1
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Amanna R, Rakshit SK. Review of nomenclature and methods of analysis of polyethylene terephthalic acid hydrolyzing enzymes activity. Biodegradation 2024; 35:341-360. [PMID: 37688750 DOI: 10.1007/s10532-023-10048-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/15/2023] [Indexed: 09/11/2023]
Abstract
Enzymatic degradation of polyethylene terephthalic acid (PET) has been gaining increasing importance. This has resulted in a significant increase in the search for newer enzymes and the development of more efficient enzyme-based systems. Due to the lack of a standard screening process, screening new enzymes has relied on other assays to determine the presence of esterase activity. This, in turn, has led to various nomenclatures and methods used to describe them and measure their activity. Since all PET-hydrolyzing enzymes are α/β hydrolases, they catalyze a serine nucleophilic attack and cleave an ester bond. They are lipases, esterases, cutinases and hydrolases. This has been used interchangeably, leading to difficulties while comparing results and evaluating progress. This review discusses the varied enzyme nomenclature being adapted, the different assays and analysis methods reported, and the strategies used to increase PET-hydrolyzing enzyme efficiency. A section on the various ways to quantify PET hydrolysis is also covered.
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Affiliation(s)
- Ruth Amanna
- Department of Biotechnology, Lakehead University, Thunder Bay, ON, Canada
- Biorefining Research Institute (BRI), Lakehead University, Thunder Bay, ON, Canada
| | - Sudip K Rakshit
- Department of Biotechnology, Lakehead University, Thunder Bay, ON, Canada.
- Biorefining Research Institute (BRI), Lakehead University, Thunder Bay, ON, Canada.
- Department of Chemical Engineering, Lakehead University, Thunder Bay, ON, Canada.
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2
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Jeon YW, Song HM, Lee KY, Kim YA, Kim HK. Synthesis of Isoamyl Fatty Acid Ester, a Flavor Compound, by Immobilized Rhodococcus Cutinase. J Microbiol Biotechnol 2024; 34:1356-1364. [PMID: 38754998 PMCID: PMC11239401 DOI: 10.4014/jmb.2402.02033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Isoamyl fatty acid esters (IAFEs) are widely used as fruity flavor compounds in the food industry. In this study, various IAFEs were synthesized from isoamyl alcohol and various fatty acids using a cutinase enzyme (Rcut) derived from Rhodococcus bacteria. Rcut was immobilized on methacrylate divinylbenzene beads and used to synthesize isoamyl acetate, butyrate, hexanoate, octanoate, and decanoate. Among them, Rcut synthesized isoamyl butyrate (IAB) most efficiently. Docking model studies showed that butyric acid was the most suitable substrate in terms of binding energy and distance from the active site serine (Ser114) γ-oxygen. Up to 250 mM of IAB was synthesized by adjusting reaction conditions such as substrate concentration, reaction temperature, and reaction time. When the enzyme reaction was performed by reusing the immobilized enzyme, the enzyme activity was maintained at least six times. These results demonstrate that the immobilized Rcut enzyme can be used in the food industry to synthesize a variety of fruity flavor compounds, including IAB.
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Affiliation(s)
- Ye Won Jeon
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Ha Min Song
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Ka Yeong Lee
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Yeong A Kim
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Hyung Kwoun Kim
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
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3
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Taxeidis G, Nikolaivits E, Nikodinovic-Runic J, Topakas E. Mimicking the enzymatic plant cell wall hydrolysis mechanism for the degradation of polyethylene terephthalate. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124347. [PMID: 38857840 DOI: 10.1016/j.envpol.2024.124347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
Plastic pollution presents a global challenge, impacting ecosystems, wildlife, and economies. Polyethylene terephthalate (PET), widely used in products like bottles, significantly contributes to this issue due to poor waste collection. In recent years, there has been increasing interest in plant biomass-degrading enzymes for plastic breakdown, due to the structural and physicochemical similarities between natural and synthetic polymers. Filamentous fungi involved in hemicellulose degradation have developed a complex mode of action that includes not only enzymes but also biosurfactants; surface-active molecules that facilitate enzyme-substrate interactions. For this reason, this study aimed to mimic the mechanism of biomass degradation by repurposing plant cell wall degrading enzymes including a cutinase and three esterases to cooperatively contribute to PET degradation. Surfactants of different charge were also introduced in the reactions, as their role is similar to biosurfactants, altering the surface tension of the polymers and thus improving enzymes' accessibility. Notably, Fusarium oxysporum cutinase combined with anionic surfactant exhibited a 2.3- and 1.6-fold higher efficacy in hydrolyzing amorphous and semi-crystalline PET, respectively. When cutinase was combined with either of two ferulic acid esterases, it resulted in complete conversion of PET intermediate products to TPA, increasing the overall product release up to 1.9- fold in presence of surfactant. The combination of cutinase with a glucuronoyl esterase demonstrated significant potential in plastic depolymerization, increasing degradation yields in semi-crystalline PET by up to 1.4-fold. The approach of incorporating enzyme cocktails and surfactants emerge as an efficient solution for PET degradation in mild reaction conditions, with potential applications in eco-friendly plastic waste management.
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Affiliation(s)
- George Taxeidis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772, 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, 11000, Belgrade, Serbia
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772, Athens, Greece.
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4
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Roman VA, Crable BR, Wagner DN, Gryganskyi A, Zelik S, Cummings L, Hung CS, Nadeau LJ, Schratz L, Haridas S, Pangilinan J, Lipzen A, Na H, Yan M, Ng V, Grigoriev IV, Barlow D, Biffinger J, Kelley-Loughnane N, Crookes-Goodson WJ, Stamps B, Varaljay VA. Identification and recombinant expression of a cutinase from Papiliotrema laurentii that hydrolyzes natural and synthetic polyesters. Appl Environ Microbiol 2024; 90:e0169423. [PMID: 38624219 PMCID: PMC11205760 DOI: 10.1128/aem.01694-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/21/2024] [Indexed: 04/17/2024] Open
Abstract
Given the multitude of extracellular enzymes at their disposal, many of which are designed to degrade nature's polymers (lignin, cutin, cellulose, etc.), fungi are adept at targeting synthetic polyesters with similar chemical composition. Microbial-influenced deterioration of xenobiotic polymeric surfaces is an area of interest for material scientists as these are important for the conservation of the underlying structural materials. Here, we describe the isolation and characterization of the Papiliotrema laurentii 5307AH (P. laurentii) cutinase, Plcut1. P. laurentii is basidiomycete yeast with the ability to disperse Impranil-DLN (Impranil), a colloidal polyester polyurethane, in agar plates. To test whether the fungal factor involved in this clearing was a secreted enzyme, we screened the ability of P. laurentii culture supernatants to disperse Impranil. Using size exclusion chromatography (SEC), we isolated fractions that contained Impranil-clearing activity. These fractions harbored a single ~22 kD band, which was excised and subjected to peptide sequencing. Homology searches using the peptide sequences identified, revealed that the protein Papla1 543643 (Plcut1) displays similarities to serine esterase and cutinase family of proteins. Biochemical assays using recombinant Plcut1 confirmed that this enzyme has the capability to hydrolyze Impranil, soluble esterase substrates, and apple cutin. Finally, we confirmed the presence of the Plcut1 in culture supernatants using a custom antibody that specifically recognizes this protein. The work shown here supports a major role for the Plcut1 in the fungal degradation of natural polyesters and xenobiotic polymer surfaces.IMPORTANCEFungi play a vital role in the execution of a broad range of biological processes that drive ecosystem function through production of a diverse arsenal of enzymes. However, the universal reactivity of these enzymes is a current problem for the built environment and the undesired degradation of polymeric materials in protective coatings. Here, we report the identification and characterization of a hydrolase from Papiliotrema laurentii 5307AH, an aircraft-derived fungal isolate found colonizing a biodeteriorated polymer-coated surface. We show that P. laurentii secretes a cutinase capable of hydrolyzing soluble esters as well as ester-based compounds forming solid surface coatings. These findings indicate that this fungus plays a significant role in biodeterioration through the production of a cutinase adept at degrading ester-based polymers, some of which form the backbone of protective surface coatings. The work shown here provides insights into the mechanisms employed by fungi to degrade xenobiotic polymers.
