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Sánchez-Ruiz MI, Santillana E, Linde D, Romero A, Martínez AT, Ruiz-Dueñas FJ. Structure-function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:74. [PMID: 38824538 PMCID: PMC11144326 DOI: 10.1186/s13068-024-02517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/11/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Manganese peroxidases (MnPs) are, together with lignin peroxidases and versatile peroxidases, key elements of the enzymatic machineries secreted by white-rot fungi to degrade lignin, thus providing access to cellulose and hemicellulose in plant cell walls. A recent genomic analysis of 52 Agaricomycetes species revealed the existence of novel MnP subfamilies differing in the amino-acid residues that constitute the manganese oxidation site. Following this in silico analysis, a comprehensive structure-function study is needed to understand how these enzymes work and contribute to transform the lignin macromolecule. RESULTS Two MnPs belonging to the subfamilies recently classified as MnP-DGD and MnP-ESD-referred to as Ape-MnP1 and Cst-MnP1, respectively-were identified as the primary peroxidases secreted by the Agaricales species Agrocybe pediades and Cyathus striatus when growing on lignocellulosic substrates. Following heterologous expression and in vitro activation, their biochemical characterization confirmed that these enzymes are active MnPs. However, crystal structure and mutagenesis studies revealed manganese coordination spheres different from those expected after their initial classification. Specifically, a glutamine residue (Gln333) in the C-terminal tail of Ape-MnP1 was found to be involved in manganese binding, along with Asp35 and Asp177, while Cst-MnP1 counts only two amino acids (Glu36 and Asp176), instead of three, to function as a MnP. These findings led to the renaming of these subfamilies as MnP-DDQ and MnP-ED and to re-evaluate their evolutionary origin. Both enzymes were also able to directly oxidize lignin-derived phenolic compounds, as seen for other short MnPs. Importantly, size-exclusion chromatography analyses showed that both enzymes cause changes in polymeric lignin in the presence of manganese, suggesting their relevance in lignocellulose transformation. CONCLUSIONS Understanding the mechanisms used by basidiomycetes to degrade lignin is of particular relevance to comprehend carbon cycle in nature and to design biotechnological tools for the industrial use of plant biomass. Here, we provide the first structure-function characterization of two novel MnP subfamilies present in Agaricales mushrooms, elucidating the main residues involved in catalysis and demonstrating their ability to modify the lignin macromolecule.
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Affiliation(s)
- María Isabel Sánchez-Ruiz
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Elena Santillana
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Antonio Romero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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2
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Pupart H, Lukk T, Väljamäe P. Dye-decolorizing peroxidase of Thermobifida halotolerance displays complex kinetics with both substrate inhibition and apparent positive cooperativity. Arch Biochem Biophys 2024; 754:109931. [PMID: 38382807 DOI: 10.1016/j.abb.2024.109931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Dye-decolorizing peroxidases (DyPs) have been intensively investigated for the purpose of industrial dye decolourization and lignin degradation. Unfortunately, the characterization of these peroxidases is hampered by their non-Michaelis-Menten kinetics, exemplified by substrate inhibition and/or positive cooperativity. Although often observed, the underlying mechanisms behind the unusual kinetics of DyPs are poorly understood. Here we studied the kinetics of the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), hydroquinones, and anthraquinone dyes by DyP from the bacterium Thermobifida halotolerans (ThDyP) and solved its crystal structure. We also provide rate equations for different kinetic mechanisms explaining the complex kinetics of heme peroxidases. Kinetic studies along with the analysis of the structure of ThDyP suggest that the substrate inhibition is caused by the non-productive binding of ABTS to the enzyme resting state. Strong irreversible inactivation of ThDyP by H2O2 in the absence of ABTS suggests that the substrate inhibition by H2O2 may be caused by the non-productive binding of H2O2 to compound I. Positive cooperativity was observed only with the oxidation of ABTS but not with the two electron-donating substrates. Although the conventional mechanism of cooperativity cannot be excluded, we propose that the oxidation of ABTS assumes the simultaneous binding of two ABTS molecules to reduce compound I to the enzyme resting state, and this causes the apparent positive cooperativity.
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Affiliation(s)
- Hegne Pupart
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
| | - Tiit Lukk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b-202, 51010, Tartu, Estonia.
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Su X, Wang S, Wang X, Ji W, Zhang H, Tu T, Hakulinen N, Luo H, Bin Yao, Zhang W, Huang H. Targeting deoxynivalenol for degradation by a chimeric manganese peroxidase/glutathione system. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116130. [PMID: 38394761 DOI: 10.1016/j.ecoenv.2024.116130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
The manganese peroxidase (MnP) can degrade multiple mycotoxins including deoxynivalenol (DON) efficiently; however, the lignin components abundant in foods and feeds were discovered to interfere with DON catalysis. Herein, using MnP from Ceriporiopsis subvermispora (CsMnP) as a model, it was demonstrated that desired catalysis of DON, but not futile reactions with lignin, in the reaction systems containing feeds could be achieved by engineering MnP and supplementing with a boosting reactant. Specifically, two successive strategies (including the fusion of CsMnP to a DON-recognizing ScFv and identification of glutathione as a specific targeting enhancer) were combined to overcome the lignin competition, which together resulted into elevation of the degradation rate from 2.5% to as high as 82.7% in the feeds. The method to construct a targeting MnP and fortify it with an additional enhancer could be similarly applied to catalyze the many other mycotoxins with yet unknown responsive biocatalysts.
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Affiliation(s)
- Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China.
| | - Shuai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 South Zhongguancun St., Haidian District, Beijing 100081, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Wangli Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 South Zhongguancun St., Haidian District, Beijing 100081, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 South Zhongguancun St., Haidian District, Beijing 100081, China.
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China.
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Takahashi S, Hori K. Long-term continuous degradation of carbon nanotubes by a bacteria-driven Fenton reaction. Front Microbiol 2023; 14:1298323. [PMID: 38098651 PMCID: PMC10720723 DOI: 10.3389/fmicb.2023.1298323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/08/2023] [Indexed: 12/17/2023] Open
Abstract
Very few bacteria are known that can degrade carbon nanotubes (CNTs), and the only known degradation mechanism is a Fenton reaction driven by Labrys sp. WJW with siderophores, which only occurs under iron-deficient conditions. No useful information is available on the degradation rates or long-term stability and continuity of the degradation reaction although several months or more are needed for CNT degradation. In this study, we investigated long-term continuous degradation of oxidized (carboxylated) single-walled CNTs (O-SWCNTs) using bacteria of the genus Shewanella. These bacteria are widely present in the environment and can drive the Fenton reaction by alternating anaerobic-aerobic growth conditions under more general environmental conditions. We first examined the effect of O-SWCNTs on the growth of S. oneidensis MR-1, and it was revealed that O-SWCNTs promote growth up to 30 μg/mL but inhibit growth at 40 μg/mL and above. Then, S. oneidensis MR-1 was subjected to incubation cycles consisting of 21-h anaerobic and 3-h aerobic periods in the presence of 30 μg/mL O-SWCNTs and 10 mM Fe(III) citrate. We determined key factors that help prolong the bacteria-driven Fenton reaction and finally achieved long-term continuous degradation of O-SWCNTs over 90 d. By maintaining a near neutral pH and replenishing Fe(III) citrate at 60 d, a degraded fraction of 56.3% was reached. S. oneidensis MR-1 produces Fe(II) from Fe(III) citrate, a final electron acceptor for anaerobic respiration during the anaerobic period. Then, ·OH is generated through the Fenton reaction by Fe(II) and H2O2 produced by MR-1 during the aerobic period. ·OH was responsible for O-SWCNT degradation, which was inhibited by scavengers of H2O2 and ·OH. Raman spectroscopy and X-ray photoelectron spectroscopy showed that the graphitic structure in O-SWCNTs was oxidized, and electron microscopy showed that long CNT fibers initially aggregated and became short and isolated during degradation. Since Shewanella spp. and iron are ubiquitous in the environment, this study suggests that a Fenton reaction driven by this genus is applicable to the degradation of CNTs under a wide range of conditions and will help researchers develop novel methods for waste treatment and environmental bioremediation against CNTs.
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Affiliation(s)
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
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5
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Mou B, Gong G, Wu S. Biodegradation mechanisms of polycyclic aromatic hydrocarbons: Combination of instrumental analysis and theoretical calculation. CHEMOSPHERE 2023; 341:140017. [PMID: 37657699 DOI: 10.1016/j.chemosphere.2023.140017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a common class of petroleum hydrocarbons, widely encountered in both environment and industrial pollution sources. Owing to their toxicity, environmental persistence, and potential bioaccumulation properties, a mounting interest has been kindled in addressing the remediation of PAHs. Biodegradation is widely employed for the removal and remediation of PAHs due to its low cost, lack of second-contamination and ease of operation. This paper reviews the degradation efficiency of degradation and the underlying mechanisms exhibited by algae, bacteria, and fungi in remediation. Additionally, it delved into the application of modern instrumental analysis techniques and theoretical investigations in the realm of PAH degradation. Advanced instrumental analysis methods such as mass spectrometry provide a powerful tool for identifying intermediates and metabolites throughout the degradation process. Meanwhile, theoretical calculations could guide the optimization of degradation processes by revealing the reaction mechanisms and energy changes in PAH degradation. The combined use of instrumental analysis and theoretical calculations allows for a comprehensive understanding of the degradation mechanisms of PAHs and provides new insights and approaches for the development of environmental remediation technologies.
