1
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Hermann E, Rodrigues CF, Martins LO, Peterbauer C, Oostenbrink C. Engineering A-type Dye-Decolorizing Peroxidases by Modification of a Conserved Glutamate Residue. Chembiochem 2024; 25:e202300872. [PMID: 38376941 DOI: 10.1002/cbic.202300872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage.
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Affiliation(s)
- Enikö Hermann
- Institute of Food Technology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190, Vienna, Austria
- Institute for Molecular Modeling and Simulation, Department of Material Science and Life Sciences, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Carolina F Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Clemens Peterbauer
- Institute of Food Technology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190, Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department of Material Science and Life Sciences, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna, Austria
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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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3
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Mangini V, Rosini E, Caliandro R, Mangiatordi GF, Delre P, Sciancalepore AG, Pollegioni L, Haidukowski M, Mazzorana M, Sumarah MW, Renaud JB, Flaig R, Mulè G, Belviso BD, Loi M. DypB peroxidase for aflatoxin removal: New insights into the toxin degradation process. CHEMOSPHERE 2024; 349:140826. [PMID: 38040262 DOI: 10.1016/j.chemosphere.2023.140826] [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: 08/18/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Aflatoxin B1 (AFB1) is one of the most potent carcinogens and a widespread food and feed contaminant. As for other toxins, many efforts are devoted to find efficient and environmentally-friendly methods to degrade AFB1, such as enzymatic treatments, thus improving the safety of food and feed products. In this regard, the dye decolorizing peroxidase of type B (DypB) can efficiently degrade AFB1. The molecular mechanism, which is required to drive protein optimization in view of the usage of DypB as a mycotoxin reduction agent in large scale application, is unknown. Here, we focused on the role of four DypB residues in the degradation of AFB1 by alanine-scanning (residues 156, 215, 239 and 246), which were identified from biochemical assays to be kinetically relevant for the degradation. As a result of DypB degradation, AFB1 is converted into four products. Interestingly, the relative abundancy of these products depends on the replaced residues. Molecular dynamics simulations were used to investigate the role of these residues in the binding step between protein and manganese, a metal ion which is expected to be involved in the degradation process. We found that the size of the haem pocket as well as conformational changes in the protein structure could play a role in determining the kinetics of AFB1 removal and, consequently, guide the process towards specific degradation products.
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Affiliation(s)
- V Mangini
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - E Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, Varese, 21100, Italy
| | - R Caliandro
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - G F Mangiatordi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - P Delre
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - A G Sciancalepore
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - L Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, Varese, 21100, Italy
| | - M Haidukowski
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
| | - M Mazzorana
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - M W Sumarah
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street London, Ontario, Canada, N5V4T3
| | - J B Renaud
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street London, Ontario, Canada, N5V4T3
| | - R Flaig
- Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - G Mulè
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy.
| | - B D Belviso
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy.
| | - M Loi
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/o, Bari, 70126, Italy
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4
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Pupart H, Vastšjonok D, Lukk T, Väljamäe P. Dye-Decolorizing Peroxidase of Streptomyces coelicolor ( ScDyPB) Exists as a Dynamic Mixture of Kinetically Different Oligomers. ACS OMEGA 2024; 9:3866-3876. [PMID: 38284010 PMCID: PMC10809370 DOI: 10.1021/acsomega.3c07963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
Dye-decolorizing peroxidases (DyPs) are heme-dependent enzymes that catalyze the oxidation of various substrates including environmental pollutants such as azo dyes and also lignin. DyPs often display complex non-Michaelis-Menten kinetics with substrate inhibition or positive cooperativity. Here, we performed in-depth kinetic characterization of the DyP of the bacterium Streptomyces coelicolor (ScDyPB). The activity of ScDyPB was found to be dependent on its concentration in the working stock used to initiate the reactions as well as on the pH of the working stock. Furthermore, the above-listed conditions had different effects on the oxidation of 2,2'-azino-di(3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS) and methylhydroquinone, suggesting that different mechanisms are used in the oxidation of these substrates. The kinetics of the oxidation of ABTS were best described by the model whereby ScDyPB exists as a mixture of two kinetically different enzyme forms. Both forms obey the ping-pong kinetic mechanism, but one form is substrate-inhibited by the ABTS, whereas the other is not. Gel filtration chromatography and dynamic light scattering analyses revealed that ScDyPB exists as a complex mixture of molecules with different sizes. We propose that ScDyPB populations with low and high degrees of oligomerization have different kinetic properties. Such enzyme oligomerization-dependent modulation of the kinetic properties adds further dimension to the complexity of the kinetics of DyPs but also suggests novel possibilities for the regulation of their catalytic activity.
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Affiliation(s)
- Hegne Pupart
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 15 Akadeemia tee, Tallinn 12618, Estonia
| | - Darja Vastšjonok
- Institute
of Molecular and Cell Biology, University
of Tartu, Riia 23b-202, Tartu 51010, Estonia
| | - Tiit Lukk
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, 15 Akadeemia tee, Tallinn 12618, Estonia
| | - Priit Väljamäe
- Institute
of Molecular and Cell Biology, University
of Tartu, Riia 23b-202, Tartu 51010, Estonia
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5
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Frade K, Silveira CM, Salgueiro BA, Mendes S, Martins LO, Frazão C, Todorovic S, Moe E. Biochemical, Biophysical, and Structural Analysis of an Unusual DyP from the Extremophile Deinococcus radiodurans. Molecules 2024; 29:358. [PMID: 38257271 PMCID: PMC10820274 DOI: 10.3390/molecules29020358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Dye-decolorizing peroxidases (DyPs) are heme proteins with distinct structural properties and substrate specificities compared to classical peroxidases. Here, we demonstrate that DyP from the extremely radiation-resistant bacterium Deinococcus radiodurans is, like some other homologues, inactive at physiological pH. Resonance Raman (RR) spectroscopy confirms that the heme is in a six-coordinated-low-spin (6cLS) state at pH 7.5 and is thus unable to bind hydrogen peroxide. At pH 4.0, the RR spectra of the enzyme reveal the co-existence of high-spin and low-spin heme states, which corroborates catalytic activity towards H2O2 detected at lower pH. A sequence alignment with other DyPs reveals that DrDyP possesses a Methionine residue in position five in the highly conserved GXXDG motif. To analyze whether the presence of the Methionine is responsible for the lack of activity at high pH, this residue is substituted with a Glycine. UV-vis and RR spectroscopies reveal that the resulting DrDyPM190G is also in a 6cLS spin state at pH 7.5, and thus the Methionine does not affect the activity of the protein. The crystal structures of DrDyP and DrDyPM190G, determined to 2.20 and 1.53 Å resolution, respectively, nevertheless reveal interesting insights. The high-resolution structure of DrDyPM190G, obtained at pH 8.5, shows that one hydroxyl group and one water molecule are within hydrogen bonding distance to the heme and the catalytic Asparagine and Arginine. This strong ligand most likely prevents the binding of the H2O2 substrate, reinforcing questions about physiological substrates of this and other DyPs, and about the possible events that can trigger the removal of the hydroxyl group conferring catalytic activity to DrDyP.
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Affiliation(s)
| | | | | | | | | | | | | | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da Republica (EAN), 2780-157 Oeiras, Portugal; (K.F.); (C.M.S.); (B.A.S.); (S.M.); (L.O.M.); (C.F.); (S.T.)
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6
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Sethupathy S, Xie R, Liang N, Shafreen RMB, Ali MY, Zhuang Z, Zhe L, Zahoor, Yong YC, Zhu D. Evaluation of a dye-decolorizing peroxidase from Comamonas serinivorans for lignin valorization potentials. Int J Biol Macromol 2023; 253:127117. [PMID: 37774822 DOI: 10.1016/j.ijbiomac.2023.127117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/17/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Although dye-decolourising peroxidases (DyPs) are well-known for lignin degradation, a comprehensive understanding of their mechanism remains unclear. Therefore, studying the mechanism of lignin degradation by DyPs is necessary for industrial applications and enzyme engineering. In this study, a dye-decolourising peroxidase (CsDyP) gene from C. serinivorans was heterologously expressed and studied for its lignin degradation potential. Molecular docking analysis predicted the binding of 2, 2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), veratryl alcohol (VA), 2, 6-dimethylphenol (2, 6- DMP), guaiacol (GUA), and lignin to the substrate-binding pocket of CsDyP. Evaluation of the enzymatic properties showed that CsDyP requires pH 4.0 and 30 °C for optimal activity and has a high affinity for ABTS. In addition, CsDyP is stable over a wide range of temperatures and pH and can tolerate 5.0 mM organic solvents. Low NaCl concentrations promoted CsDyP activity. Further, CsDyP significantly reduced the chemical oxygen demand decolourised alkali lignin (AL) and milled wood lignin (MWL). CsDyP targets the β-O-4, CO, and CC bonds linking lignin's G, S, and H units to depolymerize and produce aromatic compounds. Overall, this study delivers valuable insights into the lignin degradation mechanism of CsDyP, which can benefit its industrial applications and lignin valorization.
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Affiliation(s)
- Sivasamy Sethupathy
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Rongrong Xie
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Nian Liang
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Raja Mohamed Beema Shafreen
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Algappapuram, Karaikudi 630003, Tamil Nadu, India
| | - Mohamed Yassin Ali
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Biochemistry Department, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Zhipeng Zhuang
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Liang Zhe
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zahoor
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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7
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Barbosa C, Rodrigues CF, Lončar N, Martins LO, Todorovic S, Silveira CM. Spectroelectrochemistry for determination of the redox potential in heme enzymes: Dye-decolorizing peroxidases. BBA ADVANCES 2023; 5:100112. [PMID: 38235374 PMCID: PMC10792693 DOI: 10.1016/j.bbadva.2023.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024] Open
Abstract
Dye-decolorizing peroxidases (DyPs) are heme-containing enzymes that are structurally unrelated to other peroxidases. Some DyPs show high potential for applications in biotechnology, which critically depends on the stability and redox potential (E°') of the enzyme. Here we provide a comparative analysis of UV-Vis- and surface-enhanced resonance Raman-based spectroelectrochemical methods for determination of the E°' of DyPs from two different organisms, and their variants generated targeting E°' upshift. We show that substituting the highly conserved Arginine in the distal side of the heme pocket by hydrophobic amino acid residues impacts the heme architecture and redox potential of DyPs from the two organisms in a very distinct manner. We demonstrate the advantages and drawbacks of the used spectroelectrochemical approaches, which is relevant for other heme proteins that contain multiple heme centers or spin populations.
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Affiliation(s)
- Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Carolina F. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Nikola Lončar
- Gecco Biotech, Nijenborgh 4, Groningen 9747AG, the Netherlands
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
| | - Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, Oeiras 2780-157, Portugal
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8
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Grenier V, Laur J, Gonzalez E, Pitre FE. Glyphosate has a negligible impact on bacterial diversity and dynamics during composting. Environ Microbiol 2023; 25:2897-2912. [PMID: 36975075 DOI: 10.1111/1462-2920.16374] [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: 12/15/2022] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
The herbicide glyphosate has several potential entry points into composting sites and its impact on composting processes has not yet been evaluated. To assess its impact on bacterial diversity and abundance as well as on community composition and dynamics, we conducted a mesocosm experiment at the Montreal Botanical Garden. Glyphosate had no effect on physicochemical property evolution during composting, while it was completely dissipated by the end of the experiment. Sampling at Days 0, 2, 28 and 112 of the process followed by 16S rRNA amplicon sequencing also found no effect of glyphosate on species richness and community composition. Differential abundance analyses revealed an increase of a few taxa in the presence of glyphosate, namely TRA3-20 (order Polyangiales), Pedosphaeraceae and BIrii41 (order Burkholderiales) after 28 days. In addition, five amplicon sequence variants (ASVs) had lower relative abundance in the glyphosate treatment compared to the control on Day 2, namely Comamonadaceae, Pseudomonas sp., Streptomyces sp., Thermoclostridium sp. and Actinomadura keratinilytica, while two ASVs were less abundant on Day 112, namely Pedomicrobium sp. and Pseudorhodoplanes sp. Most differences in abundance were measured between the different sampling points within each treatment. These results present glyphosate as a poor determinant of species recruitment during composting.
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Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
| | - Joan Laur
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montreal, Québec, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Frederic E Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de recherche en biologie végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montreal, Québec, Canada
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9
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Kalkan Ö, Kantamneni S, Brings L, Han H, Bean R, Mancuso AP, Koua FHM. Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme. Front Chem 2023; 11:1220543. [PMID: 37593106 PMCID: PMC10427876 DOI: 10.3389/fchem.2023.1220543] [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: 05/12/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.
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Affiliation(s)
- Özlem Kalkan
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Türkiye
| | | | - Lea Brings
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Huijong Han
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Richard Bean
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, Schenefeld, Schleswig-Holstein, Germany
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, United Kingdom
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10
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Ley Y, Cheng XY, Ying ZY, Zhou NY, Xu Y. Characterization of Two Marine Lignin-Degrading Consortia and the Potential Microbial Lignin Degradation Network in Nearshore Regions. Microbiol Spectr 2023; 11:e0442422. [PMID: 37042774 PMCID: PMC10269927 DOI: 10.1128/spectrum.04424-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
Terrestrial organic carbon such as lignin is an important component of the global marine carbon. However, the structural complexity and recalcitrant nature of lignin are deemed challenging for biodegradation. It has been speculated that bacteria play important roles in lignin degradation in the marine system. However, the extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, two bacterial consortia capable of degrading alkali lignin (a model compound of lignin), designated LIG-B and LIG-S, were enriched from the nearshore sediments of the East and South China Seas. Consortia LIG-B and LIG-S mainly comprised of the Proteobacteria phylum with Nitratireductor sp. (71.6%) and Halomonas sp. (91.6%), respectively. Lignin degradation was found more favorable in consortium LIG-B (max 57%) than in LIG-S (max 18%). Ligninolytic enzymes laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) capable of decomposing lignin into smaller fragments were all active in both consortia. The newly emerged low-molecular-weight aromatics, organic acids, and other lignin-derived compounds in biotreated alkali lignin also evidently showed the depolymerization of lignin by both consortia. The lignin degradation pathways reconstructed from consortium LIG-S were found to be more comprehensive compared to consortium LIG-B. It was further revealed that catabolic genes, involved in the degradation of lignin and its derivatives through multiple pathways via protocatechuate and catechol, are present not only in lignin-degrading consortia LIG-B and LIG-S but also in 783 publicly available metagenomic-assembled genomes from nine nearshore regions. IMPORTANCE Numerous terrigenous lignin-containing plant materials are constantly discharged from rivers and estuaries into the marine system. However, only low levels of terrigenous organic carbon, especially lignin, are detected in the global marine system due to the abundance of active heterotrophic microorganisms driving the carbon cycle. Simultaneously, the lack of knowledge on lignin biodegradation has hindered our understanding of the oceanic carbon cycle. Moreover, bacteria have been speculated to play important roles in the marine lignin biodegradation. Here, we enriched two bacterial consortia from nearshore sediments capable of utilizing alkali lignin for cell growth while degrading it into smaller molecules and reconstructed the lignin degradation network. In particular, this study highlights that marine microorganisms in nearshore regions mostly undergo similar pathways using protocatechuate and catechol as ring-cleavage substrates to drive lignin degradation as part of the oceanic carbon cycle, regardless of whether they are in sediments or water column.
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Affiliation(s)
- Yvette Ley
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Yu Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Yue Ying
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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11
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Singh AK, Iqbal HMN, Cardullo N, Muccilli V, Fern'andez-Lucas J, Schmidt JE, Jesionowski T, Bilal M. Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology-A review. Int J Biol Macromol 2023:124968. [PMID: 37217044 DOI: 10.1016/j.ijbiomac.2023.124968] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/22/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational frameworks, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Jesús Fern'andez-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanizaci'on El Bosque, 28670 Villaviciosa de Od'on, Spain; Grupo de Investigaci'on en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002 Barranquilla, Colombia
| | - Jens Ejbye Schmidt
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Odense, Denmark
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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12
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Silva D, Rodrigues F, Lorena C, Borges PT, Martins LO. Biocatalysis for biorefineries: The case of dye-decolorizing peroxidases. Biotechnol Adv 2023; 65:108153. [PMID: 37044267 DOI: 10.1016/j.biotechadv.2023.108153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/14/2023]
Abstract
Dye-decolorizing Peroxidases (DyPs) are heme-containing enzymes in fungi and bacteria that catalyze the reduction of hydrogen peroxide to water with concomitant oxidation of various substrates, including anthraquinone dyes, lignin-related phenolic and non-phenolic compounds, and metal ions. Investigation of DyPs has shed new light on peroxidases, one of the most extensively studied families of oxidoreductases; still, details of their microbial physiological role and catalytic mechanisms remain to be fully disclosed. They display a distinctive ferredoxin-like fold encompassing anti-parallel β-sheets and α-helices, and long conserved loops surround the heme pocket with a role in catalysis and stability. A tunnel routes H2O2 to the heme pocket, whereas binding sites for the reducing substrates are in cavities near the heme or close to distal aromatic residues at the surface. Variations in reactions, the role of catalytic residues, and mechanisms were observed among different classes of DyP. They were hypothetically related to the presence or absence of distal H2O molecules in the heme pocket. The engineering of DyPs for improved properties directed their biotechnological applications, primarily centered on treating textile effluents and degradation of other hazardous pollutants, to fields such as biosensors and valorization of lignin, the most abundant renewable aromatic polymer. In this review, we track recent research contributions that furthered our understanding of the activity, stability, and structural properties of DyPs and their biotechnological applications. Overall, the study of DyP-type peroxidases has significant implications for environmental sustainability and the development of new bio-based products and materials with improved end-of-life options via biodegradation and chemical recyclability, fostering the transition to a sustainable bio-based industry in the circular economy realm.
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Affiliation(s)
- Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - F Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Constança Lorena
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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13
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Dhankhar P, Dalal V, Sharma AK, Kumar P. Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis. Proteins 2023; 91:508-517. [PMID: 36345957 DOI: 10.1002/prot.26444] [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: 06/09/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022]
Abstract
Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.
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Affiliation(s)
- Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
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14
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Cagide C, Marizcurrena JJ, Vallés D, Alvarez B, Castro-Sowinski S. A bacterial cold-active dye-decolorizing peroxidase from an Antarctic Pseudomonas strain. Appl Microbiol Biotechnol 2023; 107:1707-1724. [PMID: 36773063 DOI: 10.1007/s00253-023-12405-7] [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: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 02/12/2023]
Abstract
DyP (dye-decolorizing peroxidase) enzymes are hemeproteins that catalyze the H2O2-dependent oxidation of various molecules and also carry out lignin degradation, albeit with low activity. We identified a dyp gene in the genome of an Antarctic cold-tolerant microbe (Pseudomonas sp. AU10) that codes for a class B DyP. The recombinant protein (rDyP-AU10) was produced using Escherichia coli as a host and purified. We found that rDyP-AU10 is mainly produced as a dimer and has characteristics that resemble psychrophilic enzymes, such as high activity at low temperatures (20 °C) when using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and H2O2 as substrates, thermo-instability, low content of arginine, and a catalytic pocket surface larger than the DyPs from some mesophilic and thermophilic microbes. We also report the steady-state kinetic parameters of rDyP-AU10 for ABTS, hydroquinone, and ascorbate. Stopped-flow kinetics revealed that Compound I is formed with a rate constant of (2.07 ± 0.09) × 106 M-1 s-1 at pH 5 and that this is the predominant species during turnover. The enzyme decolors dyes and modifies kraft lignin, suggesting that this enzyme may have potential use in bioremediation and in the cellulose and biofuel industries. KEY POINTS: • An Antarctic Pseudomonas strain produces a dye-decolorizing peroxidase. • The recombinant enzyme (rDyP-AU10) was produced in E. coli and purified. • rDyP-AU10 showed high activity at low temperatures. • rDyP-AU10 is potentially useful for biotechnological applications.
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Affiliation(s)
- Célica Cagide
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Juan José Marizcurrena
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Diego Vallés
- Laboratorio de Biocatalizadores y sus Aplicaciones, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, and Centro de Investigaciones Biomédicas, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Biocatalizadores y sus Aplicaciones, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
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15
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Unexpected diversity of dye-decolorizing peroxidases. Biochem Biophys Rep 2023; 33:101401. [DOI: 10.1016/j.bbrep.2022.101401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
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16
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Li J, Dong C, Sen B, Lai Q, Gong L, Wang G, Shao Z. Lignin-oxidizing and xylan-hydrolyzing Vibrio involved in the mineralization of plant detritus in the continental slope. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158714. [PMID: 36113801 DOI: 10.1016/j.scitotenv.2022.158714] [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: 07/08/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A large amount of terrigenous organic matter (TOM) is constantly transported to the deep sea. However, relatively little is known about the microbial mineralization of TOM therein. Our recent in situ enrichment experiments revealed that Vibrio is especially enriched as one of the predominant taxa in the cultures amended with natural plant materials in the deep sea. Yet their role in the mineralization of plant-derived TOM in the deep sea remains largely unknown. Here we isolated Vibrio strains representing dominant members of the enrichments and verified their potential to degrade lignin and xylan. The isolated strains were closely related to Vibrio harveyi, V. alginolyticus, V. diabolicus, and V. parahaemolyticus. Extracellular enzyme assays, and genome and transcriptome analyses revealed diverse peroxidases, including lignin peroxidase (LiP), catalase-peroxidase (KatG), and decolorizing peroxidase (DyP), which played an important role in the depolymerization and oxidation of lignin. Superoxide dismutase was found to likely promote lignin oxidation by supplying H2O2 to LiP, DyP, and KatG. Interestingly, these deep-sea Vibrio strains could oxidize lignin and hydrolyze xylan not only through aerobic pathway, but also through anaerobic pathway. Genome analysis revealed multiple anaerobic respiratory mechanisms, including the reductions of nitrate, arsenate, tetrathionate, and dimethyl sulfoxide. The strains showed the potential to anaerobically reduce sulfite and metal oxides of iron and manganese, in contrast the non-deep-sea Vibrio strains were not retrieved of genes involved in reduction of metal oxides. This is the first report about the lignin oxidation mechanisms in Vibrio and their role in TOM mineralization in anoxic and oxic environments of the marginal sea.
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Affiliation(s)
- Jianyang Li
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China.
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17
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Properties, Physiological Functions and Involvement of Basidiomycetous Alcohol Oxidase in Wood Degradation. Int J Mol Sci 2022; 23:ijms232213808. [PMID: 36430286 PMCID: PMC9699415 DOI: 10.3390/ijms232213808] [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: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
Extensive research efforts have been devoted to describing yeast alcohol oxidase (AO) and its promoter region, which is vastly applied in studies of heterologous gene expression. However, little is known about basidiomycetous AO and its physiological role in wood degradation. This review describes several alcohol oxidases from both white and brown rot fungi, highlighting their physicochemical and kinetic properties. Moreover, the review presents a detailed analysis of available AO-encoding gene promoter regions in basidiomycetous fungi with a discussion of the manipulations of culture conditions in relation to the modification of alcohol oxidase gene expression and changes in enzyme production. The analysis of reactions catalyzed by lignin-modifying enzymes (LME) and certain lignin auxiliary enzymes (LDA) elucidated the possible involvement of alcohol oxidase in the degradation of derivatives of this polymer. Combined data on lignin degradation pathways suggest that basidiomycetous AO is important in secondary reactions during lignin decomposition by wood degrading fungi. With numerous alcoholic substrates, the enzyme is probably engaged in a variety of catalytic reactions leading to the detoxification of compounds produced in lignin degradation processes and their utilization as a carbon source by fungal mycelium.
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18
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Omura I, Ishimori K, Uchida T. Converting cytochrome c into a DyP-like metalloenzyme. Dalton Trans 2022; 51:12641-12649. [PMID: 35929826 DOI: 10.1039/d2dt02137d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dye-decolorizing peroxidase (DyP), which can degrade anthraquinone dyes using H2O2, is an attractive prospect for potential biotechnological applications for environmental purification. We previously designed an artificial DyP with an optimal pH for reactive blue 19 (RB19) degradation shifting from pH 4.5 to 6.5. We then attempted to degrade RB19 using Escherichia coli expressing this mutant, but RB19 was degraded equally compared with bacteria expressing wild-type (WT) DyP because most DyP was expressed in a heme-free form. In this study, we attempted to design an artificial peroxidase based on cytochrome c (cyt c), whose heme is covalently bound to the protein. We found that cyt c can degrade RB19, but its ability at pH 7.0 was ∼60% of that of DyP from Vibrio cholerae at pH 4.5. To enhance this activity we constructed several mutants using three approaches. Initially, to improve reactivity with H2O2, Met80 was replaced with a noncoordinating residue, Ala or Val, but catalytic efficiency (kcat/Km) was increased by only ∼1.5-fold. To enhance the substrate binding affinity we introduced an additional Trp by replacing Pro76 (P76W). The catalytic efficiency of this mutant was ∼3-fold greater than that of WT cyt c. Finally, to form a hydrogen bond to axial histidine Gly29 was replaced with Asp (G29D). This mutant exhibited an ∼80-fold greater dye-decolorizing activity. Escherichia coli expressing the G29D mutant was unable to degrade RB19 in solution due to degradation of heme itself, but this study provides new insights into the design of artificial DyPs.
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Affiliation(s)
- Issei Omura
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
| | - Takeshi Uchida
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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Du Y, Yao C, Dou M, Wu J, Su L, Xia W. Oxidative degradation of pre-oxidated polystyrene plastics by dye decolorizing peroxidases from Thermomonospora curvata and Nostocaceae. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129265. [PMID: 35739782 DOI: 10.1016/j.jhazmat.2022.129265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of PS has attracted lots of public attentions due to its environmental friendliness. However, no specific PS degrading enzyme has been identified yet. Dye decolorizing peroxidases (DyPs) are heme-containing peroxidases named for the ability to degrade a variety of organic dyes. Herein, the abilities of two DyPs from Thermomonospora curvata (TcDyP) and Nostocaceae (AnaPX) to degrade PS were evaluated. Preoxidation methods by ultraviolet (UV) irradiation and chemical oxidants were developed to initially activate C-C bonds in the PS skeleton. DyPs degradation caused obvious etching and enhanced hydrophilicity of UV-PS films, and also generated new CO and C-OH groups. The cleavage of activated C-C bonds by DyPs was experimentally proven by analyzing the degradation products of UV-PS and model substrates. Furthermore, better pre-oxidation was obtained by using chemical oxidants KMnO4/H2SO4 and mCPBA to oxidize PS materials in dissolved state. And AnaPX exhibited stronger degradation effects on KMnO4/H2SO4-PS and mCPBA-PS by causing greater changes in functional groups CO, C-O, -OH groups and substituted benzenes and higher molecular weight reductions of 19.7% and 31.0%, respectively. To our knowledge, this is the first report on the identification of PS-degrading enzymes that provides experimental evidence.
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Affiliation(s)
- Yanyi Du
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Congyu Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Mingde Dou
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wei Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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Borges PT, Silva D, Silva TF, Brissos V, Cañellas M, Lucas MF, Masgrau L, Melo EP, Machuqueiro M, Frazão C, Martins LO. Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase. Comput Struct Biotechnol J 2022; 20:3899-3910. [PMID: 35950185 PMCID: PMC9334217 DOI: 10.1016/j.csbj.2022.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 01/21/2023] Open
Abstract
DyP-type peroxidases (DyPs) are microbial enzymes that catalyze the oxidation of a wide range of substrates, including synthetic dyes, lignin-derived compounds, and metals, such as Mn2+ and Fe2+, and have enormous biotechnological potential in biorefineries. However, many questions on the molecular basis of enzyme function and stability remain unanswered. In this work, high-resolution structures of PpDyP wild-type and two engineered variants (6E10 and 29E4) generated by directed evolution were obtained. The X-ray crystal structures revealed the typical ferredoxin-like folds, with three heme access pathways, two tunnels, and one cavity, limited by three long loops including catalytic residues. Variant 6E10 displays significantly increased loops' flexibility that favors function over stability: despite the considerably higher catalytic efficiency, this variant shows poorer protein stability compared to wild-type and 29E4 variants. Constant-pH MD simulations revealed a more positively charged microenvironment near the heme pocket of variant 6E10, particularly in the neutral to alkaline pH range. This microenvironment affects enzyme activity by modulating the pK a of essential residues in the heme vicinity and should account for variant 6E10 improved activity at pH 7-8 compared to the wild-type and 29E4 that show optimal enzymatic activity close to pH 4. Our findings shed light on the structure-function relationships of DyPs at the molecular level, including their pH-dependent conformational plasticity. These are essential for understanding and engineering the catalytic properties of DyPs for future biotechnological applications.
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Affiliation(s)
- Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Diogo Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Tomás F.D. Silva
- BioISI – Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vânia Brissos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marina Cañellas
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain
| | | | - Laura Masgrau
- Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain,Department of Chemistry, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Eduardo P. Melo
- Centro de Ciências do Mar, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Miguel Machuqueiro
- BioISI – Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal,Corresponding author.
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21
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Jiang C, Yan H, Shen X, Zhang Y, Wang Y, Sun S, Jiang H, Zang H, Zhao X, Hou N, Li Z, Wang L, Wang H, Li C. Genome Functional Analysis of the Psychrotrophic Lignin-Degrading Bacterium Arthrobacter sp. C2 and the Role of DyP in Catalyzing Lignin Degradation. Front Microbiol 2022; 13:921549. [PMID: 35910642 PMCID: PMC9327799 DOI: 10.3389/fmicb.2022.921549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
In the cold regions of China, lignin-rich corn straw accumulates at high levels due to low temperatures. The application of psychrotrophic lignin-degrading bacteria should be an effective means of overcoming the low-temperature limit for lignin degradation and promoting the utilization of corn straw. However, this application is limited by the lack of suitable strains for decomposition of lignin; furthermore, the metabolic mechanism of psychrotrophic lignin-degrading bacteria is unclear. Here, the whole genome of the psychrotrophic lignin-degrading bacterium Arthrobacter sp. C2, isolated in our previous work, was sequenced. Comparative genomics revealed that C2 contained unique genes related to lignin degradation and low-temperature adaptability. DyP may participate in lignin degradation and may be a cold-adapted enzyme. Moreover, DyP was proven to catalyze lignin Cα-Cβ bond cleavage. Deletion and complementation of the DyP gene verified its ability to catalyze the first-step reaction of lignin degradation. Comparative transcriptomic analysis revealed that the transcriptional expression of the DyP gene was upregulated, and the genetic compensation mechanism allowed C2ΔDyP to degrade lignin, which provided novel insights into the survival strategy of the psychrotrophic mutant strain C2ΔdyP. This study improved our understanding of the metabolic mechanism of psychrotrophic lignin-degrading bacteria and provided potential application options for energy-saving production using cold-adapted lignin-degrading enzymes.
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Affiliation(s)
- Cheng Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- College of Life Science and Resources and Environment, Yichun University, Yichun, China
| | - Haohao Yan
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xiaohui Shen
- College of Life Science and Resources and Environment, Yichun University, Yichun, China
| | - Yuting Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Yue Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Shanshan Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hanyi Jiang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Ziwei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Liwen Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hanjun Wang
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
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22
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Yayci A, Bachmann N, Dirks T, Hofmann E, Bandow JE. Characterization of three novel DyP-type peroxidases from Streptomyces chartreusis NRRL 3882. J Appl Microbiol 2022; 133:2417-2429. [PMID: 35808848 DOI: 10.1111/jam.15707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
AIMS Actinobacteria are known to produce extracellular enzymes including DyPs. We set out to identify and characterize novel peroxidases from Streptomyces chartreusis NRRL 3882, because S. chartreusis belongs to the small group of actinobacteria with three different DyPs. METHODS AND RESULTS The genome of the actinomycete Streptomyces chartreusis NRRL 3882 was mined for novel DyP-type peroxidases. Three genes encoding for DyP-type peroxidases were cloned and overexpressed in Escherichia coli. Subsequent characterization of the recombinant proteins included examination of operating conditions such as pH, temperature, and H2 O2 concentrations, as well as substrate spectrum. Despite their high sequence similarity, the enzymes named SCDYP1-SCDYP3 presented distinct preferences regarding their operating conditions. They showed great divergence in H2 O2 tolerance and stability, with SCDYP2 being most active at concentrations above 50 mmol l-1 . Moreover, SCDYP1 and SCDYP3 preferred acidic pH (typical for DyP-type peroxidases) whereas SCDYP2 was most active at pH 8. CONCLUSIONS Regarding the function of DyPs in nature, these results suggest that availability of different DyP variants with complementary activity profiles in one organism might convey evolutionary benefits. SIGNIFICANCE AND IMPACT OF STUDY DyP-type peroxidases are able to degrade xenobiotic compounds and thus can be applied in biocatalysis and bioremediation. However, the native function of DyPs and the benefits for their producers largely remain to be elucidated.
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Affiliation(s)
- Abdulkadir Yayci
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Nathalie Bachmann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Tim Dirks
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Germany
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23
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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24
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Mahanty A, Giri S, Kar A, Ghosh S. Biocatalytic pretreatment of rice straw by ligninolytic enzymes produced by newly isolated <i>Micrococcus unnanensis</i> strain B4 for downstream cellulolytic saccharification. J GEN APPL MICROBIOL 2022; 68:184-192. [DOI: 10.2323/jgam.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ayan Mahanty
- Department of Biotechnology, University of North Bengal
| | | | - Akas Kar
- Department of Biotechnology, University of North Bengal
| | - Shilpi Ghosh
- