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Rahmati F, Sethi D, Shu W, Asgari Lajayer B, Mosaferi M, Thomson A, Price GW. Advances in microbial exoenzymes bioengineering for improvement of bioplastics degradation. CHEMOSPHERE 2024; 355:141749. [PMID: 38521099 DOI: 10.1016/j.chemosphere.2024.141749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/06/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Plastic pollution has become a major global concern, posing numerous challenges for the environment and wildlife. Most conventional ways of plastics degradation are inefficient and cause great damage to ecosystems. The development of biodegradable plastics offers a promising solution for waste management. These plastics are designed to break down under various conditions, opening up new possibilities to mitigate the negative impact of traditional plastics. Microbes, including bacteria and fungi, play a crucial role in the degradation of bioplastics by producing and secreting extracellular enzymes, such as cutinase, lipases, and proteases. However, these microbial enzymes are sensitive to extreme environmental conditions, such as temperature and acidity, affecting their functions and stability. To address these challenges, scientists have employed protein engineering and immobilization techniques to enhance enzyme stability and predict protein structures. Strategies such as improving enzyme and substrate interaction, increasing enzyme thermostability, reinforcing the bonding between the active site of the enzyme and substrate, and refining enzyme activity are being utilized to boost enzyme immobilization and functionality. Recently, bioengineering through gene cloning and expression in potential microorganisms, has revolutionized the biodegradation of bioplastics. This review aimed to discuss the most recent protein engineering strategies for modifying bioplastic-degrading enzymes in terms of stability and functionality, including enzyme thermostability enhancement, reinforcing the substrate binding to the enzyme active site, refining with other enzymes, and improvement of enzyme surface and substrate action. Additionally, discovered bioplastic-degrading exoenzymes by metagenomics techniques were emphasized.
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Affiliation(s)
- Farzad Rahmati
- Department of Microbiology, Faculty of Science, Qom Branch, Islamic Azad University (IAU), Qom 37185364, Iran
| | - Debadatta Sethi
- Sugarcane Research Station, Odisha University of Agriculture and Technology, Nayagarh, India
| | - Weixi Shu
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | | | - Mohammad Mosaferi
- Health and Environment Research Center, Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Allan Thomson
- Perennia Food and Agriculture Corporation., 173 Dr. Bernie MacDonald Dr., Bible Hill, Truro, NS, B6L 2H5, Canada
| | - G W Price
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
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2
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Choi J, Kim H, Ahn YR, Kim M, Yu S, Kim N, Lim SY, Park JA, Ha SJ, Lim KS, Kim HO. Recent advances in microbial and enzymatic engineering for the biodegradation of micro- and nanoplastics. RSC Adv 2024; 14:9943-9966. [PMID: 38528920 PMCID: PMC10961967 DOI: 10.1039/d4ra00844h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024] Open
Abstract
This review examines the escalating issue of plastic pollution, specifically highlighting the detrimental effects on the environment and human health caused by microplastics and nanoplastics. The extensive use of synthetic polymers such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS) has raised significant environmental concerns because of their long-lasting and non-degradable characteristics. This review delves into the role of enzymatic and microbial strategies in breaking down these polymers, showcasing recent advancements in the field. The intricacies of enzymatic degradation are thoroughly examined, including the effectiveness of enzymes such as PETase and MHETase, as well as the contribution of microbial pathways in breaking down resilient polymers into more benign substances. The paper also discusses the impact of chemical composition on plastic degradation kinetics and emphasizes the need for an approach to managing the environmental impact of synthetic polymers. The review highlights the significance of comprehending the physical characteristics and long-term impacts of micro- and nanoplastics in different ecosystems. Furthermore, it points out the environmental and health consequences of these contaminants, such as their ability to cause cancer and interfere with the endocrine system. The paper emphasizes the need for advanced analytical methods and effective strategies for enzymatic degradation, as well as continued research and development in this area. This review highlights the crucial role of enzymatic and microbial strategies in addressing plastic pollution and proposes methods to create effective and environmentally friendly solutions.
