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Lequan Q, Yanan F, Xianda Z, Mengyuan B, Chenyu L, Shijin W. Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria. World J Microbiol Biotechnol 2024; 40:247. [PMID: 38904858 DOI: 10.1007/s11274-024-04060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Phthalate isomers are key intermediates in the biodegradation of pollutants including waste polyethylene terephthalate (PET) plastics and plasticizers. So far, an increasing number of phthalate isomer-degrading strains have been isolated, and their degradation pathways show significant diversity. In this paper, we comprehensively review the current status of research on the degrading bacteria, degradation characteristics, aerobic and anaerobic degradation pathways, and degradation genes (clusters) of phthalate isomers, and discuss the current shortcomings and challenges. Moreover, the degradation process of phthalate isomers produces many important aromatic precursor molecules, which can be used to produce higher-value derivative chemicals, and the modification of their degradation pathways holds good prospects. Therefore, this review also highlights the current progress made in modifying the phthalate isomer degradation pathway and explores its potential for high-value applications.
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Affiliation(s)
- Qiu Lequan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
| | - Fu Yanan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhou Xianda
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Bao Mengyuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Li Chenyu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wu Shijin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
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Mahto JK, Sharma M, Neetu N, Kayastha A, Aggarwal S, Kumar P. Conformational flexibility enables catalysis of phthalate cis-4,5-dihydrodiol dehydrogenase. Arch Biochem Biophys 2022; 727:109314. [DOI: 10.1016/j.abb.2022.109314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
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Structural insights into dihydroxylation of terephthalate, a product of polyethylene terephthalate degradation. J Bacteriol 2022; 204:e0054321. [PMID: 35007143 DOI: 10.1128/jb.00543-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biodegradation of terephthalate (TPA) is a highly desired catabolic process for the bacterial utilization of this Polyethylene terephthalate (PET) depolymerization product, but to date, the structure of terephthalate dioxygenase (TPDO), a Rieske oxygenase (RO) that catalyzes the dihydroxylation of TPA to a cis-diol is unavailable. In this study, we characterized the steady-state kinetics and first crystal structure of TPDO from Comamonas testosteroni KF1 (TPDOKF1). The TPDOKF1 exhibited the substrate specificity for TPA (kcat/Km = 57 ± 9 mM-1s-1). The TPDOKF1 structure harbors characteristics RO features as well as a unique catalytic domain that rationalizes the enzyme's function. The docking and mutagenesis studies reveal that its substrate specificity to TPA is mediated by Arg309 and Arg390 residues, two residues positioned on opposite faces of the active site. Additionally, residue Gln300 is also proven to be crucial for the activity, its substitution to alanine decreases the activity (kcat) by 80%. Together, this study delineates the structural features that dictate the substrate recognition and specificity of TPDO. Importance The global plastic pollution has become the most pressing environmental issue. Recent studies on enzymes depolymerizing polyethylene terephthalate plastic into terephthalate (TPA) show some potential in tackling this. Microbial utilization of this released product, TPA is an emerging and promising strategy for waste-to-value creation. Research from the last decade has discovered terephthalate dioxygenase (TPDO), as being responsible for initiating the enzymatic degradation of TPA in a few Gram-negative and Gram-positive bacteria. Here, we have determined the crystal structure of TPDO from Comamonas testosteroni KF1 and revealed that it possesses a unique catalytic domain featuring two basic residues in the active site to recognize TPA. Biochemical and mutagenesis studies demonstrated the crucial residues responsible for the substrate specificity of this enzyme.
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Sadler JC, Wallace S. Microbial synthesis of vanillin from waste poly(ethylene terephthalate). GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2021; 23:4665-4672. [PMID: 34276250 PMCID: PMC8256426 DOI: 10.1039/d1gc00931a] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
Poly(ethylene terephthalate) (PET) is an abundant and extremely useful material, with widespread applications across society. However, there is an urgent need to develop technologies to valorise post-consumer PET waste to tackle plastic pollution and move towards a circular economy. Whilst PET degradation and recycling technologies have been reported, examples focus on repurposing the resultant monomers to produce more PET or other second-generation materials. Herein, we report a novel pathway in engineered Escherichia coli for the direct upcycling of PET derived monomer terephthalic acid into the value-added small molecule vanillin, a flavour compound ubiquitous in the food and cosmetic industries, and an important bulk chemical. After process optimisation, 79% conversion to vanillin from TA was achieved, a 157-fold improvement over our initial conditions. Parameters such as temperature, cell permeabilisation and in situ product removal were key to maximising vanillin titres. Finally, we demonstrate the conversion of post-consumer PET from a plastic bottle into vanillin by coupling the pathway with enzyme-catalysed PET hydrolysis. This work demonstrates the first biological upcycling of post-consumer plastic waste into vanillin using an engineered microorganism.