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Affiliation(s)
- Bolin Mou
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Guangyi Gong
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Shimin Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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6
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Silva EM, Milagres AMF. Production of Extracellular Enzymes by Lentinula edodes Strains in Solid-State Fermentation on Lignocellulosic Biomass Sterilized by Physical and Chemical Methods. Curr Microbiol 2023; 80:395. [PMID: 37907667 DOI: 10.1007/s00284-023-03501-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/19/2023] [Indexed: 11/02/2023]
Abstract
Two methods of sterilization of lignocellulosic biomass were performed in this study. Eucalypt waste (EW) supplemented with rice bran (RB) was added in the proportions 80:20 and 90:10 in dry weight. The compositions were sterilized by physical method (autoclaving) and by chemical method (H2O2). The production of extracellular enzymes by Lentinula edodes strains was compared within the two methods. Inactivation of catalase present in RB was achieved with 250 mM H2O2. The use of H2O2, when compared by physical method, favored high production of hydrolytic enzymes such as endoglucanase (1,600 IU/kg), twofold higher, β-glucosidase (1,000 IU/kg), fivefold higher, xylanase (55,000 IU/kg), threefold higher and β-xylosidase (225 IU/kg), similar results. Oxidative enzymes, MnP and laccase, were produced within a different profile between strains, with shorter times for laccase (2,200 IU/kg) by SJC in 45 days and MnP (2,000 IU/kg) by CCB-514 in 30 days. High production of extracellular enzymes is achieved by the use of the chemical method of sterilization of lignocellulosic biomass; in addition to no energy consumption, this process is carried out in a shorter execution time when compared to the physical process. The use of H2O2 in sterilization does not produce toxic compounds from the degradation of hemicellulose and cellulose such as furfural and hydroxy-methyl-furfural that cause inhibition of microorganisms and enzymes.
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Affiliation(s)
- Ezequiel Marcelino Silva
- Department of Biotechnology, Fundação Universidade Federal do Tocantins, Gurupi, TO, CEP 77 402 970, Brazil.
| | - Adriane Maria Ferreira Milagres
- Department of Biotechnology, Escola de Engenharia de Lorena - University of São Paulo, CP 116, Lorena, SP, CEP 12 602 810, Brazil
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7
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Kumar N, He J, Rusling JF. Electrochemical transformations catalyzed by cytochrome P450s and peroxidases. Chem Soc Rev 2023; 52:5135-5171. [PMID: 37458261 DOI: 10.1039/d3cs00461a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Cytochrome P450s (Cyt P450s) and peroxidases are enzymes featuring iron heme cofactors that have wide applicability as biocatalysts in chemical syntheses. Cyt P450s are a family of monooxygenases that oxidize fatty acids, steroids, and xenobiotics, synthesize hormones, and convert drugs and other chemicals to metabolites. Peroxidases are involved in breaking down hydrogen peroxide and can oxidize organic compounds during this process. Both heme-containing enzymes utilize active FeIVO intermediates to oxidize reactants. By incorporating these enzymes in stable thin films on electrodes, Cyt P450s and peroxidases can accept electrons from an electrode, albeit by different mechanisms, and catalyze organic transformations in a feasible and cost-effective way. This is an advantageous approach, often called bioelectrocatalysis, compared to their biological pathways in solution that require expensive biochemical reductants such as NADPH or additional enzymes to recycle NADPH for Cyt P450s. Bioelectrocatalysis also serves as an ex situ platform to investigate metabolism of drugs and bio-relevant chemicals. In this paper we review biocatalytic electrochemical reactions using Cyt P450s including C-H activation, S-oxidation, epoxidation, N-hydroxylation, and oxidative N-, and O-dealkylation; as well as reactions catalyzed by peroxidases including synthetically important oxidations of organic compounds. Design aspects of these bioelectrocatalytic reactions are presented and discussed, including enzyme film formation on electrodes, temperature, pH, solvents, and activation of the enzymes. Finally, we discuss challenges and future perspective of these two important bioelectrocatalytic systems.
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Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
| | - Jie He
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
| | - James F Rusling
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
- Department of Surgery and Neag Cancer Center, Uconn Health, Farmington, CT 06030, USA
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
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8
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Jäger C, Gregori BJ, Aho JAS, Hallamaa M, Deska J. Peroxidase-induced C-N bond formation via nitroso ene and Diels-Alder reactions. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2023; 25:3166-3174. [PMID: 37113763 PMCID: PMC10124104 DOI: 10.1039/d2gc04827b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The formation of new carbon-nitrogen bonds is indisputably one of the most important tasks in synthetic organic chemistry. Here, nitroso compounds offer a highly interesting reactivity that complements traditional amination strategies, allowing for the introduction of nitrogen functionalities via ene-type reactions or Diels-Alder cycloadditions. In this study, we highlight the potential of horseradish peroxidase as biological mediator for the generation of reactive nitroso species under environmentally benign conditions. Exploiting a non-natural peroxidase reactivity, in combination with glucose oxidase as oxygen-activating biocatalyst, aerobic activation of a broad range of N-hydroxycarbamates and hydroxamic acids is achieved. Thus both intra- and intermolecular nitroso-ene as well as nitroso-Diels-Alder reactions are performed with high efficiency. Relying on a commercial and robust enzyme system, the aqueous catalyst solution can be recycled over numerous reaction cycles without significant loss of activity. Overall, this green and scalable C-N bond-forming strategy enables the production of allylic amides and various N-heterocyclic building blocks utilizing only air and glucose as sacrificial reagents.
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Affiliation(s)
- Christina Jäger
- Department of Chemistry, University of Helsinki A.I. Virtasen aukio 1 00560 Helsinki Finland https://www.deskalab.com
| | - Bernhard J Gregori
- Department of Chemistry, University of Helsinki A.I. Virtasen aukio 1 00560 Helsinki Finland https://www.deskalab.com
- Institut für Anorganische und Angewandte Chemie Martin-Luther-King-Platz 6 20146 Hamburg Germany
| | - Juhana A S Aho
- Department of Chemistry, University of Helsinki A.I. Virtasen aukio 1 00560 Helsinki Finland https://www.deskalab.com
| | - Marleen Hallamaa
- Department of Chemistry, University of Helsinki A.I. Virtasen aukio 1 00560 Helsinki Finland https://www.deskalab.com
| | - Jan Deska
- Department of Chemistry, University of Helsinki A.I. Virtasen aukio 1 00560 Helsinki Finland https://www.deskalab.com
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Ding Y, Yuan J, Wang L, Jin N, Wang S, Li Y, Lin J. Semi-circle magnetophoretic separation under rotated magnetic field for colorimetric biosensing of Salmonella. Biosens Bioelectron 2023; 229:115230. [PMID: 36940661 DOI: 10.1016/j.bios.2023.115230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/01/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Magnetic separation was often applied to isolate and concentrate foodborne bacteria using immunomagnetic nanobeads before downstream bacterial detection. However, nanobead-bacteria conjugates (magnetic bacteria) were coexisting with excessive unbound nanobeads, limiting these nanobeads on magnetic bacteria to further act as signal probes for bacterial detection. Here, a new microfluidic magnetophoretic biosensor was elaboratively developed using a rotated high gradient magnetic field and platinum modified immunomagnetic nanobeads for continuous-flow isolation of magnetic bacteria from free nanobeads, and combined with nanozyme signal amplification for colorimetric biosensing of Salmonella. First, the platinum modified immunomagnetic nanobeads were mixed with the bacterial sample to form the magnetic bacteria, and magnetically separated to eliminate non-magnetic background. Then, the mixture of free immunomagnetic nanobeads and magnetic bacteria was injected with sheath flow (PBS) at higher flowrate into the semi-circle magnetophoretic separation channel under rotated magnetic field, which was generated by two repulsive cylindric magnets and their in-between ring iron gear, leading to continuous-flow isolation of magnetic bacteria from free immunomagnetic nanobeads because they suffered from different magnetic forces and thus had different deviating positions at the outlet. Finally, the separated magnetic bacteria and unbound magnetic nanobeads were respectively collected and used to catalyze coreless substrate into blue product, which was further analyzed using the microplate reader to obtain bacterial amount. This biosensor could determinate Salmonella as low as 41 CFU/mL in 40 min.
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Affiliation(s)
- Ying Ding
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Jing Yuan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Lei Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Nana Jin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Siyuan Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100083, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Jianhan Lin
- Key Laboratory of Smart Agriculture System Integration, Ministry of Education, China Agricultural University, Beijing, 100083, China.
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Gutierrez-Rus LI, Gamiz-Arco G, Gavira JA, Gaucher EA, Risso VA, Sanchez-Ruiz JM. Protection of catalytic cofactors by polypeptides as a driver for the emergence of primordial enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532612. [PMID: 36993774 PMCID: PMC10055001 DOI: 10.1101/2023.03.14.532612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Enzymes catalyze the chemical reactions of life. For nearly half of known enzymes, catalysis requires the binding of small molecules known as cofactors. Polypeptide-cofactor complexes likely formed at a primordial stage and became starting points for the evolution of many efficient enzymes. Yet, evolution has no foresight so the driver for the primordial complex formation is unknown. Here, we use a resurrected ancestral TIM-barrel protein to identify one potential driver. Heme binding at a flexible region of the ancestral structure yields a peroxidation catalyst with enhanced efficiency when compared to free heme. This enhancement, however, does not arise from protein-mediated promotion of catalysis. Rather, it reflects protection of bound heme from common degradation processes and a resulting longer life time and higher effective concentration for the catalyst. Protection of catalytic cofactors by polypeptides emerges as a general mechanism to enhance catalysis and may have plausibly benefited primordial polypeptide-cofactor associations.
