
|
Sun R, Chen S, Chen X, Liu X, Zhang F, Wu J, Su L. Enzymatic treatment to improve permeability and quality of cherry tomatoes for production of dried products. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:2718-2727. [PMID: 37997286 DOI: 10.1002/jsfa.13156] [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: 06/17/2023] [Revised: 11/02/2023] [Accepted: 11/23/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Cherry tomatoes are nutritious and favored by consumers. Processing them into dried cherry tomatoes can prolong their storage life and improve their flavor. The pretreatment of tomato pericarp is crucial for the subsequent processing. However, the traditional physical and chemical treatments of tomato pericarp generally cause nutrient loss and environmental pollution. RESULTS In this study, a novel enzymatic method for cherry tomatoes was performed using mixed enzymes containing cutinase, cellulase and pectinase. Results showed that the pericarp permeability of cherry tomatoes was effectively improved due to enzymatic treatment. Changes in the microscopic structure and composition of the cuticle were revealed. After treatment with different concentrations of enzymes, cherry tomatoes exhibited higher pericarp permeability and sensory quality to varying degrees. The lycopene content and total polyphenol content significantly increased 2.4- and 1.45-fold, respectively. In addition, the satisfactory effect of the six-time reuse of enzymes on cherry tomatoes could still reach the same level as the initial effect, which effectively reduced the cost of production. CONCLUSIONS This study revealed for the first time that a mixed enzymatic treatment consisting of cutinase, pectinase and cellulase could effectively degrade the cuticle, enhance the pericarp permeability and improve the quality of cherry tomatoes, with the advantages of being mildly controllable and environmentally friendly, providing a new strategy for the processing of dried cherry tomatoes. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Ruyu Sun
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Shiheng Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Xiaoqian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Xiaqing Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Fengshan Zhang
- Shangdong Huatai Paper Co. Ltd & Shangdong Yellow Triangle Biotechnology Industry Research Institute Co. Ltd, Dongying, China
| | - Jing Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| | - Lingqia Su
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
| |
Collapse
|
7
|
Yan ZF, Feng CQ, Zhou JQ, Huang QS, Chen XQ, Xia W, Wu J. Complete degradation of PET waste using a thermophilic microbe-enzyme system. Int J Biol Macromol 2024; 260:129538. [PMID: 38246467 DOI: 10.1016/j.ijbiomac.2024.129538] [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: 10/23/2023] [Revised: 12/09/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
Enzymatic degradation has been proposed as a suitable solution for addressing PET pollution, but approximately 10 % of PET is left as nonbiodegradable. Microbes can completely degrade PET at the gram level per year. Based on the complementary benefits of microbes and enzymes, a microbe-enzyme system was created to completely degrade PET. Here, a thermophilic microbe-enzyme (TME) system composed of Bacillus thermoamylovorans JQ3 and leaf-branch compost cutinase variant (ICCG) was used to demonstrate the synergistic degradation of PET, enabling 100 % degradation of PET waste at a high PET loading level (360 g/L). Six endogenous PET hydrolases of strain JQ3 were discovered by employing an ester bond hydrolysis function-first genome mining (EGM) strategy and first successfully expressed in E. coli. These hydrolases could release TPA as the final product from PET and preferentially degraded BHET instead of MHET. Of these, carboxylesterase 39_5 and ICCG could degrade PET in a synergistic manner to generate 50 μM of TPA, which was greater than the sum of the individual treatments. Finally, the degradation pathway of the TME system was speculated to include biofilm formation, PET degradation and utilization. The successful implementation of this study rendered a scale-up degradation feasible of PET at a lower cost.
