51
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Holst LH, Madsen NG, Toftgård FT, Rønne F, Moise IM, Petersen EI, Fojan P. De novo design of a polycarbonate hydrolase. Protein Eng Des Sel 2023; 36:gzad022. [PMID: 38035789 DOI: 10.1093/protein/gzad022] [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: 03/08/2023] [Revised: 10/31/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023] Open
Abstract
Enzymatic degradation of plastics is currently limited to the use of engineered natural enzymes. As of yet, all engineering approaches applied to plastic degrading enzymes retain the natural $\alpha /\beta $-fold. While mutations can be used to increase thermostability, an inherent maximum likely exists for the $\alpha /\beta $-fold. It is thus of interest to introduce catalytic activity toward plastics in a different protein fold to escape the sequence space of plastic degrading enzymes. Here, a method for designing highly thermostable enzymes that can degrade plastics is described. With the help of Rosetta an active site catalysing the hydrolysis of polycarbonate is introduced into a set of thermostable scaffolds. Through computational evaluation, a potential PCase was selected and produced recombinantly in Escherichia coli. Thermal analysis suggests that the design has a melting temperature of >95$^{\circ }$C. Activity toward polycarbonate was confirmed using atomic force spectroscopy (AFM), proving the successful design of a PCase.
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Affiliation(s)
- Laura H Holst
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Niklas G Madsen
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Freja T Toftgård
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Freja Rønne
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Ioana-Malina Moise
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Evamaria I Petersen
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
| | - Peter Fojan
- Material Science and Engineering Group, Department of Materials and Production, Aalborg University, 9000 Aalborg, Denmark
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52
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Joho Y, Vongsouthi V, Spence MA, Ton J, Gomez C, Tan LL, Kaczmarski JA, Caputo AT, Royan S, Jackson CJ, Ardevol A. Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella sakaiensis PETase and Variants with Improved Stability and Activity. Biochemistry 2023; 62:437-450. [PMID: 35951410 DOI: 10.1021/acs.biochem.2c00323] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The improved production, recycling, and removal of plastic waste, such as polyethylene terephthalate (PET), are pressing environmental and economic issues for society. Biocatalytic (enzymatic) PET depolymerization is potentially a sustainable, low-energy solution to PET recycling, especially when compared with current disposal methods such as landfills, incineration, or gasification. IsPETase has been extensively studied for its use in PET depolymerization; however, its evolution from cutinases is not fully understood, and most engineering studies have neglected the majority of the available sequence space remote from the active site. In this study, ancestral protein reconstruction (ASR) has been used to trace the evolutionary trajectory from ancient serine hydrolases to IsPETase, while ASR and the related design approach, protein repair one-stop shop, were used to identify enzyme variants with improved activity and stability. Kinetic and structural characterization of these variants reveals new insights into the evolution of PETase activity and the role of second-shell mutations around the active site. Among the designed and reconstructed variants, we identified several with melting points 20 °C higher than that of IsPETase and two variants with significantly higher catalytic activity.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia.,Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Jennifer Ton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Li Lynn Tan
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Joe A Kaczmarski
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Alessandro T Caputo
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia
| | - Santana Royan
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3168, Australia.,CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
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53
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Kaabel S, Arciszewski J, Borchers TH, Therien JPD, Friščić T, Auclair K. Solid-State Enzymatic Hydrolysis of Mixed PET/Cotton Textiles. CHEMSUSCHEM 2023; 16:e202201613. [PMID: 36165763 DOI: 10.1002/cssc.202201613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Waste polyester textiles are not recycled due to separation challenges and partial structural degradation during use and recycling. Chemical recycling of polyethylene terephthalate (PET) textiles through depolymerization can provide a feedstock of recycled monomers to make "as-new" polymers. While enzymatic PET recycling is a more selective and more sustainable approach, methods in development, however, have thus far been limited to clean, high-quality PET feedstocks, and require an energy-intensive melt-amorphization step ahead of enzymatic treatment. Here, high-crystallinity PET in mixed PET/cotton textiles could be directly and selectively depolymerized to terephthalic acid (TPA) by using a commercial cutinase from Humicola insolens under moist-solid reaction conditions, affording up to 30±2 % yield of TPA. The process was readily combined with cotton depolymerization through simultaneous or sequential application of the cellulase enzymes CTec2®, providing up to 83±4 % yield of glucose without any negative influence on the TPA yield.
