551
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Sadler JC, Wallace S. Microbial synthesis of vanillin from waste poly(ethylene terephthalate). GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2021; 23:4665-4672. [PMID: 34276250 PMCID: PMC8256426 DOI: 10.1039/d1gc00931a] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
Poly(ethylene terephthalate) (PET) is an abundant and extremely useful material, with widespread applications across society. However, there is an urgent need to develop technologies to valorise post-consumer PET waste to tackle plastic pollution and move towards a circular economy. Whilst PET degradation and recycling technologies have been reported, examples focus on repurposing the resultant monomers to produce more PET or other second-generation materials. Herein, we report a novel pathway in engineered Escherichia coli for the direct upcycling of PET derived monomer terephthalic acid into the value-added small molecule vanillin, a flavour compound ubiquitous in the food and cosmetic industries, and an important bulk chemical. After process optimisation, 79% conversion to vanillin from TA was achieved, a 157-fold improvement over our initial conditions. Parameters such as temperature, cell permeabilisation and in situ product removal were key to maximising vanillin titres. Finally, we demonstrate the conversion of post-consumer PET from a plastic bottle into vanillin by coupling the pathway with enzyme-catalysed PET hydrolysis. This work demonstrates the first biological upcycling of post-consumer plastic waste into vanillin using an engineered microorganism.
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Affiliation(s)
- Joanna C Sadler
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh Roger Land Building Alexander Crum Brown Road King's Buildings Edinburgh EH9 3FF UK
| | - Stephen Wallace
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh Roger Land Building Alexander Crum Brown Road King's Buildings Edinburgh EH9 3FF UK
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552
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Cowan AR, Costanzo CM, Benham R, Loveridge EJ, Moody SC. Fungal bioremediation of polyethylene: Challenges and perspectives. J Appl Microbiol 2021; 132:78-89. [PMID: 34218487 DOI: 10.1111/jam.15203] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/18/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022]
Abstract
Plastics have become ubiquitous in both their adoption as materials and as environmental contaminants. Widespread pollution of these versatile, man-made and largely petroleum-derived polymers has resulted from their long-term mass production, inappropriate disposal and inadequate end of life management. Polyethylene (PE) is at the forefront of this problem, accounting for one-third of plastic demand in Europe in part due to its extensive use in packaging. Current recycling and incineration processes do not represent sustainable solutions to tackle plastic waste, especially once it becomes littered, and the development of new waste-management and remediation technologies are needed. Mycoremediation (fungal-based biodegradation) of PE has been the topic of several studies over the last two decades. The utility of these studies is limited by an inconclusive definition of biodegradation and a lack of knowledge regarding the biological systems responsible. This review highlights relevant features of fungi as potential bioremediation agents, before discussing the evidence for fungal biodegradation of both high- and low-density PE. An up-to-date perspective on mycoremediation as a future solution to PE waste is provided.
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Affiliation(s)
- Andrew R Cowan
- Faculty of Sport, Health and Social Science, Solent University, Southampton, UK
| | - Chiara M Costanzo
- Department of Chemistry, College of Science, Swansea University, Swansea, UK
| | - Robert Benham
- Faculty of Creative Industries, Architecture and Engineering, Solent University, Southampton, UK
| | - E Joel Loveridge
- Department of Chemistry, College of Science, Swansea University, Swansea, UK
| | - Suzy C Moody
- School of Life Sciences, Pharmacy and Chemistry, Faculty of Science, Engineering and Computing, Kingston University, Kingston-Upon-Thames, UK
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553
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Lumio RT, Tan MA, Magpantay HD. Biotechnology-based microbial degradation of plastic additives. 3 Biotech 2021; 11:350. [PMID: 34221820 PMCID: PMC8217394 DOI: 10.1007/s13205-021-02884-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 06/06/2021] [Indexed: 10/21/2022] Open
Abstract
Plastic additives are agents responsible to the flame resistance, durability, microbial resistance, and flexibility of plastic products. High demand for production and use of plastic additives is associated with environmental accumulation and various health hazards. One of the suitable methods of depleting plastic additive in the environment is bioremediation as it offers cost-efficiency, convenience, and sustainability. Microbial activity is one of the effective ways of detoxifying various compounds as microorganisms can adapt in an environment with high prevalence of pollutants. The present review discusses the use and abundance of these plastic additives, their health-related risks, the microorganisms capable of degrading them, the proposed mechanism of biodegradation, and current innovations capable of improving the efficiency of bioremediation.
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Affiliation(s)
- Rob T. Lumio
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines
| | - Mario A. Tan
- The Graduate School, University of Santo Tomas, Manila, Philippines
- College of Science and Research Center for the Natural and Applied Sciences, University of Santo, Tomas, Manila, Philippines
| | - Hilbert D. Magpantay
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines
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554
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Biodegradation of aromatic pollutants meets synthetic biology. Synth Syst Biotechnol 2021; 6:153-162. [PMID: 34278013 PMCID: PMC8260767 DOI: 10.1016/j.synbio.2021.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/02/2023] Open
Abstract
Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.
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555
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Oda M. Structural basis for Ca 2+-dependent catalysis of a cutinase-like enzyme and its engineering: application to enzymatic PET depolymerization. Biophys Physicobiol 2021; 18:168-176. [PMID: 34386313 PMCID: PMC8326265 DOI: 10.2142/biophysico.bppb-v18.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
A cutinase-like enzyme from Saccharomonospora viridis AHK190, Cut190, can depolymerize polyethylene terephthalate (PET). As high activity at approximately 70°C is required for PET depolymerization, structure-based protein engineering of Cut190 was carried out. Crystal structure information of the Cut190 mutants was used for protein engineering and for evaluating the molecular basis of activity and thermal stability. A variety of biophysical methods were employed to unveil the mechanisms underlying the unique features of Cut190, which included the regulation of its activity and thermal stability by Ca2+. Ca2+ association and dissociation can change the enzyme conformation to regulate catalytic activity. Weak metal-ion binding would be required for the naïve conformational change of Cut190, while maintaining its fluctuation, to “switch” the enzyme on and off. The activity of Cut190 is regulated by the weak Ca2+ binding to the specific site, Site 1, while thermal stability is mainly regulated by binding to another Site 2, where a disulfide bond could be introduced to increase the stability. Recent results on the structure-activity relationship of engineered Cut190 are reviewed, including the application for PET depolymerization by enzymes.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
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556
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Nakamura A, Kobayashi N, Koga N, Iino R. Positive Charge Introduction on the Surface of Thermostabilized PET Hydrolase Facilitates PET Binding and Degradation. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01204] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Akihiko Nakamura
- Department of Applied Life Sciences, Faculty of Agriculture, 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
| | - Naoya Kobayashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Nobuyasu Koga
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa 240-0193, Japan
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557
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Improved production of biocatalysts by Yarrowia lipolytica using natural sources of the biopolyesters cutin and suberin, and their application in hydrolysis of poly (ethylene terephthalate) (PET). Bioprocess Biosyst Eng 2021; 44:2277-2287. [PMID: 34165618 DOI: 10.1007/s00449-021-02603-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
Since plastic pollution emerged as an urgent environmental problem, different biocatalysts have been tested for poly(ethylene terephthalate) (PET) hydrolysis. This work evaluated three different possible inducers for lipases and/or esterases, two natural sources of biopolymers (apple peels and commercial cork) and PET, as supplements in the solid-state fermentation of soybean bran by Yarrowia lipolytica. The obtained enzymatic extracts displaying different levels of lipase and esterase activities were then tested for PET depolymerization. Supplementation with 5 or 20 wt% of commercial cork led to an increase of 16% in lipase activity and to an increase of 131% in esterase activity, respectively. PET supplementation also led to an increase in the esterase activity of the enzymatic extracts (up to 69%). Enzymes produced in the screening step were able to act as biocatalysts in PET hydrolysis. Enzymatic extracts obtained in fermentation samples supplemented with 20 wt% PET and 20 wt% apple peels led to the highest terephthalic acid concentration (21.2 µmol L-1) in 7 days, whereas enzymes produced in commercial cork media were more efficient for bis(2-hydroxyethyl) terephthalate (BHET) hydrolysis, one of the key-PET hydrolysis intermediates. Results suggest a good potential of the biocatalysts produced by Y. lipolytica IMUFRJ 50,682 in a low-cost media for subsequent utilization in PET depolymerization reactions. This is one of the few reports on the use of a yeast for this application.