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Affiliation(s)
- Jaewon Choi
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Hongbin Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Yu-Rim Ahn
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Minse Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Seona Yu
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Nanhyeon Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Su Yeon Lim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Jeong-Ann Park
- Department of Environmental Engineering, Kangwon National University Chuncheon 24341 Republic of Korea
| | - Suk-Jin Ha
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Kwang Suk Lim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
| | - Hyun-Ouk Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University Chuncheon Korea
- Department of Smart Health Science and Technology, Kangwon National University Chuncheon Korea
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3
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Orlando C, Prejanò M, Russo N, Marino T. On the Role of Temperature in the Depolymerization of PET by FAST-PETase: An Atomistic Point of View on Possible Active Site Pre-Organization and Substrate-Destabilization Effects. Chembiochem 2023; 24:e202300412. [PMID: 37556192 DOI: 10.1002/cbic.202300412] [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: 06/21/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/10/2023]
Abstract
Enzyme FAST-PETase, recently obtained by a machine learning approach, can depolymerize poly(ethylene terephthalate) (PET), a synthetic resin employed in plastics and in clothing fibers. Therefore it represents a promising solution for the recycling of PET-based materials. In this study, a model of PET was adopted to describe the substrate, and all-atoms classical molecular dynamics (MD) simulations on apo- and substrate-bound FAST-PETase were carried out at 30 and 50 °C to provide atomistic details on the binding step of the catalytic cycle. Comparative analysis shed light on the interactions occurring between the FAST-PETase and 4PET at 50 °C, the optimal working conditions of the enzyme. Pre-organization of the enzyme active and binding sites has been highlighted, while MD simulations of FAST-PETase:4PET pointed out the occurrence of solvent-inaccessible conformations of the substrate promoted by the enzyme. Indeed, neither of these conformations was observed during MD simulations of the substrate alone in solution performed at 30, 50 and 150 °C. The analysis led us to propose that, at 50 °C, the FAST-PETase is pre-organized to bind the PET and that the interactions occurring in the binding site can promote a more reactive conformation of PET substrate, thus enhancing the catalytic activity of the enzyme.
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Affiliation(s)
- Carla Orlando
- Dipartimento di Chimica e Tecnologie Chimiche Laboratorio PROMOCS cubo 14C, Università della Calabria, 87036, Rende (CS), Italy
| | - Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche Laboratorio PROMOCS cubo 14C, Università della Calabria, 87036, Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche Laboratorio PROMOCS cubo 14C, Università della Calabria, 87036, Rende (CS), Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche Laboratorio PROMOCS cubo 14C, Università della Calabria, 87036, Rende (CS), Italy
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4
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Platero-Rochart D, Krivobokova T, Gastegger M, Reibnegger G, Sánchez-Murcia PA. Prediction of Enzyme Catalysis by Computing Reaction Energy Barriers via Steered QM/MM Molecular Dynamics Simulations and Machine Learning. J Chem Inf Model 2023; 63:4623-4632. [PMID: 37479222 PMCID: PMC10430765 DOI: 10.1021/acs.jcim.3c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 07/23/2023]
Abstract
The prediction of enzyme activity is one of the main challenges in catalysis. With computer-aided methods, it is possible to simulate the reaction mechanism at the atomic level. However, these methods are usually expensive if they are to be used on a large scale, as they are needed for protein engineering campaigns. To alleviate this situation, machine learning methods can help in the generation of predictive-decision models. Herein, we test different regression algorithms for the prediction of the reaction energy barrier of the rate-limiting step of the hydrolysis of mono-(2-hydroxyethyl)terephthalic acid by the MHETase ofIdeonella sakaiensis. As a training data set, we use steered quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation snapshots and their corresponding pulling work values. We have explored three algorithms together with three chemical representations. As an outcome, our trained models are able to predict pulling works along the steered QM/MM MD simulations with a mean absolute error below 3 kcal mol-1 and a score value above 0.90. More challenging is the prediction of the energy maximum with a single geometry. Whereas the use of the initial snapshot of the QM/MM MD trajectory as input geometry yields a very poor prediction of the reaction energy barrier, the use of an intermediate snapshot of the former trajectory brings the score value above 0.40 with a low mean absolute error (ca. 3 kcal mol-1). Altogether, we have faced in this work some initial challenges of the final goal of getting an efficient workflow for the semiautomatic prediction of enzyme-catalyzed energy barriers and catalytic efficiencies.
