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An Ultra-Sensitive Comamonas thiooxidans Biosensor for the Rapid Detection of Enzymatic Polyethylene Terephthalate (PET) Degradation. Appl Environ Microbiol 2023; 89:e0160322. [PMID: 36507653 PMCID: PMC9888244 DOI: 10.1128/aem.01603-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Polyethylene terephthalate (PET) is a prevalent synthetic polymer that is known to contaminate marine and terrestrial environments. Currently, only a limited number of PET-active microorganisms and enzymes (PETases) are known. This is in part linked to the lack of highly sensitive function-based screening assays for PET-active enzymes. Here, we report on the construction of a fluorescent biosensor based on Comamonas thiooxidans strain S23. C. thiooxidans S23 transports and metabolizes TPA, one of the main breakdown products of PET, using a specific tripartite tricarboxylate transporter (TTT) and various mono- and dioxygenases encoded in its genome in a conserved operon ranging from tphC-tphA1. TphR, an IclR-type transcriptional regulator is found upstream of the tphC-tphA1 cluster where TPA induces transcription of tphC-tphA1 up to 88-fold in exponentially growing cells. In the present study, we show that the C. thiooxidans S23 wild-type strain, carrying the sfGFP gene fused to the tphC promoter, senses TPA at concentrations as low as 10 μM. Moreover, a deletion mutant lacking the catabolic genes involved in TPA degradation thphA2-A1 (ΔtphA2A3BA1) is up to 10,000-fold more sensitive and detects TPA concentrations in the nanomolar range. This is, to our knowledge, the most sensitive reporter strain for TPA and we demonstrate that it can be used for the detection of enzymatic PET breakdown products. IMPORTANCE Plastics and microplastics accumulate in all ecological niches. The construction of more sensitive biosensors allows to monitor and screen potential PET degradation in natural environments and industrial samples. These strains will also be a valuable tool for functional screenings of novel PETase candidates and variants or monitoring of PET recycling processes using biocatalysts. Thereby they help us to enrich the known biodiversity and efficiency of PET degrading organisms and enzymes and understand their contribution to environmental plastic degradation.
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2
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Yastrebova OV, Malysheva AA, Plotnikova EG. Halotolerant Terephthalic Acid-Degrading Bacteria of the Genus Glutamicibacter. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822050167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Terephthalic acid (TPA) is an isomer of ortho-phthalic acid, which is widely used in the chemical industry to produce artificial fibers and plastics, including polyethylene terephthalate; it is a widespread environmental pollutant. The ability of two strains of Glutamicibacter spp. PB8-1 (=ВКМ Ac-2934D) and BO25 (=ВКМ Ac2935D) isolated from the salt mining area (Perm krai, Russia) to grow using terephthalic acid as the only source of carbon and energy was studied. The strains PB8-1 and BO25 could utilize high concentrations of TPA (30 g/L), which was shown for TPA-degrading bacteria for the first time. Strains PB8-1 and BO25 were halotolerant bacteria: they grew in the NaCl-free medium or at NaCl concentrations of up to 90 g/L in a rich medium and up to 60 g/L in a mineral medium supplemented with TPA. No bacteria capable of degrading TPA under saline conditions were previously described. The growth of the strain BO25 using TPA was accompanied by the accumulation and subsequent degradation of protocatechuic acid (PCA), suggesting that the TPA metabolism occurred through PCA, which was previously described for bacteria of different taxa, including actinobacteria. Thus, TPA-degrading strains Glutamicibacter spp. PB8-1 and BO25 are promising for the development of bioremediation methods for saline soils and wastewater contaminated with TPA.
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3
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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: 27] [Impact Index Per Article: 13.5] [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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4
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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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5
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Gao R, Pan H, Kai L, Han K, Lian J. Microbial degradation and valorization of poly(ethylene terephthalate) (PET) monomers. World J Microbiol Biotechnol 2022; 38:89. [PMID: 35426614 DOI: 10.1007/s11274-022-03270-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 12/22/2022]
Abstract
The polyethylene terephthalate (PET) is one of the major plastics with a huge annual production. Alongside with its mass production and wide applications, PET pollution is threatening and damaging the environment and human health. Although mechanical or chemical methods can deal with PET, the process suffers from high cost and the hydrolyzed monomers will cause secondary pollution. Discovery of plastic-degrading microbes and the corresponding enzymes emerges new hope to cope with this issue. Combined with synthetic biology and metabolic engineering, microbial cell factories not only provide a promising approach to degrade PET, but also enable the conversion of its monomers, ethylene glycol (EG) and terephthalic acid (TPA), into value-added compounds. In this way, PET wastes can be handled in environment-friendly and more potentially cost-effective processes. While PET hydrolases have been extensively reviewed, this review focuses on the microbes and metabolic pathways for the degradation of PET monomers. In addition, recent advances in the biotransformation of TPA and EG into value-added compounds are discussed in detail.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 310027, Hangzhou, China
| | - Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China
| | - Lei Kai
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, 22116, Xuzhou, China.,Jiangsu Keybio Co. LTD, 22116, Xuzhou, China
| | - Kun Han
- Jiangsu Keybio Co. LTD, 22116, Xuzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China. .,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 310027, Hangzhou, China.