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11
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Lukas J, Družeta I, Kühl T. Comparative studies of soluble and immobilized Fe(III) heme-peptide complexes as alternative heterogeneous biocatalysts. Biol Chem 2022; 403:1099-1105. [PMID: 36257922 DOI: 10.1515/hsz-2022-0199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Fe(III) heme is known to possess low catalytic activity when exposed to hydrogen peroxide and a reducing substrate. Efficient non-covalently linked Fe(III) heme-peptide complexes may represent suitable alternatives as a new group of green catalysts. Here, we evaluated a set of heme-peptide complexes by determination of their peroxidase-like activity and the kinetics of the catalytic conversion in both, the soluble and the immobilized state. We show the impact of peptide length on binding of the peptides to Fe(III) heme and the catalytic activity. Immobilization of the peptide onto a polymer support maintains the catalytic performance of the Fe(III) heme-peptide complex. This study thus opens up a new perspective with regard to the development of heterogeneous biocatalysts with a peroxidase-like activity.
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Affiliation(s)
- Joey Lukas
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Ivona Družeta
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
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Mohammadi SA, Najafi H, Zolgharnian S, Sharifian S, Asasian-Kolur N. Biological oxidation methods for the removal of organic and inorganic contaminants from wastewater: A comprehensive review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157026. [PMID: 35772531 DOI: 10.1016/j.scitotenv.2022.157026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/03/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Enzyme-based bioremediation is a simple, cost-effective, and environmentally friendly method for isolating and removing a wide range of environmental pollutants. This study is a comprehensive review of recent studies on the oxidation of pollutants by biological oxidation methods, performed individually or in combination with other methods. The main bio-oxidants capable of removing all types of pollutants, such as organic and inorganic molecules, from fungi, bacteria, algae, and plants, and different types of enzymes, as well as the removal mechanisms, were investigated. The use of mediators and modification methods to improve the performance of microorganisms and their resistance under harsh real wastewater conditions was discussed, and numerous case studies were presented and compared. The advantages and disadvantages of conventional and novel immobilization methods, and the development of enzyme engineering to adjust the content and properties of the desired enzymes, were also explained. The optimal operating parameters such as temperature and pH, which usually lead to the best performance, were presented. A detailed overview of the different combination processes was also given, including bio-oxidation in coincident or consecutive combination with adsorption, advanced oxidation processes, and membrane separation. One of the most important issues that this study has addressed is the removal of both organic and inorganic contaminants, taking into account the actual wastewaters and the economic aspect.
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Affiliation(s)
- Seyed Amin Mohammadi
- Fouman Faculty of Engineering, College of Engineering, University of Tehran, Fouman 43581-39115, Iran
| | - Hanieh Najafi
- Fouman Faculty of Engineering, College of Engineering, University of Tehran, Fouman 43581-39115, Iran
| | - Sheida Zolgharnian
- TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Seyedmehdi Sharifian
- Fouman Faculty of Engineering, College of Engineering, University of Tehran, Fouman 43581-39115, Iran
| | - Neda Asasian-Kolur
- Fouman Faculty of Engineering, College of Engineering, University of Tehran, Fouman 43581-39115, Iran.
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13
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Barber-Zucker S, Mateljak I, Goldsmith M, Kupervaser M, Alcalde M, Fleishman SJ. Designed High-Redox Potential Laccases Exhibit High Functional Diversity. ACS Catal 2022; 12:13164-13173. [PMID: 36366766 PMCID: PMC9638991 DOI: 10.1021/acscatal.2c03006] [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: 06/22/2022] [Revised: 09/29/2022] [Indexed: 11/29/2022]
Abstract
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White-rot fungi secrete an impressive repertoire of high-redox
potential laccases (HRPLs) and peroxidases for efficient oxidation
and utilization of lignin. Laccases are attractive enzymes for the
chemical industry due to their broad substrate range and low environmental
impact. Since expression of functional recombinant HRPLs is challenging,
however, iterative-directed evolution protocols have been applied
to improve their expression, activity, and stability. We implement
a rational, stabilize-and-diversify strategy to two HRPLs that we
could not functionally express. First, we use the PROSS stability-design
algorithm to allow functional expression in yeast. Second, we use
the stabilized enzymes as starting points for FuncLib active-site
design to improve their activity and substrate diversity. Four of
the FuncLib-designed HRPLs and their PROSS progenitor exhibit substantial
diversity in reactivity profiles against high-redox potential substrates,
including lignin monomers. Combinations of 3–4 subtle mutations
that change the polarity, solvation, and sterics of the substrate-oxidation
site result in orders of magnitude changes in reactivity profiles.
These stable and versatile HRPLs are a step toward generating an effective
lignin-degrading consortium of enzymes that can be secreted from yeast.
The stabilize-and-diversify strategy can be applied to other challenging
enzyme families to study and expand the utility of natural enzymes.
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Affiliation(s)
- Shiran Barber-Zucker
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Ivan Mateljak
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, Madrid 28049, Spain
- EvoEnzyme S.L., Parque Científico de Madrid, C/Faraday, 7, Campus de Cantoblanco, Madrid 28049, Spain
| | - Moshe Goldsmith
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Meital Kupervaser
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, Madrid 28049, Spain
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
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14
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FitzGerald LI, Olorunyomi JF, Singh R, Doherty CM. Towards Solving the PFAS Problem: The Potential Role of Metal-Organic Frameworks. CHEMSUSCHEM 2022; 15:e202201136. [PMID: 35843909 PMCID: PMC9804497 DOI: 10.1002/cssc.202201136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a group of recalcitrant molecules that have been used since the 1940s in a variety of applications. They are now linked to a host of negative health outcomes and are extremely resistant to degradation under environmental conditions. Currently, membrane technologies or adsorbents are used to remediate contaminated water. These techniques are either inefficient at capturing smaller PFAS molecules, have high energy demands, or result in concentrated waste that must be incinerated at high temperatures. This Review focuses on what role metal-organic frameworks (MOFs) may play in addressing the PFAS problem. Specifically, how the unique properties of MOFs such as their well-defined pore sizes, ultra-high internal surface area, and tunable surface chemistry may be a sustainable solution for PFAS contamination.
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Affiliation(s)
| | | | - Ruhani Singh
- CSIRO ManufacturingPrivate Bag 10Clayton South3169VictoriaAustralia
| | - Cara M. Doherty
- CSIRO ManufacturingPrivate Bag 10Clayton South3169VictoriaAustralia
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15
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Mao Z, Chen J, Wang Y, Xia J, Zhang Y, Zhang W, Zhu H, Hu X, Chen H. Copper metal organic framework as natural oxidase mimic for effective killing of Gram-negative and Gram-positive bacteria. NANOSCALE 2022; 14:9474-9484. [PMID: 35748350 DOI: 10.1039/d2nr01673g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanozymes have been widely studied as substitutes for natural enzymes. However, the delicacy of their structures and their unclear catalytic sites make it difficult to maintain their structural robustness and catalytic durability. By mimicking active catalytic sites of natural enzymes and combining them with distinct channels of metal organic frameworks (MOFs), an active copper mimetic oxidase enzyme (Cu-MOF) was designed and synthesized with good structure and clear catalytic sites for improvement in catalytic activity. The Cu-MOFs showed excellent oxidase-like activity with a low Km of 1.09 mM and exogenous ROS generation capacity. The Cu-MOFs exhibited antibacterial efficacy at a low concentration of 12.5 μg mL-1 by an oxidative stress response. These Cu-MOFs with their simple design and effective oxidase mimicking show attractive application prospects in the field of antibacterial and enzyme catalysis.
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Affiliation(s)
- Zhihui Mao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Jie Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Yindian Wang
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Junjie Xia
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Yajing Zhang
- School of Qianweichang, Shanghai University, Shanghai, 200444, China
| | - Weiwen Zhang
- School of Qianweichang, Shanghai University, Shanghai, 200444, China
| | - Han Zhu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Xiaojun Hu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
| | - Hongxia Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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16
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Alzahrani HA. Encapsulation of peroxidase on hydrogel sodium polyacrylate spheres incorporated by silver and gold nanoparticles: A comparative study. MAIN GROUP CHEMISTRY 2022. [DOI: 10.3233/mgc-220033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The selectivity of biocatalysts based on enzymes, eco-friendly reaction systems, and strong catalyst performance is exceptionally compelling. For improving enzyme recyclability and stability, a good option that has been proved is immobilization. For enzyme immobilization, hydrogel sodium polyacrylate combined with nanoparticles is an interesting class of support matrices as compared to others. This study synthesizes and uses the cross-linked hydrogel sodium polyacrylate-decorated gold or silver nanoparticles (HSP/AuNPs or AgNPs) as immobilized support for peroxidase and FTIR characterizes it. The novel supports immobilized system properties enhanced biocompatibility. They have attained a greater immobilization yield (91% with HSP/AuNPs and 84% with HSP/AgNPs). The rest of the immobilized peroxidase activity, after 10 recurring cycles of HSP/AuNPs was 61% and HSP/AgNPs was 54% . The remaining activity of the immobilized enzyme onto HSP/AgNPs, after storing at 4°C for 6 weeks, was 73% and HSP/AuNPs was 75% of its initial activity. It was revealed that the optimum temperature for the free enzyme and the immobilized enzyme was 50°C and 50–60°C, respectively. For the immobilized enzyme, the optimum pH is 7–7.5, as compared to the optimum pH of free enzyme pH 6.5.