Collapse
Affiliation(s)
- Zheng-Fei Yan
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Chu-Qi Feng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jian-Qiao Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Qing-Song Huang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiao-Qian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wei Xia
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| |
Collapse
|
8
|
Yang Y, Cheng S, Zheng Y, Xue T, Huang JW, Zhang L, Yang Y, Guo RT, Chen CC. Remodeling the polymer-binding cavity to improve the efficacy of PBAT-degrading enzyme. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132965. [PMID: 37979420 DOI: 10.1016/j.jhazmat.2023.132965] [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: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Poly(butylene adipate-co-terephthalate) (PBAT) is among the most widely applied synthetic polyesters that are utilized in the packaging and agricultural industries, but the accumulation of PBAT wastes has posed a great burden to ecosystems. Using renewable enzymes to decompose PBAT is an eco-friendly solution to tackle this problem. Recently, we demonstrated that cutinase is the most effective PBAT-degrading enzyme and that an engineered cutinase termed TfCut-DM could completely decompose PBAT film to terephthalate (TPA). Here, we report crystal structures of a variant of leaf compost cutinase in complex with soluble fragments of PBAT, including BTa and TaBTa. In the TaBTa complex, one TPA moiety was located at a polymer-binding site distal to the catalytic center that has never been experimentally validated. Intriguingly, the composition of the distal TPA-binding site shows higher diversity relative to the one proximal to the catalytic center in various cutinases. We thus modified the distal TPA-binding site of TfCut-DM and obtained variants that exhibit higher activity. Notably, the time needed to completely degrade the PBAT film to TPA was shortened to within 24 h by TfCut-DM Q132Y (5813 mol per mol protein). Taken together, the structural information regarding the substrate-binding behavior of PBAT-degrading enzymes could be useful guidance for direct enzyme engineering.
Collapse
Affiliation(s)
- Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Shujing Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Yingyu Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Ting Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Yunyun Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, People's Republic of China.
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, People's Republic of China; Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, People's Republic of China.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Aer L, Qin H, Wo P, Feng J, Tang L. Signal peptide independent secretion of bifunctional dual-hydrolase to enhance the bio-depolymerization of polyethylene terephthalate. BIORESOURCE TECHNOLOGY 2024; 391:129884. [PMID: 37852506 DOI: 10.1016/j.biortech.2023.129884] [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: 08/03/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023]
Abstract
The use of polyethylene terephthalate (PET) results in a significant amount of plastic waste, which poses a threat to the environment and human health. Dual-enzyme system is promising candidate for PET depolymerization. However, its production in Escherichia coli is challenging, especially for secretory expression. Herein, a novel bifunctional dual-enzyme, TfH-FPE, was constructed through fusion of FAST-PETase and TfH. TfH modifies cell membrane permeability via phospholipid degradation, thus facilitating the secretion of TfH-FPE into the medium. After systematic optimization, purified secreted TfH-FPE reached 104 ± 5.2 mg/L, which is 32.5-fold higher than that of the secreted enzyme using a signal peptide. TfH-FPE exhibits remarkable PET depolymerization capacity compared to FAST-PETase, releasing 6-fold more product than FAST-PETase and 2-fold more product than an equimolar enzyme mixture. Collectively, this study explores a novel secretory approach for efficient production of TfH-FPE and provides a valuable tool to promote PET bio-depolymerization via multi-enzyme cascades.
Collapse
Affiliation(s)
- Lizhu Aer
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Huiling Qin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Peng Wo
- School of Life Science and Technology, 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
| | - 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.