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6
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Mutanda I, Sun J, Jiang J, Zhu D. Bacterial membrane transporter systems for aromatic compounds: Regulation, engineering, and biotechnological applications. Biotechnol Adv 2022; 59:107952. [PMID: 35398204 DOI: 10.1016/j.biotechadv.2022.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
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7
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Biochemical and structural characterization of an aromatic ring-hydroxylating dioxygenase for terephthalic acid catabolism. Proc Natl Acad Sci U S A 2022; 119:e2121426119. [PMID: 35312352 PMCID: PMC9060491 DOI: 10.1073/pnas.2121426119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SignificanceMore than 400 million tons of plastic waste is produced each year, the overwhelming majority of which ends up in landfills. Bioconversion strategies aimed at plastics have emerged as important components of enabling a circular economy for synthetic plastics, especially those that exhibit chemically similar linkages to those found in nature, such as polyesters. The enzyme system described in this work is essential for mineralization of the xenobiotic components of poly(ethylene terephthalate) (PET) in the biosphere. Our description of its structure and substrate preferences lays the groundwork for in vivo or ex vivo engineering of this system for PET upcycling.
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8
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Suvorova IA, Gelfand MS. Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content. Front Microbiol 2021; 12:675815. [PMID: 34177859 PMCID: PMC8222616 DOI: 10.3389/fmicb.2021.675815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
The IclR-family is a large group of transcription factors (TFs) regulating various biological processes in diverse bacteria. Using comparative genomics techniques, we have identified binding motifs of IclR-family TFs, reconstructed regulons and analyzed their content, finding co-occurrences between the regulated COGs (clusters of orthologous genes), useful for future functional characterizations of TFs and their regulated genes. We describe two main types of IclR-family motifs, similar in sequence but different in the arrangement of the half-sites (boxes), with GKTYCRYW3-4RYGRAMC and TGRAACAN1-2TGTTYCA consensuses, and also predict that TFs in 32 orthologous groups have binding sites comprised of three boxes with alternating direction, which implies two possible alternative modes of dimerization of TFs. We identified trends in site positioning relative to the translational gene start, and show that TFs in 94 orthologous groups bind tandem sites with 18-22 nucleotides between their centers. We predict protein-DNA contacts via the correlation analysis of nucleotides in binding sites and amino acids of the DNA-binding domain of TFs, and show that the majority of interacting positions and predicted contacts are similar for both types of motifs and conform well both to available experimental data and to general protein-DNA interaction trends.
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Affiliation(s)
- Inna A Suvorova
- Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
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9
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Pardo I, Jha RK, Bermel RE, Bratti F, Gaddis M, McIntyre E, Michener W, Neidle EL, Dale T, Beckham GT, Johnson CW. Gene amplification, laboratory evolution, and biosensor screening reveal MucK as a terephthalic acid transporter in Acinetobacter baylyi ADP1. Metab Eng 2020; 62:260-274. [DOI: 10.1016/j.ymben.2020.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/11/2020] [Accepted: 09/19/2020] [Indexed: 12/19/2022]
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10
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Gibu N, Arata T, Kuboki S, Linh DV, Fukuda M, Steinbüchel A, Kasai D. Characterization of the genes responsible for rubber degradation in Actinoplanes sp. strain OR16. Appl Microbiol Biotechnol 2020; 104:7367-7376. [PMID: 32681242 PMCID: PMC7413915 DOI: 10.1007/s00253-020-10700-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 10/25/2022]
Abstract
A Gram-positive rubber-degrading bacterium, Actinoplanes sp. strain OR16 (strain NBRC 114529), is able to grow on agar plates containing natural and synthetic rubber as the sole sources of carbon and energy. When this strain was grown on natural rubber latex overlay agar plates, translucent halos around the cells were observed. To identify the natural rubber degradation genes and other features of its metabolism, its complete genome sequence was determined. The genome of OR16 consists of 9,293,892 bp and comprises one circular chromosome (GenBank accession number AP019371.1) with a G + C content of 70.3%. The genome contains 8238 protein-coding and 18 rRNA genes. A homology search of the genome sequence revealed that three genes (lcp1, lcp2, and lcp3) are homologous to an extracellular latex-clearing protein (Lcp) of Streptomyces sp. K30. RT-PCR analysis revealed that lcp1 and lcp2 seem to constitute an operon. Purified lcp gene products have oxygen consumption activity toward natural rubber latex, suggesting that all these genes encode rubber-degrading enzymes in OR16. Quantitative reverse transcription-PCR analysis indicated that the transcription of these genes is induced during the growth of OR16 on natural rubber. The genes located adjacent to lcp1 and lcp3, which code for a TetR/AcrR-type transcriptional regulator, can bind to the promoter regions of these lcp genes. It is suggested that the putative regulators play a role in regulating the transcription of the lcp genes. These results strongly suggested that three lcp genes are required for the utilization of natural rubber in strain OR16. Key Points • The complete genome sequence of Actinoplanes sp. strain OR16 was determined. • Three lcp genes which are involved in the natural rubber degradation in OR16 were identified. • Transcription of these lcp genes is induced during utilization of rubber in OR16. • Two regulators, which bind to the promoter regions of lcp, were determined.