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Affiliation(s)
- Joanna C Sadler
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh Roger Land Building Alexander Crum Brown Road King's Buildings Edinburgh EH9 3FF UK
| | - Stephen Wallace
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh Roger Land Building Alexander Crum Brown Road King's Buildings Edinburgh EH9 3FF UK
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Kocyła A, Tran JB, Krężel A. Galvanization of Protein-Protein Interactions in a Dynamic Zinc Interactome. Trends Biochem Sci 2020; 46:64-79. [PMID: 32958327 DOI: 10.1016/j.tibs.2020.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
The presence of Zn2+ at protein-protein interfaces modulates complex function, stability, and introduces structural flexibility/complexity, chemical selectivity, and reversibility driven in a Zn2+-dependent manner. Recent studies have demonstrated that dynamically changing Zn2+ affects numerous cellular processes, including protein-protein communication and protein complex assembly. How Zn2+-involved protein-protein interactions (ZPPIs) are formed and dissociate and how their stability and reactivity are driven in a zinc interactome remain poorly understood, mostly due to experimental obstacles. Here, we review recent research advances on the role of Zn2+ in the formation of interprotein sites, their architecture, function, and stability. Moreover, we underline the importance of zinc networks in intersystemic communication and highlight bioinformatic and experimental challenges required for the identification and investigation of ZPPIs.
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Affiliation(s)
- Anna Kocyła
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Józef Ba Tran
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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Boll M, Geiger R, Junghare M, Schink B. Microbial degradation of phthalates: biochemistry and environmental implications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:3-15. [PMID: 31364812 DOI: 10.1111/1758-2229.12787] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 05/10/2023]
Abstract
The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.
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Affiliation(s)
- Matthias Boll
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Robin Geiger
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Madan Junghare
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
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Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, de Crécy-Lagard V. Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite. ACS Chem Biol 2016; 11:2304-11. [PMID: 27294475 DOI: 10.1021/acschembio.6b00279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DUF1537 is a novel family of kinases identified by comparative genomic approaches. The family is widespread and found in all sequenced plant genomes and 16% of sequenced bacterial genomes. DUF1537 is not a monofunctional family and contains subgroups that can be separated by phylogenetic and genome neighborhood context analyses. A subset of the DUF1537 proteins is strongly associated by physical clustering and gene fusion with the PdxA2 family, demonstrated here to be a functional paralog of the 4-phosphohydroxy-l-threonine dehydrogenase enzyme (PdxA), a central enzyme in the synthesis of pyridoxal-5'-phosphate (PLP) in proteobacteria. Some members of this DUF1537 subgroup phosphorylate l-4-hydroxythreonine (4HT) into 4-phosphohydroxy-l-threonine (4PHT), the substrate of PdxA, in vitro and in vivo. This provides an alternative route to PLP from the toxic antimetabolite 4HT that can be directly generated from the toxic intermediate glycolaldehyde. Although the kinetic and physical clustering data indicate that these functions in PLP synthesis are not the main roles of the DUF1537-PdxA2 enzymes, genetic and physiological data suggest these side activities function has been maintained in diverse sets of organisms.
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Affiliation(s)
- Jennifer J. Thiaville
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Jake Flood
- Department
of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado United States
| | - Svetlana Yurgel
- Dalhousie University, 6299 South
St., Halifax, NS B3H 4R2, Canada
| | - Laurence Prunetti
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | | | - Geoffrey Hutinet
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Farhad Forouhar
- Department
of Biological Sciences, Columbia University, New York, New York, United States
| | - Xinshuai Zhang
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Venkateswaran Ganesan
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Patrick Reddy
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center, UC Davis, Davis, California, United States
- King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia
| | - J. A. Gerlt
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John F. Hunt
- Department
of Biological Sciences, Columbia University, New York, New York, United States
| | - Shelley D. Copley
- Department
of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
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