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Affiliation(s)
- Hassan A.H. Alzahrani
- Department of Chemistry, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
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17
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Barber-Zucker S, Mindel V, Garcia-Ruiz E, Weinstein JJ, Alcalde M, Fleishman SJ. Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences. J Am Chem Soc 2022; 144:3564-3571. [PMID: 35179866 PMCID: PMC8895400 DOI: 10.1021/jacs.1c12433] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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White-rot fungi secrete a repertoire
of high-redox potential oxidoreductases
to efficiently decompose lignin. Of these enzymes, versatile peroxidases
(VPs) are the most promiscuous biocatalysts. VPs are attractive enzymes
for research and industrial use but their recombinant production is
extremely challenging. To date, only a single VP has been structurally
characterized and optimized for recombinant functional expression,
stability, and activity. Computational enzyme optimization methods
can be applied to many enzymes in parallel but they require accurate
structures. Here, we demonstrate that model structures computed by
deep-learning-based ab initio structure prediction
methods are reliable starting points for one-shot PROSS stability-design
calculations. Four designed VPs encoding as many as 43 mutations relative
to the wildtype enzymes are functionally expressed in yeast, whereas
their wildtype parents are not. Three of these designs exhibit substantial
and useful diversity in their reactivity profiles and tolerance to
environmental conditions. The reliability of the new generation of
structure predictors and design methods increases the scale and scope
of computational enzyme optimization, enabling efficient discovery
and exploitation of the functional diversity in natural enzyme families
directly from genomic databases.
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Affiliation(s)
- Shiran Barber-Zucker
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Vladimir Mindel
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Eva Garcia-Ruiz
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, Madrid 28094, Spain
| | - Jonathan J Weinstein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, Madrid 28094, Spain
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7600001, Israel
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18
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González-Rodríguez S, Lu-Chau TA, Trueba-Santiso A, Eibes G, Moreira MT. Bundling the removal of emerging contaminants with the production of ligninolytic enzymes from residual streams. Appl Microbiol Biotechnol 2022; 106:1299-1311. [PMID: 35075520 PMCID: PMC8816780 DOI: 10.1007/s00253-022-11776-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/09/2021] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
Abstract Enzymes offer interesting features as biological catalysts for industry: high specificity, activity under mild conditions, accessibility, and environmental friendliness. Being able to produce enzymes in large quantities and having them available in a stable and reusable form reduces the production costs of any enzyme-based process. Agricultural residues have recently demonstrated their potential as substrates to produce ligninolytic enzymes by different white rot fungi. In this study, the biotechnological production of a manganese peroxidase (MnP) by Irpex lacteus was conducted through solid-state fermentation (SSF) with wheat straw as substrate and submerged fermentation (SmF) employing wheat straw extract (WSE). The obtained enzyme cocktail also showed manganese-independent activity (MiP), related to the presence of a short MnP and a dye-decolorizing peroxidase (DyP) which was confirmed by shotgun proteomic analyses. In view of the enhanced production of ligninolytic enzymes in SmF, different parameters such as WSE concentration and nitrogen source were evaluated. The highest enzyme titers were obtained with a medium formulated with glucose and peptone (339 U/L MnP and 15 U/L MiP). The scale-up to a 30 L reactor achieved similar activities, demonstrating the feasibility of enzyme production from the residual substrate at different production scales. Degradation of five emerging pollutants was performed to demonstrate the high oxidative capacity of the enzyme. Complete removal of hormones and bisphenol A was achieved in less than 1 h, whereas almost 30% degradation of carbamazepine was achieved in 24 h, which is a significant improvement compared to previous enzymatic treatments of this compound. Key points • Wheat straw extract is suitable for the growth of I. lacteus. • The enzyme cocktail obtained allows the degradation of emerging contaminants. • Mn-dependent and Mn-independent activities increases the catalytic potential. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11776-7.
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19
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Li K, Yang Q, Zhang P, Zhang W. Research Progress of Peroxygenase-Catalyzed Reactions Driven by in-situ Generation of H 2 O 2. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Valle-Altamirano RG, Baratto MC, Badillo-Ramírez I, Gasteazoro F, Pogni R, Saniger JM, Valderrama B. Identification of Fe( iii)–OH species as a catalytic intermediate in plant peroxidases at high H 2O 2 concentration. NEW J CHEM 2022. [DOI: 10.1039/d1nj04837f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The structure for compound III formed after exposure of plant heme peroxidases to excess H2O2 seems to be a hydroxylated form, providing new evidence for understanding the structural basis of the substrate-induced suicidal behavior of these enzymes.
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Affiliation(s)
- Rodolfo G. Valle-Altamirano
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Maria Camilla Baratto
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Francisco Gasteazoro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
| | - Rebecca Pogni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro, 53100 Siena, Italy
| | - José M. Saniger
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Brenda Valderrama
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 62210 Morelos, Mexico
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21
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Adeoye RI, Okaiyeto K, Oguntibeju OO. Global mapping of research outputs on nanoparticles with peroxidase mimetic activity from 2010–2019. INORG NANO-MET CHEM 2021. [DOI: 10.1080/24701556.2021.2020841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Raphael Idowu Adeoye
- Enzymology and Drug Design Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria
| | - Kunle Okaiyeto
- Phytomedicine and Phytochemistry Group, Oxidative Stress Research Centre, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Oluwafemi Omoniyi Oguntibeju
- Phytomedicine and Phytochemistry Group, Oxidative Stress Research Centre, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
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22
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Characterization of Two Hydrogen Peroxide Resistant Peroxidases from Rhodococcus opacus 1CP. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11177941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dye-decolorizing peroxidases (DyP) are a family of heme-dependent enzymes present on a broad spectrum of microorganisms. While the natural function of these enzymes is not fully understood, their capacity to degrade highly contaminant pigments such as azo dyes or anthraquinones make them excellent candidates for applications in bioremediation and organic synthesis. In this work, two novel DyP peroxidases from the organism Rhodococcus opacus 1CP (DypA and DypB) were cloned and expressed in Escherichia coli. The enzymes were purified and biochemically characterized. The activities of the two DyPs via 2,2′-azino-bis [3-ethylbenzthiazoline-6-sulphonic acid] (ABTS) assay and against Reactive Blue 5 were assessed and optimized. Results showed varying trends for DypA and DypB. Remarkably, these enzymes presented a particularly high tolerance towards H2O2, retaining its activities at about 10 mM H2O2 for DypA and about 4.9 mM H2O2 for DypB.
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23
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Ether Oxidation by an Evolved Fungal Heme-Peroxygenase: Insights into Substrate Recognition and Reactivity. J Fungi (Basel) 2021; 7:jof7080608. [PMID: 34436147 PMCID: PMC8396878 DOI: 10.3390/jof7080608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
Ethers can be found in the environment as structural, active or even pollutant molecules, although their degradation is not efficient under environmental conditions. Fungal unspecific heme-peroxygenases (UPO were reported to degrade low-molecular-weight ethers through an H2O2-dependent oxidative cleavage mechanism. Here, we report the oxidation of a series of structurally related aromatic ethers, catalyzed by a laboratory-evolved UPO (PaDa-I) aimed at elucidating the factors influencing this unusual biochemical reaction. Although some of the studied ethers were substrates of the enzyme, they were not efficiently transformed and, as a consequence, secondary reactions (such as the dismutation of H2O2 through catalase-like activity and suicide enzyme inactivation) became significant, affecting the oxidation efficiency. The set of reactions that compete during UPO-catalyzed ether oxidation were identified and quantified, in order to find favorable conditions that promote ether oxidation over the secondary reactions.
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24
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Yang N, Tian Y, Zhang M, Peng X, Li F, Li J, Li Y, Fan B, Wang F, Song H. Photocatalyst-enzyme hybrid systems for light-driven biotransformation. Biotechnol Adv 2021; 54:107808. [PMID: 34324993 DOI: 10.1016/j.biotechadv.2021.107808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/26/2021] [Accepted: 07/21/2021] [Indexed: 11/02/2022]
Abstract
Enzymes catalyse target reactions under mild conditions with high efficiency, as well as excellent regional-, stereo-, and enantiomeric selectivity. Photocatalysis utilises sustainable and environment-friendly light power to realise efficient chemical conversion. By combining the interdisciplinary advantages of photo- and enzymatic catalysis, the photocatalyst-enzyme hybrid systems have proceeded various light-driven biotransformation with high efficiency under environmentally benign conditions, thus, attracting unparalleled focus during the last decades. It has also been regarded as a promising pathway towards green chemistry utilising ubiquitous solar energy. This systematic review gives insight into this research field by classifying the existing photocatalyst-enzyme hybrid systems into three sections based on different hybridizing modes between photo- and enzymatic catalysis. Furthermore, existing challenges and proposed strategies are discussed within this context. The first system summarised is the cofactor-mediated hybrid system, in which natural/artificial cofactors act as reducing equivalents that connect photocatalysts with enzymes for light-driven enzymatic biotransformation. Second, the direct contact-based photocatalyst-enzyme hybrid systems are described, including two different kinds of electron exchange sites on the enzyme molecules. Third, some cases where photocatalysts and enzymes are integrated into a reaction cascade with specific intermediates will be discussed in the following chapter. Finally, we provide perspective concerning the future of this field.
