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Pham VHT, Kim J, Chang S. A Valuable Source of Promising Extremophiles in Microbial Plastic Degradation. Polymers (Basel) 2024; 16:2109. [PMID: 39125136 PMCID: PMC11314448 DOI: 10.3390/polym16152109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Plastics have accumulated in open environments, such as oceans, rivers, and land, for centuries, but their effect has been of concern for only decades. Plastic pollution is a global challenge at the forefront of public awareness worldwide due to its negative effects on ecological systems, animals, human health, and national economies. Therefore, interest has increased regarding specific circular economies for the development of plastic production and the investigation of green technologies for plastic degradation after use on an appropriate timescale. Moreover, biodegradable plastics have been found to contain potential new hazards compared with conventional plastics due to the physicochemical properties of the polymers involved. Recently, plastic biodegradation was defined as microbial conversion using functional microorganisms and their enzymatic systems. This is a promising strategy for depolymerizing organic components into carbon dioxide, methane, water, new biomass, and other higher value bioproducts under both oxic and anoxic conditions. This study reviews microplastic pollution, the negative consequences of plastic use, and the current technologies used for plastic degradation and biodegradation mediated by microorganisms with their drawbacks; in particular, the important and questionable role of extremophilic multi-enzyme-producing bacteria in synergistic systems of plastic decomposition is discussed. This study emphasizes the key points for enhancing the plastic degradation process using extremophiles, such as cell hydrophobicity, amyloid protein, and other relevant factors. Bioprospecting for novel mechanisms with unknown information about the bioproducts produced during the plastic degradation process is also mentioned in this review with the significant goals of CO2 evolution and increasing H2/CH4 production in the future. Based on the potential factors that were analyzed, there may be new ideas for in vitro isolation techniques for unculturable/multiple-enzyme-producing bacteria and extremophiles from various polluted environments.
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Affiliation(s)
- Van Hong Thi Pham
- Department of Environmental Energy Engineering, College of Creative Engineering, Kyonggi University, Suwon 16227, Republic of Korea;
- Department of Life Science, College of Natural Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Soonwoong Chang
- Department of Environmental Energy Engineering, College of Creative Engineering, Kyonggi University, Suwon 16227, Republic of Korea;
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Winiarska A, Ramírez-Amador F, Hege D, Gemmecker Y, Prinz S, Hochberg G, Heider J, Szaleniec M, Schuller JM. A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire. SCIENCE ADVANCES 2023; 9:eadg6689. [PMID: 37267359 PMCID: PMC10413684 DOI: 10.1126/sciadv.adg6689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/28/2023] [Indexed: 06/04/2023]
Abstract
Aldehyde oxidoreductases (AORs) are tungsten enzymes catalyzing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacterium Aromatoleum aromaticum (AORAa) consists of three different subunits (AorABC) and uses nicotinamide adenine dinucleotide (NAD) as an electron acceptor. Here, we reveal that the enzyme forms filaments of repeating AorAB protomers that are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with quantum mechanics:molecular mechanics (QM:MM)-based modeling for the coordination of the W-co, enables formulation of a hypothetical catalytic mechanism that paves the way to further engineering for applications in synthetic biology and biotechnology.
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Affiliation(s)
- Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków, Poland
| | - Fidel Ramírez-Amador
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Dominik Hege
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Yvonne Gemmecker
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Simone Prinz
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Georg Hochberg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Johann Heider
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków, Poland
| | - Jan Michael Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
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Atanasova N, Stoitsova S, Paunova-Krasteva T, Kambourova M. Plastic Degradation by Extremophilic Bacteria. Int J Mol Sci 2021; 22:ijms22115610. [PMID: 34070607 PMCID: PMC8198520 DOI: 10.3390/ijms22115610] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 01/03/2023] Open
Abstract
Intensive exploitation, poor recycling, low repeatable use, and unusual resistance of plastics to environmental and microbiological action result in accumulation of huge waste amounts in terrestrial and marine environments, causing enormous hazard for human and animal life. In the last decades, much scientific interest has been focused on plastic biodegradation. Due to the comparatively short evolutionary period of their appearance in nature, sufficiently effective enzymes for their biodegradation are not available. Plastics are designed for use in conditions typical for human activity, and their physicochemical properties roughly change at extreme environmental parameters like low temperatures, salt, or low or high pH that are typical for the life of extremophilic microorganisms and the activity of their enzymes. This review represents a first attempt to summarize the extraordinarily limited information on biodegradation of conventional synthetic plastics by thermophilic, alkaliphilic, halophilic, and psychrophilic bacteria in natural environments and laboratory conditions. Most of the available data was reported in the last several years and concerns moderate extremophiles. Two main questions are highlighted in it: which extremophilic bacteria and their enzymes are reported to be involved in the degradation of different synthetic plastics, and what could be the impact of extremophiles in future technologies for resolving of pollution problems.