| |
Collapse
|
11
|
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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
12
|
Sui B, Wang T, Fang J, Hou Z, Shu T, Lu Z, Liu F, Zhu Y. Recent advances in the biodegradation of polyethylene terephthalate with cutinase-like enzymes. Front Microbiol 2023; 14:1265139. [PMID: 37849919 PMCID: PMC10577388 DOI: 10.3389/fmicb.2023.1265139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Polyethylene terephthalate (PET) is a synthetic polymer in the polyester family. It is widely found in objects used daily, including packaging materials (such as bottles and containers), textiles (such as fibers), and even in the automotive and electronics industries. PET is known for its excellent mechanical properties, chemical resistance, and transparency. However, these features (e.g., high hydrophobicity and high molecular weight) also make PET highly resistant to degradation by wild-type microorganisms or physicochemical methods in nature, contributing to the accumulation of plastic waste in the environment. Therefore, accelerated PET recycling is becoming increasingly urgent to address the global environmental problem caused by plastic wastes and prevent plastic pollution. In addition to traditional physical cycling (e.g., pyrolysis, gasification) and chemical cycling (e.g., chemical depolymerization), biodegradation can be used, which involves breaking down organic materials into simpler compounds by microorganisms or PET-degrading enzymes. Lipases and cutinases are the two classes of enzymes that have been studied extensively for this purpose. Biodegradation of PET is an attractive approach for managing PET waste, as it can help reduce environmental pollution and promote a circular economy. During the past few years, great advances have been accomplished in PET biodegradation. In this review, current knowledge on cutinase-like PET hydrolases (such as TfCut2, Cut190, HiC, and LCC) was described in detail, including the structures, ligand-protein interactions, and rational protein engineering for improved PET-degrading performance. In particular, applications of the engineered catalysts were highlighted, such as improving the PET hydrolytic activity by constructing fusion proteins. The review is expected to provide novel insights for the biodegradation of complex polymers.
Collapse
Affiliation(s)
- Beibei Sui
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Jingxiang Fang
- Rizhao Administration for Market Regulation, Rizhao, Shandong, China
| | - Zuoxuan Hou
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Ting Shu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Zhenhua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| | - Youshuang Zhu
- School of Biological Science, Jining Medical University, Jining, Shandong, China
| |
Collapse
|
13
|
Liu F, Wang T, Yang W, Zhang Y, Gong Y, Fan X, Wang G, Lu Z, Wang J. Current advances in the structural biology and molecular engineering of PETase. Front Bioeng Biotechnol 2023; 11:1263996. [PMID: 37795175 PMCID: PMC10546322 DOI: 10.3389/fbioe.2023.1263996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023] Open
Abstract
Poly(ethylene terephthalate) (PET) is a highly useful synthetic polyester plastic that is widely used in daily life. However, the increase in postconsumer PET as plastic waste that is recalcitrant to biodegradation in landfills and the natural environment has raised worldwide concern. Currently, traditional PET recycling processes with thermomechanical or chemical methods also result in the deterioration of the mechanical properties of PET. Therefore, it is urgent to develop more efficient and green strategies to address this problem. Recently, a novel mesophilic PET-degrading enzyme (IsPETase) from Ideonella sakaiensis was found to streamline PET biodegradation at 30°C, albeit with a lower PET-degrading activity than chitinase or chitinase-like PET-degrading enzymes. Consequently, the molecular engineering of more efficient PETases is still required for further industrial applications. This review details current knowledge on IsPETase, MHETase, and IsPETase-like hydrolases, including the structures, ligand‒protein interactions, and rational protein engineering for improved PET-degrading performance. In particular, applications of the engineered catalysts are highlighted, including metabolic engineering of the cell factories, enzyme immobilization or cell surface display. The information is expected to provide novel insights for the biodegradation of complex polymers.
