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Zheng L, Wang M, Li Y, Xiong Y, Wu C. Recycling and Degradation of Polyamides. Molecules 2024; 29:1742. [PMID: 38675560 PMCID: PMC11052090 DOI: 10.3390/molecules29081742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/31/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
As one of the five major engineering plastics, polyamide brings many benefits to humans in the fields of transportation, clothing, entertainment, health, and more. However, as the production of polyamide increases year by year, the pollution problems it causes are becoming increasingly severe. This article reviews the current recycling and treatment processes of polyamide, such as chemical, mechanical, and energy recovery, and degradation methods such as thermal oxidation, photooxidation, enzyme degradation, etc. Starting from the synthesis mechanism of polyamide, it discusses the advantages and disadvantages of different treatment methods of polyamide to obtain more environmentally friendly and economical treatment schemes. Finding enzymes that can degrade high-molecular-weight polyamides, exploring the recovery of polyamides under mild conditions, synthesizing environmentally degradable polyamides through copolymerization or molecular design, and finally preparing degradable bio-based polyamides may be the destination of polyamide.
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Affiliation(s)
- Lin Zheng
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Collaborative Innovation Center of Green Light-Weight Materials and Processing, New Materials and Green Manufacturing Talent Introduction and Innovation Demonstration Base, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (L.Z.); (M.W.); (Y.L.); (Y.X.)
| | - Mengjin Wang
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Collaborative Innovation Center of Green Light-Weight Materials and Processing, New Materials and Green Manufacturing Talent Introduction and Innovation Demonstration Base, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (L.Z.); (M.W.); (Y.L.); (Y.X.)
| | - Yaoqin Li
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Collaborative Innovation Center of Green Light-Weight Materials and Processing, New Materials and Green Manufacturing Talent Introduction and Innovation Demonstration Base, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (L.Z.); (M.W.); (Y.L.); (Y.X.)
| | - Yan Xiong
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Collaborative Innovation Center of Green Light-Weight Materials and Processing, New Materials and Green Manufacturing Talent Introduction and Innovation Demonstration Base, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (L.Z.); (M.W.); (Y.L.); (Y.X.)
- Hubei Longzhong Laboratory, Xiangyang 441000, China
| | - Chonggang Wu
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Collaborative Innovation Center of Green Light-Weight Materials and Processing, New Materials and Green Manufacturing Talent Introduction and Innovation Demonstration Base, School of Materials and Chemical Engineering, Hubei University of Technology, Wuhan 430068, China; (L.Z.); (M.W.); (Y.L.); (Y.X.)
- Hubei Longzhong Laboratory, Xiangyang 441000, China
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Oluwoye I, Machuca LL, Higgins S, Suh S, Galloway TS, Halley P, Tanaka S, Iannuzzi M. Degradation and lifetime prediction of plastics in subsea and offshore infrastructures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166719. [PMID: 37673242 DOI: 10.1016/j.scitotenv.2023.166719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023]
Abstract
Engineering and civil developments have relied on synthetic polymers and plastics (including polyethylene, polypropylene, polyamide, etc.) for decades, especially where their durability protects engineering structures against corrosion and other environmental stimuli. Offshore oil and gas infrastructure and renewable energy platforms are typical examples, where these plastics (100,000 s of metric tonnes worldwide) are used primarily as functional material to protect metallic flowlines and subsea equipment against seawater corrosion. Despite this, the current literature on polymers is limited to sea-surface environments, and a model for subsea degradation of plastics is needed. In this review, we collate relevant studies on the degradation of plastics and synthetic polymers in marine environments to gain insight into the fate of these materials when left in subsea conditions. We present a new mathematical model that accounts for various physicochemical changes in the oceanic environment as a function of depth to predict the lifespan of synthetic plastics and the possible formation of plastic debris, e.g., microplastics. We found that the degradation rate of the plastics decreases significantly as a function of water depth and can be estimated quantitatively by the mathematical model that accounts for the effect (and sensitivity) of geographical location, temperature, light intensity, hydrostatic pressure, and marine sediments. For instance, it takes a subsea polyethylene coating about 800 years to degrade on ocean floor (as opposed to <400 years in shallow coastal waters), generating 1000s of particles per g of degradation under certain conditions. Our results demonstrate how suspended sediments in the water column are likely to compensate for the decreasing depth-corrected degradation rates, resulting in surface abrasion and the formation of plastic debris such as microplastics. This review, and the complementing data, will be significant for the environmental impact assessment of plastics in subsea infrastructures. Moreover, as these infrastructures reach the end of their service life, the management of the plastic components becomes of great interest to environmental regulators, industry, and the community, considering the known sizeable impacts of plastics on global biogeochemical cycles.