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Affiliation(s)
- Sandra Kaabel
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, QC H3A 0B8, Canada
- Department of Bioproducts and Biosystems, Aalto University, 02150, Espoo, Finland
| | - Jane Arciszewski
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, QC H3A 0B8, Canada
| | - Tristan H Borchers
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, QC H3A 0B8, Canada
| | - J P Daniel Therien
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, QC H3A 0B8, Canada
| | - Tomislav Friščić
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, QC H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, QC H3A 0B8, Canada
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54
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von Haugwitz G, Han X, Pfaff L, Li Q, Wei H, Gao J, Methling K, Ao Y, Brack Y, Mican J, Feiler CG, Weiss MS, Bednar D, Palm GJ, Lalk M, Lammers M, Damborsky J, Weber G, Liu W, Bornscheuer UT, Wei R. Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization. ACS Catal 2022; 12:15259-15270. [PMID: 36570084 PMCID: PMC9764356 DOI: 10.1021/acscatal.2c03772] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/09/2022] [Indexed: 12/03/2022]
Abstract
TfCa, a promiscuous carboxylesterase from Thermobifida fusca, was found to hydrolyze polyethylene terephthalate (PET) degradation intermediates such as bis(2-hydroxyethyl) terephthalate (BHET) and mono-(2-hydroxyethyl)-terephthalate (MHET). In this study, we elucidated the structures of TfCa in its apo form, as well as in complex with a PET monomer analogue and with BHET. The structure-function relationship of TfCa was investigated by comparing its hydrolytic activity on various ortho- and para-phthalate esters of different lengths. Structure-guided rational engineering of amino acid residues in the substrate-binding pocket resulted in the TfCa variant I69W/V376A (WA), which showed 2.6-fold and 3.3-fold higher hydrolytic activity on MHET and BHET, respectively, than the wild-type enzyme. TfCa or its WA variant was mixed with a mesophilic PET depolymerizing enzyme variant [Ideonella sakaiensis PETase (IsPETase) PM] to degrade PET substrates of various crystallinity. The dual enzyme system with the wild-type TfCa or its WA variant produced up to 11-fold and 14-fold more terephthalate (TPA) than the single IsPETase PM, respectively. In comparison to the recently published chimeric fusion protein of IsPETase and MHETase, our system requires 10% IsPETase and one-fourth of the reaction time to yield the same amount of TPA under similar PET degradation conditions. Our simple dual enzyme system reveals further advantages in terms of cost-effectiveness and catalytic efficiency since it does not require time-consuming and expensive cross-linking and immobilization approaches.
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Affiliation(s)
- Gerlis von Haugwitz
- Department
of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Xu Han
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China,National
Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Lara Pfaff
- Department
of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Qian Li
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China,National
Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Hongli Wei
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China,National
Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Jian Gao
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China,National
Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Karen Methling
- Department
of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Yufei Ao
- Department
of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany,University
of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yannik Brack
- Department
of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Jan Mican
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic,International
Clinical Research Center, St. Anne’s
University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Christian G. Feiler
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Alber-Einstein-Straße 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Alber-Einstein-Straße 15, 12489 Berlin, Germany
| | - David Bednar
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic,International
Clinical Research Center, St. Anne’s
University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gottfried J. Palm
- Department
of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Michael Lalk
- Department
of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Michael Lammers
- Department
of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic,International
Clinical Research Center, St. Anne’s
University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gert Weber
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Alber-Einstein-Straße 15, 12489 Berlin, Germany
| | - Weidong Liu
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China,National
Technology Innovation Center of Synthetic Biology, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China,University
of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China,
| | - Uwe T. Bornscheuer
- Department
of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany,
| | - Ren Wei
- Department
of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany,
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55
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Tarazona NA, Wei R, Brott S, Pfaff L, Bornscheuer UT, Lendlein A, Machatschek R. Rapid depolymerization of poly(ethylene terephthalate) thin films by a dual-enzyme system and its impact on material properties. CHEM CATALYSIS 2022; 2:3573-3589. [PMID: 37350932 PMCID: PMC10284027 DOI: 10.1016/j.checat.2022.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 06/24/2023]
Abstract
Enzymatic hydrolysis holds great promise for plastic waste recycling and upcycling. The interfacial catalysis mode, and the variability of polymer specimen properties under different degradation conditions, add to the complexity and difficulty of understanding polymer cleavage and engineering better biocatalysts. We present a systemic approach to studying the enzyme-catalyzed surface erosion of poly(ethylene terephthalate) (PET) while monitoring/controlling operating conditions in real time with simultaneous detection of mass loss and changes in viscoelastic behavior. PET nanofilms placed on water showed a porous morphology and a thickness-dependent glass transition temperature (Tg) between 40°C and 44°C, which is >20°C lower than the Tg of bulk amorphous PET. Hydrolysis by a dual-enzyme system containing thermostabilized variants of Ideonella sakaiensis PETase and MHETase resulted in a maximum depolymerization of 70% in 1 h at 50°C. We demonstrate that increased accessible surface area, amorphization, and Tg reduction speed up PET degradation while simultaneously lowering the threshold for degradation-induced crystallization.