Collapse
Affiliation(s)
- Fei Liu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Wentao Yang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yingkang Zhang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yuming Gong
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Xinxin Fan
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Guocheng Wang
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Zhenhua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianmin Wang
- School of Pharmacy, Jining Medical University, Rizhao, China
| |
Collapse
|
14
|
Fransen KA, Av-Ron SHM, Buchanan TR, Walsh DJ, Rota DT, Van Note L, Olsen BD. High-throughput experimentation for discovery of biodegradable polyesters. Proc Natl Acad Sci U S A 2023; 120:e2220021120. [PMID: 37252959 PMCID: PMC10266013 DOI: 10.1073/pnas.2220021120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/08/2023] [Indexed: 06/01/2023] Open
Abstract
The consistent rise of plastic pollution has stimulated interest in the development of biodegradable plastics. However, the study of polymer biodegradation has historically been limited to a small number of polymers due to costly and slow standard methods for measuring degradation, slowing new material innovation. High-throughput polymer synthesis and a high-throughput polymer biodegradation method are developed and applied to generate a biodegradation dataset for 642 chemically distinct polyesters and polycarbonates. The biodegradation assay was based on the clear-zone technique, using automation to optically observe the degradation of suspended polymer particles under the action of a single Pseudomonas lemoignei bacterial colony. Biodegradability was found to depend strongly on aliphatic repeat unit length, with chains less than 15 carbons and short side chains improving biodegradability. Aromatic backbone groups were generally detrimental to biodegradability; however, ortho- and para-substituted benzene rings in the backbone were more likely to be degradable than metasubstituted rings. Additionally, backbone ether groups improved biodegradability. While other heteroatoms did not show a clear improvement in biodegradability, they did demonstrate increases in biodegradation rates. Machine learning (ML) models were leveraged to predict biodegradability on this large dataset with accuracies over 82% using only chemical structure descriptors.
Collapse
Affiliation(s)
- Katharina A. Fransen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Sarah H. M. Av-Ron
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Tess R. Buchanan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Dylan J. Walsh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Dechen T. Rota
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Lana Van Note
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Bradley D. Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| |
Collapse
|
15
|
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: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
16
|
Determinants for an Efficient Enzymatic Catalysis in Poly(Ethylene Terephthalate) Degradation. Catalysts 2023. [DOI: 10.3390/catal13030591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
The enzymatic degradation of the recalcitrant poly(ethylene terephthalate) (PET) has been an important biotechnological goal. The present review focuses on the state of the art in enzymatic degradation of PET, and the challenges ahead. This review covers (i) enzymes acting on PET, (ii) protein improvements through selection or engineering, (iii) strategies to improve biocatalyst–polymer interaction and monomer yields. Finally, this review discusses critical points on PET degradation, and their related experimental aspects, that include the control of physicochemical parameters. The search for, and engineering of, PET hydrolases, have been widely studied to achieve this, and several examples are discussed here. Many enzymes, from various microbial sources, have been studied and engineered, but recently true PET hydrolases (PETases), active at moderate temperatures, were reported. For a circular economy process, terephtalic acid (TPA) production is critical. Some thermophilic cutinases and engineered PETases have been reported to release terephthalic acid in significant amounts. Some bottlenecks in enzyme performance are discussed, including enzyme activity, thermal stability, substrate accessibility, PET microstructures, high crystallinity, molecular mass, mass transfer, and efficient conversion into reusable fragments.
Collapse
|
17
|
Liu K, Xu Z, Zhao Z, Chen Y, Chai Y, Ma L, Li S. A Dual Fluorescence Assay Enables High-Throughput Screening for Poly(ethylene terephthalate) Hydrolases. CHEMSUSCHEM 2023; 16:e202202019. [PMID: 36511949 DOI: 10.1002/cssc.202202019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/03/2022] [Indexed: 06/17/2023]
Abstract
The drastically increasing consumption of petroleum-derived plastics hasserious environmental impacts and raises public concerns. Poly(ethylene terephthalate) (PET) is amongst the most extensively produced synthetic polymers. Enzymatic hydrolysis of PET recently emerged as an enticing path for plastic degradation and recycling. In-lab directed evolution has revealed the great potential of PET hydrolases (PETases). However, the time-consuming and laborious PETase assays hinder the identification of effective variants in large mutant libraries. Herein, we devise and validate a dual fluorescence-based high-throughput screening (HTS) assay for a representative IsPETase. The two-round HTS of a pilot library consisting of 2850 IsPETase variants yields six mutant IsPETases with 1.3-4.9 folds improved activities. Compared to the currently used structure- or computational redesign-based PETase engineering, this HTS approach provides a new strategy for discovery of new beneficial mutation patterns of PETases.