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Affiliation(s)
- Ibukun Oluwoye
- Curtin Corrosion Centre, Western Australian School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Perth, Australia; Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan.
| | - Laura L Machuca
- Curtin Corrosion Centre, Western Australian School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Perth, Australia
| | - Stuart Higgins
- Curtin University, GPO Box U1987, Perth, WA 6824, Australia
| | - Sangwon Suh
- Bren School of Environmental Science and Management, University of California, Santa Barbara, CA 93106, USA
| | - Tamara S Galloway
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Peter Halley
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shuhei Tanaka
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan
| | - Mariano Iannuzzi
- Curtin Corrosion Centre, Western Australian School of Mines: Minerals, Energy and Chemical Engineering, Curtin University, Perth, Australia
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Negoro S, Shibata N, Kato DI, Tanaka Y, Yasuhira K, Nagai K, Oshima S, Furuno Y, Yokoyama R, Miyazaki K, Takeo M, Hengphasatporn K, Shigeta Y, Lee YH, Higuchi Y. X-ray crystallographic and mutational analysis of the NylC precursor: catalytic mechanism of autocleavage and substrate hydrolysis of nylon hydrolase. FEBS J 2023. [PMID: 36799721 DOI: 10.1111/febs.16755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 02/18/2023]
Abstract
Nylon hydrolase (NylC), a member of the N-terminal nucleophile (Ntn) hydrolase superfamily, is responsible for the degradation of various aliphatic nylons, including nylon-6 and nylon-66. NylC is initially expressed as an inactive precursor (36 kDa), but the precursor is autocatalytically cleaved at Asn266/Thr267 to generate an active enzyme composed of 27 and 9 kDa subunits. We isolated various mutants with amino acid changes at the catalytic centre. X-ray crystallographic analysis revealed that the NylC precursor forms a doughnut-shaped quaternary structure composed of four monomers (molecules A-D) with D2 symmetry. Catalytic residues in the precursor are covered by loop regions at the A/B interface (equivalent to the C/D interface). However, the catalytic residues are exposed to the solvent environment through autocleavage followed by movements of the loop regions. T267A, D306A and D308A mutations resulted in a complete loss of autocleavage. By contrast, in the T267S mutant, autocleavage proceeded slowly at a constant reaction rate (k = 2.8 × 10-5 s-1 ) until complete conversion, but the reaction was inhibited by K189A and N219A mutations. Based on the crystallographic and molecular dynamic simulation analyses, we concluded that the Asp308-Asp306-Thr267 triad, resembling the Glu-Ser-Ser triad conserved in Ntn-hydrolase family enzymes, is responsible for autocleavage and that hydrogen-bonding networks connecting Thr267 with Lys189 and Asn219 are required for increasing the nucleophilicity of Thr267-OH in both the water accessible and water inaccessible systems. Furthermore, we determined that NylC employs the Asp308-Asp306-Thr267 triad as catalytic residues for substrate hydrolysis, but the reaction requires Lys189 and Tyr146 as additional catalytic/substrate-binding residues specific for nylon hydrolysis.
