1
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Ogura Y, Hashino Y, Nakamura A. Direct Screening of PET Hydrolase Activity in Culture Medium Based on Turbidity Reduction. ACS OMEGA 2024; 9:34151-34160. [PMID: 39130604 PMCID: PMC11307985 DOI: 10.1021/acsomega.4c05488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/13/2024]
Abstract
The development of an efficient screening method for the activity of PET-degrading enzymes represents a significant technological advance in the field of enzyme research, with the potential to facilitate the advancement of enzymes for PET recycling. By examining the stable conditions of PET suspension and enzyme production conditions, we developed a method to quantify PET-degrading enzyme activity in E. coli culture medium using turbidity reduction as an indicator. High PET concentration or ionic strength caused aggregation of PET, and the best condition for activity detection was 0.5 mg mL-1 PET in 50 mM sodium phosphate pH 7.0. Preculture of E. coli increased the purity of enzyme secreted in medium. To evaluate the screening method, 720 colonies of the PET2-7M-H229X-F233X mutant library were analyzed and three candidates of high-activity mutants were obtained. The thermostability of the mutants could also be easily measured by measuring the residual activity after heat treatment. The H229T-F233M mutant showed 3.4 times higher degradation rate against PET film than the template enzyme at the initial time. The molecular dynamics simulation implied that the F233M mutation makes space for making an α helix and that the H229T mutation resolved the steric hindrance with Trp199. These mutations were speculated to change the angle of the Trp199 side chain of PET2 to an angle similar to that of the Trp185 of IsPETase, making it suitable for PET binding to the active center. Screening of activity using PET suspensions is compatible with robotic automation and is expected to be useful for validating computationally predicted mutations.
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Affiliation(s)
- Yui Ogura
- Department
of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yoshihito Hashino
- Department
of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Akihiko Nakamura
- Department
of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research
Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Shizuoka
Institute for the Study of Marine Biology and Chemistry, Shizuoka, Shizuoka 422-8529, Japan
- Institute
for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama Myodaijicho, Okazaki, Aichi 444-8787, Japan
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2
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Carr CM, Göttsch F, de Oliveira BFR, Murcia PAS, Jackson SA, Wei R, Clarke DJ, Bornscheuer UT, Dobson ADW. Identification and expression of MarCE, a marine carboxylesterase with synthetic ester-degrading activity. Microb Biotechnol 2024; 17:e14479. [PMID: 38881500 PMCID: PMC11180994 DOI: 10.1111/1751-7915.14479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Carboxylic ester hydrolases with the capacity to degrade polyesters are currently highly sought after for their potential use in the biological degradation of PET and other chemically synthesized polymers. Here, we describe MarCE, a carboxylesterase family protein identified via genome mining of a Maribacter sp. isolate from the marine sponge Stelligera stuposa. Based on phylogenetic analysis, MarCE and its closest relatives belong to marine-associated genera from the Cytophaga-Flavobacterium-Bacteroides taxonomic group and appear evolutionarily distinct to any homologous carboxylesterases that have been studied to date in terms of structure or function. Molecular docking revealed putative binding of BHET, a short-chain PET derivative, onto the predicted MarCE three-dimensional structure. The synthetic ester-degrading activity of MarCE was subsequently confirmed by MarCE-mediated hydrolysis of 2 mM BHET substrate, indicated by the release of its breakdown products MHET and TPA, which were measured, respectively, as 1.28 and 0.12 mM following 2-h incubation at 30°C. The findings of this study provide further insight into marine carboxylic ester hydrolases, which have the potential to display unique functional plasticity resulting from their adaptation to complex and fluctuating marine environmentsw.