Collapse
Affiliation(s)
- Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Ziping Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Zhiyi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yuexing Chen
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Yating Chai
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Li Ma
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, P. R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, No. 168 Wenhai Middle Rd, Qingdao, Shandong, 266237, P. R. China
| |
Collapse
|
18
|
Mrigwani A, Pitaliya M, Kaur H, Kasilingam B, Thakur B, Guptasarma P. Rational mutagenesis of Thermobifida fusca cutinase to modulate the enzymatic degradation of polyethylene terephthalate. Biotechnol Bioeng 2023; 120:674-686. [PMID: 36514261 DOI: 10.1002/bit.28305] [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: 07/08/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
Thermobifida fusca cutinase (TfCut2) is a carboxylesterase (CE) which degrades polyethylene terephthalate (PET) as well as its degradation intermediates [such as oligoethylene terephthalate (OET), or bis-/mono-hydroxyethyl terephthalate (BHET/MHET)] into terephthalic acid (TPA). Comparisons of the surfaces of certain CEs (including TfCut2) were combined with docking and molecular dynamics simulations involving 2HE-(MHET)3, a three-terephthalate OET, to support the rational design of 22 variants with potential for improved generation of TPA from PET, comprising 15 single mutants (D12L, E47F, G62A, L90A, L90F, H129W, W155F, ΔV164, A173C, H184A, H184S, F209S, F209I, F249A, and F249R), 6 double mutants [H129W/T136S, A173C/A206C, A173C/A210C, G62A/L90F, G62A/F209I, and G62A/F249R], and 1 triple mutant [G62A/F209I/F249R]. Of these, nine displayed no activity, three displayed decreased activity, three displayed comparable activity, and seven displayed increased (~1.3- to ~7.2-fold) activity against solid PET, while all variants displayed activity against BHET. Of the variants that displayed increased activity against PET, four displayed more activity than G62A, the most-active mutant of TfCut2 known till date. Of these four, three displayed even more activity than LCC (G62A/F209I, G62A/F249R, and G62A/F209I/F249R), a CE known to be ~5-fold more active than wild-type TfCut2. These improvements derived from changes in PET binding and not changes in catalytic efficiency.
Collapse
Affiliation(s)
- Arpita Mrigwani
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Madhav Pitaliya
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Harman Kaur
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Bharathraj Kasilingam
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Bhishem Thakur
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India
| |
Collapse
|
19
|
Yuan H, Liu G, Chen Y, Yi Z, Jin W, Zhang G. A versatile tag for simple preparation of cutinase towards enhanced biodegradation of polyethylene terephthalate. Int J Biol Macromol 2023; 225:149-161. [PMID: 36403765 DOI: 10.1016/j.ijbiomac.2022.11.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/26/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
Enzymatic degradation of polyethylene terephthalate (PET) suffered from challenges such as complex and costly enzyme preparation, difficult access to PET substrates, poor reusability of free enzymes and sometimes MHET inhibitions. Herein, we propose an "all-in-one" strategy to address these issues with a well-designed elastin-like polypeptides (ELPs) tag. The preparation of the ELPs-tagged cutinase (ET-C) was efficient and easy to scale up by centrifugation, with an activity recovery of 57.55 % and a yield of 160 mg/L. Besides, the activity of the ET-C was 1.3 and 1.66-fold higher in degrading PET micro- and macro-plastics compared to wild-type cutinase. The self-immobilized cutinase (ET-C@SiO2) obtained by the ELPs-mediated biosilicification exhibited high loading capacity, activity, and thermostability and maintained 77.65 % of the original activity after 10 reuses. Interestingly, the product of the ET-C was TPA, whereas the wild-type was TPA and MHET. This is a simple way to release the intermediates inhibition compared with the existing methods. Our results demonstrated the feasibility of the versatile ELPs tag, which will pave an alternative economic way for scalable PET biodegradation.