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558
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Shieh P, Hill MR, Zhang W, Kristufek SL, Johnson JA. Clip Chemistry: Diverse (Bio)(macro)molecular and Material Function through Breaking Covalent Bonds. Chem Rev 2021; 121:7059-7121. [PMID: 33823111 DOI: 10.1021/acs.chemrev.0c01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the two decades since the introduction of the "click chemistry" concept, the toolbox of "click reactions" has continually expanded, enabling chemists, materials scientists, and biologists to rapidly and selectively build complexity for their applications of interest. Similarly, selective and efficient covalent bond breaking reactions have provided and will continue to provide transformative advances. Here, we review key examples and applications of efficient, selective covalent bond cleavage reactions, which we refer to herein as "clip reactions." The strategic application of clip reactions offers opportunities to tailor the compositions and structures of complex (bio)(macro)molecular systems with exquisite control. Working in concert, click chemistry and clip chemistry offer scientists and engineers powerful methods to address next-generation challenges across the chemical sciences.
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Affiliation(s)
- Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan R Hill
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenxu Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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559
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Nikolaivits E, Pantelic B, Azeem M, Taxeidis G, Babu R, Topakas E, Brennan Fournet M, Nikodinovic-Runic J. Progressing Plastics Circularity: A Review of Mechano-Biocatalytic Approaches for Waste Plastic (Re)valorization. Front Bioeng Biotechnol 2021; 9:696040. [PMID: 34239864 PMCID: PMC8260098 DOI: 10.3389/fbioe.2021.696040] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/28/2021] [Indexed: 01/10/2023] Open
Abstract
Inspirational concepts, and the transfer of analogs from natural biology to science and engineering, has produced many excellent technologies to date, spanning vaccines to modern architectural feats. This review highlights that answers to the pressing global petroleum-based plastic waste challenges, can be found within the mechanics and mechanisms natural ecosystems. Here, a suite of technological and engineering approaches, which can be implemented to operate in tandem with nature's prescription for regenerative material circularity, is presented as a route to plastics sustainability. A number of mechanical/green chemical (pre)treatment methodologies, which simulate natural weathering and arthropodal dismantling activities are reviewed, including: mechanical milling, reactive extrusion, ultrasonic-, UV- and degradation using supercritical CO2. Akin to natural mechanical degradation, the purpose of the pretreatments is to render the plastic materials more amenable to microbial and biocatalytic activities, to yield effective depolymerization and (re)valorization. While biotechnological based degradation and depolymerization of both recalcitrant and bioplastics are at a relatively early stage of development, the potential for acceleration and expedition of valuable output monomers and oligomers yields is considerable. To date a limited number of independent mechano-green chemical approaches and a considerable and growing number of standalone enzymatic and microbial degradation studies have been reported. A convergent strategy, one which forges mechano-green chemical treatments together with the enzymatic and microbial actions, is largely lacking at this time. An overview of the reported microbial and enzymatic degradations of petroleum-based synthetic polymer plastics, specifically: low-density polyethylene (LDPE), high-density polyethylene (HDPE), polystyrene (PS), polyethylene terephthalate (PET), polyurethanes (PU) and polycaprolactone (PCL) and selected prevalent bio-based or bio-polymers [polylactic acid (PLA), polyhydroxyalkanoates (PHAs) and polybutylene succinate (PBS)], is detailed. The harvesting of depolymerization products to produce new materials and higher-value products is also a key endeavor in effectively completing the circle for plastics. Our challenge is now to effectively combine and conjugate the requisite cross disciplinary approaches and progress the essential science and engineering technologies to categorically complete the life-cycle for plastics.
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Affiliation(s)
- Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Brana Pantelic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - George Taxeidis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Ramesh Babu
- AMBER Centre, CRANN Institute, School of Chemistry, Trinity College Dublin, Dublin, Ireland
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | | | - Jasmina Nikodinovic-Runic
- Eco-Biotechnology & Drug Development Group, Laboratory for Microbial Molecular Genetics and Ecology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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560
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Gercke D, Furtmann C, Tozakidis IEP, Jose J. Highly Crystalline Post‐Consumer PET Waste Hydrolysis by Surface Displayed PETase Using a Bacterial Whole‐Cell Biocatalyst. ChemCatChem 2021. [DOI: 10.1002/cctc.202100443] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- David Gercke
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
| | - Christoph Furtmann
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
| | - Iasson E. P. Tozakidis
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie PharmaCampus Westfälische Wilhelms-Universität Münster Corrensstrasse 48 48149 Münster Germany
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561
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Hu K, Tian W, Yang Y, Nie G, Zhou P, Wang Y, Duan X, Wang S. Microplastics remediation in aqueous systems: Strategies and technologies. WATER RESEARCH 2021; 198:117144. [PMID: 33933920 DOI: 10.1016/j.watres.2021.117144] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/05/2021] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
In recent years, the ubiquitous detection and accumulation of microplastics (MPs) in the aquatic environment have raised significant concerns on water security and long-term ecological impacts all around the world. Nevertheless, critical reviews on strategic control and effective remediation of MPs in the aqueous phase are still lacking. In this work, we summarise the origins and types of MPs, and then introduce the methodologies for extraction, identification and quantification. More importantly, we for the first time provide a comprehensive overview of the recent advances in the emerging MPs removal and transformation technologies. Except for biodegradation, this review presents new applications of advanced oxidation processes (AOPs) for MPs degradation and utilisation, including photocatalysis, photoreforming and Fenton-like reactions. Physical or catalytic thermal treatment can transform plastics into value-added nanocarbons or hydrocarbons. These transformation technologies demonstrate great potentials in dealing with MPs. The review will guide researchers to further explore the feasible approaches and develop new strategies for advanced control and remediation of MPs in the future.
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Affiliation(s)
- Kunsheng Hu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide SA 5005, Australia
| | - Wenjie Tian
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide SA 5005, Australia
| | - Yangyang Yang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide SA 5005, Australia
| | - Gang Nie
- Department of Environmental Science and Engineering, Wuhan University, Wuhan 430079, China
| | - Peng Zhou
- College of Architecture & Environment, Sichuan University, Chengdu 610065, China
| | - Yuxian Wang
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China
| | - Xiaoguang Duan
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide SA 5005, Australia.
| | - Shaobin Wang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide SA 5005, Australia.