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Affiliation(s)
- Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Naoki Shibata
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Japan
| | - Dai-Ichiro Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Yusuke Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Kengo Yasuhira
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Keisuke Nagai
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Shohei Oshima
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Yoko Furuno
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Risa Yokoyama
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Kaito Miyazaki
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | | | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Suita, Japan.,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju-si, South Korea.,Bio-Analytical Science, University of Science and Technology, Daejeon, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Japan
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Lopes AR, Bunin E, Viana AT, Froufe H, Muñoz-Merida A, Pinho D, Figueiredo J, Barroso C, Vaz-Moreira I, Bellanger X, Egas C, Nunes OC. In silico prediction of the enzymes involved in the degradation of the herbicide molinate by Gulosibacter molinativorax ON4T. Sci Rep 2022; 12:15502. [PMID: 36109598 PMCID: PMC9477822 DOI: 10.1038/s41598-022-18732-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Abstract
Gulosibacter molinativorax ON4T is the only known organism to produce molinate hydrolase (MolA), which catalyses the breakdown of the thiocarbamate herbicide into azepane-1-carboxylic acid (ACA) and ethanethiol. A combined genomic and transcriptomic strategy was used to fully characterize the strain ON4T genome, particularly the molA genetic environment, to identify the potential genes encoding ACA degradation enzymes. Genomic data revealed that molA is the only catabolic gene of a novel composite transposon (Tn6311), located in a novel low copy number plasmid (pARLON1) harbouring a putative T4SS of the class FATA. pARLON1 had an ANI value of 88.2% with contig 18 from Agrococcus casei LMG 22410T draft genome. Such results suggest that pARLON1 is related to genomic elements of other Actinobacteria, although Tn6311 was observed only in strain ON4T. Furthermore, genomic and transcriptomic data demonstrated that the genes involved in ACA degradation are chromosomal. Based on their overexpression when growing in the presence of molinate, the enzymes potentially involved in the heterocyclic ring breakdown were predicted. Among these, the activity of a protein related to caprolactone hydrolase was demonstrated using heterologous expression. However, further studies are needed to confirm the role of the other putative enzymes.
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Tiso T, Winter B, Wei R, Hee J, de Witt J, Wierckx N, Quicker P, Bornscheuer UT, Bardow A, Nogales J, Blank LM. The metabolic potential of plastics as biotechnological carbon sources - Review and targets for the future. Metab Eng 2021; 71:77-98. [PMID: 34952231 DOI: 10.1016/j.ymben.2021.12.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 12/19/2022]
Abstract
The plastic crisis requires drastic measures, especially for the plastics' end-of-life. Mixed plastic fractions are currently difficult to recycle, but microbial metabolism might open new pathways. With new technologies for degradation of plastics to oligo- and monomers, these carbon sources can be used in biotechnology for the upcycling of plastic waste to valuable products, such as bioplastics and biosurfactants. We briefly summarize well-known monomer degradation pathways and computed their theoretical yields for industrially interesting products. With this information in hand, we calculated replacement scenarios of existing fossil-based synthesis routes for the same products. Thereby, we highlight fossil-based products for which plastic monomers might be attractive alternative carbon sources. Notably, not the highest yield of product on substrate of the biochemical route, but rather the (in-)efficiency of the petrochemical routes (i.e., carbon, energy use) determines the potential of biochemical plastic upcycling. Our results might serve as a guide for future metabolic engineering efforts towards a sustainable plastic economy.
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Affiliation(s)
- Till Tiso
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Benedikt Winter
- Energy & Process Systems Engineering, ETH Zurich, Zurich, Switzerland; Institute of Technical Thermodynamics, RWTH Aachen University, Germany
| | - Ren Wei
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Johann Hee
- Unit of Technology of Fuels, RWTH Aachen University, Aachen, Germany
| | - Jan de Witt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Peter Quicker
- Unit of Technology of Fuels, RWTH Aachen University, Aachen, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - André Bardow
- Energy & Process Systems Engineering, ETH Zurich, Zurich, Switzerland; Institute of Technical Thermodynamics, RWTH Aachen University, Germany; Institute of Energy and Climate Research (IEK 10), Research Center Jülich GmbH, Germany
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany.
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Abda EM, Muleta A, Tafesse M, Prabhu SV, Aemro A. Recent endeavors in microbial remediation of micro- and nanoplastics. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2021-0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Petrochemical plastics are frequently utilized in our daily lives for various purposes such as packaging and transportation, but their burden on the environment is considered one of the most man-made pollution crises. These pollutants are slowly fragmented in the environment into microplastics and nanoplastics by consolidated actions of abiotic and biotic factors. Microplastics and nanoplastics can easily be dispersed in the atmosphere and be harmful to all kinds of life. As a result, the remediation of micro- and nanoplastics has recently received a tremendous research impetus in the realm of an ecologically benign approach, notably microbial-based remediation. Thus, the current article looks at the formation, properties, analysis, and biological effects of micro- and nanoplastics. The content is then streamlined towards a comprehensive discussion on microbial-mediated degradation of microplastics and nanoplastics, with an emphasis on front-line bacteria and enzymes, as well as remediation mechanisms. Further, technologies for the removal of microplastics and nanoplastics from the environment are presented for possible remedial considerations. An attempt is also made to highlight the practical snags of microbial plastic degradation while aiming to alleviate the environmental burden of plastic waste.