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Affiliation(s)
- Nan Yang
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Yao Tian
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Mai Zhang
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Xiting Peng
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Feng Li
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Jianxun Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Yi Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Bei Fan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
| | - Fengzhong Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China.
| | - Hao Song
- Frontier Science Centre for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China.
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25
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Xia Y, Wu Z, He R, Gao Y, Qiu Y, Cheng Q, Ma X, Wang Z. Simultaneous degradation of two mycotoxins enabled by a fusion enzyme in food-grade recombinant Kluyveromyces lactis. BIORESOUR BIOPROCESS 2021; 8:62. [PMID: 38650290 PMCID: PMC10991947 DOI: 10.1186/s40643-021-00395-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
Aflatoxin B1 (AFB1) and zearalenone (ZEN) are two predominant mycotoxins ubiquitously found in corn, peanuts, and other grains, which pose a great threat to human health. Therefore, safe and effective methods for detoxification of these mycotoxins are urgently needed. To achieve simultaneous degradation of multiple mycotoxins, a fusion enzyme ZPF1 was constructed by linking zearalenone hydrolase and manganese peroxidase with a linker peptide GGGGS. This fusion enzyme was secretory expressed successfully in the newly constructed food-grade recombinant strain Kluyveromyces lactis GG799(pKLAC1-ZPF1), and was investigated with the mycotoxins degradation efficiency in two reaction systems. Results showed that both AFB1 and ZEN can be degraded by ZPF1 in reaction system 1 (70.0 mmol/L malonic buffer with 1.0 mmol/L MnSO4, 0.1 mmol/L H2O2, 5.0 µg/mL AFB1 and ZEN, respectively) with the ratios of 46.46% and 38.76%, respectively. In reaction system 2 (50.0 mmol/L Tris-HCl, with 5.0 µg/mL AFB1 and ZEN, respectively), AFB1 cannot be degraded while ZEN can be degraded with the ratio of 35.38%. To improve the degradation efficiency of these mycotoxins, optimization of the induction and degradation conditions were fulfilled subsequently. The degradation ratios of AFB1 and ZEN by ZPF1 in reaction system 1 reached 64.11% ± 2.93% and 46.21% ± 3.17%, respectively. While in reaction system 2, ZEN was degraded by ZPF1 at a ratio of 41.45% ± 3.34%. The increases of degradation ratios for AFB1 and ZEN in reaction system 1 were 17.65% and 7.45%, respectively, while that for ZEN in reaction system 2 was 6.07%, compared with the unoptimized results.
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Affiliation(s)
- Yu Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, 214122, China.
| | - Zifeng Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Rui He
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yahui Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yangyu Qiu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Qianqian Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, 214122, China
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26
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Kinner A, Rosenthal K, Lütz S. Identification and Expression of New Unspecific Peroxygenases - Recent Advances, Challenges and Opportunities. Front Bioeng Biotechnol 2021; 9:705630. [PMID: 34307325 PMCID: PMC8293615 DOI: 10.3389/fbioe.2021.705630] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
In 2004, the fungal heme-thiolate enzyme subfamily of unspecific peroxygenases (UPOs) was first described in the basidiomycete Agrocybe aegerita. As UPOs naturally catalyze a broad range of oxidative transformations by using hydrogen peroxide as electron acceptor and thus possess a great application potential, they have been extensively studied in recent years. However, despite their versatility to catalyze challenging selective oxyfunctionalizations, the availability of UPOs for potential biotechnological applications is restricted. Particularly limiting are the identification of novel natural biocatalysts, their production, and the description of their properties. It is hence of great interest to further characterize the enzyme subfamily as well as to identify promising new candidates. Therefore, this review provides an overview of the state of the art in identification, expression, and screening approaches of fungal UPOs, challenges associated with current protein production and screening strategies, as well as potential solutions and opportunities.
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Affiliation(s)
- Alina Kinner
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
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Bideh NZ, Mashhadi N, Taylor KE, Biswas N. Elimination of selected heterocyclic aromatic emerging contaminants from water using soybean peroxidase. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:37570-37579. [PMID: 33715130 DOI: 10.1007/s11356-021-13403-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Widespread occurrence of various heterocyclic aromatic compounds is reported in concentrations from 1 to 20 μg/L in surface and groundwater as well as influents and effluents of wastewater treatment plants around the world. These so-called emerging contaminants and their metabolites can cause adverse effects on the environment and humans, even at very low concentration, hence raised environmental concerns. In this study, feasibility of soybean peroxidase-catalyzed removal of three selected heterocyclic aromatics from water was investigated, including sensitivity to the most important operational conditions, pH (range 3.6-9.0), H2O2 concentration (range 0.10-1.50 mM), and enzyme activity (range 0.001-5.0 U/mL). 3-Hydroxycoumarin and 2-aminobenzoxaozle were found to be substrates for the enzyme, having ≥95% and 45% removal efficiency with most effective pHs of 7.0 and 6.0, respectively. Time course study was also conducted to determine the initial first-order rate constants and half-lives; half-lives normalized for enzyme activity (0.0257 and 452 min for the respective substrates) are compared with those of 21 other compounds reactive with soybean peroxidase. High-resolution mass spectrometry was employed to characterize the plausible oligomerization products of enzymatic treatment, which revealed formation of dimers and trimers of the two substrates.
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Affiliation(s)
- Negin Ziayee Bideh
- Department of Civil and Environmental Engineering, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - Neda Mashhadi
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
| | - Keith E Taylor
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada.
| | - Nihar Biswas
- Department of Civil and Environmental Engineering, University of Windsor, 401 Sunset Avenue, Windsor, ON, N9B 3P4, Canada
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Pandey AK, Gaur VK, Udayan A, Varjani S, Kim SH, Wong JWC. Biocatalytic remediation of industrial pollutants for environmental sustainability: Research needs and opportunities. CHEMOSPHERE 2021; 272:129936. [PMID: 35534980 DOI: 10.1016/j.chemosphere.2021.129936] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/24/2021] [Accepted: 02/06/2021] [Indexed: 06/14/2023]
Abstract
An increasing quantum of pollutants from various industrial sector activities represents a severe menace to environmental & ecological balance. Bioremediation is gaining flow globally due to its cost-effective and environment-friendly nature. Understanding biodegradation mechanisms is of high ecological significance. Application of microbial enzymes has been reported as sustainable approach to mitigate the pollution. Immobilized enzyme catalyzed transformations are getting accelerated attention as potential alternatives to physical and chemical methods. The attention is now also focused on developing novel protein engineering strategies and bioreactor design systems to ameliorate overall biocatalysis and waste treatment further. This paper presents and discusses the most advanced and state of the art scientific & technical developments about biocatalytic remediation of industrial pollutants. It also covers various biocatalysts and the associated sustainable technologies to remediate various pollutants from waste streams. Enzyme production and immobilization in bioreactors have also been discussed. This paper also covers challenges and future research directions in this field.
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Affiliation(s)
| | - Vivek K Gaur
- CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Aswathy Udayan
- CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, 695 019, India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, 382010, Gujarat, India.
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jonathan W C Wong
- Institute of Bioresource and Agriculture, Hong Kong Baptist University, Hong Kong
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29
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Mechanism of action, sources, and application of peroxidases. Food Res Int 2021; 143:110266. [PMID: 33992367 DOI: 10.1016/j.foodres.2021.110266] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/28/2021] [Accepted: 02/21/2021] [Indexed: 02/06/2023]
Abstract
Peroxidase is an enzyme in the group of oxidoreductases that is widely distributed in nature. It can catalyze the oxidation of various organic and inorganic substrates by reacting with hydrogen peroxide and similar molecules. Due to its wide catalytic activity, peroxidases can act in the removal of both phenolic compounds and peroxides, in chemical synthesis and, according to recent studies, in mycotoxin degradation. Therefore, this study aimed at introducing an overview of the mechanism of peroxidase action, extraction sources, mycotoxin degradation capacity and other potential applications in the food industry.
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Characterization of a Dye-Decolorizing Peroxidase from Irpex lacteus Expressed in Escherichia coli: An Enzyme with Wide Substrate Specificity Able to Transform Lignosulfonates. J Fungi (Basel) 2021; 7:jof7050325. [PMID: 33922393 PMCID: PMC8145141 DOI: 10.3390/jof7050325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
A dye-decolorizing peroxidase (DyP) from Irpex lacteus was cloned and heterologously expressed as inclusion bodies in Escherichia coli. The protein was purified in one chromatographic step after its in vitro activation. It was active on ABTS, 2,6-dimethoxyphenol (DMP), and anthraquinoid and azo dyes as reported for other fungal DyPs, but it was also able to oxidize Mn2+ (as manganese peroxidases and versatile peroxidases) and veratryl alcohol (VA) (as lignin peroxidases and versatile peroxidases). This corroborated that I. lacteus DyPs are the only enzymes able to oxidize high redox potential dyes, VA and Mn+2. Phylogenetic analysis grouped this enzyme with other type D-DyPs from basidiomycetes. In addition to its interest for dye decolorization, the results of the transformation of softwood and hardwood lignosulfonates suggest a putative biological role of this enzyme in the degradation of phenolic lignin.