Collapse
Affiliation(s)
- Hang Yuan
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Guanzhang Liu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Yaxin Chen
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Zhiwei Yi
- Third Institute of Oceanography, Ministry of Nature Resources, Xiamen 361005, Fujian Province, PR China
| | - Wenhui Jin
- Third Institute of Oceanography, Ministry of Nature Resources, Xiamen 361005, Fujian Province, PR China
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
| |
Collapse
|
20
|
Synergism Between Multi-Pseudomonas and Cutinase for Biodegradation of Crude Oil-Based Derivatives. Curr Microbiol 2022; 80:30. [PMID: 36474116 DOI: 10.1007/s00284-022-03139-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Polyethylene terephthalate (PET) as one of the main crude oil-based derivatives, produces a significant amount of waste that is difficult to degrade. Currently, microbial degradation of PET is an eco-friendly, efficient, and economical method. This study was conducted to propose a novel screening strategy for PET-degrading bacteria, and evaluate their degradation efficiency of PET. Two strains, Pseudomonas nitroreducens S8 and Pseudomonas monteilii S17, were isolated and could utilize PET as a carbon source by co-culture. The combined use of both bacteria gave a synergistic effect on the disruption of the PET surface through colonization behavior, which could enhance the subsequent degradation of PET. Its time of reaching a peak value of PET degradation rate (94.5% at 6 d) was 2 days earlier than these of single bacteria. A similar synergistic effect was also observed in the metabolization of PET monomers, and the metabolic rate was expressed as 82.4% of bis (2-hydroxyethyl) terephthalate (BHET), 64.0% of mono (2-hydroxyethyl) terephthalate (MHET), and 20.0% of terephthalic acid (TPA), respectively. This study is novel in showing the degradation of PET waste by combinations of bacterial pretreatment and enzymatic treatment, which can be a promising method.
Collapse
|
21
|
Weigert S, Perez‐Garcia P, Gisdon FJ, Gagsteiger A, Schweinshaut K, Ullmann GM, Chow J, Streit WR, Höcker B. Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes. Protein Sci 2022; 31:e4500. [PMID: 36336469 PMCID: PMC9679969 DOI: 10.1002/pro.4500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.
Collapse
Affiliation(s)
| | - Pablo Perez‐Garcia
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | | | | | | | | | - Jennifer Chow
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Wolfgang R. Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
| |
Collapse
|
22
|
Kawai F, Furushima Y, Mochizuki N, Muraki N, Yamashita M, Iida A, Mamoto R, Tosha T, Iizuka R, Kitajima S. Efficient depolymerization of polyethylene terephthalate (PET) and polyethylene furanoate by engineered PET hydrolase Cut190. AMB Express 2022; 12:134. [DOI: 10.1186/s13568-022-01474-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractThe enzymatic recycling of polyethylene terephthalate (PET) can be a promising approach to tackle the problem of plastic waste. The thermostability and activity of PET-hydrolyzing enzymes are still insufficient for practical application. Pretreatment of PET waste is needed for bio-recycling. Here, we analyzed the degradation of PET films, packages, and bottles using the newly engineered cutinase Cut190. Using gel permeation chromatography and high-performance liquid chromatography, the degradation of PET films by the Cut190 variant was shown to proceed via a repeating two-step hydrolysis process; initial endo-type scission of a surface polymer chain, followed by exo-type hydrolysis to produce mono/bis(2-hydroxyethyl) terephthalate and terephthalate from the ends of fragmented polymer molecules. Amorphous PET powders were degraded more than twofold higher than amorphous PET film with the same weight. Moreover, homogenization of post-consumer PET products, such as packages and bottles, increased their degradability, indicating the importance of surface area for the enzymatic hydrolysis of PET. In addition, it was required to maintain an alkaline pH to enable continuous enzymatic hydrolysis, by increasing the buffer concentration (HEPES, pH 9.0) depending on the level of the acidic products formed. The cationic surfactant dodecyltrimethylammonium chloride promoted PET degradation via adsorption on the PET surface and binding to the anionic surface of the Cut190 variant. The Cut190 variant also hydrolyzed polyethylene furanoate. Using the best performing Cut190 variant (L136F/Q138A/S226P/R228S/D250C-E296C/Q123H/N202H/K305del/L306del/N307del) and amorphous PET powders, more than 90 mM degradation products were obtained in 3 days and approximately 80 mM in 1 day.