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Affiliation(s)
- Victor A. Roman
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Bryan R. Crable
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Dominique N. Wagner
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Andrii Gryganskyi
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Stephen Zelik
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Logan Cummings
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Chia S. Hung
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
| | - Lloyd J. Nadeau
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
| | - Lucas Schratz
- Chemistry Department, University of Dayton, Dayton, Ohio, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyunsoo Na
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | | | | | - Nancy Kelley-Loughnane
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
| | | | - Blake Stamps
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
| | - Vanessa A. Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Ohio, USA
- The Ohio State University, Infectious Diseases Institute, Columbus, Ohio, USA
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5
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Taxeidis G, Djapovic M, Nikolaivits E, Maslak V, Nikodinovic-Runic J, Topakas E. New Labeled PET Analogues Enable the Functional Screening and Characterization of PET-Degrading Enzymes. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024; 12:5943-5952. [PMID: 38903150 PMCID: PMC11187625 DOI: 10.1021/acssuschemeng.4c00143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 06/22/2024]
Abstract
The discovery and engineering of novel biocatalysts capable of depolymerizing polyethylene terephthalate (PET) have gained significant attention since the need for green technologies to combat plastic pollution has become increasingly urgent. This study focuses on the development of novel substrates that can indicate enzymes with PET hydrolytic activity, streamlining the process of enzyme evaluation and selection. Four novel substrates, mimicking the structure of PET, were chemically synthesized and labeled with fluorogenic or chromogenic moieties, enabling the direct analysis of candidate enzymes without complex preparatory or analysis steps. The fluorogenic substrates, mUPET1, mUPET2, and mUPET3, not only identify enzymes capable of PET breakdown but also differentiate those with exceptional performance on the polymer, such as the benchmark PETase, LCCICCG. Among the substrates, the chromogenic p-NPhPET3 stands out as a reliable tool for screening both pure and crude enzymes, offering advantages over fluorogenic substrates such as ease of assay using UV-vis spectroscopy and compatibility with crude enzyme samples. However, ferulic acid esterases and mono-(2-hydroxyethyl) terephthalate esterases (MHETases), which exhibit remarkably high affinity for PET oligomers, also show high catalytic activity on these substrates. The substrates introduced in this study hold significant value in the function-based screening and characterization of enzymes that degrade PET, as well as the the potential to be used in screening mutant libraries derived from directed evolution experiments. Following this approach, a rapid and dependable assay method can be carried out using basic laboratory infrastructure, eliminating the necessity for intricate preparatory procedures before analysis.
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Affiliation(s)
- George Taxeidis
- Industrial
Biotechnology & Biocatalysis Group, Biotechnology Laboratory,
School of Chemical Engineering, National
Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772 Athens, Greece
| | - Milica Djapovic
- Faculty
of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Belgrade, Serbia
| | - Efstratios Nikolaivits
- Industrial
Biotechnology & Biocatalysis Group, Biotechnology Laboratory,
School of Chemical Engineering, National
Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772 Athens, Greece
| | - Veselin Maslak
- Faculty
of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Belgrade, Serbia
| | - Jasmina Nikodinovic-Runic
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Evangelos Topakas
- Industrial
Biotechnology & Biocatalysis Group, Biotechnology Laboratory,
School of Chemical Engineering, National
Technical University of Athens, Heroon Polytechniou 9, Zografou, 15772 Athens, Greece
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6
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Makryniotis K, Nikolaivits E, Taxeidis G, Nikodinovic-Runic J, Topakas E. Exploring the substrate spectrum of phylogenetically distinct bacterial polyesterases. Biotechnol J 2024; 19:e2400053. [PMID: 38593303 DOI: 10.1002/biot.202400053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/09/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
The rapid escalation of plastic waste accumulation presents a significant threat of the modern world, demanding an immediate solution. Over the last years, utilization of the enzymatic machinery of various microorganisms has emerged as an environmentally friendly asset in tackling this pressing global challenge. Thus, various hydrolases have been demonstrated to effectively degrade polyesters. Plastic waste streams often consist of a variety of different polyesters, as impurities, mainly due to wrong disposal practices, rendering recycling process challenging. The elucidation of the selective degradation of polyesters by hydrolases could offer a proper solution to this problem, enhancing the recyclability performance. Towards this, our study focused on the investigation of four bacterial polyesterases, including DaPUase, IsPETase, PfPHOase, and Se1JFR, a novel PETase-like lipase. The enzymes, which were biochemically characterized and structurally analyzed, demonstrated degradation ability of synthetic plastics. While a consistent pattern of polyesters' degradation was observed across all enzymes, Se1JFR stood out in the degradation of PBS, PLA, and polyether PU. Additionally, it exhibited comparable results to IsPETase, a benchmark mesophilic PETase, in the degradation of PCL and semi-crystalline PET. Our results point out the wide substrate spectrum of bacterial hydrolases and underscore the significant potential of PETase-like enzymes in polyesters degradation.
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Affiliation(s)
- Konstantinos Makryniotis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - George Taxeidis
- 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
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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7
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Torres de Oliveira C, Alexandrino de Assis M, Lourenço Franco Cairo JP, Damasio A, Guimarães Pereira GA, Mazutti MA, de Oliveira D. Functional characterization and structural insights of three cutinases from the ascomycete Fusarium verticillioides. Protein Expr Purif 2024; 216:106415. [PMID: 38104791 DOI: 10.1016/j.pep.2023.106415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Cutinases are serine esterases that belong to the α/β hydrolases superfamily. The natural substrates for these enzymes are cutin and suberin, components of the plant cuticle, the first barrier in the defense system against pathogen invasion. It is well-reported that plant pathogens produce cutinases to facilitate infection. Fusarium verticillioides, one important corn pathogens, is an ascomycete upon which its cutinases are poorly explored. Consequently, the objective of this study was to perform the biochemical characterization of three precursor cutinases (FvCut1, FvCut2, and FvCut3) from F. verticillioides and to obtain structural insights about them. The cutinases were produced in Escherichia coli and purified. FvCut1, FvCut2, and FvCut3 presented optimal temperatures of 20, 40, and 35 °C, and optimal pH of 9, 7, and 8, respectively. Some chemicals stimulated the enzymatic activity. The kinetic parameters revealed that FvCut1 has higher catalytic efficiency (Kcat/Km) in the p-nitrophenyl-butyrate (p-NPB) substrate. Nevertheless, the enzymes were not able to hydrolyze polyethylene terephthalate (PET). Furthermore, the three-dimensional models of these enzymes showed structural differences among them, mainly FvCut1, which presented a narrower opening cleft to access the catalytic site. Therefore, our study contributes to exploring the diversity of fungal cutinases and their potential biotechnological applications.
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Affiliation(s)
- Caroline Torres de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil
| | - Michelle Alexandrino de Assis
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - Marcio Antonio Mazutti
- Department of Chemical Engineering, Technology Center, Federal University of Santa Maria, UFSM, Santa Maria, Brazil
| | - Débora de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil.
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8
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Cognigni F, Temporiti MEE, Nicola L, Gueninchault N, Tosi S, Rossi M. Exploring the infiltrative and degradative ability of Fusarium oxysporum on polyethylene terephthalate (PET) using correlative microscopy and deep learning. Sci Rep 2023; 13:22987. [PMID: 38151495 PMCID: PMC10752890 DOI: 10.1038/s41598-023-50199-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/16/2023] [Indexed: 12/29/2023] Open
Abstract
Managing the worldwide steady increase in the production of plastic while mitigating the Earth's global pollution is one of the greatest challenges nowadays. Fungi are often involved in biodegradation processes thanks to their ability to penetrate into substrates and release powerful catabolic exoenzymes. However, studying the interaction between fungi and plastic substrates is challenging due to the deep hyphal penetration, which hinders visualisation and evaluation of fungal activity. In this study, a multiscale and multimodal correlative microscopy workflow was employed to investigate the infiltrative and degradative ability of Fusarium oxysporum fungal strain on polyethylene terephthalate (PET) fragments. The use of non-destructive high-resolution 3D X-ray microscopy (XRM) coupled with a state-of-art Deep Learning (DL) reconstruction algorithm allowed optimal visualisation of the distribution of the fungus on the PET fragment. The fungus preferentially developed on the edges and corners of the fragment, where it was able to penetrate into the material through fractures. Additional analyses with scanning electron microscopy (SEM), Raman and energy dispersive X-ray spectroscopy (EDX) allowed the identification of the different phases detected by XRM. The correlative microscopy approach unlocked a more comprehensive understanding of the fungus-plastic interaction, including elemental information and polymeric composition.