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Ben Ayed A, Saint-Genis G, Vallon L, Linde D, Turbé-Doan A, Haon M, Daou M, Bertrand E, Faulds CB, Sciara G, Adamo M, Marmeisse R, Comtet-Marre S, Peyret P, Abrouk D, Ruiz-Dueñas FJ, Marchand C, Hugoni M, Luis P, Mechichi T, Record E. Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts. J Fungi (Basel) 2021; 7:jof7050321. [PMID: 33919051 PMCID: PMC8143184 DOI: 10.3390/jof7050321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 01/21/2023] Open
Abstract
The functional diversity of the New Caledonian mangrove sediments was examined, observing the distribution of fungal dye-decolorizing peroxidases (DyPs), together with the complete biochemical characterization of the main DyP. Using a functional metabarcoding approach, the diversity of expressed genes encoding fungal DyPs was investigated in surface and deeper sediments, collected beneath either Avicennia marina or Rhizophora stylosa trees, during either the wet or the dry seasons. The highest DyP diversity was observed in surface sediments beneath the R. stylosa area during the wet season, and one particular operational functional unit (OFU1) was detected as the most abundant DyP isoform. This OFU was found in all sediment samples, representing 51–100% of the total DyP-encoding sequences in 70% of the samples. The complete cDNA sequence corresponding to this abundant DyP (OFU 1) was retrieved by gene capture, cloned, and heterologously expressed in Pichia pastoris. The recombinant enzyme, called DyP1, was purified and characterized, leading to the description of its physical–chemical properties, its ability to oxidize diverse phenolic substrates, and its potential to decolorize textile dyes; DyP1 was more active at low pH, though moderately stable over a wide pH range. The enzyme was very stable at temperatures up to 50 °C, retaining 60% activity after 180 min incubation. Its ability to decolorize industrial dyes was also tested on Reactive Blue 19, Acid Black, Disperse Blue 79, and Reactive Black 5. The effect of hydrogen peroxide and sea salt on DyP1 activity was studied and compared to what is reported for previously characterized enzymes from terrestrial and marine-derived fungi.
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Affiliation(s)
- Amal Ben Ayed
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Geoffroy Saint-Genis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Laurent Vallon
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Annick Turbé-Doan
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Mireille Haon
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Marianne Daou
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Department of Chemistry, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Emmanuel Bertrand
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Craig B. Faulds
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Giuliano Sciara
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Martino Adamo
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Roland Marmeisse
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Cyril Marchand
- IMPMC, Institut de Recherche Pour le Développement (IRD), UPMC, CNRS, MNHN, 98851 Noumea, France;
- ISEA, EA, Université de la Nouvelle-Calédonie (UNC), 3325, BP R4, 98851 Noumea, France
| | - Mylène Hugoni
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Patricia Luis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Tahar Mechichi
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Eric Record
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Correspondence:
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Liao HX, Jia HY, Dai JR, Zong MH, Li N. Bioinspired Cooperative Photobiocatalytic Regeneration of Oxidized Nicotinamide Cofactors for Catalytic Oxidations. CHEMSUSCHEM 2021; 14:1687-1691. [PMID: 33559949 DOI: 10.1002/cssc.202100184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Inspired by water-forming NAD(P)H oxidases, a cooperative photobiocatalytic system has been designed to aerobically regenerate the oxidized nicotinamide cofactors. Photocatalysts enable NAD(P)H oxidation with O2 under visible-light irradiation, producing H2 O2 as a byproduct, which is subsequently used as an oxidant by the horseradish peroxidase mediator system (PMS) to oxidize NAD(P)H. The photobiocatalytic system shows a turnover frequency of 8800 min-1 in the oxidation of NAD(P)H. Photobiocatalytic NAD(P)H oxidation proceeds smoothly at pH 6-9. In addition to natural NAD(P)H, synthetic biomimetics are also good substrates for this regeneration system. Total turnover numbers of up to 180000 are obtained for the cofactor when the photobiocatalytic regeneration system is coupled with dehydrogenase-catalyzed oxidations. It may be a promising protocol to recycle the oxidized cofactors for catalytic oxidations.
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Affiliation(s)
- Huan-Xin Liao
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P. R. China
| | - Hao-Yu Jia
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P. R. China
| | - Jian-Rong Dai
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P. R. China
| | - Min-Hua Zong
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P. R. China
| | - Ning Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, P. R. China
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The steadfast Au@Pt soldier: Peroxide-tolerant nanozyme for signal enhancement in lateral flow immunoassay of peroxidase-containing samples. Talanta 2021; 225:121961. [DOI: 10.1016/j.talanta.2020.121961] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 02/05/2023]
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Tomášková N, Novák P, Kožár T, Petrenčáková M, Jancura D, Yassaghi G, Man P, Sedlák E. Early modification of cytochrome c by hydrogen peroxide triggers its fast degradation. Int J Biol Macromol 2021; 174:413-423. [PMID: 33529629 DOI: 10.1016/j.ijbiomac.2021.01.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/16/2022]
Abstract
Cytochrome c (cyt c), in addition to its function as an electron shuttle in respiratory chain, is able to perform as a pseudo-peroxidase with a critical role during apoptosis. Incubation of cyt c with an excess of hydrogen peroxide leads to a suicide inactivation of the protein, which is accompanied by heme destruction and covalent modification of numerous amino acid residues. Although steady-state reactions of cyt c with an excess of hydrogen peroxide represent non-physiological conditions, they might be used for analysis of the first-modified amino acid in in vivo. Here, we observed oxidation of tyrosine residues 67 and 74 and heme as the first modifications found upon incubation with hydrogen peroxide. The positions of the oxidized tyrosines suggest a possible migration pathway of hydrogen peroxide-induced radicals from the site of heme localization to the protein surface. Analysis of a size of folded fraction of cyt c upon limited incubation with hydrogen peroxide indicates that the early oxidation of amino acids triggers an accelerated destruction of cyt c. Position of channels from molecular dynamics simulation structures of cyt c points to a location of amino acid residues exposed to reactive oxidants that are thus more prone to covalent modification.
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Affiliation(s)
- Nataša Tomášková
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Petr Novák
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Martina Petrenčáková
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Daniel Jancura
- Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Ghazaleh Yassaghi
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Man
- Institute of Microbiology - BioCeV, Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Erik Sedlák
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia.
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Li F, Shao R, Mao Y, Yu W, Yu H. Enzyme Cascade Reaction Involving Lytic Polysaccharide Monooxygenase and Dye-Decolorizing Peroxidase for Chitosan Functionalization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1049-1056. [PMID: 33428421 DOI: 10.1021/acs.jafc.0c06856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In situ H2O2 generation systems are efficient for H2O2-dependent biocatalytic oxidation reactions. Here, we report that lytic polysaccharide monooxygenases (LPMOs), copper-dependent polysaccharide monooxygenases, can efficiently supply H2O2 in situ to dye-decolorizing peroxidases (DyPs) using substrate gallic acid (GA) for chitosan functionalization. The maximum grafting ratio induced by the cascade reaction was significantly higher than that achieved by a reaction with initial exogenous H2O2. The maximum grafting ratio was obtained with 12 g/L GA, 5.6 mg/L DyP, 20-30 mg/L LPMO, and pH 4.5-5.0. UV-vis, Fourier transform infrared (FT-IR), and nuclear magnetic resonance (1H NMR) spectroscopy confirmed GA grafting onto chitosan. X-ray diffraction (XRD) analysis and thermogravimetric analysis (TGA) indicated that GA-chitosan conjugates had lower thermal stability and crystallinity than chitosan. The GA-chitosan conjugates had significantly higher antioxidant activity than chitosan. This study supplies a green and high-efficiency approach to achieve an enzymatic cascade reaction for chitosan functionalization and has potential applications in H2O2-dependent biocatalytic oxidation reactions.
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Affiliation(s)
- Fei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Ruijian Shao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Yingzheng Mao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Wen Yu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P. R. China
| | - Hongbo Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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Abstract
A biocatalytic cascade system using a cocktail of oxidoreductase enzymes (2-1B peroxidase and M120 laccase) was designed for the allylic oxidation of (+)-α-pinene into value-added products (e.g., verbenol and verbenone). The oxidative transformation involved a two-step process as follows: (+)-α-pinene was (i) oxidized on the allylic position with H2O2 mainly assisted by 2-1B peroxidase leading to verbenol as the principal reaction product, and (ii) directed to verbenone in the presence of M120 laccase responsible for further oxidation of verbenol to verbenone. The reaction environment was ensured by the acetate buffer (0.1 M, pH = 5). Optimum values for the experimental parameters (e.g., concentration of 2-1B peroxidase, M120 laccase, and H2O2) were set up. The biocatalytic cascade process was monitored for 24 h in order to evaluate the process pathway. Maximum performance under optimum conditions was reached after 5 h incubation time (e.g., 80% (+)-α-pinene conversion and 70% yield in verbenol). Therefore, the developed biocatalytic cascade system offered promising perspectives for (+)-α-pinene valorization.
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Vinnik V, Zhang F, Park H, Cook TB, Throckmorton K, Pfleger BF, Bugni TS, Thomas MG. Structural and Biosynthetic Analysis of the Fabrubactins, Unusual Siderophores from Agrobacterium fabrum Strain C58. ACS Chem Biol 2021; 16:125-135. [PMID: 33373180 DOI: 10.1021/acschembio.0c00809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Siderophores are iron-chelating molecules produced by microorganisms and plants to acquire exogenous iron. Siderophore biosynthetic enzymology often produces elaborate and unique molecules through unusual reactions to enable specific recognition by the producing organisms. Herein, we report the structure of two siderophore analogs from Agrobacterium fabrum strain C58, which we named fabrubactin (FBN) A and FBN B. Additionally, we characterized the substrate specificities of the NRPS and PKS components. The structures suggest unique Favorskii-like rearrangements of the molecular backbone that we propose are catalyzed by the flavin-dependent monooxygenase, FbnE. FBN A and B contain a 1,1-dimethyl-3-amino-1,2,3,4-tetrahydro-7,8-dihydroxy-quinolin (Dmaq) moiety previously seen only in the anachelin cyanobacterial siderophores. We provide evidence that Dmaq is derived from l-DOPA and propose a mechanism for the formation of the mature Dmaq moiety. Our bioinformatic analyses suggest that FBN A and B and the anachelins belong to a large and diverse siderophore family widespread throughout the Rhizobium/Agrobacterium group, α-proteobacteria, and cyanobacteria.