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Affiliation(s)
- Clodagh M. Carr
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
| | - Frederike Göttsch
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | | | - Pedro A. Sánchez Murcia
- Laboratory of Computer‐Aided Molecular Design, Division of Medicinal Chemistry, Otto‐Loewi Research CenterMedical University of GrazGrazAustria
- BioTechMed‐GrazGrazAustria
| | - Stephen A. Jackson
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Ren Wei
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - David J. Clarke
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Alan D. W. Dobson
- School of MicrobiologyUniversity College CorkCorkIreland
- SSPC‐SFI Research Centre for PharmaceuticalsUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
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3
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Joho Y, Royan S, Caputo AT, Newton S, Peat TS, Newman J, Jackson C, Ardevol A. Enhancing PET Degrading Enzymes: A Combinatory Approach. Chembiochem 2024; 25:e202400084. [PMID: 38584134 DOI: 10.1002/cbic.202400084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Plastic waste has become a substantial environmental issue. A potential strategy to mitigate this problem is to use enzymatic hydrolysis of plastics to depolymerize post-consumer waste and allow it to be reused. Over the last few decades, the use of enzymatic PET-degrading enzymes has shown promise as a great solution for creating a circular plastic waste economy. PsPETase from Piscinibacter sakaiensis has been identified as an enzyme with tremendous potential for such applications. But to improve its efficiency, enzyme engineering has been applied aiming at enhancing its thermal stability, enzymatic activity, and ease of production. Here, we combine different strategies such as structure-based rational design, ancestral sequence reconstruction and machine learning to engineer a more highly active Combi-PETase variant with a melting temperature of 70 °C and optimal performance at 60 °C. Furthermore, this study demonstrates that these approaches, commonly used in other works of enzyme engineering, are most effective when utilized in combination, enabling the improvement of enzymes for industrial applications.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Santana Royan
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Alessandro T Caputo
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Sophia Newton
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
| | - Thomas S Peat
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Janet Newman
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, 3168, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
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4
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Zhong-Johnson EZL, Dong Z, Canova CT, Destro F, Cañellas M, Hoffman MC, Maréchal J, Johnson TM, Zheng M, Schlau-Cohen GS, Lucas MF, Braatz RD, Sprenger KG, Voigt CA, Sinskey AJ. Analysis of Poly(ethylene terephthalate) degradation kinetics of evolved IsPETase variants using a surface crowding model. J Biol Chem 2024; 300:105783. [PMID: 38395309 PMCID: PMC10963241 DOI: 10.1016/j.jbc.2024.105783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/10/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
Poly(ethylene terephthalate) (PET) is a major plastic polymer utilized in the single-use and textile industries. The discovery of PET-degrading enzymes (PETases) has led to an increased interest in the biological recycling of PET in addition to mechanical recycling. IsPETase from Ideonella sakaiensis is a candidate catalyst, but little is understood about its structure-function relationships with regards to PET degradation. To understand the effects of mutations on IsPETase productivity, we develop a directed evolution assay to identify mutations beneficial to PET film degradation at 30 °C. IsPETase also displays enzyme concentration-dependent inhibition effects, and surface crowding has been proposed as a causal phenomenon. Based on total internal reflectance fluorescence microscopy and adsorption experiments, IsPETase is likely experiencing crowded conditions on PET films. Molecular dynamics simulations of IsPETase variants reveal a decrease in active site flexibility in free enzymes and reduced probability of productive active site formation in substrate-bound enzymes under crowding. Hence, we develop a surface crowding model to analyze the biochemical effects of three hit mutations (T116P, S238N, S290P) that enhanced ambient temperature activity and/or thermostability. We find that T116P decreases susceptibility to crowding, resulting in higher PET degradation product accumulation despite no change in intrinsic catalytic rate. In conclusion, we show that a macromolecular crowding-based biochemical model can be used to analyze the effects of mutations on properties of PETases and that crowding behavior is a major property to be targeted for enzyme engineering for improved PET degradation.
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Affiliation(s)
| | - Ziyue Dong
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher T Canova
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Francesco Destro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Mikaila C Hoffman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jeanne Maréchal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; AgroParisTech, Palaiseau, France
| | - Timothy M Johnson
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Maya Zheng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kayla G Sprenger
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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5
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Cribari MA, Unger MJ, Unarta IC, Ogorek AN, Huang X, Martell JD. Ultrahigh-Throughput Directed Evolution of Polymer-Degrading Enzymes Using Yeast Display. J Am Chem Soc 2023; 145:27380-27389. [PMID: 38051911 PMCID: PMC11058326 DOI: 10.1021/jacs.3c08291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Enzymes that degrade synthetic polymers have attracted intense interest for eco-friendly plastic recycling. However, because enzymes did not evolve for the cleavage of abiotic polymers, directed evolution strategies are needed to enhance activity for plastic degradation. Previous directed evolution efforts relied on polymer degradation assays that were limited to screening ∼104 mutants. Here, we report a high-throughput yeast surface display platform to rapidly evaluate >107 enzyme mutants for increased activity in cleaving synthetic polymers. In this platform, individual yeast cells display distinct mutants, and enzyme activity is detected by a change in fluorescence upon the cleavage of a synthetic probe resembling a polymer of interest. Highly active mutants are isolated by fluorescence activated cell sorting and identified through DNA sequencing. To demonstrate this platform, we performed directed evolution of a polyethylene terephthalate (PET)-depolymerizing enzyme, leaf and branch compost cutinase (LCC). We identified activity-boosting mutations that substantially increased the kinetics of degradation of solid PET films. Biochemical assays and molecular dynamics (MD) simulations of the most active variants suggest that the H218Y mutation improves the binding of the enzyme to PET. Overall, this evolution platform increases the screening throughput of polymer-degrading enzymes by 3 orders of magnitude and identifies mutations that enhance kinetics for depolymerizing solid substrates.