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Affiliation(s)
- Flavio Cognigni
- Department of Basic and Applied Sciences for Engineering (SBAI), University of Rome LA SAPIENZA, 00185, Rome, Italy
| | - Marta Elisabetta Eleonora Temporiti
- Laboratory of Mycology, Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
- National Biodiversity Future Centre, 90133, Palermo, Italy
| | - Lidia Nicola
- Laboratory of Mycology, Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy.
| | | | - Solveig Tosi
- Laboratory of Mycology, Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
- National Biodiversity Future Centre, 90133, Palermo, Italy
| | - Marco Rossi
- Department of Basic and Applied Sciences for Engineering (SBAI), University of Rome LA SAPIENZA, 00185, Rome, Italy
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9
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Degli-Innocenti F, Breton T, Chinaglia S, Esposito E, Pecchiari M, Pennacchio A, Pischedda A, Tosin M. Microorganisms that produce enzymes active on biodegradable polyesters are ubiquitous. Biodegradation 2023; 34:489-518. [PMID: 37354274 DOI: 10.1007/s10532-023-10031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Biodegradability standards measure ultimate biodegradation of polymers by exposing the material under test to a natural microbial inoculum. Available tests developed by the International Organization for Standardization (ISO) use inoculums sampled from different environments e.g. soil, marine sediments, seawater. Understanding whether each inoculum is to be considered as microbially unique or not can be relevant for the interpretation of tests results. In this review, we address this question by consideration of the following: (i) the chemical nature of biodegradable plastics (virtually all biodegradable plastics are polyesters) (ii) the diffusion of ester bonds in nature both in simple molecules and in polymers (ubiquitous); (iii) the diffusion of decomposers capable of producing enzymes, called esterases, which accelerate the hydrolysis of esters, including polyesters (ubiquitous); (iv) the evidence showing that synthetic polyesters can be depolymerized by esterases (large and growing); (v) the evidence showing that these esterases are ubiquitous (growing and confirmed by bioinformatics studies). By combining the relevant available facts it can be concluded that if a certain polyester shows ultimate biodegradation when exposed to a natural inoculum, it can be considered biodegradable and need not be retested using other inoculums. Obviously, if the polymer does not show ultimate biodegradation it must be considered recalcitrant, until proven otherwise.
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Affiliation(s)
| | - Tony Breton
- Novamont S.p.A., via Fauser 8, 28100, Novara, Italy
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10
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Metagenome-Assembled Genomes of Four Southern Ocean Archaea Harbor Multiple Genes Linked to Polyethylene Terephthalate and Polyhydroxybutyrate Plastic Degradation. Microbiol Resour Announc 2023; 12:e0109822. [PMID: 36794928 PMCID: PMC10019265 DOI: 10.1128/mra.01098-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Here, we present four archaeal metagenome-assembled genomes (MAGs) (three Thaumarchaeota MAGs and one Thermoplasmatota MAG) from a polar upwelling zone in the Southern Ocean. These archaea harbor putative genes encoding enzymes such as polyethylene terephthalate (PET) hydrolases (PETases) and polyhydroxybutyrate (PHB) depolymerases, which are associated with microbial degradation of PET and PHB plastics.
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11
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Tournier V, Duquesne S, Guillamot F, Cramail H, Taton D, Marty A, André I. Enzymes' Power for Plastics Degradation. Chem Rev 2023; 123:5612-5701. [PMID: 36916764 DOI: 10.1021/acs.chemrev.2c00644] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.
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Affiliation(s)
- Vincent Tournier
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Sophie Duquesne
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Frédérique Guillamot
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Henri Cramail
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Daniel Taton
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Alain Marty
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
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12
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Birolli WG, Porto ALM. Esfenvalerate biodegradation by marine fungi is affected by seawater and emulsifier formulation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38394-38408. [PMID: 36580257 DOI: 10.1007/s11356-022-24921-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Pesticides already were detected in the oceans, and their fates require evaluation in these environmental conditions. Therefore, marine-derived fungi were assessed for Esfenvalerate biodegradation, approaching the effects of seawater and use of commercial emulsifiable formulation. Residual pesticide and four metabolites were quantified. Furthermore, kinetics were determined for the three tested strains (Microsphaeropsis sp. CBMAI 1675, Acremonium sp. CBMAI 1676, and Westerdykella sp. CBMAI 1679). These facultative marine fungi biodegraded up to 87 ± 2% of 100 mg L-1 Esfenvalerate in liquid media. However, Esfenvalerate biodegradation was faster in low salinity conditions than in artificial seawater. Moreover, rates of consumption were higher for Esfenvalerate in the pure form than for the commercial emulsifiable formulation. These results suggest that half-life of Esfenvalerate formulated with inert ingredients in seawater can have a double prolongation effect that can contribute to health and environmental issues.
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Affiliation(s)
- Willian Garcia Birolli
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, Avenida João Dagnone, 1100, Ed. Prof. Douglas Wagner Franco, Jd. Santa Angelina, Sao Carlos, SP, 13563-120, Brazil.
| | - André Luiz Meleiro Porto
- Laboratory of Organic Chemistry and Biocatalysis, São Carlos Institute of Chemistry, University of São Paulo, Avenida João Dagnone, 1100, Ed. Prof. Douglas Wagner Franco, Jd. Santa Angelina, Sao Carlos, SP, 13563-120, Brazil
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13
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Al-Tohamy R, Ali SS, Zhang M, Sameh M, Mahmoud YAG, Waleed N, Okasha KM, Sun S, Sun J. Can wood-feeding termites solve the environmental bottleneck caused by plastics? A critical state-of-the-art review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 326:116606. [PMID: 36403319 DOI: 10.1016/j.jenvman.2022.116606] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The abundance of synthetic polymers has become an ever-increasing environmental threat in the world. The excessive utilization of plastics leads to the accumulation of such recalcitrant pollutants in the environment. For example, during the COVID-19 pandemic, unprecedented demand for personal protective equipment (PPE) kits, face masks, and gloves made up of single-use items has resulted in the massive generation of plastic biomedical waste. As secondary pollutants, microplastic particles (<5 mm) are derived from pellet loss and degradation of macroplastics. Therefore, urgent intervention is required for the management of these hazardous materials. Physicochemical approaches have been employed to degrade synthetic polymers, but these approaches have limited efficiency and cause the release of hazardous metabolites or by-products into the environment. Therefore, bioremediation is a proper option as it is both cost-efficient and environmentally friendly. On the other hand, plants evolved lignocellulose to be resistant to destruction, whereas insects, such as wood-feeding termites, possess diverse microorganisms in their guts, which confer physiological and ecological benefits to their host. Plastic and lignocellulose polymers share a number of physical and chemical properties, despite their structural and recalcitrance differences. Among these similarities are a hydrophobic nature, a carbon skeleton, and amorphous/crystalline regions. Compared with herbivorous mammals, lignocellulose digestion in termites is accomplished at ordinary temperatures. This unique characteristic has been of great interest for the development of a plastic biodegradation approach by termites and their gut symbionts. Therefore, transferring knowledge from research on lignocellulosic degradation by termites and their gut symbionts to that on synthetic polymers has become a new research hotspot and technological development direction to solve the environmental bottleneck caused by synthetic plastic polymers.
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Affiliation(s)
- Rania Al-Tohamy
- Biofuels Institute, School of the Environmnt and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Sameh S Ali
- Biofuels Institute, School of the Environmnt and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Meng Zhang
- Biofuels Institute, School of the Environmnt and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Mariam Sameh
- Clinical Pharmacy Practice Department, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo, Egypt
| | - Yehia A-G Mahmoud
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Nadeen Waleed
- Faculty of Medicine, Tanta University, Tanta, 31527, Egypt
| | - Kamal M Okasha
- Internal Medicine and Nephrology Department, Faculty of Medicine, Tanta University, Tanta, 31527, Egypt
| | - Sarina Sun
- Institute of Textiles and Clothing, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Jianzhong Sun
- Biofuels Institute, School of the Environmnt and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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14
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Jiddah Usman N, Rodrid K, Sabo Ajingi Y, Tuncharoen N, Meegnoen K, Pason P, Jongruja N. Characterization of recombinant cutinase from Thermobifida cellulosilytica and its application in tomato cutin degradation. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Zhou Y, Kumar V, Harirchi S, Vigneswaran VS, Rajendran K, Sharma P, Wah Tong Y, Binod P, Sindhu R, Sarsaiya S, Balakrishnan D, Mofijur M, Zhang Z, Taherzadeh MJ, Kumar Awasthi M. Recovery of value-added products from biowaste: A review. BIORESOURCE TECHNOLOGY 2022; 360:127565. [PMID: 35788392 DOI: 10.1016/j.biortech.2022.127565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
This review provides an update on the state-of-the art technologies for the valorization of solid waste and its mechanism to generate various bio-products. The organic content of these wastes can be easily utilized by the microbes and produce value-added compounds. Microbial fermentation techniques can be utilized for developing waste biorefinery processes. The utilization of lignocellulosic and plastics wastes for the generation of carbon sources for microbial utilization after pre-processing steps will make the process a multi-product biorefinery. The C1 and C2 gases generated from different industries could also be utilized by various microbes, and this will help to control global warming. The review seeks to expand expertise about the potential application through several perspectives, factors influencing remediation, issues, and prospects.