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Affiliation(s)
- Vladimir Vinnik
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Fan Zhang
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Hyunjun Park
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- CATALOG, Boston, Massachusetts 02129, United States
| | - Taylor B. Cook
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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38
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Naveen Prasad S, Weerathunge P, Karim MN, Anderson S, Hashmi S, Mariathomas PD, Bansal V, Ramanathan R. Non-invasive detection of glucose in human urine using a color-generating copper NanoZyme. Anal Bioanal Chem 2021; 413:1279-1291. [PMID: 33399880 DOI: 10.1007/s00216-020-03090-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/13/2020] [Accepted: 11/23/2020] [Indexed: 01/06/2023]
Abstract
Renal complications are long-term effect of diabetes mellitus where glucose is excreted in urine. Therefore, reliable glucose detection in urine is critical. While commercial urine strips offer a simple way to detect urine sugar, poor sensitivity and low reliability limit their use. A hybrid glucose oxidase (GOx)/horseradish peroxidase (HRP) assay remains the gold standard for pathological detection of glucose. A key restriction is poor stability of HRP and its suicidal inactivation by hydrogen peroxide, a key intermediate of the GOx-driven reaction. An alternative is to replace HRP with a robust inorganic enzyme-mimic or NanoZyme. While colloidal NanoZymes show promise in glucose sensing, they detect low concentrations of glucose, while urine has high (mM) glucose concentration. In this study, a free-standing copper NanoZyme is used for the colorimetric detection of glucose in human urine. The sensor could operate in a biologically relevant dynamic linear range of 0.5-15 mM, while showing minimal sample matrix effect such that glucose could be detected in urine without significant sample processing or dilution. This ability could be attributed to the Cu NanoZyme that for the first time showed an ability to promote the oxidation of a TMB substrate to its double oxidation diimine product rather than the charge-transfer complex product commonly observed. Additionally, the sensor could operate at a single pH without the need to use different pH conditions as used during the gold standard assay. These outcomes outline the high robustness of the NanoZyme sensing system for direct detection of glucose in human urine. Graphical abstract.
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Affiliation(s)
- Sanjana Naveen Prasad
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia
| | - Pabudi Weerathunge
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia
| | - Md Nurul Karim
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia
| | - Samuel Anderson
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia
| | - Sabeen Hashmi
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia
| | - Pyria D Mariathomas
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia
| | - Vipul Bansal
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia.
| | - Rajesh Ramanathan
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory (NBRL), School of Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3000, Australia.
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39
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Ton TP, Nguyen VT, Doan P, Nguyen DT, Nguyen TP, Huynh CK, Ngo TCQ, Dang LH, Tran NQ. Hematin-conjugated gelatin as an effective catalyst for preparing biological hydrogels. NEW J CHEM 2021. [DOI: 10.1039/d1nj01426a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of Ge–He provides feasible strategies for mimicking HRP enzyme to fabricate biomedical hydrogels.
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Affiliation(s)
- Tan Phuoc Ton
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, HCMC, Vietnam
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, HCMC, Vietnam
| | - Van Toan Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, HCMC, Vietnam
- Institute of Fundamental and Applied Sciences, Duy Tan University, HCMC 700000, Vietnam
| | - Phuong Doan
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, HCMC, Vietnam
| | - Dinh Trung Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, HCMC, Vietnam
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, HCMC, Vietnam
| | - Thi Phuong Nguyen
- Faculty of Chemical Technology, HCMC University of Food Industry, HCMC, Vietnam
| | - Chan Khon Huynh
- Department of Biomedical Engineering, International University, Vietnam National University - HCMC, HCMC, Vietnam
| | - Thi Cam Quyen Ngo
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, HCMC, Vietnam
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, HCMC, Vietnam
| | - Le Hang Dang
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, HCMC, Vietnam
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, HCMC, Vietnam
| | - Ngoc Quyen Tran
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, HCMC, Vietnam
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40
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Zhang W, Liu H, van Schie MMCH, Hagedoorn PL, Alcalde M, Denkova AG, Djanashvili K, Hollmann F. Nuclear Waste and Biocatalysis: A Sustainable Liaison? ACS Catal 2020; 10:14195-14200. [PMID: 33312749 PMCID: PMC7723303 DOI: 10.1021/acscatal.0c03059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/27/2020] [Indexed: 12/14/2022]
Abstract
![]()
It
is well-known that energy-rich radiation induces water splitting,
eventually yielding hydrogen peroxide. Synthetic applications, however,
are scarce and to the best of our knowledge, the combination of radioactivity
with enzyme-catalysis has not been considered yet. Peroxygenases utilize
H2O2 as an oxidant to promote highly selective
oxyfunctionalization reactions but are also irreversibly inactivated
in the presence of too high H2O2 concentrations.
Therefore, there is a need for efficient in situ H2O2 generation methods. Here, we show that radiolytic water splitting
can be used to promote specific biocatalytic oxyfunctionalization
reactions. Parameters influencing the efficiency of the reaction and
current limitations are shown. Particularly, oxidative inactivation
of the biocatalyst by hydroxyl radicals influences the robustness
of the overall reaction. Radical scavengers can alleviate this issue,
but eventually, physical separation of the enzymes from the ionizing
radiation will be necessary to achieve robust reaction schemes. We
demonstrate that nuclear waste can also be used to drive selective,
peroxygenase-catalyzed oxyfunctionalization reactions, challenging
our view on nuclear waste in terms of sustainability.
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Affiliation(s)
- Wuyuan Zhang
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, 300308 Tianjin, China
| | - Huanhuan Liu
- Radiation Science and Technology, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - Morten M. C. H. van Schie
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain
| | - Antonia G. Denkova
- Radiation Science and Technology, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
| | - Kristina Djanashvili
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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41
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El-Shishtawy RM, Aldhahri M, Almulaiky YQ. Dual immobilization of α-amylase and horseradish peroxidase via electrospinning: A proof of concept study. Int J Biol Macromol 2020; 163:1353-1360. [DOI: 10.1016/j.ijbiomac.2020.07.278] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/09/2020] [Accepted: 07/19/2020] [Indexed: 11/25/2022]
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42
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Wang Z, Jian Y, Han Y, Fu Z, Lu D, Wu J, Liu Z. Recent progress in enzymatic functionalization of carbon-hydrogen bonds for the green synthesis of chemicals. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Current state and future perspectives of engineered and artificial peroxygenases for the oxyfunctionalization of organic molecules. Nat Catal 2020. [DOI: 10.1038/s41929-020-00507-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Musengi A, Durrell K, Prins A, Khan N, Agunbiade M, Kudanga T, Kirby-McCullough B, Pletschke BI, Burton SG, Le Roes-Hill M. Production and characterisation of a novel actinobacterial DyP-type peroxidase and its application in coupling of phenolic monomers. Enzyme Microb Technol 2020; 141:109654. [PMID: 33051013 DOI: 10.1016/j.enzmictec.2020.109654] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
The extracellular peroxidase from Streptomyces albidoflavus BSII#1 was purified to near homogeneity using sequential steps of acid and acetone precipitation, followed by ultrafiltration. The purified peroxidase was characterised and tested for the ability to catalyse coupling reactions between selected phenolic monomer pairs. A 46-fold purification of the peroxidase was achieved, and it was shown to be a 46 kDa haem peroxidase. Unlike other actinobacteria-derived peroxidases, it was only inhibited (27 % inhibition) by relatively high concentrations of sodium azide (5 mM) and was capable of oxidising eleven (2,4-dichlorophenol, 2,6-dimethoxyphenol, 4-tert-butylcatechol, ABTS, caffeic acid, catechol, guaiacol, l-DOPA, o-aminophenol, phenol, pyrogallol) of the seventeen substrates tested. The peroxidase remained stable at temperatures of up to 80 °C for 60 min and retained >50 % activity after 24 h between pH 5.0-9.0, but was most sensitive to incubation with hydrogen peroxide (H2O2; 0.01 mM), l-cysteine (0.02 mM) and ascorbate (0.05 mM) for one hour. It was significantly inhibited by all organic solvents tested (p ≤ 0.05). The Km and Vmax values of the partially purified peroxidase with the substrate 2,4-DCP were 0.95 mM and 0.12 mmol min-1, respectively. The dyes reactive blue 4, reactive black 5, and Azure B, were all decolourised to a certain extent: approximately 30 % decolourisation was observed after 24 h (1 μM dye). The peroxidase successfully catalysed coupling reactions between several phenolic monomer pairs including catechin-caffeic acid, catechin-catechol, catechin-guaiacol and guaiacol-syringaldazine under the non-optimised conditions used in this study. Genome sequencing confirmed the identity of strain BSII#1 as a S. albidoflavus strain. In addition, the genome sequence revealed the presence of one peroxidase gene that includes the twin arginine translocation signal sequence of extracellular proteins. Functional studies confirmed that the peroxidase produced by S. albidoflavus BSII#1 is part of the dye-decolourising peroxidase (DyP-type) family.