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562
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Vogel K, Wei R, Pfaff L, Breite D, Al-Fathi H, Ortmann C, Estrela-Lopis I, Venus T, Schulze A, Harms H, Bornscheuer UT, Maskow T. Enzymatic degradation of polyethylene terephthalate nanoplastics analyzed in real time by isothermal titration calorimetry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145111. [PMID: 33940717 DOI: 10.1016/j.scitotenv.2021.145111] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Plastics are globally used for a variety of benefits. As a consequence of poor recycling or reuse, improperly disposed plastic waste accumulates in terrestrial and aquatic ecosystems to a considerable extent. Large plastic waste items become fragmented to small particles through mechanical and (photo)chemical processes. Particles with sizes ranging from millimeter (microplastics, <5 mm) to nanometer (nanoplastics, NP, <100 nm) are apparently persistent and have adverse effects on ecosystems and human health. Current research therefore focuses on whether and to what extent microorganisms or enzymes can degrade these NP. In this study, we addressed the question of what information isothermal titration calorimetry, which tracks the heat of reaction of the chain scission of a polyester, can provide about the kinetics and completeness of the degradation process. The majority of the heat represents the cleavage energy of the ester bonds in polymer backbones providing real-time kinetic information. Calorimetry operates even in complex matrices. Using the example of the cutinase-catalyzed degradation of polyethylene terephthalate (PET) nanoparticles, we found that calorimetry (isothermal titration calorimetry-ITC) in combination with thermokinetic models is excellently suited for an in-depth analysis of the degradation processes of NP. For instance, we can separately quantify i) the enthalpy of surface adsorption ∆AdsH = 129 ± 2 kJ mol-1, ii) the enthalpy of the cleavage of the ester bonds ∆EBH = -58 ± 1.9 kJ mol-1 and the apparent equilibrium constant of the enzyme substrate complex K = 0.046 ± 0.015 g L-1. It could be determined that the heat production of PET NP degradation depends to 95% on the reaction heat and only to 5% on the adsorption heat. The fact that the percentage of cleaved ester bonds (η = 12.9 ± 2.4%) is quantifiable with the new method is of particular practical importance. The new method promises a quantification of enzymatic and microbial adsorption to NP and their degradation in mimicked real-world aquatic conditions.
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Affiliation(s)
- Kristina Vogel
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraße 15, D-04318 Leipzig, Germany; Institute for Drug Discovery, Leipzig University Medical School, Leipzig University, Bruederstr, 34, D-04103 Leipzig, Germany
| | - Ren Wei
- Department of Biotechnology and Enzyme Catalysis, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
| | - Lara Pfaff
- Department of Biotechnology and Enzyme Catalysis, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Daniel Breite
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, D-04318 Leipzig, Germany
| | - Hassan Al-Fathi
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
| | | | - Irina Estrela-Lopis
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstr, 16-18, D-04107 Leipzig, Germany
| | - Tom Venus
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstr, 16-18, D-04107 Leipzig, Germany
| | - Agnes Schulze
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, D-04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Thomas Maskow
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Permoserstraße 15, D-04318 Leipzig, Germany.
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563
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Sales JCS, Santos AG, de Castro AM, Coelho MAZ. A critical view on the technology readiness level (TRL) of microbial plastics biodegradation. World J Microbiol Biotechnol 2021; 37:116. [DOI: 10.1007/s11274-021-03089-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022]
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564
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da Costa CHS, Dos Santos AM, Alves CN, Martí S, Moliner V, Santana K, Lameira J. Assessment of the PETase conformational changes induced by poly(ethylene terephthalate) binding. Proteins 2021; 89:1340-1352. [PMID: 34075621 DOI: 10.1002/prot.26155] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/13/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022]
Abstract
Recently, a bacterium strain of Ideonella sakaiensis was identified with the uncommon ability to degrade the poly(ethylene terephthalate) (PET). The PETase from I. sakaiensis strain 201-F6 (IsPETase) catalyzes the hydrolysis of PET converting it to mono(2-hydroxyethyl) terephthalic acid (MHET), bis(2-hydroxyethyl)-TPA (BHET), and terephthalic acid (TPA). Despite the potential of this enzyme for mitigation or elimination of environmental contaminants, one of the limitations of the use of IsPETase for PET degradation is the fact that it acts only at moderate temperature due to its low thermal stability. Besides, molecular details of the main interactions of PET in the active site of IsPETase remain unclear. Herein, molecular docking and molecular dynamics (MD) simulations were applied to analyze structural changes of IsPETase induced by PET binding. Results from the essential dynamics revealed that the β1-β2 connecting loop is very flexible. This loop is located far from the active site of IsPETase and we suggest that it can be considered for mutagenesis to increase the thermal stability of IsPETase. The free energy landscape (FEL) demonstrates that the main change in the transition between the unbound to the bound state is associated with the β7-α5 connecting loop, where the catalytic residue Asp206 is located. Overall, the present study provides insights into the molecular binding mechanism of PET into the IsPETase structure and a computational strategy for mapping flexible regions of this enzyme, which can be useful for the engineering of more efficient enzymes for recycling plastic polymers using biological systems.
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Affiliation(s)
| | - Alberto M Dos Santos
- Centro de Ciências Exatas e Tecnologias, Federal University of Maranhão, São Luis, Maranhão, Brazil
| | - Cláudio Nahum Alves
- Institute of Natural Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Sérgio Martí
- Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain
| | - Kauê Santana
- Institute of Biodiversity, Federal University of Western Pará, Santarém, Pará, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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565
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Chen K, Hu Y, Dong X, Sun Y. Molecular Insights into the Enhanced Performance of EKylated PETase Toward PET Degradation. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01062] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Yang Hu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- 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, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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566
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Boneta S, Arafet K, Moliner V. QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate. J Chem Inf Model 2021; 61:3041-3051. [PMID: 34085821 PMCID: PMC8576761 DOI: 10.1021/acs.jcim.1c00394] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
The
environmental problems derived from the generalized plastic
consumption and disposal could find a friendly solution in enzymatic
biodegradation. Recently, two hydrolases from Ideonella sakaiensis 201-F6 and the metagenome-derived leaf-branch compost cutinase (LCC),
more specially the improved ICCG variant, have revealed degradation
activity toward poly ethylene terephthalate (PET). In the present
study, the reaction mechanism of this polymer breakage is studied
at an atomic level by multiscale QM/MM molecular dynamics simulations,
using semiempirical and DFT Hamiltonians to describe the QM region.
The obtained free energy surfaces confirmed a characteristic four-step
path for both systems, with activation energies in agreement with
the experimental observations. Structural analysis of the evolution
of the active site along the reaction progress and the study of electrostatic
effects generated by the proteins reveal the similarity in the behavior
of the active site of these two enzymes. The origin of the apparent
better performance of the LCC-ICCG protein over PETase must be due
to its capabilities of working at higher temperature and its intrinsic
relationship with the crystallinity grade of the polymer. Our results
may be useful for the development of more efficient enzymes in the
biodegradation of PET.
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Affiliation(s)
- Sergio Boneta
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain.,Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Kemel Arafet
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
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567
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Fu J, Wu YN. A Showcase of Green Chemistry: Sustainable Synthetic Approach of Zirconium-Based MOF Materials. Chemistry 2021; 27:9967-9987. [PMID: 33955075 DOI: 10.1002/chem.202005151] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 11/08/2022]
Abstract
Zirconium-based metal-organic framework materials (Zr-MOFs) have more practical usage over most conventional benchmark porous materials and even many other MOFs due to the excellent structural stability, rich coordination forms, and various active sites. However, their mass-production and application are restricted by the high-cost raw materials, complex synthesis procedures, harsh reaction conditions, and unexpected environmental impact. Based on the principles of "Green Chemistry", considerable efforts have been done for breaking through the limitations, and significant progress has been made in the sustainable synthesis of Zr-MOFs over the past decade. In this review, the advancements of green raw materials and green synthesis methods in the synthesis of Zr-MOFs are reviewed, along with the corresponding drawbacks. The challenges and prospects are discussed and outlooked, expecting to provide guidance for the acceleration of the industrialization and commercialization of Zr-MOFs.