Graphical Abstract
Collapse
|
23
|
Chen K, Dong X, Sun Y. Sequentially co-immobilized PET and MHET hydrolases via Spy chemistry in calcium phosphate nanocrystals present high-performance PET degradation. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129517. [PMID: 35809363 DOI: 10.1016/j.jhazmat.2022.129517] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Accumulation of polyethylene terephthalate (PET) has brought an enormous threat to the ecosystem. The recently reported PET hydrolase (DuraPETase) and MHET hydrolase (MHETase) can synergistically catalyze the complete PET degradation. Hence, this work was designed to develop a bienzymatic cascade catalysis by co-immobilizing the two enzymes for PET biodegradation. DuraPETase and MHETase were sequentially co-immobilized in calcium phosphate nanocrystals (CaP) through SpyTag/SpyCatcher system. MHETase-SpyCatcher was first embedded inside the nanocrystals via biomimetic mineralization, and DuraPETase-SpyTag was then conjugated on the outlayer (~1.5 µm). The bienzyme compartmentalization facilitated DuraPETase interaction with the solid substrate, and the layered structures of the nanocrystals protected the enzymes, thus enhancing their stability. The high specific surface area of the nanocrystals and the proximity effects from the bienzymatic cascade were beneficial to the improved enzyme activity. Experimental data and molecular dynamics simulations revealed the activation effect of Ca2+ on DuraPETase. Taken together, the final results indicate that the PET degradation efficiency of DuraPETase-MHETase@CaP increased by 6.1 and 1.5 times over the free bienzyme system within 10 d at 40 °C and 50 °C, with weight losses at 32.2% and 50.3%, respectively. The bienzymatic cascade with DuraPETase-MHETase@CaP can completely degrade PET, contributing to the recycling of PET.
Collapse
Affiliation(s)
- 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
| | - Xiaoyan Dong
- 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.
| |
Collapse
|
24
|
Charupanit K, Tipmanee V, Sutthibutpong T, Limsakul P. In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103353. [PMID: 35630830 PMCID: PMC9143596 DOI: 10.3390/molecules27103353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
The accumulation of polyethylene terephthalate (PET) seriously harms the environment because of its high resistance to degradation. The recent discovery of the bacteria-secreted biodegradation enzyme, PETase, sheds light on PET recycling; however, the degradation efficiency is far from practical use. Here, in silico alanine scanning mutagenesis (ASM) and site-saturation mutagenesis (SSM) were employed to construct the protein sequence space from binding energy of the PETase–PET interaction to identify the number and position of mutation sites and their appropriate side-chain properties that could improve the PETase–PET interaction. The binding mechanisms of the potential PETase variant were investigated through atomistic molecular dynamics simulations. The results show that up to two mutation sites of PETase are preferable for use in protein engineering to enhance the PETase activity, and the proper side chain property depends on the mutation sites. The predicted variants agree well with prior experimental studies. Particularly, the PETase variants with S238C or Q119F could be a potential candidate for improving PETase. Our combination of in silico ASM and SSM could serve as an alternative protocol for protein engineering because of its simplicity and reliability. In addition, our findings could lead to PETase improvement, offering an important contribution towards a sustainable future.
Collapse
Affiliation(s)
- Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (K.C.); (V.T.)
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (K.C.); (V.T.)
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand;
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Praopim Limsakul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Center of Excellence for Trace Analysis and Biosensor (TAB-CoE), Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Correspondence:
| |
Collapse
|