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Affiliation(s)
- Amos Musengi
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa; Biotechnology Department, Harare Institute of Technology, P. O. Box BE 277, Belvedere, Harare, Zimbabwe
| | - Kim Durrell
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Alaric Prins
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa; Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Nuraan Khan
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Mayowa Agunbiade
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Tukayi Kudanga
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa; Department of Biotechnology and Food Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Bronwyn Kirby-McCullough
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Brett I Pletschke
- Department of Biochemistry and Microbiology, Rhodes University, PO Box 94, Makhanda (Grahamstown), 6140, South Africa
| | - Stephanie G Burton
- Vice-Principal: Research and Postgraduate Education and Department of Biochemistry, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Marilize Le Roes-Hill
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa.
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45
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Exploring the Role of Phenylalanine Residues in Modulating the Flexibility and Topography of the Active Site in the Peroxygenase Variant PaDa-I. Int J Mol Sci 2020; 21:ijms21165734. [PMID: 32785123 PMCID: PMC7460833 DOI: 10.3390/ijms21165734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 11/28/2022] Open
Abstract
Unspecific peroxygenases (UPOs) are fungal heme-thiolate enzymes able to catalyze a wide range of oxidation reactions, such as peroxidase-like, catalase-like, haloperoxidase-like, and, most interestingly, cytochrome P450-like. One of the most outstanding properties of these enzymes is the ability to catalyze the oxidation a wide range of organic substrates (both aromatic and aliphatic) through cytochrome P450-like reactions (the so-called peroxygenase activity), which involves the insertion of an oxygen atom from hydrogen peroxide. To catalyze this reaction, the substrate must access a channel connecting the bulk solution to the heme group. The composition, shape, and flexibility of this channel surely modulate the catalytic ability of the enzymes in this family. In order to gain an understanding of the role of the residues comprising the channel, mutants derived from PaDa-I, a laboratory-evolved UPO variant from Agrocybe aegerita, were obtained. The two phenylalanine residues at the surface of the channel, which regulate the traffic towards the heme active site, were mutated by less bulky residues (alanine and leucine). The mutants were experimentally characterized, and computational studies (i.e., molecular dynamics (MD)) were performed. The results suggest that these residues are necessary to reduce the flexibility of the region and maintain the topography of the channel.
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46
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Nagarajan S, Nagarajan R, Kumar J, Salemme A, Togna AR, Saso L, Bruno F. Antioxidant Activity of Synthetic Polymers of Phenolic Compounds. Polymers (Basel) 2020; 12:E1646. [PMID: 32722059 PMCID: PMC7464737 DOI: 10.3390/polym12081646] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 01/10/2023] Open
Abstract
In recent years, developing potent antioxidants has been a very active area of research. In this context, phenolic compounds have been evaluated for their antioxidant activity. However, the use of phenolic compounds has also been limited by poor antioxidant activity in several in vivo studies. Polymeric phenols have received much attention owing to their potent antioxidant properties and increased stability in aqueous systems. To be truly effective in biological applications, it is important that these polymers be synthesized using benign methods. In this context, enzyme catalyzed synthesis of polymeric phenols has been explored as an environmentally friendly and safer approach. This review summarizes work in enzymatic syntheses of polymers of phenols. Several assays have been developed to determine the antioxidant potency of these polymeric phenols. These assays are discussed in detail along with structure-property relationships. A deeper understanding of factors affecting antioxidant activity would provide an opportunity for the design of versatile, high performing polymers with enhanced antioxidant activity.
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Affiliation(s)
- Subhalakshmi Nagarajan
- Department of Natural and Social Sciences, Bowling Green State University-Firelands, Huron, OH 44839, USA
| | - Ramaswamy Nagarajan
- Department of Plastics Engineering and Center for Advanced Materials, University of Massachusetts, Lowell, MA 01854, USA;
| | - Jayant Kumar
- Department of Physics and Center for Advanced Materials, University of Massachusetts, Lowell, MA 01854, USA;
| | - Adele Salemme
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; (A.S.); (A.R.T.); (L.S.)
| | - Anna Rita Togna
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; (A.S.); (A.R.T.); (L.S.)
| | - Luciano Saso
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; (A.S.); (A.R.T.); (L.S.)
| | - Ferdinando Bruno
- Combat Capabilities Development Command Soldier Center, Natick, MA 01760, USA
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47
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Guo J, Yang L, Gao Z, Zhao C, Mei Y, Song YY. Insight of MOF Environment-Dependent Enzyme Activity via MOFs-in-Nanochannels Configuration. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00591] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Junli Guo
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Lingling Yang
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Zhida Gao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Chenxi Zhao
- College of Sciences, Northeastern University, Shenyang 110004, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Yan-Yan Song
- College of Sciences, Northeastern University, Shenyang 110004, China
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48
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Yayci A, Baraibar ÁG, Krewing M, Fueyo EF, Hollmann F, Alcalde M, Kourist R, Bandow JE. Plasma-Driven in Situ Production of Hydrogen Peroxide for Biocatalysis. CHEMSUSCHEM 2020; 13:2072-2079. [PMID: 32026604 PMCID: PMC7216967 DOI: 10.1002/cssc.201903438] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Peroxidases and peroxygenases are promising classes of enzymes for biocatalysis because of their ability to carry out one-electron oxidation reactions and stereoselective oxyfunctionalizations. However, industrial application is limited, as the major drawback is the sensitivity toward the required peroxide substrates. Herein, we report a novel biocatalysis approach to circumvent this shortcoming: in situ production of H2 O2 by dielectric barrier discharge plasma. The discharge plasma can be controlled to produce hydrogen peroxide at desired rates, yielding desired concentrations. Using horseradish peroxidase, it is demonstrated that hydrogen peroxide produced by plasma treatment can drive the enzymatic oxidation of model substrates. Fungal peroxygenase is then employed to convert ethylbenzene to (R)-1-phenylethanol with an ee of >96 % using plasma-generated hydrogen peroxide. As direct treatment of the reaction solution with plasma results in reduced enzyme activity, the use of plasma-treated liquid and protection strategies are investigated to increase total turnover. Technical plasmas present a noninvasive means to drive peroxide-based biotransformations.
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Affiliation(s)
- Abdulkadir Yayci
- Applied MicrobiologyFaculty of Biology and BiotechnologyRuhr University BochumUniversitätsstraße 15044780BochumGermany
| | - Álvaro Gómez Baraibar
- Microbial BiotechnologyFaculty of Biology and BiotechnologyRuhr University BochumUniversitätsstraße 15044780BochumGermany
| | - Marco Krewing
- Applied MicrobiologyFaculty of Biology and BiotechnologyRuhr University BochumUniversitätsstraße 15044780BochumGermany
| | - Elena Fernandez Fueyo
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629HZDelftThe Netherlands
| | - Miguel Alcalde
- Department of BiocatalysisInstitute of Catalysis and Petrochemistry (CSIC)Campus Cantoblanco28049MadridSpain
| | - Robert Kourist
- Microbial BiotechnologyFaculty of Biology and BiotechnologyRuhr University BochumUniversitätsstraße 15044780BochumGermany
- current address: Institute for Molecular BiotechnologyGraz University of TechnologyPetersgasse 14GrazAustria
| | - Julia E. Bandow
- Applied MicrobiologyFaculty of Biology and BiotechnologyRuhr University BochumUniversitätsstraße 15044780BochumGermany
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49
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Morsi R, Bilal M, Iqbal HMN, Ashraf SS. Laccases and peroxidases: The smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136572. [PMID: 31986384 DOI: 10.1016/j.scitotenv.2020.136572] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/05/2020] [Accepted: 01/05/2020] [Indexed: 02/08/2023]
Abstract
Various organic pollutants so-called emerging pollutants (EPs), including active residues from pharmaceuticals, pesticides, surfactants, hormones, and personal care products, are increasingly being detected in numerous environmental matrices including water. The persistence of these EPs can cause adverse ecological and human health effects even at very small concentrations in the range of micrograms per liter or lower, hence called micropollutants (MPs). The existence of EPs/MPs tends to be challenging to mitigate from the environment effectively. Unfortunately, most of them are not removed during the present-day treatment plants. So far, a range of treatment processes and degradation methods have been introduced and deployed against various EPs and/or MPs, such as ultrafiltration, nanofiltration, advanced oxidation processes (AOPs) and enzyme-based treatments coupled with membrane filtrations. To further strengthen the treatment processes and to overcome the EPs/MPs effective removal dilemma, numerous studies have revealed the applicability and notable biocatalytic potentialities of laccases and peroxidases to degrade different classes of organic pollutants. Exquisite selectivity and unique catalytic properties make these enzymes powerful biocatalytic candidates for bio-transforming an array of toxic contaminants to harmless entities. This review focuses on the use of laccases and peroxidases, such as soybean peroxidase (SBP), horseradish peroxidase (HRP), lignin peroxidase (LiP), manganese peroxidase (MnP), and chloroperoxidase (CPO) as a greener oxidation route towards efficient and effective removal or degradation of EPs/MPs.
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Affiliation(s)
- Rana Morsi
- Department of Chemistry, College of Science, UAE University, Al Ain, United Arab Emirates.
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Science, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, NL CP 64849, Mexico.
| | - S Salman Ashraf
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.
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50
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Improvement in oxidative stability of versatile peroxidase by flow cytometry-based high-throughput screening system. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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