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Affiliation(s)
- Jiarui Fu
- College of Environmental Science and Engineering State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Siping Rd 1239, 200092, Shanghai, P.R. China.,Shanghai Institute of Pollution Control and Ecological Security, Siping Rd 1239, 200092, Shanghai, P.R. China
| | - Yi-Nan Wu
- College of Environmental Science and Engineering State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Siping Rd 1239, 200092, Shanghai, P.R. China.,Shanghai Institute of Pollution Control and Ecological Security, Siping Rd 1239, 200092, Shanghai, P.R. China
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568
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569
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Dissanayake L, Jayakody LN. Engineering Microbes to Bio-Upcycle Polyethylene Terephthalate. Front Bioeng Biotechnol 2021; 9:656465. [PMID: 34124018 PMCID: PMC8193722 DOI: 10.3389/fbioe.2021.656465] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
Polyethylene terephthalate (PET) is globally the largest produced aromatic polyester with an annual production exceeding 50 million metric tons. PET can be mechanically and chemically recycled; however, the extra costs in chemical recycling are not justified when converting PET back to the original polymer, which leads to less than 30% of PET produced annually to be recycled. Hence, waste PET massively contributes to plastic pollution and damaging the terrestrial and aquatic ecosystems. The global energy and environmental concerns with PET highlight a clear need for technologies in PET "upcycling," the creation of higher-value products from reclaimed PET. Several microbes that degrade PET and corresponding PET hydrolase enzymes have been successfully identified. The characterization and engineering of these enzymes to selectively depolymerize PET into original monomers such as terephthalic acid and ethylene glycol have been successful. Synthetic microbiology and metabolic engineering approaches enable the development of efficient microbial cell factories to convert PET-derived monomers into value-added products. In this mini-review, we present the recent progress of engineering microbes to produce higher-value chemical building blocks from waste PET using a wholly biological and a hybrid chemocatalytic-biological strategy. We also highlight the potent metabolic pathways to bio-upcycle PET into high-value biotransformed molecules. The new synthetic microbes will help establish the circular materials economy, alleviate the adverse energy and environmental impacts of PET, and provide market incentives for PET reclamation.
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Affiliation(s)
- Lakshika Dissanayake
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, United States
| | - Lahiru N. Jayakody
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, United States
- Fermentation Science Institute, Southern Illinois University, Carbondale, IL, United States
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570
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571
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García-Depraect O, Bordel S, Lebrero R, Santos-Beneit F, Börner RA, Börner T, Muñoz R. Inspired by nature: Microbial production, degradation and valorization of biodegradable bioplastics for life-cycle-engineered products. Biotechnol Adv 2021; 53:107772. [PMID: 34015389 DOI: 10.1016/j.biotechadv.2021.107772] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/01/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
The global environmental pollution by micro- and macro-plastics reveals the consequences of an extensive use of recalcitrant plastic products together with inappropriate waste management practices that fail to sufficiently recycle the broad types of conventional plastic waste. Biobased and biodegradable plastics are experiencing an uprising as their properties offer alternative waste management solutions for a more circular material economy. However, although the production of such bioplastics has advanced on scale, the end-of-life (EOL) (bio)technologies to promote circularity are lacking behind. While composting and biogas plants are the only managed EOL options today, advanced biotechnological recycling technologies for biodegradable bioplastics are still in an embryonic stage. Thus, developing efficient biotechnologies capable of transforming bioplastic waste into high-value chemical building blocks or into the constituents of the original polymer offers promising routes towards life-cycle-engineered products. This review aims at providing a comprehensive state-of-the-art overview of microbial-based processes involved in the complete lifecycle of bioplastics. The current trends in the bioplastic market, the beginning and EOL scenarios of bioplastics, and a critical discussion on the key factors and mechanisms governing microbial degradation are systematically presented. Also, a critical evaluation of terminology and international standards to quantify polymer biodegradability is provided together with the latest biotechnological recycling strategies, including the use of different pre-treatments for (bio)plastic waste. Finally, the challenges and future perspectives for the development of life-cycle-engineered biobased and biodegradable plastic products are discussed.
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Affiliation(s)
- Octavio García-Depraect
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Sergio Bordel
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Raquel Lebrero
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Fernando Santos-Beneit
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Rosa Aragão Börner
- Nestlé Research, Société des Produits Nestlé S.A, Route du Jorat 57, 1000 Lausanne, Switzerland
| | - Tim Börner
- Nestlé Research, Société des Produits Nestlé S.A, Route du Jorat 57, 1000 Lausanne, Switzerland.
| | - Raúl Muñoz
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain.
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572
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From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi. Biotechnol Adv 2021; 50:107770. [PMID: 33989704 DOI: 10.1016/j.biotechadv.2021.107770] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/04/2021] [Accepted: 05/08/2021] [Indexed: 01/21/2023]
Abstract
In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation.
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573
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Ackermann YS, Li WJ, Op de Hipt L, Niehoff PJ, Casey W, Polen T, Köbbing S, Ballerstedt H, Wynands B, O'Connor K, Blank LM, Wierckx N. Engineering adipic acid metabolism in Pseudomonas putida. Metab Eng 2021; 67:29-40. [PMID: 33965615 DOI: 10.1016/j.ymben.2021.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/12/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022]
Abstract
Bio-upcycling of plastics is an upcoming alternative approach for the valorization of diverse polymer waste streams that are too contaminated for traditional recycling technologies. Adipic acid and other medium-chain-length dicarboxylates are key components of many plastics including polyamides, polyesters, and polyurethanes. This study endows Pseudomonas putida KT2440 with efficient metabolism of these dicarboxylates. The dcaAKIJP genes from Acinetobacter baylyi, encoding initial uptake and activation steps for dicarboxylates, were heterologously expressed. Genomic integration of these dca genes proved to be a key factor in efficient and reliable expression. In spite of this, adaptive laboratory evolution was needed to connect these initial steps to the native metabolism of P. putida, thereby enabling growth on adipate as sole carbon source. Genome sequencing of evolved strains revealed a central role of a paa gene cluster, which encodes parts of the phenylacetate metabolic degradation pathway with parallels to adipate metabolism. Fast growth required the additional disruption of the regulator-encoding psrA, which upregulates redundant β-oxidation genes. This knowledge enabled the rational reverse engineering of a strain that can not only use adipate, but also other medium-chain-length dicarboxylates like suberate and sebacate. The reverse engineered strain grows on adipate with a rate of 0.35 ± 0.01 h-1, reaching a final biomass yield of 0.27 ± 0.00 gCDW gadipate-1. In a nitrogen-limited medium this strain produced polyhydroxyalkanoates from adipate up to 25% of its CDW. This proves its applicability for the upcycling of mixtures of polymers made from fossile resources into biodegradable counterparts.
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Affiliation(s)
- Yannic S Ackermann
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Wing-Jin Li
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Leonie Op de Hipt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Paul-Joachim Niehoff
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - William Casey
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Dublin, Ireland
| | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Sebastian Köbbing
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Hendrik Ballerstedt
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Kevin O'Connor
- UCD Earth Institute and School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland; BiOrbic Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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574
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Damayanti, Wu HS. Strategic Possibility Routes of Recycled PET. Polymers (Basel) 2021; 13:1475. [PMID: 34063330 PMCID: PMC8125656 DOI: 10.3390/polym13091475] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022] Open
Abstract
The polyethylene terephthalate (PET) application has many challenges and potential due to its sustainability. The conventional PET degradation was developed for several technologies to get higher yield products of ethylene glycol, bis(2-hydroxyethyl terephthalate) and terephthalic acid. The chemical recycling of PET is reviewed, such as pyrolysis, hydrolysis, methanolysis, glycolysis, ionic-liquid, phase-transfer catalysis and combination of glycolysis-hydrolysis, glycolysis-methanolysis and methanolysis-hydrolysis. Furthermore, the reaction kinetics and reaction conditions were investigated both theoretically and experimentally. The recycling of PET is to solve environmental problems and find another source of raw material for petrochemical products and energy.