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Affiliation(s)
- Mario A. Cribari
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Maxwell J. Unger
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ilona C. Unarta
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ashley N. Ogorek
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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6
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Shen W, Dalby PA, Guo Z, Li W, Zhu C, Fan D. Residue Effect-Guided Design: Engineering of S. Solfataricus β-Glycosidase to Enhance Its Thermostability and Bioproduction of Ginsenoside Compound K. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16669-16680. [PMID: 37812684 DOI: 10.1021/acs.jafc.3c04575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
β-Glycosidase from Sulfolobus solfataricus (SS-BGL) is a highly effective biocatalyst for the synthesis of compound K (CK) from glycosylated protopanaxadiol ginsenosides. In order to improve the thermal stability of SS-BGL, molecular dynamics simulations were used to determine the residue-level binding energetics of ginsenoside Rd in the SS-BGL-Rd docked complex and to identify the top ten critical contributors. Target sites for mutations were determined using dynamic cross-correlation mapping of residues via the Ohm server to identify networks of distal residues that interact with the key binding residues. Target mutations were determined rationally based on site characteristics. Single mutants and then recombination of top hits led to the two most promising variants SS-BGL-Q96E/N97D/N302D and SS-BGL-Q96E/N97D/N128D/N302D with 2.5-fold and 3.3-fold increased half-lives at 95 °C, respectively. The enzyme activities relative to those of wild-type for ginsenoside conversion were 161 and 116%, respectively..
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Affiliation(s)
- Wenfeng Shen
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Paul A Dalby
- Department of Biochemical Engineering, UCL, London WCIE 6BT, U.K
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Science and Technology, Aarhus University, Gustav Wied Vej 10, Aarhus 8000, Denmark
| | - Weina Li
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Chenhui Zhu
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
| | - Daidi Fan
- Engineering Research Center of Western Resource Innovation Medicine Green Manufacturing, Ministry of Education, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an 710069, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an 710069, China
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7
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Blázquez‐Sánchez P, Vargas JA, Furtado AA, Griñen A, Leonardo DA, Sculaccio SA, Pereira HD, Sonnendecker C, Zimmermann W, Díez B, Garratt RC, Ramírez‐Sarmiento CA. Engineering the catalytic activity of an Antarctic PET-degrading enzyme by loop exchange. Protein Sci 2023; 32:e4757. [PMID: 37574805 PMCID: PMC10464292 DOI: 10.1002/pro.4757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Several hydrolases have been described to degrade polyethylene terephthalate (PET) at moderate temperatures ranging from 25°C to 40°C. These mesophilic PET hydrolases (PETases) are less efficient in degrading this plastic polymer than their thermophilic homologs and have, therefore, been the subject of many protein engineering campaigns. However, enhancing their enzymatic activity through rational design or directed evolution poses a formidable challenge due to the need for exploring a large number of mutations. Additionally, evaluating the improvements in both activity and stability requires screening numerous variants, either individually or using high-throughput screening methods. Here, we utilize instead the design of chimeras as a protein engineering strategy to increase the activity and stability of Mors1, an Antarctic PETase active at 25°C. First, we obtained the crystal structure of Mors1 at 1.6 Å resolution, which we used as a scaffold for structure- and sequence-based chimeric design. Then, we designed a Mors1 chimera via loop exchange of a highly divergent active site loop from the thermophilic leaf-branch compost cutinase (LCC) into the equivalent region in Mors1. After restitution of an active site disulfide bond into this chimera, the enzyme exhibited a shift in optimal temperature for activity to 45°C and an increase in fivefold in PET hydrolysis when compared with wild-type Mors1 at 25°C. Our results serve as a proof of concept of the utility of chimeric design to further improve the activity and stability of PETases active at moderate temperatures.
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Affiliation(s)
- Paula Blázquez‐Sánchez
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID—Millennium Science Initiative ProgramMillennium Institute for Integrative Biology (iBio)SantiagoChile
- Institute of Analytical ChemistryLeipzig UniversityLeipzigGermany
| | - Jhon A. Vargas
- São Carlos Institute of PhysicsUniversity of São PauloSão CarlosBrazil
| | | | - Aransa Griñen
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID—Millennium Science Initiative ProgramMillennium Institute for Integrative Biology (iBio)SantiagoChile
| | - Diego A. Leonardo
- São Carlos Institute of PhysicsUniversity of São PauloSão CarlosBrazil
| | | | | | | | | | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, School of Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- Center for Climate and Resilience Research (CR)SantiagoChile
- Millennium Institute Center for Genome Regulation (CGR)SantiagoChile
| | | | - César A. Ramírez‐Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID—Millennium Science Initiative ProgramMillennium Institute for Integrative Biology (iBio)SantiagoChile
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8
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Jayasekara SK, Joni HD, Jayantha B, Dissanayake L, Mandrell C, Sinharage MM, Molitor R, Jayasekara T, Sivakumar P, Jayakody LN. Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Comput Struct Biotechnol J 2023; 21:3513-3521. [PMID: 37484494 PMCID: PMC10362282 DOI: 10.1016/j.csbj.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 07/25/2023] Open
Abstract
Polyethylene terephthalate (PET) is the largest produced polyester globally, and less than 30% of all the PET produced globally (∼6 billion pounds annually) is currently recycled into lower-quality products. The major drawbacks in current recycling methods (mechanical and chemical), have inspired the exploration of potentially efficient and sustainable PET depolymerization using biological approaches. Researchers have discovered efficient PET hydrolyzing enzymes in the plastisphere and have demonstrated the selective degradation of PET to original monomers thus enabling biological recycling or upcycling. However, several significant hurdles such as the less efficiency of the hydrolytic reaction, low thermostability of the enzymes, and the inability of the enzyme to depolymerize crystalline PET must be addressed in order to establish techno-economically feasible commercial-scale biological PET recycling or upcycling processes. Researchers leverage a synthetic biology-based design; build, test, and learn (DBTL) methodology to develop commercially applicable efficient PET hydrolyzing enzymes through 1) high-throughput metagenomic and proteomic approaches to discover new PET hydrolyzing enzymes with superior properties: and, 2) enzyme engineering approaches to modify and optimize PET hydrolyzing properties. Recently, in-silico platforms including molecular mechanics and machine learning concepts are emerging as innovative tools for the development of more efficient and effective PET recycling through the exploration of novel mutations in PET hydrolyzing enzymes. In-silico-guided PET hydrolyzing enzyme engineering with DBTL cycles enables the rapid development of efficient variants of enzymes over tedious conventional enzyme engineering methods such as random or directed evolution. This review highlights the potential of in-silico-guided PET degrading enzyme engineering to create more efficient variants, including Ideonella sakaiensis PETase (IsPETase) and leaf-branch compost cutinases (LCC). Furthermore, future research prospects are discussed to enable a sustainable circular economy through the bioconversion of PET to original or high-value platform chemicals.
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Affiliation(s)
- Sandhya K. Jayasekara
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Hriday Dhar Joni
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Bhagya Jayantha
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lakshika Dissanayake
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Christopher Mandrell
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Manuka M.S. Sinharage
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Ryan Molitor
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Thushari Jayasekara
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Poopalasingam Sivakumar
- School of Physics and Applied Physics, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Lahiru N. Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA
- Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA
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9
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Yang Y, Min J, Xue T, Jiang P, Liu X, Peng R, Huang JW, Qu Y, Li X, Ma N, Tsai FC, Dai L, Zhang Q, Liu Y, Chen CC, Guo RT. Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases. Nat Commun 2023; 14:1645. [PMID: 36964144 PMCID: PMC10039075 DOI: 10.1038/s41467-023-37374-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/15/2023] [Indexed: 03/26/2023] Open
Abstract
Poly(butylene adipate-co-terephthalate) (PBAT), a polyester made of terephthalic acid (TPA), 1,4-butanediol, and adipic acid, is extensively utilized in plastic production and has accumulated globally as environmental waste. Biodegradation is an attractive strategy to manage PBAT, but an effective PBAT-degrading enzyme is required. Here, we demonstrate that cutinases are highly potent enzymes that can completely decompose PBAT films in 48 h. We further show that the engineered cutinases, by applying a double mutation strategy to render a more flexible substrate-binding pocket exhibit higher decomposition rates. Notably, these variants produce TPA as a major end-product, which is beneficial feature for the future recycling economy. The crystal structures of wild type and double mutation of a cutinase from Thermobifida fusca in complex with a substrate analogue are also solved, elucidating their substrate-binding modes. These structural and biochemical analyses enable us to propose the mechanism of cutinase-mediated PBAT degradation.
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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
| | - Jian Min
- 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
| | - Pengcheng Jiang
- 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
| | - Xin Liu
- 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
| | - Rouming Peng
- 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
| | - Yingying Qu
- 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
| | - Xian Li
- 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
| | - Ning Ma
- Hubei Key Laboratory of Polymer Materials, Key Laboratory for the Green Preparation and Application of Functional Materials (Ministry of Education), Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, School of Materials Science and Engineering, Hubei University, 430062, Wuhan, People's Republic of China
| | - Fang-Chang Tsai
- Hubei Key Laboratory of Polymer Materials, Key Laboratory for the Green Preparation and Application of Functional Materials (Ministry of Education), Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, School of Materials Science and Engineering, Hubei University, 430062, Wuhan, People's Republic of China
| | - Longhai Dai
- 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
| | - Qi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, 430072, Wuhan, People's Republic of China
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, 430072, Wuhan, 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.
| | - 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.
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