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Affiliation(s)
- Namiko Gibu
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Tomoka Arata
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Saya Kuboki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Dao Viet Linh
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.,Department of Biological Chemistry, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany.,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.
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11
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Salvador M, Abdulmutalib U, Gonzalez J, Kim J, Smith AA, Faulon JL, Wei R, Zimmermann W, Jimenez JI. Microbial Genes for a Circular and Sustainable Bio-PET Economy. Genes (Basel) 2019; 10:E373. [PMID: 31100963 PMCID: PMC6562992 DOI: 10.3390/genes10050373] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 02/03/2023] Open
Abstract
Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for the synthesis of novel PET as well as become a potential carbon source for microorganisms. In addition, microorganisms and biomass can be used for the synthesis of the constituent monomers of PET from renewable sources. The combination of both biodegradation and biosynthesis would enable a completely circular bio-PET economy beyond the conventional recycling processes. Circular strategies like this could contribute to significantly decreasing the environmental impact of our dependence on this polymer. Here we review the efforts made towards turning PET into a viable feedstock for microbial transformations. We highlight current bottlenecks in degradation of the polymer and metabolism of the monomers, and we showcase fully biological or semisynthetic processes leading to the synthesis of PET from sustainable substrates.
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Affiliation(s)
- Manuel Salvador
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Umar Abdulmutalib
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Jaime Gonzalez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Juhyun Kim
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Alex A Smith
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
- CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, 91000 Évry, France.
| | - Ren Wei
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
| | - Jose I Jimenez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
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12
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Kasai D, Iwasaki T, Nagai K, Araki N, Nishi T, Fukuda M. 2,3-Dihydroxybenzoate meta-Cleavage Pathway is Involved in o-Phthalate Utilization in Pseudomonas sp. strain PTH10. Sci Rep 2019; 9:1253. [PMID: 30718753 PMCID: PMC6362003 DOI: 10.1038/s41598-018-38077-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 12/18/2018] [Indexed: 11/09/2022] Open
Abstract
Pseudomonas sp. strain PTH10 can utilize o-phthalate which is a key intermediate in the bacterial degradation of some polycyclic aromatic hydrocarbons. In this strain, o-phthalate is degraded to 2,3-dihydroxybenzoate and further metabolized via the 2,3-dihydroxybenzoate meta-cleavage pathway. Here, the opa genes which are involved in the o-phthalate catabolism were identified. Based on the enzymatic activity of the opa gene products, opaAaAbAcAd, opaB, opaC, and opaD were found to code for o-phthalate 2,3-dioxygenase, dihydrodiol dehydrogenase, 2,3-dihydroxybenzoate 3,4-dioxygenase, and 3-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase, respectively. Collectively, these enzymes are thought to catalyze the conversion of o-phthalate to 2-hydroxymuconate-6-semialdehyde. Deletion mutants of the above opa genes indicated that their products were required for the utilization of o-phthalate. Transcriptional analysis showed that the opa genes were organized in the same transcriptional unit. Quantitative analysis of opaAa, opaB, opaC, opaD, opaE, and opaN revealed that, except for opaB and opaC, all other genes were transcriptionally induced during growth on o-phthalate. The constitutive expression of opaB and opaC, and the transcriptional induction of opaD located downstream of opaB, suggest several possible internal promoters are existence in the opa cluster. Together, these results strongly suggest that the opa genes are involved in a novel o-phthalate catabolic pathway in strain PTH10.
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Affiliation(s)
- Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.
| | | | - Kazuki Nagai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Naoto Araki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | | | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.,Department of Biological Chemistry, Chubu University, Kasugai, Aichi, 487-8501, Japan
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13
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Draft Genome Sequence of Comamonas sp. Strain E6 (NBRC 107749), a Degrader of Phthalate Isomers through the Protocatechuate 4,5-Cleavage Pathway. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00643-15. [PMID: 26089421 PMCID: PMC4472898 DOI: 10.1128/genomea.00643-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Comamonas sp. strain E6 can degrade o-phthalate, terephthalate, and isophthalate via the protocatechuate 4,5-cleavage pathway. Here, we report the draft genome sequence of E6 in order to provide insights into its mechanisms in o-phthalate catabolism and its potential use for biotechnological applications.