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Affiliation(s)
- Damayanti
- Department of Chemical Engineering, Institut Teknologi Sumatera, Lampung Selatan, Lampung 35365, Indonesia;
- Department of Chemical Engineering and Materials Science, Yuan Ze University, 135 Yuan-Tung Road, Chung-Li, Taoyuan 32003, Taiwan
| | - Ho-Shing Wu
- Department of Chemical Engineering and Materials Science, Yuan Ze University, 135 Yuan-Tung Road, Chung-Li, Taoyuan 32003, Taiwan
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575
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Jin K, Sun Q, Feng Y, Guo J, Wang C. High-performance polymers adapted to facile melt processing through structure design of benzocyclobutene-containing precursors. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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576
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DelRe C, Jiang Y, Kang P, Kwon J, Hall A, Jayapurna I, Ruan Z, Ma L, Zolkin K, Li T, Scown CD, Ritchie RO, Russell TP, Xu T. Near-complete depolymerization of polyesters with nano-dispersed enzymes. Nature 2021; 592:558-563. [DOI: 10.1038/s41586-021-03408-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
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577
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Tiso T, Narancic T, Wei R, Pollet E, Beagan N, Schröder K, Honak A, Jiang M, Kenny ST, Wierckx N, Perrin R, Avérous L, Zimmermann W, O'Connor K, Blank LM. Towards bio-upcycling of polyethylene terephthalate. Metab Eng 2021; 66:167-178. [PMID: 33865980 DOI: 10.1016/j.ymben.2021.03.011] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/24/2021] [Accepted: 03/13/2021] [Indexed: 12/29/2022]
Abstract
Over 359 million tons of plastics were produced worldwide in 2018, with significant growth expected in the near future, resulting in the global challenge of end-of-life management. The recent identification of enzymes that degrade plastics previously considered non-biodegradable opens up opportunities to steer the plastic recycling industry into the realm of biotechnology. Here, the sequential conversion of post-consumer polyethylene terephthalate (PET) into two types of bioplastics is presented: a medium chain-length polyhydroxyalkanoate (PHA) and a novel bio-based poly(amide urethane) (bio-PU). PET films are hydrolyzed by a thermostable polyester hydrolase yielding highly pure terephthalate and ethylene glycol. The obtained hydrolysate is used directly as a feedstock for a terephthalate-degrading Pseudomonas umsongensis GO16, also evolved to efficiently metabolize ethylene glycol, to produce PHA. The strain is further modified to secrete hydroxyalkanoyloxy-alkanoates (HAAs), which are used as monomers for the chemo-catalytic synthesis of bio-PU. In short, a novel value-chain for PET upcycling is shown that circumvents the costly purification of PET monomers, adding technological flexibility to the global challenge of end-of-life management of plastics.
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Affiliation(s)
- Till Tiso
- iAMB - Institute of Applied Microbiology. ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Tanja Narancic
- BiOrbic - SFI Bioeconomy Research Centre, University College Dublin, Belfield, Dublin 4, Ireland; School of Biomolecular and Biomedical Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ren Wei
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, Johannisallee 23, D-04103, Leipzig, Germany
| | - Eric Pollet
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Strasbourg University, 25 rue Becquerel, F-67087, Strasbourg Cedex 2, France
| | - Niall Beagan
- BiOrbic - SFI Bioeconomy Research Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - Katja Schröder
- iAMB - Institute of Applied Microbiology. ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Annett Honak
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, Johannisallee 23, D-04103, Leipzig, Germany
| | - Mengying Jiang
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Strasbourg University, 25 rue Becquerel, F-67087, Strasbourg Cedex 2, France; SOPREMA, 14 rue de Saint-Nazaire, F-67025 Strasbourg Cedex, France
| | - Shane T Kenny
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nick Wierckx
- iAMB - Institute of Applied Microbiology. ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Rémi Perrin
- SOPREMA, 14 rue de Saint-Nazaire, F-67025 Strasbourg Cedex, France
| | - Luc Avérous
- BioTeam/ICPEES-ECPM, UMR CNRS 7515, Strasbourg University, 25 rue Becquerel, F-67087, Strasbourg Cedex 2, France
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, Johannisallee 23, D-04103, Leipzig, Germany
| | - Kevin O'Connor
- BiOrbic - SFI Bioeconomy Research Centre, University College Dublin, Belfield, Dublin 4, Ireland; School of Biomolecular and Biomedical Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Lars M Blank
- iAMB - Institute of Applied Microbiology. ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany.
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578
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Affiliation(s)
- Jonathan M. Millican
- Macromolecular Chemistry II, Bavarian Polymer Institute, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Seema Agarwal
- Macromolecular Chemistry II, Bavarian Polymer Institute, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
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579
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Li Y, Li S, Sun J. Degradable Poly(vinyl alcohol)-Based Supramolecular Plastics with High Mechanical Strength in a Watery Environment. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007371. [PMID: 33634522 DOI: 10.1002/adma.202007371] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/17/2021] [Indexed: 06/12/2023]
Abstract
It is challenging to fabricate degradable poly(vinyl alcohol) (PVA)-based plastics that can be used in watery environments because PVA is soluble in water. In this study, PVA-based supramolecular plastics with excellent degradability in soil and high mechanical strength in watery environments are fabricated by the complexation of vanillin-grafted PVA (VPVA), hydrophobic humic acid (HA), and Fe3+ ions (hereafter denoted as VPVA-HA-Fe complexes). Large-area PVA-based plastics can be easily prepared from a solution of VPVA-HA-Fe complexes using a blade-coating method. The high-density of hydrogen bonds and coordination interactions, as well as the reinforcement of self-assembled Fe3+ -chelated HA nanoparticles, facilitate the fabrication of PVA-based plastics with a breaking strength of ≈85.0 MPa. After immersion in water at room temperature for 7 d, the PVA-based plastics exhibit a breaking strength of ≈26.2 MPa, which is similar to that of polyethylene in its dry state. Furthermore, owing to the reversibility of the hydrogen bonds and coordination interactions, the VPVA-HA-Fe plastics are recyclable and can be conveniently processed into plastic products with desired shapes. After being placed under soil for ≈108 d, the PVA-based plastics are completely degraded into nontoxic species without requiring manual interference.
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Affiliation(s)
- Yixuan Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Siheng Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Junqi Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
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580
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Borchert E, Hammerschmidt K, Hentschel U, Deines P. Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology. Trends Microbiol 2021; 29:908-918. [PMID: 33812769 DOI: 10.1016/j.tim.2021.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022]
Abstract
Environmental accumulation of anthropogenic pollutants is a pressing global issue. The biodegradation of these pollutants by microbes is an emerging field but is hampered by inefficient degradation rates and a limited knowledge of potential enzymes and pathways. Here, we advocate the view that significant progress can be achieved by harnessing artificial community selection for a desired biological process, an approach that makes use of eco-evolutionary principles. The selected communities can either be directly used in bioremediation applications or further be analyzed and modified, for instance through a combination of systems biology, synthetic biology, and genetic engineering. This knowledge can then inform machine learning and enhance the discovery of novel biodegradation pathways.