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Affiliation(s)
- Daniel Platero-Rochart
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Tatyana Krivobokova
- Department
of Statistics and Operations Research, University
of Vienna, Oskar-Morgenstern-Platz 1, A-1090 Vienna, Austria
| | - Michael Gastegger
- Institute
of Software Engineering and Theoretical Computer Science, Machine
Learning Group, Technische Universität, 10587 Berlin, Germany
| | - Gilbert Reibnegger
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Pedro A. Sánchez-Murcia
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
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5
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Tournier V, Duquesne S, Guillamot F, Cramail H, Taton D, Marty A, André I. Enzymes' Power for Plastics Degradation. Chem Rev 2023; 123:5612-5701. [PMID: 36916764 DOI: 10.1021/acs.chemrev.2c00644] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.
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Affiliation(s)
- Vincent Tournier
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Sophie Duquesne
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Frédérique Guillamot
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Henri Cramail
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Daniel Taton
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Alain Marty
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
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6
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Schubert S, Schaller K, Bååth JA, Hunt C, Borch K, Jensen K, Brask J, Westh P. Reaction Pathways for the Enzymatic Degradation of Poly(Ethylene Terephthalate): What Characterizes an Efficient PET-Hydrolase? Chembiochem 2023; 24:e202200516. [PMID: 36399069 PMCID: PMC10108200 DOI: 10.1002/cbic.202200516] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Bioprocessing of polyester waste has emerged as a promising tool in the quest for a cyclic plastic economy. One key step is the enzymatic breakdown of the polymer, and this entails a complicated pathway with substrates, intermediates, and products of variable size and solubility. We have elucidated this pathway for poly(ethylene terephthalate) (PET) and four enzymes. Specifically, we combined different kinetic measurements and a novel stochastic model and found that the ability to hydrolyze internal bonds in the polymer (endo-lytic activity) was a key parameter for overall enzyme performance. Endo-lytic activity promoted the release of soluble PET fragments with two or three aromatic rings, which, in turn, were broken down with remarkable efficiency (kcat /KM values of about 105 M-1 s-1 ) in the aqueous bulk. This meant that approximatly 70 % of the final, monoaromatic products were formed via soluble di- or tri-aromatic intermediates.
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Affiliation(s)
- Sune Schubert
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs., Lyngby, Denmark
| | - Kay Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs., Lyngby, Denmark
| | | | - Cameron Hunt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs., Lyngby, Denmark
| | - Kim Borch
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs., Lyngby, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs., Lyngby, Denmark
| | - Jesper Brask
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs., Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs., Lyngby, Denmark
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7
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An NMR look at an engineered PET depolymerase. Biophys J 2022; 121:2882-2894. [PMID: 35794828 PMCID: PMC9388554 DOI: 10.1016/j.bpj.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 12/30/2022] Open
Abstract
Plastic environmental pollution is a major issue that our generation must face to protect our planet. Plastic recycling has the potential not only to reduce the pollution but also to limit the need for fossil-fuel-based production of new plastics. Enzymes capable of breaking down plastic could thereby support such a circular economy. Polyethylene terephthalate (PET) degrading enzymes have recently attracted considerable interest and have been subjected to intensive enzyme engineering to improve their characteristics. A quadruple mutant of Leaf-branch Compost Cutinase (LCC) was identified as a most efficient and promising enzyme. Here, we use NMR to follow the initial LCC enzyme through its different mutations that lead to its improved performance. We experimentally define the two calcium-binding sites and show their importance on the all-or-nothing thermal unfolding process, which occurs at a temperature of 72°C close to the PET glass transition temperature. Using various NMR probes such as backbone amide, methyl group, and histidine side-chain resonances, we probe the interaction of the enzymes with mono-(2-hydroxyethyl)terephthalic acid. The latter experiments are interpreted in terms of accessibility of the active site to the polymer chain.