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Affiliation(s)
- Natalia A. Tarazona
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany
| | - Ren Wei
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany
| | - Stefan Brott
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany
| | - Lara Pfaff
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany
| | - Andreas Lendlein
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14469 Potsdam, Germany
| | - Rainhard Machatschek
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany
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56
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Weigert S, Perez‐Garcia P, Gisdon FJ, Gagsteiger A, Schweinshaut K, Ullmann GM, Chow J, Streit WR, Höcker B. Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes. Protein Sci 2022; 31:e4500. [PMID: 36336469 PMCID: PMC9679969 DOI: 10.1002/pro.4500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.
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Affiliation(s)
| | - Pablo Perez‐Garcia
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | | | | | | | | | - Jennifer Chow
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Wolfgang R. Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Birte Höcker
- Department of BiochemistryUniversity of BayreuthBayreuthGermany
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57
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Lomwongsopon P, Varrone C. Critical Review on the Progress of Plastic Bioupcycling Technology as a Potential Solution for Sustainable Plastic Waste Management. Polymers (Basel) 2022; 14:polym14224996. [PMID: 36433123 PMCID: PMC9692586 DOI: 10.3390/polym14224996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Plastic production worldwide has doubled in the last two decades and is expected to reach a four-fold increase by 2050. The durability of plastic makes them a perfect material for many applications, but it is also a key limitation to their end-of-life management. The current plastic lifecycle is far from circular, with only 13% being collected for recycling and 9% being successfully recycled, indicating the failure of current recycling technology. The remaining plastic waste streams are thus incinerated, landfilled, or worse, mismanaged, leading to them leaking into the environment. To promote plastic circularity, keeping material in the loop is a priority and represents a more sustainable solution. This can be achieved through the reuse of plastic items, or by using plastic waste as a resource for new materials, instead of discarding them as waste. As the discovery of plastic-degrading/utilizing microorganisms and enzymes has been extensively reported recently, the possibility of developing biological plastic upcycling processes is opening up. An increasing amount of studies have investigated the use of plastic as a carbon source for biotechnological processes to produce high-value compounds such as bioplastics, biochemicals, and biosurfactants. In the current review, the advancements in fossil-based plastic bio- and thermochemical upcycling technologies are presented and critically discussed. In particular, we highlight the developed (bio)depolymerization coupled with bioconversion/fermentation processes to obtain industrially valuable products. This review is expected to contribute to the future development and scale-up of effective plastic bioupcycling processes that can act as a drive to increase waste removal from the environment and valorize post-consumer plastic streams, thus accelerating the implementation of a circular (plastic) economy.
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58
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Zlobin A, Golovin A. Between Protein Fold and Nucleophile Identity: Multiscale Modeling of the TEV Protease Enzyme-Substrate Complex. ACS OMEGA 2022; 7:40279-40292. [PMID: 36385818 PMCID: PMC9647873 DOI: 10.1021/acsomega.2c05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
The cysteine protease from the tobacco etch virus (TEVp) is a well-known and widely utilized enzyme. TEVp's chymotrypsin-like fold is generally associated with serine catalytic triads that differ in terms of a reaction mechanism from the most well-studied papain-like cysteine proteases. The question of what dominates the TEVp mechanism, nucleophile identity, or structural composition has never been previously addressed. Here, we use enhanced sampling multiscale modeling to uncover that TEVp combines the features of two worlds in such a way that potentially hampers its activity. We show that TEVp cysteine is strictly in the anionic form in a free enzyme similar to papain. Peptide binding shifts the equilibrium toward the nucleophile's protonated form, characteristic of chymotrypsin-like proteases, although the cysteinyl anion form is still present and interconversion is rapid. This way cysteine protonation generates enzyme states that are a diversion from the most effective course of action, with only 13.2% of Michaelis complex sub-states able to initiate the reaction. As a result, we propose an updated view on the reaction mechanism catalyzed by TEVp. We also demonstrate that AlphaFold is able to construct protease-substrate complexes with high accuracy. We propose that our findings open a way for its industrious use in enzymological tasks. Unique features of TEVp discovered in this work open a discussion on the evolutionary history and trade-offs of optimizing serine triad-associated folds to cysteine as a nucleophile.