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Affiliation(s)
- Erik Borchert
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Ute Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany; University of Kiel, Kiel, Germany
| | - Peter Deines
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
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581
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Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021; 433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
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Affiliation(s)
- Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kai-En Chen
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Emma K Livingstone
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kathryn Perez
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gro E K Bjerga
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Øivind Larsen
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shira Albeck
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anja Schuetz
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany; University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany; Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Paola Storici
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marta S Semrau
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Christian Aigner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Sabine Suppmann
- Max-Planck Institute of Biochemistry, Biochemistry Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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582
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Kim DH, Han DO, In Shim K, Kim JK, Pelton JG, Ryu MH, Joo JC, Han JW, Kim HT, Kim KH. One-Pot Chemo-bioprocess of PET Depolymerization and Recycling Enabled by a Biocompatible Catalyst, Betaine. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dong Hyun Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Dong Oh Han
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Kyu In Shim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jae Kyun Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Jeffrey G. Pelton
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Mi Hee Ryu
- Bio-based Chemistry Research Center, Advanced Convergent Chemistry Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Jeong Chan Joo
- Bio-based Chemistry Research Center, Advanced Convergent Chemistry Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Jeong Woo Han
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hee Taek Kim
- Bio-based Chemistry Research Center, Advanced Convergent Chemistry Division, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Republic of Korea
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583
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Berselli A, Ramos MJ, Menziani MC. Novel Pet-Degrading Enzymes: Structure-Function from a Computational Perspective. Chembiochem 2021; 22:2032-2050. [PMID: 33470503 DOI: 10.1002/cbic.202000841] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Indexed: 12/12/2022]
Abstract
The bacterium strain Ideonella sakaiensis 201-F6 is able to hydrolyze low-crystallinity PET films at 30 °C due to two enzymes named PETase and MHETase. Since its discovery, many efforts have been dedicated to elucidating the structure and features of those two enzymes, and various authors have highlighted the necessity to optimize both the substrate binding site and the global structure in order to enhance the stability and catalytic activity of these PET biocatalysts so as to make them more suitable for industrial applications. In this review, the strategies adopted by different research groups to investigate the structure and functionality of both PETase and MHETase in depth are described, emphasizing the advantages provided by the use of computational methods to complement and drive experiments. Subsequently, the modifications implemented with protein engineering are discussed. The versatility of the enzymes secreted by I. sakaiensis enables the prediction that they will find several applications in the disposal of PET debris, encouraging a prioritization of efforts in this prolific research field.
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Affiliation(s)
- Alessandro Berselli
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Maria J Ramos
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
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584
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Modelling Microplastics in the River Thames: Sources, Sinks and Policy Implications. WATER 2021. [DOI: 10.3390/w13060861] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
With widespread, long-term historical use of plastics and the presence of microplastics in a range of new and existing products, there is rising concern about their potential impacts on freshwater ecosystems. Understanding how microplastics are transported and distributed along river systems is key to assessing impacts. Modelling the main flow dynamics, mixing, sedimentation and resuspension processes is essential for an understanding of the transport processes. We use the new, processed based, dynamic, integrated catchments (INCA) microplastics model and apply this to the whole of the freshwater catchment of the River Thames, UK, to evaluate inputs, loads and concentrations along the river system. Recent data from UK water industry studies on microplastics in effluent discharges and sewage sludge disposal has been utilised to drive the INCA microplastics model. Predicted concentrations and microplastic loads moving along the river system are shown to be significant, with a build-up of concentrations along the river, with increasing deposition on the riverbed. The potential impacts on aquatic ecosystems are evaluated and a review of policy implications is explored.
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585
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Meng X, Yang L, Liu H, Li Q, Xu G, Zhang Y, Guan F, Zhang Y, Zhang W, Wu N, Tian J. Protein engineering of stable IsPETase for PET plastic degradation by Premuse. Int J Biol Macromol 2021; 180:667-676. [PMID: 33753197 DOI: 10.1016/j.ijbiomac.2021.03.058] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/25/2022]
Abstract
Poly(ethylene terephthalate) (PET) is used widely by human beings, but is very difficult to degrade. Up to now, the PET degradation effect of PETase from Ideonella sakaiensis 201-F6 (IsPETase) variants with low stability and activity was not ideal. In this study, a mutation design tool, Premuse, was developed to integrate the sequence alignment and quantitative selection of the preferred mutations based on natural sequence evolution. Ten single point mutants were selected from 1486 homologous sequences using Premuse, and then two mutations (W159H and F229Y) with improved stability were screened from them. The derived double point mutant, W159H/F229Y, exhibited a strikingly enhanced enzymatic performance. Its Tm and catalytic efficiency values (kcat/Km) respectively increased by 10.4 °C and 2.0-fold using p-NPP as the substrate compared with wild type. The degradation activity for amorphous PET was increased by almost 40-fold in comparison with wild type at 40 °C in 24 h. Additionally, the variant could catalyze biodegradation of PET bottle preform at a mean rate of 23.4 mgPET/h/mgenzyme. This study allowed us to design the mutation more efficiently, and provides a tool for achieving biodegradation of PET pollution under mild natural environments.
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Affiliation(s)
- Xiangxi Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lixin Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hanqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingbin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guoshun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Food Science and Technology, Agricultural University of Hebei, Baoding, Hebei Province 071001, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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586
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Borrero-de Acuña JM, Rohde M, Saldias C, Poblete-Castro I. Fed-Batch mcl- Polyhydroxyalkanoates Production in Pseudomonas putida KT2440 and Δ phaZ Mutant on Biodiesel-Derived Crude Glycerol. Front Bioeng Biotechnol 2021; 9:642023. [PMID: 33796510 PMCID: PMC8007980 DOI: 10.3389/fbioe.2021.642023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
Crude glycerol has emerged as a suitable feedstock for the biotechnological production of various industrial chemicals given its high surplus catalyzed by the biodiesel industry. Pseudomonas bacteria metabolize the polyol into several biopolymers, including alginate and medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHAs). Although P. putida is a suited platform to derive these polyoxoesters from crude glycerol, the attained concentrations in batch and fed-batch cultures are still low. In this study, we employed P. putida KT2440 and the hyper-PHA producer ΔphaZ mutant in two different fed-batch modes to synthesize mcl-PHAs from raw glycerol. Initially, the cells grew in a batch phase (μmax 0.21 h–1) for 22 h followed by a carbon-limiting exponential feeding, where the specific growth rate was set at 0.1 (h–1), resulting in a cell dry weight (CDW) of nearly 50 (g L–1) at 40 h cultivation. During the PHA production stage, we supplied the substrate at a constant rate of 50 (g h–1), where the KT2440 and the ΔphaZ produced 9.7 and 12.7 gPHA L–1, respectively, after 60 h cultivation. We next evaluated the PHA production ability of the P. putida strains using a DO-stat approach under nitrogen depletion. Citric acid was the main by-product secreted by the cells, accumulating in the culture broth up to 48 (g L–1) under nitrogen limitation. The mutant ΔphaZ amassed 38.9% of the CDW as mcl-PHA and exhibited a specific PHA volumetric productivity of 0.34 (g L–1 h–1), 48% higher than the parental KT2440 under the same growth conditions. The biosynthesized mcl-PHAs had average molecular weights ranging from 460 to 505 KDa and a polydispersity index (PDI) of 2.4–2.6. Here, we demonstrated that the DO-stat feeding approach in high cell density cultures enables the high yield production of mcl-PHA in P. putida strains using the industrial crude glycerol, where the fed-batch process selection is essential to exploit the superior biopolymer production hallmarks of engineered bacterial strains.