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Affiliation(s)
- Yuwen Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Vinay Kumar
- Department of Biotechnology, Indian Institute of Technology (IIT) Roorkee, Roorkee 247667, Uttarakhand, India
| | - Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, Borås 50190, Sweden
| | - V S Vigneswaran
- Department of Environmental Science and Engineering, School of Engineering and Sciences, SRM University-AP, Amaravati, Andhra Pradesh 522240, India
| | - Karthik Rajendran
- Department of Environmental Science and Engineering, School of Engineering and Sciences, SRM University-AP, Amaravati, Andhra Pradesh 522240, India
| | - Pooja Sharma
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technology Enterprise (CREATE), 1 CREATE Way, Singapore 138602, Singapore
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore; Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technology Enterprise (CREATE), 1 CREATE Way, Singapore 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive, 117585, Singapore
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 691505, Kerala, India
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Deepanraj Balakrishnan
- Department of Mechanical Engineering, College of Engineering, Prince Mohammad Bin Fahd University, Al Khobar, 31952, Saudi Arabia
| | - M Mofijur
- Faculty of Engineering and IT, University of Technology Sydney, NSW 2007, Australia; Mechanical Engineering Department, Prince Mohammad Bin Fahd University, Al Khobar 31952, Saudi Arabia
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | | | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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16
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A Review of the Fungi That Degrade Plastic. J Fungi (Basel) 2022; 8:jof8080772. [PMID: 35893140 PMCID: PMC9330918 DOI: 10.3390/jof8080772] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Plastic has become established over the world as an essential basic need for our daily life. Current global plastic production exceeds 300 million tons annually. Plastics have many characteristics such as low production costs, inertness, relatively low weight, and durability. The primary disadvantage of plastics is their extremely slow natural degradation. The latter results in an accumulation of plastic waste in nature. The amount of plastic waste as of 2015 was 6300 million tons worldwide, and 79% of this was placed in landfills or left in the natural environment. Moreover, recent estimates report that 12,000 million tons of plastic waste will have been accumulated on the earth by 2050. Therefore, it is necessary to develop an effective plastic biodegradation process to accelerate the natural degradation rate of plastics. More than 400 microbes have been identified as capable of plastic degradation. This is the first paper of the series on plastic-degrading fungi. This paper provides a summary of the current global production of plastic and plastic waste accumulation in nature. A list is given of all the plastic-degrading fungi recorded thus far, based on the available literature, and comments are made relating to the major fungal groups. In addition, the phylogenetic relationships of plastic-degrading fungi were analyzed using a combined ITS, LSU, SSU, TEF, RPB1, and RPB2 dataset consisting of 395 strains. Our results confirm that plastic-degrading fungi are found in eleven classes in the fungal phyla Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes, Saccharomycetes, and Sordariomycetes), Basidiomycota (Agaricomycetes, Microbotryomycetes, Tremellomycetes, Tritirachiomycetes, and Ustilaginomy-cetes), and Mucoromycota (Mucoromycetes). The taxonomic placement of plastic-degrading fungal taxa is briefly discussed. The Eurotiomycetes include the largest number of plastic degraders in the kingdom Fungi. The results presented herein are expected to influence the direction of future research on similar topics in order to find effective plastic-degrading fungi that can eliminate plastic wastes. The next publication of the series on plastic-degrading fungi will be focused on major metabolites, degradation pathways, and enzyme production in plastic degradation by fungi.
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17
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Nikolaivits E, Taxeidis G, Gkountela C, Vouyiouka S, Maslak V, Nikodinovic-Runic J, Topakas E. A polyesterase from the Antarctic bacterium Moraxella sp. degrades highly crystalline synthetic polymers. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128900. [PMID: 35452981 DOI: 10.1016/j.jhazmat.2022.128900] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/24/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
The uncontrolled release of plastics in the environment has rendered them ubiquitous around the planet, threatening the wildlife and human health. Biodegradation and valorization of plastics has emerged as an eco-friendly alternative to conventional management techniques. Discovery of novel polymer-degrading enzymes with diversified properties is hence an important task in order to explore different operational conditions for plastic-waste upcycling. In the present study, a barely studied psychrophilic enzyme (MoPE) from the Antractic bacterium Moraxella sp. was heterologously expressed, characterized and its potential in polymer degradation was further investigated. Based on its amino acid composition and structure, MoPE resembled PET-degrading enzymes, sharing features from both mesophilic and thermophilic homologues. MoPE hydrolyzes non-biodegradable plastics, such as polyethylene terephthalate and polyurethane, as well as biodegradable synthetic polyesters, such as polycaprolactone, polyhydroxy butyrate, polybutylene succinate and polylactic acid. The mass fraction crystallinity of the aliphatic polymers tested ranged from 11% to 64% highlighting the potential of the enzyme to hydrolyze highly crystalline plastics. MoPE was able to degrade different types of amorphous and semi-crystalline PET, releasing water-soluble monomers and showed synergy with a feruloyl esterase of the tannase family for the release of terephthalic acid. Based on the above, MoPE was characterized as a versatile psychrophilic polyesterase demonstrating a broad-range plastics degradation potential.
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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
| | - George Taxeidis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Gkountela
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Stamatina Vouyiouka
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Veselin Maslak
- University of Belgrade, Faculty of Chemistry, Belgrade, Serbia
| | - 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
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
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18
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Fungal Enzymes Involved in Plastics Biodegradation. Microorganisms 2022; 10:microorganisms10061180. [PMID: 35744698 PMCID: PMC9230134 DOI: 10.3390/microorganisms10061180] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/04/2022] Open
Abstract
Plastic pollution is a growing environmental problem, in part due to the extremely stable and durable nature of this polymer. As recycling does not provide a complete solution, research has been focusing on alternative ways of degrading plastic. Fungi provide a wide array of enzymes specialized in the degradation of recalcitrant substances and are very promising candidates in the field of plastic degradation. This review examines the present literature for different fungal enzymes involved in plastic degradation, describing their characteristics, efficacy and biotechnological applications. Fungal laccases and peroxidases, generally used by fungi to degrade lignin, show good results in degrading polyethylene (PE) and polyvinyl chloride (PVC), while esterases such as cutinases and lipases were successfully used to degrade polyethylene terephthalate (PET) and polyurethane (PUR). Good results were also obtained on PUR by fungal proteases and ureases. All these enzymes were isolated from many different fungi, from both Basidiomycetes and Ascomycetes, and have shown remarkable efficiency in plastic biodegradation under laboratory conditions. Therefore, future research should focus on the interactions between the genes, proteins, metabolites and environmental conditions involved in the processes. Further steps such as the improvement in catalytic efficiency and genetic engineering could lead these enzymes to become biotechnological applications in the field of plastic degradation.
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19
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Delangiz N, Aliyar S, Pashapoor N, Nobaharan K, Asgari Lajayer B, Rodríguez-Couto S. Can polymer-degrading microorganisms solve the bottleneck of plastics' environmental challenges? CHEMOSPHERE 2022; 294:133709. [PMID: 35074325 DOI: 10.1016/j.chemosphere.2022.133709] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Increasing world population and industrial activities have enhanced anthropogenic pollution, plastic pollution being especially alarming. So, plastics should be recycled and/or make them biodegradable. Chemical and physical remediating methods are usually energy consuming and costly. In addition, they are not ecofriendly and usually produce toxic byproducts. Bioremediation is a proper option as it is cost-efficient and environmentally friendly. Plastic production and consumption are increasing daily, and, as a consequence, more microorganisms are exposed to these nonbiodegradable polymers. Therefore, investigating new efficient microorganisms and increasing the knowledge about their biology can pave the way for efficient and feasible plastic bioremediation processes. In this sense, omics, systems biology and bioinformatics are three important fields to analyze the biodegradation pathways in microorganisms. Based on the above-mentioned technologies, researchers can engineer microorganisms with specific desired properties to make bioremediation more efficient.
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Affiliation(s)
- Nasser Delangiz
- Department of Plant Biotechnology and Breeding, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Sajad Aliyar
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Neda Pashapoor
- Department of Soil Science, Faculty of Agriculture, Urmia University, Urmia, Iran
| | | | - Behnam Asgari Lajayer
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
| | - Susana Rodríguez-Couto
- Department of Separation Science, LUT School of Engineering Science, LUT University, Sammonkatu 12, FI-50130 Mikkeli, Finland
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20
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Recent Advances in Biological Recycling of Polyethylene Terephthalate (PET) Plastic Wastes. Bioengineering (Basel) 2022; 9:bioengineering9030098. [PMID: 35324787 PMCID: PMC8945055 DOI: 10.3390/bioengineering9030098] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Polyethylene terephthalate (PET) is one of the most commonly used polyester plastics worldwide but is extremely difficult to be hydrolyzed in a natural environment. PET plastic is an inexpensive, lightweight, and durable material, which can readily be molded into an assortment of products that are used in a broad range of applications. Most PET is used for single-use packaging materials, such as disposable consumer items and packaging. Although PET plastics are a valuable resource in many aspects, the proliferation of plastic products in the last several decades have resulted in a negative environmental footprint. The long-term risk of released PET waste in the environment poses a serious threat to ecosystems, food safety, and even human health in modern society. Recycling is one of the most important actions currently available to reduce these impacts. Current clean-up strategies have attempted to alleviate the adverse impacts of PET pollution but are unable to compete with the increasing quantities of PET waste exposed to the environment. In this review paper, current PET recycling methods to improve life cycle and waste management are discussed, which can be further implemented to reduce plastics pollution and its impacts on health and environment. Compared with conventional mechanical and chemical recycling processes, the biotechnological recycling of PET involves enzymatic degradation of the waste PET and the followed bioconversion of degraded PET monomers into value-added chemicals. This approach creates a circular PET economy by recycling waste PET or upcycling it into more valuable products with minimal environmental footprint.