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Affiliation(s)
- Alexander Zlobin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrey Golovin
- Belozersky
Institute of Physico-Chemical Biology, Lomonosov
Moscow State University, 119991 Moscow, Russia
- Shemyakin
and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Sirius
University of Science and Technology, 354340 Sochi, Russia
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59
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Cutinase fused with C-terminal residues of α-synuclein improves polyethylene terephthalate degradation by enhancing the substrate binding. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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60
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Kawai F, Furushima Y, Mochizuki N, Muraki N, Yamashita M, Iida A, Mamoto R, Tosha T, Iizuka R, Kitajima S. Efficient depolymerization of polyethylene terephthalate (PET) and polyethylene furanoate by engineered PET hydrolase Cut190. AMB Express 2022; 12:134. [DOI: 10.1186/s13568-022-01474-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractThe enzymatic recycling of polyethylene terephthalate (PET) can be a promising approach to tackle the problem of plastic waste. The thermostability and activity of PET-hydrolyzing enzymes are still insufficient for practical application. Pretreatment of PET waste is needed for bio-recycling. Here, we analyzed the degradation of PET films, packages, and bottles using the newly engineered cutinase Cut190. Using gel permeation chromatography and high-performance liquid chromatography, the degradation of PET films by the Cut190 variant was shown to proceed via a repeating two-step hydrolysis process; initial endo-type scission of a surface polymer chain, followed by exo-type hydrolysis to produce mono/bis(2-hydroxyethyl) terephthalate and terephthalate from the ends of fragmented polymer molecules. Amorphous PET powders were degraded more than twofold higher than amorphous PET film with the same weight. Moreover, homogenization of post-consumer PET products, such as packages and bottles, increased their degradability, indicating the importance of surface area for the enzymatic hydrolysis of PET. In addition, it was required to maintain an alkaline pH to enable continuous enzymatic hydrolysis, by increasing the buffer concentration (HEPES, pH 9.0) depending on the level of the acidic products formed. The cationic surfactant dodecyltrimethylammonium chloride promoted PET degradation via adsorption on the PET surface and binding to the anionic surface of the Cut190 variant. The Cut190 variant also hydrolyzed polyethylene furanoate. Using the best performing Cut190 variant (L136F/Q138A/S226P/R228S/D250C-E296C/Q123H/N202H/K305del/L306del/N307del) and amorphous PET powders, more than 90 mM degradation products were obtained in 3 days and approximately 80 mM in 1 day.
Graphical Abstract
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61
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Chen K, Dong X, Sun Y. Sequentially co-immobilized PET and MHET hydrolases via Spy chemistry in calcium phosphate nanocrystals present high-performance PET degradation. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129517. [PMID: 35809363 DOI: 10.1016/j.jhazmat.2022.129517] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Accumulation of polyethylene terephthalate (PET) has brought an enormous threat to the ecosystem. The recently reported PET hydrolase (DuraPETase) and MHET hydrolase (MHETase) can synergistically catalyze the complete PET degradation. Hence, this work was designed to develop a bienzymatic cascade catalysis by co-immobilizing the two enzymes for PET biodegradation. DuraPETase and MHETase were sequentially co-immobilized in calcium phosphate nanocrystals (CaP) through SpyTag/SpyCatcher system. MHETase-SpyCatcher was first embedded inside the nanocrystals via biomimetic mineralization, and DuraPETase-SpyTag was then conjugated on the outlayer (~1.5 µm). The bienzyme compartmentalization facilitated DuraPETase interaction with the solid substrate, and the layered structures of the nanocrystals protected the enzymes, thus enhancing their stability. The high specific surface area of the nanocrystals and the proximity effects from the bienzymatic cascade were beneficial to the improved enzyme activity. Experimental data and molecular dynamics simulations revealed the activation effect of Ca2+ on DuraPETase. Taken together, the final results indicate that the PET degradation efficiency of DuraPETase-MHETase@CaP increased by 6.1 and 1.5 times over the free bienzyme system within 10 d at 40 °C and 50 °C, with weight losses at 32.2% and 50.3%, respectively. The bienzymatic cascade with DuraPETase-MHETase@CaP can completely degrade PET, contributing to the recycling of PET.