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Salii I, Szaleniec M, Zein AA, Seyhan D, Sekuła A, Schühle K, Kaplieva-Dudek I, Linne U, Meckenstock RU, Heider J. Determinants for Substrate Recognition in the Glycyl Radical Enzyme Benzylsuccinate Synthase Revealed by Targeted Mutagenesis. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iryna Salii
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, 30-239 Kraków, Poland
| | - Ammar Alhaj Zein
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Deniz Seyhan
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | - Anna Sekuła
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Science, 30-239 Kraków, Poland
| | - Karola Schühle
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
| | | | - Uwe Linne
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Philipps University Marburg, 35043 Marburg, Germany
| | | | - Johann Heider
- Department of Biology, Laboratory for Microbial Biochemistry, Philipps University Marburg, 35043 Marburg, Germany
- Synmikro-Center for Synthetic Microbiology, Philipps University Marburg, 35043 Marburg, Germany
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Nissen LS, Basen M. The emerging role of aldehyde:ferredoxin oxidoreductases in microbially-catalyzed alcohol production. J Biotechnol 2019; 306:105-117. [DOI: 10.1016/j.jbiotec.2019.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
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Two Different Quinohemoprotein Amine Dehydrogenases Initiate Anaerobic Degradation of Aromatic Amines in Aromatoleum aromaticum EbN1. J Bacteriol 2019; 201:JB.00281-19. [PMID: 31138631 DOI: 10.1128/jb.00281-19] [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: 04/18/2019] [Accepted: 05/23/2019] [Indexed: 11/20/2022] Open
Abstract
Aromatic amines like 2-phenylethylamine (2-PEA) and benzylamine (BAm) have been identified as novel growth substrates of the betaproteobacterium Aromatoleum aromaticum EbN1, which degrades a wide variety of aromatic compounds in the absence of oxygen under denitrifying growth conditions. The catabolic pathway of these amines was identified, starting with their oxidative deamination to the corresponding aldehydes, which are then further degraded via the enzymes of the phenylalanine or benzyl alcohol metabolic pathways. Two different periplasmic quinohemoprotein amine dehydrogenases involved in 2-PEA or BAm metabolism were identified and characterized. Both enzymes consist of three subunits, contain two heme c cofactors in their α-subunits, and exhibit extensive processing of their γ-subunits, generating four intramolecular thioether bonds and a cysteine tryptophylquinone (CTQ) cofactor. One of the enzymes was present in cells grown with 2-PEA or other substrates, showed an α2β2γ2 composition, and had a rather broad substrate spectrum, which included 2-PEA, BAm, tyramine, and 1-butylamine. In contrast, the other enzyme was specifically induced in BAm-grown cells, showing an αβγ composition and activity only with BAm and 2-PEA. Since the former enzyme showed the highest catalytic efficiency with 2-PEA and the latter with BAm, they were designated 2-PEADH and benzylamine dehydrogenase (BAmDH). The catalytic properties and inhibition patterns of 2-PEADH and BAmDH showed considerable differences and were compared to previously characterized quinohemoproteins of the same enzyme family.IMPORTANCE The known substrate spectrum of A. aromaticum EbN1 is expanded toward aromatic amines, which are metabolized as sole substrates coupled to denitrification. The characterization of the two quinohemoprotein isoenzymes involved in degrading either 2-PEA or BAm expands the knowledge of this enzyme family and establishes for the first time that the necessary maturation of their quinoid CTQ cofactors does not require the presence of molecular oxygen. Moreover, the study revealed a highly interesting regulatory phenomenon, suggesting that growth with BAm leads to a complete replacement of 2-PEADH by BAmDH, which has considerably different catalytic and inhibition properties.
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Arndt F, Schmitt G, Winiarska A, Saft M, Seubert A, Kahnt J, Heider J. Characterization of an Aldehyde Oxidoreductase From the Mesophilic Bacterium Aromatoleum aromaticum EbN1, a Member of a New Subfamily of Tungsten-Containing Enzymes. Front Microbiol 2019; 10:71. [PMID: 30766522 PMCID: PMC6365974 DOI: 10.3389/fmicb.2019.00071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
The biochemical properties of a new tungsten-containing aldehyde oxidoreductase from the mesophilic betaproteobacterium Aromatoleum aromaticum EbN1 (AORAa) are presented in this study. The enzyme was purified from phenylalanine-grown cells of an overexpressing mutant lacking the gene for an aldehyde dehydrogenase normally involved in anaerobic phenylalanine degradation. AORAa catalyzes the oxidation of a broad variety of aldehydes to the respective acids with either viologen dyes or NAD+ as electron acceptors. In contrast to previously known AORs, AORAa is a heterohexameric protein consisting of three different subunits, a large subunit containing the W-cofactor and an Fe-S cluster, a small subunit containing four Fe-S clusters, and a medium subunit containing an FAD cofactor. The presence of the expected cofactors have been confirmed by elemental analysis and spectrophotometric methods. AORAa has a pH optimum of 8.0, a temperature optimum of 40°C and is completely inactive at 50°C. Compared to archaeal AORs, AORAa is remarkably resistant against exposure to air, exhibiting a half-life time of 1 h as purified enzyme and being completely unaffected in cell extracts. Kinetic parameters of AORAa have been obtained for the oxidation of one aliphatic and two aromatic aldehydes, resulting in about twofold higher kcat values with benzyl viologen than with NAD+ as electron acceptor. Finally, we obtained evidence that AORAa is also catalyzing the reverse reaction, reduction of benzoate to benzaldehyde, albeit at very low rates and under conditions strongly favoring acid reduction, e.g., low pH and using Ti(III) citrate as electron donor of very low redox potential. AORAa appears to be a prototype of a new subfamily of bacterial AOR-like tungsten-enzymes, which differ from the previously known archaeal AORs mostly by their multi-subunit composition, their low sensitivity against oxygen, and the ability to use NAD+ as electron acceptor.
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Affiliation(s)
- Fabian Arndt
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Georg Schmitt
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Poland
| | - Martin Saft
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Seubert
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jörg Kahnt
- Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
| | - Johann Heider
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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