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14
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Weiss M, Kesberg AI, Labutti KM, Pitluck S, Bruce D, Hauser L, Copeland A, Woyke T, Lowry S, Lucas S, Land M, Goodwin L, Kjelleberg S, Cook AM, Buhmann M, Thomas T, Schleheck D. Permanent draft genome sequence of Comamonas testosteroni KF-1. Stand Genomic Sci 2013; 8:239-54. [PMID: 23991256 PMCID: PMC3746432 DOI: 10.4056/sigs.3847890] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel biochemical degradation pathways for xenobiotic 4-sulfophenylcarboxylates (SPC) formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear alkylbenzenesulfonates, LAS) by bacterial communities. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,026,527 bp long chromosome (one sequencing gap) exhibits an average G+C content of 61.79% and is predicted to encode 5,492 protein-coding genes and 114 RNA genes.
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Affiliation(s)
- Michael Weiss
- Department of Biological Sciences, University of Konstanz, Germany ; Konstanz Research School Chemical Biology, University of Konstanz, Germany
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15
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Kasai D, Kamimura N, Tani K, Umeda S, Abe T, Fukuda M, Masai E. Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6. FEMS Microbiol Lett 2012; 332:68-75. [PMID: 22515452 DOI: 10.1111/j.1574-6968.2012.02576.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/12/2012] [Accepted: 04/16/2012] [Indexed: 11/28/2022] Open
Abstract
Sphingobium sp. strain SYK-6 is able to degrade various lignin-derived aromatic compounds including ferulate, vanillate, and syringate. In the SYK-6 cells, ferulate is converted to vanillin and acetyl-coenzyme A (acetyl-CoA) through the reactions catalyzed by feruloyl-CoA synthetase and feruloyl-CoA hydratase/lyase encoded by ferA and ferB, respectively. Here, we characterized the transcriptional regulation of ferBA controlled by a MarR-type transcriptional regulator, FerC. The ferC gene is located upstream of ferB. Reverse transcription (RT)-PCR analysis suggested that the ferBA genes form an operon. Quantitative RT-PCR analyses of SYK-6 and its mutant cells revealed that the transcription of the ferBA operon is negatively regulated by FerC, and feruloyl-CoA was identified as an inducer. The transcription start site of ferB was mapped at 30 nucleotides upstream from the ferB initiation codon. Purified His-tagged FerC bound to the ferC-ferB intergenic region. This region contains an inverted repeat sequence, which overlaps with a part of the -10 sequence and the transcriptional start site of ferB. The binding of FerC to the operator sequence was inhibited by the addition of feruloyl-CoA, indicating that FerC interacts with feruloyl-CoA as an effector molecule. Furthermore, hydroxycinnamoyl-CoAs, including p-coumaroyl-CoA, caffeoyl-CoA, and sinapoyl-CoA also acted as effector.
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Affiliation(s)
- Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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Kamimura N, Inakazu K, Kasai D, Fukuda M, Masai E. Regulation of the isophthalate catabolic operon controlled by IphR in Comamonas sp. strain E6. FEMS Microbiol Lett 2012; 329:186-92. [PMID: 22313288 DOI: 10.1111/j.1574-6968.2012.02521.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 01/26/2012] [Accepted: 02/02/2012] [Indexed: 11/29/2022] Open
Abstract
The isophthalate (IPA) catabolic operon (iphACBDR) of Comamonas sp. strain E6 responsible for the conversion of IPA into protocatechuate is negatively regulated by an IclR-type transcriptional regulator, IphR. Promoter analysis showed that the region sufficient for the IPA-dependent induction of the iphA promoter was located within the 87 bp region upstream from the iphA start codon. The transcription start site of the iph operon was mapped at a cytosine located 49 bp upstream of the iphA start codon. Two inverted repeat sequences IR1 (positions -21 to -7 relative to the iphA transcription start site) and IR2 (-2 to +10) were found in the binding region of IphR identified by electrophoretic mobility shift assays (EMSA) using purified IphR. Mutation analysis of each half-site of these inverted repeat sequences indicated that both IR2 and a downstream half-site of IR1 are necessary for the binding of IphR. EMSA in the presence of IPA or its analogous substrates demonstrated that IPA had the ability to inhibit the binding of IphR to this operator region. In conclusion, the iph operon is negatively autoregulated by the binding of IphR to the operator region, and this repression is released by the presence of IPA.
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Affiliation(s)
- Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata, Japan
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