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21
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Haernvall K, Fladischer P, Schoeffmann H, Zitzenbacher S, Pavkov-Keller T, Gruber K, Schick M, Yamamoto M, Kuenkel A, Ribitsch D, Guebitz GM, Wiltschi B. Residue-Specific Incorporation of the Non-Canonical Amino Acid Norleucine Improves Lipase Activity on Synthetic Polyesters. Front Bioeng Biotechnol 2022; 10:769830. [PMID: 35155387 PMCID: PMC8826565 DOI: 10.3389/fbioe.2022.769830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/07/2022] [Indexed: 11/19/2022] Open
Abstract
Environmentally friendly functionalization and recycling processes for synthetic polymers have recently gained momentum, and enzymes play a central role in these procedures. However, natural enzymes must be engineered to accept synthetic polymers as substrates. To enhance the activity on synthetic polyesters, the canonical amino acid methionine in Thermoanaerobacter thermohydrosulfuricus lipase (TTL) was exchanged by the residue-specific incorporation method for the more hydrophobic non-canonical norleucine (Nle). Strutural modelling of TTL revealed that residues Met-114 and Met-142 are in close vicinity of the active site and their replacement by the norleucine could modulate the catalytic activity of the enzyme. Indeed, hydrolysis of the polyethylene terephthalate model substrate by the Nle variant resulted in significantly higher amounts of release products than the Met variant. A similar trend was observed for an ionic phthalic polyester containing a short alkyl diol (C5). Interestingly, a 50% increased activity was found for TTL [Nle] towards ionic phthalic polyesters containing different ether diols compared to the parent enzyme TTL [Met]. These findings clearly demonstrate the high potential of non-canonical amino acids for enzyme engineering.
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Affiliation(s)
| | - Patrik Fladischer
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | | | | | - Tea Pavkov-Keller
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | | | | | | | - Doris Ribitsch
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute for Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- *Correspondence: Doris Ribitsch,
| | - Georg M. Guebitz
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute for Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Birgit Wiltschi
- Acib–Austrian Centre of Industrial Biotechnology, Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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22
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Magalhães RP, Fernandes HS, Sousa SF. The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase. Catal Sci Technol 2022. [DOI: 10.1039/d1cy02271g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We described the catalytic mechanism of IsPETase, a polyethylene-terephthalate degrading enzyme. The reaction was found to progress in four steps, divided in two events: formation of the first transition intermediate and hydrolysis of the adduct.
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Affiliation(s)
- Rita P. Magalhães
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Henrique S. Fernandes
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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23
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Viljakainen VR, Hug LA. New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes. Comput Struct Biotechnol J 2021; 19:6191-6200. [PMID: 34900132 PMCID: PMC8632723 DOI: 10.1016/j.csbj.2021.11.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 12/04/2022] Open
Abstract
Plastics in the environment represent new substrates for microbial colonization, and recent methodological advances allow for in-depth characterization of plastic-associated microbial communities (PAMCs). Over the past several decades, discovery of plastic degrading enzymes (PDEs) and plastic degrading microorganisms (PDMs) has been driven by efforts to understand microbially-mediated plastic degradation in the environment and to discover biocatalysts for plastic processing. In this review, we discuss the evolution of methodology in plastic microbiology and highlight major advancements in the field stemming from computational microbiology. Initial research relied largely on culture-based approaches like clear-zone assays to screen for PDMs and microscopy to characterize PAMCs. New computational tools and sequencing technologies are accelerating discoveries in the field through culture-independent and multi-omic approaches, rapidly generating targets for protein engineering and improving the potential for plastic-waste management.
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Affiliation(s)
- V R Viljakainen
- University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
| | - L A Hug
- University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
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24
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Zerva A, Pentari C, Ferousi C, Nikolaivits E, Karnaouri A, Topakas E. Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2021; 342:126058. [PMID: 34597805 DOI: 10.1016/j.biortech.2021.126058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The field of enzymatic degradation of lignocellulose is actively growing and the recent updates of the last few years indicate that there is still much to learn. The growing number of protein sequences with unknown function in microbial genomes indicates that there is still much to learn on the mechanisms of lignocellulose degradation. In this review, a summary of the progress in the field is presented, including recent discoveries on the nature of the structural polysaccharides, new technologies for the discovery and functional annotation of gene sequences including omics technologies, and the novel lignocellulose-acting enzymes described. Novel enzymatic activities and enzyme families as well as accessory enzymes and their synergistic relationships regarding biomass breakdown are described. Moreover, it is shown that all the valuable knowledge of the enzymatic decomposition of plant biomass polymers can be employed towards the decomposition and upgrading of synthetic polymers, such as plastics.
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Affiliation(s)
- Anastasia Zerva
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Pentari
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Ferousi
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Anthi Karnaouri
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece; Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
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Tamoor M, Samak NA, Jia Y, Mushtaq MU, Sher H, Bibi M, Xing J. Potential Use of Microbial Enzymes for the Conversion of Plastic Waste Into Value-Added Products: A Viable Solution. Front Microbiol 2021; 12:777727. [PMID: 34917057 PMCID: PMC8670383 DOI: 10.3389/fmicb.2021.777727] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/04/2021] [Indexed: 01/24/2023] Open
Abstract
The widespread use of commercial polymers composed of a mixture of polylactic acid and polyethene terephthalate (PLA-PET) in bottles and other packaging materials has caused a massive environmental crisis. The valorization of these contaminants via cost-effective technologies is urgently needed to achieve a circular economy. The enzymatic hydrolysis of PLA-PET contaminants plays a vital role in environmentally friendly strategies for plastic waste recycling and degradation. In this review, the potential roles of microbial enzymes for solving this critical problem are highlighted. Various enzymes involved in PLA-PET recycling and bioconversion, such as PETase and MHETase produced by Ideonella sakaiensis; esterases produced by Bacillus and Nocardia; lipases produced by Thermomyces lanuginosus, Candida antarctica, Triticum aestivum, and Burkholderia spp.; and leaf-branch compost cutinases are critically discussed. Strategies for the utilization of PLA-PET's carbon content as C1 building blocks were investigated for the production of new plastic monomers and different value-added products, such as cyclic acetals, 1,3-propanediol, and vanillin. The bioconversion of PET-PLA degradation monomers to polyhydroxyalkanoate biopolymers by Pseudomonas and Halomonas strains was addressed in detail. Different solutions to the production of biodegradable plastics from food waste, agricultural residues, and polyhydroxybutyrate (PHB)-accumulating bacteria were discussed. Fuel oil production via PLA-PET thermal pyrolysis and possible hybrid integration techniques for the incorporation of thermostable plastic degradation enzymes for the conversion into fuel oil is explained in detail.
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Affiliation(s)
- Muhammad Tamoor
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Nadia A. Samak
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- Biofilm Centre, Aquatic Microbiology Department, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Yunpu Jia
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Umar Mushtaq
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
- Department of Chemical Engineering, Wah Engineering College, University of Wah, Wah Cantt, Pakistan
| | - Hassan Sher
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Maryam Bibi
- Department of Chemical Engineering, Wah Engineering College, University of Wah, Wah Cantt, Pakistan
| | - Jianmin Xing
- CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
- College of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, China
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Bright Side of Fusarium oxysporum: Secondary Metabolites Bioactivities and Industrial Relevance in Biotechnology and Nanotechnology. J Fungi (Basel) 2021; 7:jof7110943. [PMID: 34829230 PMCID: PMC8625159 DOI: 10.3390/jof7110943] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/31/2022] Open
Abstract
Fungi have been assured to be one of the wealthiest pools of bio-metabolites with remarkable potential for discovering new drugs. The pathogenic fungi, Fusarium oxysporum affects many valuable trees and crops all over the world, producing wilt. This fungus is a source of different enzymes that have variable industrial and biotechnological applications. Additionally, it is widely employed for the synthesis of different types of metal nanoparticles with various biotechnological, pharmaceutical, industrial, and medicinal applications. Moreover, it possesses a mysterious capacity to produce a wide array of metabolites with a broad spectrum of bioactivities such as alkaloids, jasmonates, anthranilates, cyclic peptides, cyclic depsipeptides, xanthones, quinones, and terpenoids. Therefore, this review will cover the previously reported data on F. oxysporum, especially its metabolites and their bioactivities, as well as industrial relevance in biotechnology and nanotechnology in the period from 1967 to 2021. In this work, 180 metabolites have been listed and 203 references have been cited.