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Affiliation(s)
- Kun Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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62
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Chow J, Perez‐Garcia P, Dierkes R, Streit WR. Microbial enzymes will offer limited solutions to the global plastic pollution crisis. Microb Biotechnol 2022; 16:195-217. [PMID: 36099200 PMCID: PMC9871534 DOI: 10.1111/1751-7915.14135] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/09/2022] [Accepted: 08/14/2022] [Indexed: 01/27/2023] Open
Abstract
Global economies depend on the use of fossil-fuel-based polymers with 360-400 million metric tons of synthetic polymers being produced per year. Unfortunately, an estimated 60% of the global production is disposed into the environment. Within this framework, microbiologists have tried to identify plastic-active enzymes over the past decade. Until now, this research has largely failed to deliver functional biocatalysts acting on the commodity polymers such as polyethylene (PE), polypropylene (PP), polyvinylchloride (PVC), ether-based polyurethane (PUR), polyamide (PA), polystyrene (PS) and synthetic rubber (SR). However, few enzymes are known to act on low-density and low-crystalline (amorphous) polyethylene terephthalate (PET) and ester-based PUR. These above-mentioned polymers represent >95% of all synthetic plastics produced. Therefore, the main challenge microbiologists are currently facing is in finding polymer-active enzymes targeting the majority of fossil-fuel-based plastics. However, identifying plastic-active enzymes either to implement them in biotechnological processes or to understand their potential role in nature is an emerging research field. The application of these enzymes is still in its infancy. Here, we summarize the current knowledge on microbial plastic-active enzymes, their global distribution and potential impact on plastic degradation in industrial processes and nature. We further outline major challenges in finding novel plastic-active enzymes, optimizing known ones by synthetic approaches and problems arising through falsely annotated and unfiltered use of database entries. Finally, we highlight potential biotechnological applications and possible re- and upcycling concepts using microorganisms.
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Affiliation(s)
- Jennifer Chow
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Pablo Perez‐Garcia
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Robert Dierkes
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
| | - Wolfgang R. Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgHamburgGermany
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63
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio-Functionalization of PET. Angew Chem Int Ed Engl 2022; 61:e202203061. [PMID: 35656865 PMCID: PMC7613822 DOI: 10.1002/anie.202203061] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 11/24/2022]
Abstract
We report a bioinformatic workflow and subsequent discovery of a new polyethylene terephthalate (PET) hydrolase, which we named MG8, from the human saliva metagenome. MG8 has robust PET plastic degradation activities under different temperature and salinity conditions, outperforming several naturally occurring and engineered hydrolases in degrading PET. Moreover, we genetically encoded 2,3-diaminopropionic acid (DAP) in place of the catalytic serine residue of MG8, thereby converting a PET hydrolase into a covalent binder for bio-functionalization of PET. We show that MG8(DAP), in conjunction with a split green fluorescent protein system, can be used to attach protein cargos to PET as well as other polyester plastics. The discovery of a highly active PET hydrolase from the human metagenome-currently an underexplored resource for industrial enzyme discovery-as well as the repurposing of such an enzyme into a plastic functionalization tool, should facilitate ongoing efforts to degrade and maximize reusability of PET.
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Affiliation(s)
- Bhumrapee Eiamthong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Piyachat Meesawat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Thanakrit Wongsatit
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Jariya Jitdee
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Raweewan Sangsri
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Maturada Patchsung
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Kanokpol Aphicho
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | | | - Shan Tang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Wipa Suginta
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | | | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Worawan Bhanthumnavin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
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64
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Li Z, Zhao Y, Wu P, Wang H, Li Q, Gao J, Qin HM, Wei H, Bornscheuer UT, Han X, Wei R, Liu W. Structural insight and engineering of a plastic degrading hydrolase Ple629. Biochem Biophys Res Commun 2022; 626:100-106. [DOI: 10.1016/j.bbrc.2022.07.103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/30/2022]
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65
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Pfaff L, Gao J, Li Z, Jäckering A, Weber G, Mican J, Chen Y, Dong W, Han X, Feiler CG, Ao YF, Badenhorst CPS, Bednar D, Palm GJ, Lammers M, Damborsky J, Strodel B, Liu W, Bornscheuer UT, Wei R. Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase. ACS Catal 2022; 12:9790-9800. [PMID: 35966606 PMCID: PMC9361285 DOI: 10.1021/acscatal.2c02275] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/06/2022] [Indexed: 12/13/2022]
Abstract
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Thermophilic polyester hydrolases (PES-H) have recently
enabled
biocatalytic recycling of the mass-produced synthetic polyester polyethylene
terephthalate (PET), which has found widespread use in the packaging
and textile industries. The growing demand for efficient PET hydrolases
prompted us to solve high-resolution crystal structures of two metagenome-derived
enzymes (PES-H1 and PES-H2) and notably also in complex with various
PET substrate analogues. Structural analyses and computational modeling
using molecular dynamics simulations provided an understanding of
how product inhibition and multiple substrate binding modes influence
key mechanistic steps of enzymatic PET hydrolysis. Key residues involved
in substrate-binding and those identified previously as mutational
hotspots in homologous enzymes were subjected to mutagenesis. At 72
°C, the L92F/Q94Y variant of PES-H1 exhibited 2.3-fold and 3.4-fold
improved hydrolytic activity against amorphous PET films and pretreated
real-world PET waste, respectively. The R204C/S250C variant of PES-H1
had a 6.4 °C higher melting temperature than the wild-type enzyme
but retained similar hydrolytic activity. Under optimal reaction conditions,
the L92F/Q94Y variant of PES-H1 hydrolyzed low-crystallinity PET materials
2.2-fold more efficiently than LCC ICCG, which was previously the
most active PET hydrolase reported in the literature. This property
makes the L92F/Q94Y variant of PES-H1 a good candidate for future
applications in industrial plastic recycling processes.