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Affiliation(s)
- José Manuel Borrero-de Acuña
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility of Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Cesar Saldias
- Departamento de Química Física, Facultad de Química y Farmacia, Pontificia Universidad Católica de Chile, Macul, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Faculty of Life Sciences, Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Santiago, Chile
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587
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Park K, Mrsny R. Are controlled release scientists doing enough for our environment? J Control Release 2021; 332:620-622. [PMID: 33741384 DOI: 10.1016/j.jconrel.2021.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/04/2021] [Accepted: 03/07/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Kinam Park
- Purdue University, West Lafayette, Indiana, United States of America
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588
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Liu J, He J, Xue R, Xu B, Qian X, Xin F, Blank LM, Zhou J, Wei R, Dong W, Jiang M. Biodegradation and up-cycling of polyurethanes: Progress, challenges, and prospects. Biotechnol Adv 2021; 48:107730. [PMID: 33713745 DOI: 10.1016/j.biotechadv.2021.107730] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/07/2021] [Indexed: 10/21/2022]
Abstract
Polyurethanes (PUR) are ranked globally as the 6th most abundant synthetic polymer material. Most PUR materials are specifically designed to ensure long-term durability and high resistance to environmental factors. As the demand for diverse PUR materials is increasing annually in many industrial sectors, a large amount of PUR waste is also being generated, which requires proper disposal. In contrast to other mass-produced plastics such as PE, PP, and PET, PUR is a family of synthetic polymers, which differ considerably in their physical properties due to different building blocks (for example, polyester- or polyether-polyol) used in the synthesis. Despite its xenobiotic properties, PUR has been found to be susceptible to biodegradation by different microorganisms, albeit at very low rate under environmental and laboratory conditions. Discovery and characterization of highly efficient PUR-degrading microbes and enzymes capable of disassembling PUR polymer chains into oligo- and monomeric compounds is of fundamental importance for a circular plastic economy. In this review, the main methods used for screening PUR-degrading microbes and enzymes are summarized and compared in terms of their catalytic mechanisms. Furthermore, recycling and upcycling strategies of waste PUR polymers, including microbial conversion of PUR monomers into value added products, are presented.
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Affiliation(s)
- Jiawei Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jie He
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Rui Xue
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Bin Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Xiujuan Qian
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Lars M Blank
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Ren Wei
- Junior Research Group Plastic Biodegradation, Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
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589
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Wayman C, Niemann H. The fate of plastic in the ocean environment - a minireview. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:198-212. [PMID: 33475108 DOI: 10.1039/d0em00446d] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The presence of plastics in the marine environment poses a threat to ocean life and has received much scientific and public attention in recent years. Plastics were introduced to the market in the 1950s and since then, global production figures and ocean plastic littering have increased exponentially. Of the 359 million tonnes (Mt) produced in 2018, an estimated 14.5 Mt has entered the ocean. In particular smaller plastic particles can be ingested by marine biota causing hazardous effects. Plastic marine debris (PMD) is exposed to physical, chemical and biological stressors. These cause macro and microplastic to break down into smaller fragments, including sub micrometre sized nanoplastic particles, which may account for an important but so far unevaluated fraction of the ocean plastic budget. Physicochemical and biological deterioration of PMD also leads to the release of more volatile compounds and the terminal oxidation of PMD, which most likely accounts for an important but also unevaluated fraction in the ocean plastic budget. This minireview provides an overview on (1) the quantity of plastic production and waste, pathways for plastics to enter the marine realm, the inventory of PMD and the negative effects of PMD to ocean life. (2) We discuss plastic degradation mechanisms in the ocean, expanding on the processes of photodegradation and biodegradation. (3) This review also highlights the emerging topic of nanoplastics in the sea and provides an overview on their specific physical and chemical properties, potential harm to ocean life, and nanoplastic detection techniques.
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Affiliation(s)
- Chloe Wayman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
| | - Helge Niemann
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje, The Netherlands. and Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands and CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, 9037 Tromsø, Norway
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590
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Tan YQ, Xue B, Yew WS. Genetically Encodable Scaffolds for Optimizing Enzyme Function. Molecules 2021; 26:molecules26051389. [PMID: 33806660 PMCID: PMC7961827 DOI: 10.3390/molecules26051389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted.
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Affiliation(s)
- Yong Quan Tan
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Correspondence: ; Tel.: +65-6516-8624
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591
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Kan Y, He L, Luo Y, Bao R. IsPETase Is a Novel Biocatalyst for Poly(ethylene terephthalate) (PET) Hydrolysis. Chembiochem 2021; 22:1706-1716. [PMID: 33434375 DOI: 10.1002/cbic.202000767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/10/2021] [Indexed: 02/05/2023]
Abstract
Poly(ethylene terephthalate) (PET) is one of the most widely used synthetic polyesters, but also a major cause of plastic pollution. Because the chemical degradation of PET would be uneconomical and rather burdensome, considerable efforts have been devoted to exploring enzymatic processes for the disposal of PET waste. Many PET-hydrolyzing enzymes have been reported in recent decades, some of which demonstrate excellent potential for industrial applications. This review sets out to summarize the state of investigation into IsPETase, a cutinase-like enzyme from Ideonella sakaiensis possessing ability to degrade crystalline PET, and to gain further insight into the structure-function relationship of IsPETase. Benefiting from the continuing identification of novel cutinase-like proteins and growing availability of the engineered IsPETase, we may anticipate future developments in this type of enzyme would generate suitable biocatalyst for industrial use.
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Affiliation(s)
- Yeyi Kan
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, P. R. China
| | - Lihui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, P. R. China
| | - Yunzi Luo
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, P. R. China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, P. R. China
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592
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Zhu B, Wang D, Wei N. Enzyme Discovery and Engineering for Sustainable Plastic Recycling. Trends Biotechnol 2021; 40:22-37. [PMID: 33676748 DOI: 10.1016/j.tibtech.2021.02.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
The drastically increasing amount of plastic waste is causing an environmental crisis that requires innovative technologies for recycling post-consumer plastics to achieve waste valorization while meeting environmental quality goals. Biocatalytic depolymerization mediated by enzymes has emerged as an efficient and sustainable alternative for plastic treatment and recycling. A variety of plastic-degrading enzymes have been discovered from microbial sources. Meanwhile, protein engineering has been exploited to modify and optimize plastic-degrading enzymes. This review highlights the recent trends and up-to-date advances in mining novel plastic-degrading enzymes through state-of-the-art omics-based techniques and improving the enzyme catalytic efficiency and stability via various protein engineering strategies. Future research prospects and challenges are also discussed.
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Affiliation(s)
- Baotong Zhu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Dong Wang
- Department of Computer Science and Engineering, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, Indiana 46556, USA.
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593
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Shi C, Li ZC, Caporaso L, Cavallo L, Falivene L, Chen EYX. Hybrid monomer design for unifying conflicting polymerizability, recyclability, and performance properties. Chem 2021. [DOI: 10.1016/j.chempr.2021.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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594
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Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors. Int J Mol Sci 2021; 22:ijms22052332. [PMID: 33652738 PMCID: PMC7956259 DOI: 10.3390/ijms22052332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/28/2022] Open
Abstract
Esters are organic compounds widely represented in cellular structures and metabolism, originated by the condensation of organic acids and alcohols. Esterification reactions are also used by chemical industries for the production of synthetic plastic polymers. Polyester plastics are an increasing source of environmental pollution due to their intrinsic stability and limited recycling efforts. Bioremediation of polyesters based on the use of specific microbial enzymes is an interesting alternative to the current methods for the valorization of used plastics. Microbial esterases are promising catalysts for the biodegradation of polyesters that can be engineered to improve their biochemical properties. In this work, we analyzed the structure-activity relationships in microbial esterases, with special focus on the recently described plastic-degrading enzymes isolated from marine microorganisms and their structural homologs. Our analysis, based on structure-alignment, molecular docking, coevolution of amino acids and surface electrostatics determined the specific characteristics of some polyester hydrolases that could be related with their efficiency in the degradation of aromatic polyesters, such as phthalates.
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595
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Becerril-Arreola R, Bucklin RE. Beverage bottle capacity, packaging efficiency, and the potential for plastic waste reduction. Sci Rep 2021; 11:3542. [PMID: 33633137 PMCID: PMC7907389 DOI: 10.1038/s41598-021-82983-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 01/25/2021] [Indexed: 11/09/2022] Open
Abstract
Plastic pollution is a pressing issue because authorities struggle to contain and process the enormous amount of waste produced. We study the potential for reducing plastic waste by examining the efficiency with which different polyethylene terephthalate (PET) bottles deliver beverages. We find that 80% of the variation in bottle weight is explained by bottle capacity, 16% by product category, and 1% by brand. Bottle weight is quadratic and convex function of capacity, which implies that medium capacity bottles are most efficient at delivering consumable product. Local data on PET bottle sales and municipal waste recovery validate the findings. A 20% shift in consumption from smaller to larger bottles could reduce the production of PET waste by over 10,000 t annually in the U.S. alone.