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Ahmaditabatabaei S, Kyazze G, Iqbal HMN, Keshavarz T. Fungal Enzymes as Catalytic Tools for Polyethylene Terephthalate (PET) Degradation. J Fungi (Basel) 2021; 7:931. [PMID: 34829219 PMCID: PMC8625934 DOI: 10.3390/jof7110931] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 02/05/2023] Open
Abstract
The ubiquitous persistence of plastic waste in diverse forms and different environmental matrices is one of the main challenges that modern societies are facing at present. The exponential utilization and recalcitrance of synthetic plastics, including polyethylene terephthalate (PET), results in their extensive accumulation, which is a significant threat to the ecosystem. The growing amount of plastic waste ending up in landfills and oceans is alarming due to its possible adverse effects on biota. Thus, there is an urgent need to mitigate plastic waste to tackle the environmental crisis of plastic pollution. With regards to PET, there is a plethora of literature on the transportation route, ingestion, environmental fate, amount, and the adverse ecological and human health effects. Several studies have described the deployment of various microbial enzymes with much focus on bacterial-enzyme mediated removal and remediation of PET. However, there is a lack of consolidated studies on the exploitation of fungal enzymes for PET degradation. Herein, an effort has been made to cover this literature gap by spotlighting the fungi and their unique enzymes, e.g., esterases, lipases, and cutinases. These fungal enzymes have emerged as candidates for the development of biocatalytic PET degradation processes. The first half of this review is focused on fungal biocatalysts involved in the degradation of PET. The latter half explains three main aspects: (1) catalytic mechanism of PET hydrolysis in the presence of cutinases as a model fungal enzyme, (2) limitations hindering enzymatic PET biodegradation, and (3) strategies for enhancement of enzymatic PET biodegradation.
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Affiliation(s)
- Seyedehazita Ahmaditabatabaei
- School of Life sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK; (S.A.); (G.K.)
| | - Godfrey Kyazze
- School of Life sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK; (S.A.); (G.K.)
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico;
| | - Tajalli Keshavarz
- School of Life sciences, College of Liberal Arts and Sciences, University of Westminster, London W1W 6UW, UK; (S.A.); (G.K.)
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Magalhães RP, Cunha JM, Sousa SF. Perspectives on the Role of Enzymatic Biocatalysis for the Degradation of Plastic PET. Int J Mol Sci 2021; 22:11257. [PMID: 34681915 PMCID: PMC8540959 DOI: 10.3390/ijms222011257] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 12/25/2022] Open
Abstract
Plastics are highly durable and widely used materials. Current methodologies of plastic degradation, elimination, and recycling are flawed. In recent years, biodegradation (the usage of microorganisms for material recycling) has grown as a valid alternative to previously used methods. The evolution of bioengineering techniques and the discovery of novel microorganisms and enzymes with degradation ability have been key. One of the most produced plastics is PET, a long chain polymer of terephthalic acid (TPA) and ethylene glycol (EG) repeating monomers. Many enzymes with PET degradation activity have been discovered, characterized, and engineered in the last few years. However, classification and integrated knowledge of these enzymes are not trivial. Therefore, in this work we present a summary of currently known PET degrading enzymes, focusing on their structural and activity characteristics, and summarizing engineering efforts to improve activity. Although several high potential enzymes have been discovered, further efforts to improve activity and thermal stability are necessary.
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Affiliation(s)
- Rita P. Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM—Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (R.P.M.); (J.M.C.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Jorge M. Cunha
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM—Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (R.P.M.); (J.M.C.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM—Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; (R.P.M.); (J.M.C.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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Djapovic M, Milivojevic D, Ilic-Tomic T, Lješević M, Nikolaivits E, Topakas E, Maslak V, Nikodinovic-Runic J. Synthesis and characterization of polyethylene terephthalate (PET) precursors and potential degradation products: Toxicity study and application in discovery of novel PETases. CHEMOSPHERE 2021; 275:130005. [PMID: 33640747 DOI: 10.1016/j.chemosphere.2021.130005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 05/29/2023]
Abstract
Polyethylene terephthalate (PET) is widely used material and as such became highly enriched in nature. It is generally considered inert and safe plastic, but due to the recent increased efforts to break-down PET using biotechnological approaches, we realized the scarcity of information about structural analysis of possible degradation products and their ecotoxicological assessment. Therefore, in this study, 11 compounds belonging to the group of PET precursors and possible degradation products have been comprehensively characterized. Seven of these compounds including 1-(2-hydroxyethyl)-4-methylterephthalate, ethylene glycol bis(methyl terephthalate), methyl bis(2-hydroxyethyl terephtahalate), 1,4-benzenedicarboxylic acid, 1,4-bis[2-[[4-(methoxycarbonyl)benzoyl]oxy]ethyl] ester and methyl tris(2-hydroxyethyl terephthalate) corresponding to mono-, 1.5-, di-, 2,5- and trimer of PET were synthetized and structurally characterized for the first time. In-silico druglikeness and physico-chemical properties of these compounds were predicted using variety of platforms. No antimicrobial properties were detected even at 1000 μg/mL. Ecotoxicological impact of the compounds against marine bacteria Allivibrio fischeri proved that the 6 out of 11 tested PET-associated compounds may be classified as harmful to aquatic microorganisms, with PET trimer being one of the most toxic. In comparison, most of the compounds were not toxic on human lung fibroblasts (MRC-5) at 200 μg/mL with inhibiting concentration (IC50) values of 30 μg/mL and 50 μg/mL determined for PET dimer and trimer. Only three of these compounds including PET monomer were toxic to nematode Caenorhabditis elegans at high concentration of 500 μg/mL. In terms of the applicative potential, PET dimer can be used as suitable substrate for the screening, identification and characterization of novel PET-depolymerizing enzymes.
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Affiliation(s)
- Milica Djapovic
- University of Belgrade, Faculty of Chemistry, Studentski Trg 16, P.O. Box 51, Belgrade, 11158, Serbia
| | - Dusan Milivojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000, Belgrade, Serbia
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000, Belgrade, Serbia
| | - Marija Lješević
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Njegoseva 12, 11000, Belgrade, Serbia
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, 15780, Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, Iroon Polytechniou 9, 15780, Athens, Greece
| | - Veselin Maslak
- University of Belgrade, Faculty of Chemistry, Studentski Trg 16, P.O. Box 51, Belgrade, 11158, Serbia.
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000, Belgrade, Serbia.
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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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31
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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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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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33
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Sequential biocatalytic decomposition of BHET as valuable intermediator of PET recycling strategy. Catal Today 2021. [DOI: 10.1016/j.cattod.2020.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Maurya A, Bhattacharya A, Khare SK. Enzymatic Remediation of Polyethylene Terephthalate (PET)-Based Polymers for Effective Management of Plastic Wastes: An Overview. Front Bioeng Biotechnol 2020; 8:602325. [PMID: 33330434 PMCID: PMC7710609 DOI: 10.3389/fbioe.2020.602325] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
Globally, plastic-based pollution is now recognized as one of the serious threats to the environment. Among different plastics, polyethylene terephthalate (PET) occupies a pivotal place, its excess presence as a waste is a major environmental concern. Mechanical, thermal, and chemical-based treatments are generally used to manage PET pollution. However, these methods are usually expensive or generate secondary pollutants. Hence, there is a need for a cost-effective and environment-friendly method for efficient management of PET-based plastic wastes. Considering this, enzymatic treatment or recycling is one of the important methods to curb PET pollution. In this regard, PET hydrolases have been explored for the treatment of PET wastes. These enzymes act on PET and end its breakdown into monomeric units and subsequently results in loss of weight. However, various factors, specifically PET crystallinity, temperature, and pH, are known to affect this enzymatic process. For effective hydrolysis of PET, high temperature is required, which facilitates easy accessibility of substrate (PET) to enzymes. However, to function at this high temperature, there is a requirement of thermostable enzymes. The thermostability could be enhanced using glycosylation, immobilization, and enzyme engineering. Furthermore, the use of surfactants, additives such as Ca2+, Mg2+, and hydrophobins (cysteine-rich proteins), has also been reported to enhance the enzymatic PET hydrolysis through facilitating easy accessibility of PET polymers. The present review encompasses a brief overview of the use of enzymes toward the management of PET wastes. Various methods affecting the treatment process and different constraints arising thereof are also systematically highlighted in the review.