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Affiliation(s)
- Lara Pfaff
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Jian Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin
Airport Economic Area, Tianjin 300308, China
| | - Zhishuai Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049 China
| | - Anna Jäckering
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University, Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Gert Weber
- Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - Jan Mican
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic
| | - Yinping Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xu Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin
Airport Economic Area, Tianjin 300308, China
| | - Christian G. Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - Yu-Fei Ao
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
- CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun North First Street 2, Beijing 100190, China
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gottfried J. Palm
- Department Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University, Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West Seventh Avenue, Tianjin
Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049 China
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Ren Wei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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66
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Meyer Cifuentes IE, Wu P, Zhao Y, Liu W, Neumann-Schaal M, Pfaff L, Barys J, Li Z, Gao J, Han X, Bornscheuer UT, Wei R, Öztürk B. Molecular and Biochemical Differences of the Tandem and Cold-Adapted PET Hydrolases Ple628 and Ple629, Isolated From a Marine Microbial Consortium. Front Bioeng Biotechnol 2022; 10:930140. [PMID: 35935485 PMCID: PMC9350882 DOI: 10.3389/fbioe.2022.930140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
Polybutylene adipate terephthalate (PBAT) is a biodegradable alternative to polyethylene and can be broadly used in various applications. These polymers can be degraded by hydrolases of terrestrial and aquatic origin. In a previous study, we identified tandem PETase-like hydrolases (Ples) from the marine microbial consortium I1 that were highly expressed when a PBAT blend was supplied as the only carbon source. In this study, the tandem Ples, Ple628 and Ple629, were recombinantly expressed and characterized. Both enzymes are mesophilic and active on a wide range of oligomers. The activities of the Ples differed greatly when model substrates, PBAT-modified polymers or PET nanoparticles were supplied. Ple629 was always more active than Ple628. Crystal structures of Ple628 and Ple629 revealed a structural similarity to other PETases and can be classified as member of the PETases IIa subclass, α/β hydrolase superfamily. Our results show that the predicted functions of Ple628 and Ple629 agree with the bioinformatic predictions, and these enzymes play a significant role in the plastic degradation by the consortium.
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Affiliation(s)
- Ingrid E. Meyer Cifuentes
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pan Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yipei Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Lara Pfaff
- Junior Research Group Plastic Biodegradation, Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Greifswald, Germany
| | - Justyna Barys
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Zhishuai Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jian Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xu Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Ren Wei
- Junior Research Group Plastic Biodegradation, Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Greifswald, Germany
| | - Başak Öztürk
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- *Correspondence: Başak Öztürk,
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67
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Reetz M. Witnessing the Birth of Directed Evolution of Stereoselective Enzymes as Catalysts in Organic Chemistry. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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68
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Abstract
In the Anthropocene, plastic pollution is a worldwide concern that must be tackled from different viewpoints, bringing together different areas of science. Microbial transformation of polymers is a broad-spectrum research topic that has become a keystone in the circular economy of fossil-based and biobased plastics. To have an open discussion about these themes, experts in the synthesis of polymers and biodegradation of lignocellulose and plastics convened within the framework of The Transnational Network for Research and Innovation in Microbial Biodiversity, Enzymes Technology and Polymer Science (MENZYPOL-NET), which was recently created by early-stage scientists from Colombia and Germany. In this context, the international workshop “Microbial Synthesis and Degradation of Polymers: Toward a Sustainable Bioeconomy” was held on 27 September 2021 via Zoom. The workshop was divided into two sections, and questions were raised for discussion with panelists and expert guests. Several key points and relevant perspectives were delivered, mainly related to (i) the microbial evolution driven by plastic pollution; (ii) the relevance of and interplay between polymer structure/composition, enzymatic mechanisms, and assessment methods in plastic biodegradation; (iii) the recycling and valorization of plastic waste; (iv) engineered plastic-degrading enzymes; (v) the impact of (micro)plastics on environmental microbiomes; (vi) the isolation of plastic-degrading (PD) microbes and design of PD microbial consortia; and (vii) the synthesis and applications of biobased plastics. Finally, research priorities from these key points were identified within the microbial, enzyme, and polymer sciences.