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Affiliation(s)
- Ebrahim M. Abda
- Department of Biotechnology , Addis Ababa Science and Technology University , P.O. Box 16417, Akaki Kality , Addis Ababa , Ethiopia
- Centre of Excellence- Biotechnology and Bioprocessing, Addis Ababa Science and Technology University , P.O. Box 16417, Akaki Kality , Addis Ababa , Ethiopia
| | - Atsede Muleta
- Department of Biology , University of Gondar , P.O. Box 196 , Gondar , Ethiopia
| | - Mesfin Tafesse
- Department of Biotechnology , Addis Ababa Science and Technology University , P.O. Box 16417, Akaki Kality , Addis Ababa , Ethiopia
- Centre of Excellence- Biotechnology and Bioprocessing, Addis Ababa Science and Technology University , P.O. Box 16417, Akaki Kality , Addis Ababa , Ethiopia
| | - Sundramurthy Venkatesa Prabhu
- Department of Chemical Engineering , Addis Ababa Science and Technology University , P.O. Box 16417, Akaki Kality , Addis Ababa , Ethiopia
| | - Afework Aemro
- Department of Environmental Engineering , Addis Ababa Science and Technology University , P.O. Box 16417, Akaki Kality , Addis Ababa , Ethiopia
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Ji Y, Lu Y, Puetz H, Schwaneberg U. Anchor peptides promote degradation of mixed plastics for recycling. Methods Enzymol 2021; 648:271-292. [PMID: 33579408 DOI: 10.1016/bs.mie.2020.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Resource stewardship and sustainable use of natural resources is mandatory for a circular plastic economy. The discovery of microbes and enzymes that can selectively degrade mixed-plastic waste enables to recycle plastics. Knowledge on how to achieve efficient and selective enzymatic plastic degradation is a key prerequisite for biocatalytic recycling of plastics. Wild-type natural polymer degrading enzymes such as cellulases pose often selective non-catalytic binding domains that facilitate a targeting and efficient degradation of polymeric substrates. Recently identified polyester hydrolases with synthetic polymer degrading activities, however, lack in general such selective domains. Inspired by nature, we herein report a protocol for the identification and engineering of anchor peptides which serve as non-catalytic binding domains specifically toward synthetic plastics. The identified anchor peptides hold the promise to be fused to known plastic degrading enzymes and thereby enhance the efficiency of biocatalytic plastic recycling processes.
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Affiliation(s)
- Yu Ji
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Yi Lu
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Hendrik Puetz
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany; DWI-Leibniz Institute for Interactive Materials, Aachen, Germany.
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Negoro S, Kato DI, Ohki T, Yasuhira K, Kawashima Y, Nagai K, Takeo M, Shibata N, Kamiya K, Shigeta Y. Structural and functional characterization of nylon hydrolases. Methods Enzymol 2020; 648:357-389. [PMID: 33579412 DOI: 10.1016/bs.mie.2020.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Biodegradation of synthetic polymers is recognized as a useful way to reduce their environmental load and pollution, loss of natural resources, extensive energy consumption, and generation of greenhouse gases. The potential use of enzymes responsible for the degradation of the targeted polymers is an effective approach which enables the conversion of the used polymers to original monomers and/or other useful compounds. In addition, the enzymes are expected to be applicable in industrial processes such as improving the surface structures of the polymers. Especially, conversion of the solid polymers to soluble oligomers/monomers is a key step for the biodegradation of the polymers. Regarding the hydrolysis of polyamides, three enzymes, 6-aminohexanoate-cyclic-dimer hydrolase (NylA), 6-aminohexanoate-dimer hydrolase (NylB), and 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC), are found in several bacterial strains. In this chapter, we describe our approach for the screening of microorganisms which degrade nylons and related compounds; preparation of substrates; assay of hydrolytic activity for soluble and insoluble substrates; and X-ray crystallographic and computational approaches for analysis of structure and catalytic mechanisms of the nylon-degrading enzymes.
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Affiliation(s)
- Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan.
| | - Dai-Ichiro Kato
- Department of Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Taku Ohki
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Kengo Yasuhira
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Yasuyuki Kawashima
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Keisuke Nagai
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Japan
| | - Naoki Shibata
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Katsumasa Kamiya
- Education Development Center, Kanagawa Institute of Technology, Atsugi, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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Gatz-Schrupp J, Deckard P, Hufford B, Ly S, Tupa P, Masuda H. Isolation and genomic analysis of 11-aminoundecanoic acid-degrading bacterium Pseudomonas sp. JG-B from nylon 11 enrichment culture. J Genomics 2020; 8:16-20. [PMID: 32064005 PMCID: PMC7019077 DOI: 10.7150/jgen.42095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/02/2020] [Indexed: 11/05/2022] Open
Abstract
Nylon 11 is a polymer synthesized from 11-aminoundecanoic acid, and widely used in commercial manufacturing. In this study, we describe the isolation of the first organism capable of metabolizing 11-aminoundecanoic acid from nylon 11 enrichment culture. The strain shows rapid growth on 11-aminoundecanoic acid as a sole source of carbon, nitrogen, and energy. Furthermore, the genome sequence of strain JG-B was deciphered and shown to belong to genus Pseudomonas. Many genes encoding putative extracellular hydrolases, as well as homologues of nylon 6 hydrolases (NylB and NylA) were identified, suggesting the metabolic versatility and possibility that this organism could also depolymerase nylon 11 polymers.
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Danso D, Chow J, Streit WR. Plastics: Environmental and Biotechnological Perspectives on Microbial Degradation. Appl Environ Microbiol 2019; 85:e01095-19. [PMID: 31324632 PMCID: PMC6752018 DOI: 10.1128/aem.01095-19] [Citation(s) in RCA: 295] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Plastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question of if and to what extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production. Thus, further research is needed to significantly increase the diversity of enzymes and microorganisms acting on these polymers. This can be achieved by tapping into the global metagenomes of noncultivated microorganisms and dark matter proteins. Only then can novel biocatalysts and organisms be delivered that allow rapid degradation, recycling, or value-added use of the vast majority of most human-made polymers.
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Affiliation(s)
- Dominik Danso
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
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11
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Palacio CM, Rozeboom HJ, Lanfranchi E, Meng Q, Otzen M, Janssen DB. Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism. FEBS J 2019; 286:4086-4102. [PMID: 31162815 DOI: 10.1111/febs.14950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/29/2019] [Accepted: 06/01/2019] [Indexed: 01/31/2023]
Abstract
The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).
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Affiliation(s)
- Cyntia M Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
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Otzen M, Palacio C, Janssen DB. Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics. Appl Microbiol Biotechnol 2018; 102:6699-6711. [PMID: 29850960 PMCID: PMC6061476 DOI: 10.1007/s00253-018-9073-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 01/04/2023]
Abstract
Some bacterial cultures are capable of growth on caprolactam as sole carbon and nitrogen source, but the enzymes of the catabolic pathway have not been described. We isolated a caprolactam-degrading strain of Pseudomonas jessenii from soil and identified proteins and genes putatively involved in caprolactam metabolism using quantitative mass spectrometry-based proteomics. This led to the discovery of a caprolactamase and an aminotransferase that are involved in the initial steps of caprolactam conversion. Additionally, various proteins were identified that likely are involved in later steps of the pathway. The caprolactamase consists of two subunits and demonstrated high sequence identity to the 5-oxoprolinases. Escherichia coli cells expressing this caprolactamase did not convert 5-oxoproline but were able to hydrolyze caprolactam to form 6-aminocaproic acid in an ATP-dependent manner. Characterization of the aminotransferase revealed that the enzyme deaminates 6-aminocaproic acid to produce 6-oxohexanoate with pyruvate as amino acceptor. The amino acid sequence of the aminotransferase showed high similarity to subgroup II ω-aminotransferases of the PLP-fold type I proteins. Finally, analyses of the genome sequence revealed the presence of a caprolactam catabolism gene cluster comprising a set of genes involved in the conversion of caprolactam to adipate.
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Affiliation(s)
- Marleen Otzen
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Cyntia Palacio
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dick B Janssen
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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