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Affiliation(s)
- Ankita Maurya
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Amrik Bhattacharya
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
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Gururaj P, Khushbu S, Monisha B, Selvakumar N, Chakravarthy M, Gautam P, Nandhini Devi G. Production, purification and application of Cutinase in enzymatic scouring of cotton fabric isolated from Acinetobacter baumannii AU10. Prep Biochem Biotechnol 2020; 51:550-561. [PMID: 33108946 DOI: 10.1080/10826068.2020.1836655] [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] [Indexed: 01/04/2023]
Abstract
Conventional cotton scouring in the textile industry using alkali results in huge environmental impact which can be overcome by using enzymes. Pectinase along with cutinase gives enhanced bioscouring results. Cutin was extracted from tomato peels and was used as substrate in the microbial media. The strain isolated from tomato peel was identified as Acinetobacter baumannii AU10 by 16S rDNA sequencing. The cutinase production was optimized by Placket-Burman and Response Surface Methodology (RSM) and the maximum production of 82.75 U/mL obtained at sucrose 6.68% (w/v), gelatin 2.74 g/L at a temperature of 35.93 °C. Cutinase was purified by ammonium sulfate precipitation, hydrophobic interaction chromatography and ion exchange chromatography with a recovery of 25.6% and specific activity of 38030 U/mg. The confirmation test for the purity of cutinase was analyzed by RP-HPLC. The molecular mass of cutinase was determined as 28.9 kDa by SDS-PAGE technique. Scanning electron microscopic analysis showed a rough and open primary wall surface on the cutinase bioscoured fabric which confirmed its activity on cutin present in the cotton fabric. Additionally, the cutinase-bioscoured samples showed better absorbency than the untreated samples. Therefore, enzymatic scouring increases wetting capacity of scoured cotton and also helps to reduce environmental pollution.
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Affiliation(s)
- P Gururaj
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - S Khushbu
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - B Monisha
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - N Selvakumar
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - M Chakravarthy
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - P Gautam
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - G Nandhini Devi
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
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Zhang H, Zhao C, Na H. Theoretical Design of Biodegradable Phthalic Acid Ester Derivatives in Marine and Freshwater Environments. ChemistryOpen 2020; 9:1033-1045. [PMID: 33101830 PMCID: PMC7570447 DOI: 10.1002/open.202000093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/07/2020] [Indexed: 11/19/2022] Open
Abstract
The biodegradability of phtalic acid esters in marine and freshwater environments was characterized by their binding free energy with corresponding degrading enzymes. According to comprehensive biodegradation effects weights, the binding free energy values were converted into dimensionless efficacy coefficient using ratio normalization method. Then, considering comprehensive dual biodegradation effects value and the structural parameters of PAEs in both marine and freshwater environments, a 3D‐QSAR pharmacophore model was constructed, five PAE derivatives (DBP−COOH, DBP−CHO, DBP−OH, DINP−NH2, and DINP−NO2) were screened out based on their environmental friendliness, functionality and stability. The prediction of biodegradation effects on five PAE derivatives by biodegradation models in marine and freshwater environment increased by 15.90 %, 15.84 %, 27.21 %, 12.33 %, and 8.32 %, and 21.57 %, 15.21 %, 20.99 %, 15.10 %, and 9.74 %, respectively. By simulating the photodegradation path of the PAE derivative molecular, it was found that DBP−OH can generate .OH and provides free radicals for the photodegradation of microplastics in the environment.
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Affiliation(s)
- Haigang Zhang
- Alan G. MacDiarmid Institute, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun City, 130012, Jilin Province, PR China
| | - Chengji Zhao
- Alan G. MacDiarmid Institute, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun City, 130012, Jilin Province, PR China
| | - Hui Na
- Alan G. MacDiarmid Institute, College of Chemistry, Jilin University, No. 2699 Qianjin Street, Changchun City, 130012, Jilin Province, PR China
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Elfgen R, Gehrke S, Hollóczki O. Ionic Liquids as Extractants for Nanoplastics. CHEMSUSCHEM 2020; 13:5449-5459. [PMID: 32780462 PMCID: PMC7692928 DOI: 10.1002/cssc.202001749] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/06/2020] [Indexed: 05/23/2023]
Abstract
Plastic waste in the ocean and on land in the form of nanoplastics is endangering food and drinking water supplies, raising the need for new strategies for the removal of plastic nanoparticles from complex media. In the present contribution we suggest considering ionic liquids as extractants, since they show several advantageous properties that may facilitate the design of efficient separation processes. Through varying the anion and the side chain at the cation, the interactions between the extractant and the polymer can be strengthened and tuned, and thereby the disintegration of the particle into separate polymer chains can be controlled. Oxidized moieties can also be efficiently solvated, given the amphiphilic nature of the considered ionic liquids, allowing also realistic particles to be extracted into these solvents. The phase transfer was found to be thermodynamically and kinetically possible, which is supported by the complicated structure of the ionic liquid-water interface through the rearrangement of the interfacial ions, and the formation of a micelle around the plastic already at the edge of the aqueous phase.
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Affiliation(s)
- Roman Elfgen
- Mulliken Center for Theoretical ChemistryUniversity of BonnBeringstr. 4+6D-53115BonnGermany
| | - Sascha Gehrke
- Mulliken Center for Theoretical ChemistryUniversity of BonnBeringstr. 4+6D-53115BonnGermany
| | - Oldamur Hollóczki
- Mulliken Center for Theoretical ChemistryUniversity of BonnBeringstr. 4+6D-53115BonnGermany
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Wu P, Tang Y, Cao G, Li J, Wang S, Chang X, Dang M, Jin H, Zheng C, Cai Z. Determination of Environmental Micro(Nano)Plastics by Matrix-Assisted Laser Desorption/Ionization–Time-of-Flight Mass Spectrometry. Anal Chem 2020; 92:14346-14356. [DOI: 10.1021/acs.analchem.0c01928] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Pengfei Wu
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR 999077, P. R. China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
| | - Yuanyuan Tang
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
| | - Guodong Cao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR 999077, P. R. China
| | - Jiangpeng Li
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
| | - Siqing Wang
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
| | - Xinyi Chang
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
| | - Miao Dang
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P. R. China
| | - Chunmiao Zheng
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, P. R. China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR 999077, P. R. China
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Taniguchi I, Yoshida S, Hiraga K, Miyamoto K, Kimura Y, Oda K. Biodegradation of PET: Current Status and Application Aspects. ACS Catal 2019. [DOI: 10.1021/acscatal.8b05171] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ikuo Taniguchi
- Department of Polymer Science, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Shosuke Yoshida
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kazumi Hiraga
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kenji Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yoshiharu Kimura
- Department of Polymer Science, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kohei Oda
- Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
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Fecker T, Galaz-Davison P, Engelberger F, Narui Y, Sotomayor M, Parra LP, Ramírez-Sarmiento CA. Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase. Biophys J 2019; 114:1302-1312. [PMID: 29590588 DOI: 10.1016/j.bpj.2018.02.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/21/2022] Open
Abstract
Polyethylene terephthalate (PET) is one of the most-consumed synthetic polymers, with an annual production of 50 million tons. Unfortunately, PET accumulates as waste and is highly resistant to biodegradation. Recently, fungal and bacterial thermophilic hydrolases were found to catalyze PET hydrolysis with optimal activities at high temperatures. Strikingly, an enzyme from Ideonella sakaiensis, termed PETase, was described to efficiently degrade PET at room temperature, but the molecular basis of its activity is not currently understood. Here, a crystal structure of PETase was determined at 2.02 Å resolution and employed in molecular dynamics simulations showing that the active site of PETase has higher flexibility at room temperature than its thermophilic counterparts. This flexibility is controlled by a novel disulfide bond in its active site, with its removal leading to destabilization of the catalytic triad and reduction of the hydrolase activity. Molecular docking of a model substrate predicts that PET binds to PETase in a unique and energetically favorable conformation facilitated by several residue substitutions within its active site when compared to other enzymes. These computational predictions are in excellent agreement with recent mutagenesis and PET film degradation analyses. Finally, we rationalize the increased catalytic activity of PETase at room temperature through molecular dynamics simulations of enzyme-ligand complexes for PETase and other thermophilic PET-degrading enzymes at 298, 323, and 353 K. Our results reveal that both the binding pose and residue substitutions within PETase favor proximity between the catalytic residues and the labile carbonyl of the substrate at room temperature, suggesting a more favorable hydrolytic reaction. These results are valuable for enabling detailed evolutionary analysis of PET-degrading enzymes and for rational design endeavors aiming at increasing the efficiency of PETase and similar enzymes toward plastic degradation.