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596
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Shi L, Liu H, Gao S, Weng Y, Zhu L. Enhanced Extracellular Production of IsPETase in Escherichia coli via Engineering of the pelB Signal Peptide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2245-2252. [PMID: 33576230 DOI: 10.1021/acs.jafc.0c07469] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Poly(ethylene terephthalate) (PET) is one of the most commonly used plastics worldwide and its accumulation in the environment is a global problem. PETase from Ideonella sakaiensis 201-F6 was reported to exhibit higher hydrolytic activity and specificity for PET than other enzymes at ambient temperature. Enzymatic degradation of PET using PETase provides an attractive approach for plastic degradation and recycling. In this work, extracellular PETase was achieved by Escherichia coli BL21 using a Sec-dependent translocation signal peptide, pelB, for secretion. Furthermore, engineering of the pelB through random mutagenesis and screening was performed to improve the secretion efficiency of PETase. Evolved pelB enabled higher PETase secretion by up to 1.7-fold. The improved secretion of PETase led to more efficient hydrolysis of the PET model compound, bis (2-hydroxyethyl) terephthalic acid (BHET), PET powder, and PET film. Our study presents the first example of the increasing secretion of PETase by an engineered signal peptide, providing a promising approach to obtain extracellular PETase for efficient enzymatic degradation of PET.
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Affiliation(s)
- Lixia Shi
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Haifeng Liu
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, Graz 8010, Austria
| | - Songfeng Gao
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yunxuan Weng
- Beijing Key Laboratory of Quality Evaluation Technology for Hygiene and Safety of Plastics, Beijing Technology and Business University, Beijing 100048, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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597
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A Computational Method to Predict Effects of Residue Mutations on the Catalytic Efficiency of Hydrolases. Catalysts 2021. [DOI: 10.3390/catal11020286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
With scientific and technological advances, growing research has focused on engineering enzymes that acquire enhanced efficiency and activity. Thereinto, computer-based enzyme modification makes up for the time-consuming and labor-intensive experimental methods and plays a significant role. In this study, for the first time, we collected and manually curated a data set for hydrolases mutation, including structural information of enzyme-substrate complexes, mutated sites and Kcat/Km obtained from vitro assay. We further constructed a classification model using the random forest algorithm to predict the effects of residue mutations on catalytic efficiency (increase or decrease) of hydrolases. This method has achieved impressive performance on a blind test set with the area under the receiver operating characteristic curve of 0.86 and the Matthews Correlation Coefficient of 0.659. Our results demonstrate that computational mutagenesis has an instructive effect on enzyme modification, which may expedite the design of engineering hydrolases.
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598
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Decarpigny C, Bleta R, Ponchel A, Monflier E. Oxidation of 2,5-diformfylfuran to 2,5-furandicarboxylic acid catalyzed by Candida antarctica Lipase B immobilized in a cyclodextrin-templated mesoporous silica. The critical role of pore characteristics on the catalytic performance. Colloids Surf B Biointerfaces 2021; 200:111606. [PMID: 33601112 DOI: 10.1016/j.colsurfb.2021.111606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 11/26/2022]
Abstract
HYPOTHESIS Porous silica has been extensively used as suitable carrier for the immobilization of various enzymes. Randomly Methylated β-Cyclodextrin (RaMeβCD) has surface active properties and very high solubility in water and could therefore be used as template in the fabrication of silica particles with tunable pore size. EXPERIMENTS Silica particles were prepared by sol-gel process in alkaline medium with and without use of RaMeβCD. Lipase Bfrom Candida antarctica (CALB) was either incorporated within the pores of RaMeβCD-derived support or covalently attached on the surface of CD-free silica particles and its catalytic performance was assayed in the oxidation of 2,5-diformylfuran (DFF) to 2,5-furandicarboxylic acid (FDCA). Enzymatic reactors were characterized by N2-adsorption analysis, small angle XRD, TG/DSC experiments, ATR-FTIR spectroscopy, HR-TEM and LSCM, while reaction products were determined based on 1H NMR spectroscopy combined with HPLC. FINDINGS Results showed that the use of RaMeβCD as structure directing agent led to mesoporous silica composed of uniform 8 nm-sized particles with 11 nm-sized mesopores compatible with the dimensions of CALB (3.0 nm × 4.0 nm × 5.0 nm). Incorporation of CALB within the pores of RaMeβCD-derived silica caused almost a two-fold increase in specific activity after 7 h at 40 °C when compared to lipase immobilized on the surface of CD-free silica particles (33.2 μmol g-1 min-1vs. 14.4 μmol g-1 min-1). Moreover, the RaMeβCD-derived biocatalyst demonstrated enhanced operational stability during the recycling experiments, retaining more than 90% of its initial activity after five 24 h-reaction cycles. These findings open up new avenues for future research on the use of cyclodextrins in the development of enzyme-based nanoreactors.
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Affiliation(s)
- Cédric Decarpigny
- Univ. Artois, CNRS, Centrale Lille, ENSCL, Univ. Lille, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, F-62300, Lens, France
| | - Rudina Bleta
- Univ. Artois, CNRS, Centrale Lille, ENSCL, Univ. Lille, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, F-62300, Lens, France.
| | - Anne Ponchel
- Univ. Artois, CNRS, Centrale Lille, ENSCL, Univ. Lille, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, F-62300, Lens, France
| | - Eric Monflier
- Univ. Artois, CNRS, Centrale Lille, ENSCL, Univ. Lille, UMR 8181-UCCS-Unité de Catalyse et Chimie du Solide, F-62300, Lens, France
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599
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600
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Bååth JA, Borch K, Jensen K, Brask J, Westh P. Comparative Biochemistry of Four Polyester (PET) Hydrolases*. Chembiochem 2021; 22:1627-1637. [PMID: 33351214 DOI: 10.1002/cbic.202000793] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/22/2020] [Indexed: 11/08/2022]
Abstract
The potential of bioprocessing in a circular plastic economy has strongly stimulated research into the enzymatic degradation of different synthetic polymers. Particular interest has been devoted to the commonly used polyester, poly(ethylene terephthalate) (PET), and a number of PET hydrolases have been described. However, a kinetic framework for comparisons of PET hydrolases (or other plastic-degrading enzymes) acting on the insoluble substrate has not been established. Herein, we propose such a framework, which we have tested against kinetic measurements for four PET hydrolases. The analysis provided values of kcat and KM , as well as an apparent specificity constant in the conventional units of M-1 s-1 . These parameters, together with experimental values for the number of enzyme attack sites on the PET surface, enabled comparative analyses. A variant of the PET hydrolase from Ideonella sakaiensis was the most efficient enzyme at ambient conditions; it relied on a high kcat rather than a low KM . Moreover, both soluble and insoluble PET fragments were consistently hydrolyzed much faster than intact PET. This suggests that interactions between polymer strands slow down PET degradation, whereas the chemical steps of catalysis and the low accessibility associated with solid substrate were less important for the overall rate. Finally, the investigated enzymes showed a remarkable substrate affinity, and reached half the saturation rate on PET when the concentration of attack sites in the suspension was only about 50 nM. We propose that this is linked to nonspecific adsorption, which promotes the nearness of enzyme and attack sites.
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Affiliation(s)
- Jenny Arnling Bååth
- 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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