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8
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Sonnendecker C, Oeser J, Richter PK, Hille P, Zhao Z, Fischer C, Lippold H, Blázquez‐Sánchez P, Engelberger F, Ramírez‐Sarmiento CA, Oeser T, Lihanova Y, Frank R, Jahnke H, Billig S, Abel B, Sträter N, Matysik J, Zimmermann W. Low Carbon Footprint Recycling of Post-Consumer PET Plastic with a Metagenomic Polyester Hydrolase. CHEMSUSCHEM 2022; 15:e202101062. [PMID: 34129279 PMCID: PMC9303343 DOI: 10.1002/cssc.202101062] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/14/2021] [Indexed: 06/01/2023]
Abstract
Earth is flooded with plastics and the need for sustainable recycling strategies for polymers has become increasingly urgent. Enzyme-based hydrolysis of post-consumer plastic is an emerging strategy for closed-loop recycling of polyethylene terephthalate (PET). The polyester hydrolase PHL7, isolated from a compost metagenome, completely hydrolyzes amorphous PET films, releasing 91 mg of terephthalic acid per hour and mg of enzyme. Vertical scanning interferometry shows degradation rates of the PET film of 6.8 μm h-1 . Structural analysis indicates the importance of leucine at position 210 for the extraordinarily high PET-hydrolyzing activity of PHL7. Within 24 h, 0.6 mgenzyme gPET -1 completely degrades post-consumer thermoform PET packaging in an aqueous buffer at 70 °C without any energy-intensive pretreatments. Terephthalic acid recovered from the enzymatic hydrolysate is then used to synthesize virgin PET, demonstrating the potential of polyester hydrolases as catalysts in sustainable PET recycling processes with a low carbon footprint.
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Affiliation(s)
| | - Juliane Oeser
- Department of Microbiology and Bioprocess Technology Institute of BiochemistryLeipzig University04103LeipzigGermany
| | - P. Konstantin Richter
- Institute of Bioanalytical Chemistry, Centre for Biotechnology and BiomedicineLeipzig University04103LeipzigGermany
| | - Patrick Hille
- Department of Microbiology and Bioprocess Technology Institute of BiochemistryLeipzig University04103LeipzigGermany
| | - Ziyue Zhao
- Institute of Analytical ChemistryLeipzig University04103LeipzigGermany
| | - Cornelius Fischer
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Institut für Ressourcenökologie Abteilung Reaktiver TransportD-04318LeipzigGermany
| | - Holger Lippold
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR)Institut für Ressourcenökologie Abteilung Reaktiver TransportD-04318LeipzigGermany
| | - Paula Blázquez‐Sánchez
- Institute for Biological and Medical Engineering Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiago7820436Chile
- ANID—Millennium Science Initiative ProgramMillennium Institute for Integrative Biology (iBio)Santiago8331150Chile
| | - Felipe Engelberger
- Institute for Biological and Medical Engineering Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiago7820436Chile
- ANID—Millennium Science Initiative ProgramMillennium Institute for Integrative Biology (iBio)Santiago8331150Chile
| | - César A. Ramírez‐Sarmiento
- Institute for Biological and Medical Engineering Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiago7820436Chile
- ANID—Millennium Science Initiative ProgramMillennium Institute for Integrative Biology (iBio)Santiago8331150Chile
| | - Thorsten Oeser
- Department of Microbiology and Bioprocess Technology Institute of BiochemistryLeipzig University04103LeipzigGermany
| | - Yuliia Lihanova
- Institute of Analytical ChemistryLeipzig University04103LeipzigGermany
| | - Ronny Frank
- Centre for Biotechnology and Biomedicine Molecular Biological-Biochemical Processing TechnologyLeipzig University04103LeipzigGermany
| | - Heinz‐Georg Jahnke
- Centre for Biotechnology and Biomedicine Molecular Biological-Biochemical Processing TechnologyLeipzig University04103LeipzigGermany
| | - Susan Billig
- Institute of Analytical ChemistryLeipzig University04103LeipzigGermany
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM)Wilhelm-Ostwald-Institute of Physical and Theoretical Chemistry04103LeipzigGermany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Centre for Biotechnology and BiomedicineLeipzig University04103LeipzigGermany
| | - Jörg Matysik
- Institute of Analytical ChemistryLeipzig University04103LeipzigGermany
| | - Wolfgang Zimmermann
- Institute of Analytical ChemistryLeipzig University04103LeipzigGermany
- Department of Microbiology and Bioprocess Technology Institute of BiochemistryLeipzig University04103LeipzigGermany
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9
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Li J, Nina MRH, Zhang X, Bai Y. Engineering Transcription Factor XylS for Sensing Phthalic Acid and Terephthalic Acid: An Application for Enzyme Evolution. ACS Synth Biol 2022; 11:1106-1113. [PMID: 35192317 DOI: 10.1021/acssynbio.1c00275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Poly(ethylene terephthalate) (PET) and phthalate esters (PAEs) are used extensively as plastics and plasticizers. Enzymatic degradation of PET and PAEs has drawn great attention in recent years; however, evolution of PET- and PAE-degrading enzymes is still a big challenge, partly because of the lack of an effective screening method to detect phthalic acid (PA) and terephthalic acid (TPA), which are the main hydrolysis products of PAEs and PET. Here, by directed evolution of a promiscuous transcription factor, XylS from Pseudomonas putida, we created two novel variants, XylS-K38R-L224Q and XylS-W88C-L224Q, that are able to bind PA and TPA and activate the downstream expression of a fluorescent reporter protein. Based on these elements, whole-cell biosensors were constructed, which enabled the fluorimetric detection of as little as 10 μM PA or TPA. A PAE hydrolase, GoEst15, was preliminarily engineered using this new biosensor, yielding a mutant GoEst15-V3 whose activity toward dibutyl phthalate (DBP) and p-nitrophenyl butyrate was enhanced 2.0- and 2.5-fold, respectively. It was shown that 96.5% DBP (5 mM) was degraded by GoEst15-V3 in 60 min, while the wild-type enzyme degraded only 55% DBP. This study provides an effective screening tool for directed evolution of PAE-/PET-degrading enzymes.
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Affiliation(s)
- Jiawei Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mario Roque Huanca Nina
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiaoyan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yunpeng Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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10
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Guo B, Vanga SR, Lopez-Lorenzo X, Saenz-Mendez P, Ericsson SR, Fang Y, Ye X, Schriever K, Bäckström E, Biundo A, Zubarev RA, Furó I, Hakkarainen M, Syrén PO. Conformational Selection in Biocatalytic Plastic Degradation by PETase. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05548] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Boyang Guo
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Sudarsana Reddy Vanga
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Ximena Lopez-Lorenzo
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Patricia Saenz-Mendez
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Sara Rönnblad Ericsson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Yuan Fang
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Chemistry, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Xinchen Ye
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Karen Schriever
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Eva Bäckström
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Antonino Biundo
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Roman A. Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden
- SciLifeLab, SE-171 21 Solna, Sweden
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
| | - István Furó
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Chemistry, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Minna Hakkarainen
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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Qi X, Ma Y, Chang H, Li B, Ding M, Yuan Y. Evaluation of PET Degradation Using Artificial Microbial Consortia. Front Microbiol 2021; 12:778828. [PMID: 35003008 PMCID: PMC8733400 DOI: 10.3389/fmicb.2021.778828] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 01/30/2023] Open
Abstract
Polyethylene terephthalate (PET) biodegradation is regarded as an environmentally friendly degradation method. In this study, an artificial microbial consortium composed of Rhodococcus jostii, Pseudomonas putida and two metabolically engineered Bacillus subtilis was constructed to degrade PET. First, a two-species microbial consortium was constructed with two engineered B. subtilis that could secrete PET hydrolase (PETase) and monohydroxyethyl terephthalate hydrolase (MHETase), respectively; it could degrade 13.6% (weight loss) of the PET film within 7 days. A three-species microbial consortium was further obtained by adding R. jostii to reduce the inhibition caused by terephthalic acid (TPA), a breakdown product of PET. The weight of PET film was reduced by 31.2% within 3 days, achieving about 17.6% improvement compared with the two-species microbial consortium. Finally, P. putida was introduced to reduce the inhibition caused by ethylene glycol (EG), another breakdown product of PET, obtaining a four-species microbial consortium. With the four-species consortium, the weight loss of PET film reached 23.2% under ambient temperature. This study constructed and evaluated the artificial microbial consortia in PET degradation, which demonstrated the great potential of artificial microbial consortia in the utilization of complex substrates, providing new insights for biodegradation of complex polymers.
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Affiliation(s)
- Xinhua Qi
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yuan Ma
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Hanchen Chang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Bingzhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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