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Affiliation(s)
- Tobias Fecker
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Engelberger
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Yoshie Narui
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.
| | - Loreto P Parra
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine, and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Mandic M, Spasic J, Ponjavic M, Nikolic MS, Cosovic VR, O'Connor KE, Nikodinovic-Runic J, Djokic L, Jeremic S. Biodegradation of poly(ε-caprolactone) (PCL) and medium chain length polyhydroxyalkanoate (mcl-PHA) using whole cells and cell free protein preparations of Pseudomonas and Streptomyces strains grown on waste cooking oil. Polym Degrad Stab 2019. [DOI: 10.1016/j.polymdegradstab.2019.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chen S, Wu Y, Su L, Wu J. Contribution of disulfide bond to the stability of Thermobifida fusca cutinase. FOOD BIOSCI 2019. [DOI: 10.1016/j.fbio.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Abstract
Cutinases are α/β hydrolases, and their role in nature is the degradation of cutin. Such enzymes are usually produced by phytopathogenic microorganisms in order to penetrate their hosts. The first focused studies on cutinases started around 50 years ago. Since then, numerous cutinases have been isolated and characterized, aiming at the elucidation of their structure–function relations. Our deeper understanding of cutinases determines the applications by which they could be utilized; from food processing and detergents, to ester synthesis and polymerizations. However, cutinases are mainly efficient in the degradation of polyesters, a natural function. Therefore, these enzymes have been successfully applied for the biodegradation of plastics, as well as for the delicate superficial hydrolysis of polymeric materials prior to their functionalization. Even though research on this family of enzymes essentially began five decades ago, they are still involved in many reports; novel enzymes are being discovered, and new fields of applications arise, leading to numerous related publications per year. Perhaps the future of cutinases lies in their evolved descendants, such as polyesterases, and particularly PETases. The present article reviews the biochemical and structural characteristics of cutinases and cutinase-like hydrolases, and their applications in the field of bioremediation and biocatalysis.
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Versatile Fungal Polyphenol Oxidase with Chlorophenol Bioremediation Potential: Characterization and Protein Engineering. Appl Environ Microbiol 2018; 84:AEM.01628-18. [PMID: 30266731 PMCID: PMC6238066 DOI: 10.1128/aem.01628-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/21/2018] [Indexed: 12/24/2022] Open
Abstract
Polyphenol oxidases (PPOs) have been mostly associated with the undesirable postharvest browning in fruits and vegetables and have implications in human melanogenesis. Nonetheless, they are considered useful biocatalysts in the food, pharmaceutical, and cosmetic industries. The aim of the present work was to characterize a novel PPO and explore its potential as a bioremediation agent. A gene encoding an extracellular tyrosinase-like enzyme was amplified from the genome of Thermothelomyces thermophila and expressed in Pichia pastoris The recombinant enzyme (TtPPO) was purified and biochemically characterized. Its production reached 40 mg/liter, and it appeared to be a glycosylated and N-terminally processed protein. TtPPO showed broad substrate specificity, as it could oxidize 28/30 compounds tested, including polyphenols, substituted phenols, catechols, and methoxyphenols. Its optimum temperature was 65°C, with a half-life of 18.3 h at 50°C, while its optimum pH was 7.5. The homology model of TtPPO was constructed, and site-directed mutagenesis was performed in order to increase its activity on mono- and dichlorophenols (di-CPs). The G292N/Y296V variant of TtPPO 5.3-fold increased activity on 3,5-dichlorophenol (3,5-diCP) compared to the wild type.IMPORTANCE A novel fungal PPO was heterologously expressed and biochemically characterized. Construction of single and double mutants led to the generation of variants with altered specificity against CPs. Through this work, knowledge is gained regarding the effect of mutations on the substrate specificity of PPOs. This work also demonstrates that more potent biocatalysts for the bioremediation of harmful CPs can be developed by applying site-directed mutagenesis.
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Biundo A, Ribitsch D, Guebitz GM. Surface engineering of polyester-degrading enzymes to improve efficiency and tune specificity. Appl Microbiol Biotechnol 2018; 102:3551-3559. [PMID: 29511846 DOI: 10.1007/s00253-018-8850-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/08/2018] [Accepted: 02/10/2018] [Indexed: 01/06/2023]
Abstract
Certain members of the carboxylesterase superfamily can act at the interface between water and water-insoluble substrates. However, nonnatural bulky polyesters usually are not efficiently hydrolyzed. In the recent years, the potential of enzyme engineering to improve hydrolysis of synthetic polyesters has been demonstrated. Regions on the enzyme surface have been modified by using site-directed mutagenesis in order to tune sorption processes through increased hydrophobicity of the enzyme surface. Such modifications can involve specific amino acid substitutions, addition of binding modules, or truncation of entire domains improving sorption properties and/or dynamics of the enzyme. In this review, we provide a comprehensive overview on different strategies developed in the recent years for enzyme surface engineering to improve the activity of polyester-hydrolyzing enzymes.
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Affiliation(s)
- Antonino Biundo
- Austrian Centre of Industrial Biotechnology (ACIB), Tulln an der Donau, Austria
| | - Doris Ribitsch
- Austrian Centre of Industrial Biotechnology (ACIB), Tulln an der Donau, Austria. .,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Tulln an der Donau, Austria.
| | - Georg M Guebitz
- Austrian Centre of Industrial Biotechnology (ACIB), Tulln an der Donau, Austria.,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences (BOKU), Tulln an der Donau, Austria
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Characterization of a cutinase from Myceliophthora thermophila and its application in polyester hydrolysis and deinking process. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.11.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nikolaivits E, Makris G, Topakas E. Immobilization of a Cutinase from Fusarium oxysporum and Application in Pineapple Flavor Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3505-3511. [PMID: 28403608 DOI: 10.1021/acs.jafc.7b00659] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In the present study, the immobilization of a cutinase from Fusarium oxysporum was carried out as cross-linked enzyme aggregates. Under optimal immobilization conditions, acetonitrile was selected as precipitant, utilizing 9.4 mg protein/mL and 10 mM glutaraldehyde as cross-linker. The immobilized cutinase (imFocut5a) was tested in isooctane for the synthesis of short-chain butyrate esters, displaying enhanced thermostability compared to the free enzyme. Pineapple flavor (butyl butyrate) synthesis was optimized, leading to a conversion yield of >99% after 6 h, with an initial reaction rate of 18.2 mmol/L/h. Optimal reaction conditions were found to be 50 °C, a vinyl butyrate/butanol molar ratio of 3:1, vinyl butyrate concentration of 100 mM, and enzyme loading of 11 U. Reusability studies of imFocut5a showed that after four consecutive runs, the reaction yield reaches 54% of the maximum. The efficient bioconversion offers a sustainable and environmentally friendly process for the production of "natural" aroma compounds essential for the food industry.
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Affiliation(s)
- Efstratios Nikolaivits
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens , 9 Heroon Polytechniou Street, Zographou Campus, 15780 Athens, Greece
| | - Georgios Makris
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens , 9 Heroon Polytechniou Street, Zographou Campus, 15780 Athens, Greece
| | - Evangelos Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens , 9 Heroon Polytechniou Street, Zographou Campus, 15780 Athens, Greece
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Duan X, Liu Y, You X, Jiang Z, Yang S, Yang S. High-level expression and characterization of a novel cutinase from Malbranchea cinnamomea suitable for butyl butyrate production. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:223. [PMID: 28932264 PMCID: PMC5606096 DOI: 10.1186/s13068-017-0912-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/11/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Butyl butyrate has been considered as a promising fuel source because it is a kind of natural ester which can be converted from renewable and sustainable lignocellulosic biomass. Compared with the conventional chemical methods for butyl butyrate production, the enzymatic approach has been demonstrated to be more attractive, mainly owing to the mild reaction conditions, high specificity, low energy consumption, and environmental friendliness. Cutinases play an important role in the butyl butyrate production process. However, the production level of cutinases is still relatively low. Thus, to identify novel cutinases suitable for butyl butyrate synthesis and enhance their yields is of great value in biofuel industry. RESULTS A novel cutinase gene (McCut) was cloned from a thermophilic fungus Malbranchea cinnamomea and expressed in Pichia pastoris. The highest cutinase activity of 12, 536 U/mL was achieved in 5-L fermentor, which is by far the highest production for a cutinase. McCut was optimally active at pH 8.0 and 45 °C. It exhibited excellent stability within the pH range of 3.0-10.5 and up to 75 °C. The cutinase displayed broad substrate specificity with the highest activity towards p-nitrophenyl butyrate and tributyrin. It was capable of hydrolyzing cutin, polycaprolactone, and poly(butylene succinate). Moreover, McCut efficiently synthesized butyl butyrate with a maximum esterification efficiency of 96.9% at 4 h. The overall structure of McCut was resolved as a typical α/β-hydrolase fold. The structural differences between McCut and Aspergillus oryzae cutinase in groove and loop provide valuable information for redesign of McCut. These excellent features make it useful in biosynthesis and biodegradation fields. CONCLUSIONS A novel cutinase from M. cinnamomea was identified and characterized for the first time. High-level expression by P. pastoris is by far the highest for a cutinase. The enzyme exhibited excellent stability and high esterification efficiency for butyl butyrate production, which may make it a good candidate in biofuel and chemical industries.
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Affiliation(s)
- Xiaojie Duan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100083 China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Yu Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100083 China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Xin You
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100083 China
- College of Engineering, China Agricultural University, Beijing, 100083 China
| | - Zhengqiang Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100083 China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Shaoxiang Yang
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), Beijing, 100048 China
| | - Shaoqing Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100083 China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
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50
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Nature Inspired Solutions for Polymers: Will Cutinase Enzymes Make Polyesters and Polyamides Greener? Catalysts 2016. [DOI: 10.3390/catal6120205] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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