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69
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Eiamthong B, Meesawat P, Wongsatit T, Jitdee J, Sangsri R, Patchsung M, Aphicho K, Suraritdechachai S, Huguenin-Dezot N, Tang S, Suginta W, Paosawatyanyong B, Babu MM, Chin JW, Pakotiprapha D, Bhanthumnavin W, Uttamapinant C. Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio‐Functionalization of PET. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bhumrapee Eiamthong
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Piyachat Meesawat
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Thanakrit Wongsatit
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering THAILAND
| | - Jariya Jitdee
- Chulalongkorn University Faculty of Science Chemistry THAILAND
| | | | - Maturada Patchsung
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Kanokpol Aphicho
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | - Surased Suraritdechachai
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - Shan Tang
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | - Wipa Suginta
- Vidyasirimedhi Institute of Science and Technology Biomolecular Science and Engineering THAILAND
| | | | - M. Madan Babu
- St Jude Children's Research Hospital Department of Structural Biology Structural Biology UNITED STATES
| | - Jason W Chin
- MRC Laboratory of Molecular Biology Protein and nucleic acid chemistry UNITED KINGDOM
| | | | | | - Chayasith Uttamapinant
- Vidyasirimedhi Institute of Science and Technology School of Biomolecular Science and Engineering 555 Moo 1 PayupnaiWangchan Valley 21210 Rayong THAILAND
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70
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Arnling Bååth J, Jensen K, Borch K, Westh P, Kari J. Sabatier Principle for Rationalizing Enzymatic Hydrolysis of a Synthetic Polyester. JACS AU 2022; 2:1223-1231. [PMID: 35647598 PMCID: PMC9131473 DOI: 10.1021/jacsau.2c00204] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 05/04/2023]
Abstract
Interfacial enzyme reactions are common in Nature and in industrial settings, including the enzymatic deconstruction of poly(ethylene terephthalate) (PET) waste. Kinetic descriptions of PET hydrolases are necessary for both comparative analyses, discussions of structure-function relations and rational optimization of technical processes. We investigated whether the Sabatier principle could be used for this purpose. Specifically, we compared the kinetics of two well-known PET hydrolases, leaf-branch compost cutinase (LCC) and a cutinase from the bacterium Thermobifida fusca (TfC), when adding different concentrations of the surfactant cetyltrimethylammonium bromide (CTAB). We found that CTAB consistently lowered the strength of enzyme-PET interactions, while its effect on enzymatic turnover was strongly biphasic. Thus, at gradually increasing CTAB concentrations, turnover was initially promoted and subsequently suppressed. This correlation with maximal turnover at an intermediate binding strength was in accordance with the Sabatier principle. One consequence of these results was that both enzymes had too strong intrinsic interaction with PET for optimal turnover, especially TfC, which showed a 20-fold improvement of k cat at the maximum. LCC on the other hand had an intrinsic substrate affinity closer to the Sabatier optimum, and the turnover rate was 5-fold improved at weakened substrate binding. Our results showed that the Sabatier principle may indeed rationalize enzymatic PET degradation and support process optimization. Finally, we suggest that future discovery efforts should consider enzymes with weakened substrate binding because strong adsorption seems to limit their catalytic performance.
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Affiliation(s)
- Jenny Arnling Bååth
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, Kgs. Lyngby DK-2800, Denmark
| | - Kenneth Jensen
- Novozymes
A/S, Biologiens Vej 2, Kgs. Lyngby DK-2800, Denmark
| | - Kim Borch
- Novozymes
A/S, Biologiens Vej 2, Kgs. Lyngby DK-2800, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads, Kgs. Lyngby DK-2800, Denmark
- . Phone: +45 45 25 26 41
| | - Jeppe Kari
- Department
of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000, Denmark
- . Phone: +45 46 74 27 20
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71
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Bayer T, Pfaff L, Branson Y, Becker A, Wu S, Bornscheuer UT, Wei R. Biosensor and chemo-enzymatic one-pot cascade applications to detect and transform PET-derived terephthalic acid in living cells. iScience 2022; 25:104326. [PMID: 35602945 PMCID: PMC9117539 DOI: 10.1016/j.isci.2022.104326] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/04/2022] [Accepted: 04/26/2022] [Indexed: 01/14/2023] Open
Abstract
Plastic waste imposes a serious problem to the environment and society. Hence, strategies for a circular plastic economy are demanded. One strategy is the engineering of polyester hydrolases toward higher activity for the biotechnological recycling of polyethylene terephthalate (PET). To provide tools for the rapid characterization of PET hydrolases and the detection of degradation products like terephthalic acid (TPA), we coupled a carboxylic acid reductase (CAR) and the luciferase LuxAB. CAR converted TPA into the corresponding aldehydes in Escherichia coli, which yielded bioluminescence that not only semiquantitatively reflected amounts of TPA in hydrolysis samples but is suitable as a high-throughput screening assay to assess PET hydrolase activity. Furthermore, the CAR-catalyzed synthesis of terephthalaldehyde was combined with a reductive amination cascade in a one-pot setup yielding the corresponding diamine, suggesting a new strategy for the transformation of TPA as a product obtained from PET biodegradation. First bioreduction of terephthalic acid (TPA) by a carboxylic acid reductase in vivo Real-time, high-throughput detection of TPA-derived aldehydes by luciferase LuxAB Bioluminescence reflects TPA amounts, assessing (engineered) PET hydrolase activity Transformation of TPA into the diamine through chemo-enzymatic one-pot cascade
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Affiliation(s)
- Thomas Bayer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
- Institute of Molecular Biotechnology, TU Graz, Petersgasse 14, 8010 Graz, Austria
- Corresponding author
| | - Lara Pfaff
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Yannick Branson
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Aileen Becker
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Shuke Wu
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
- College of Life Science & Technology, Huazhong Agricultural University, Shizishan Street 1, Wuhan 430070, China
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
| | - Ren Wei
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487 Greifswald, Germany
- Corresponding author
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Reetz MT. Making Enzymes Suitable for Organic Chemistry by Rational Protein Design. Chembiochem 2022; 23:e202200049. [PMID: 35389556 PMCID: PMC9401064 DOI: 10.1002/cbic.202200049] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/07/2022] [Indexed: 11/25/2022]
Abstract
This review outlines recent developments in protein engineering of stereo‐ and regioselective enzymes, which are of prime interest in organic and pharmaceutical chemistry as well as biotechnology. The widespread application of enzymes was hampered for decades due to limited enantio‐, diastereo‐ and regioselectivity, which was the reason why most organic chemists were not interested in biocatalysis. This attitude began to change with the advent of semi‐rational directed evolution methods based on focused saturation mutagenesis at sites lining the binding pocket. Screening constitutes the labor‐intensive step (bottleneck), which is the reason why various research groups are continuing to develop techniques for the generation of small and smart mutant libraries. Rational enzyme design, traditionally an alternative to directed evolution, provides small collections of mutants which require minimal screening. This approach first focused on thermostabilization, and did not enter the field of stereoselectivity until later. Computational guides such as the Rosetta algorithms, HotSpot Wizard metric, and machine learning (ML) contribute significantly to decision making. The newest advancements show that semi‐rational directed evolution such as CAST/ISM and rational enzyme design no longer develop on separate tracks, instead, they have started to merge. Indeed, researchers utilizing the two approaches have learned from each other. Today, the toolbox of organic chemists includes enzymes, primarily because the possibility of controlling stereoselectivity by protein engineering has ensured reliability when facing synthetic challenges. This review was also written with the hope that undergraduate and graduate education will include enzymes more so than in the past.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut fur Kohlenforschung, Biocatalysis, Kaiser-Wilhelm-Platz 1, 45470, Muelheim an der Ruhr, GERMANY
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Cheng Y, Kuboyama K, Akasaka S, Araki T, Masai E, Nakamura M, Michinobu T. Polyurethanes based on lignin-derived metabolic intermediate with strong adhesion to metals. Polym Chem 2022. [DOI: 10.1039/d2py01128j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Polyurethanes based on lignin-derived 2-pyrone-4,6-dicarboxylic acid (PDC) were successfully synthesized in one-pot, and their thermal, mechanical, and adhesive properties were investigated.
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Affiliation(s)
- Ye Cheng
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Keiichi Kuboyama
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Shuichi Akasaka
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Takuma Araki
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Masaya Nakamura
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Tsuyoshi Michinobu
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8552, Japan
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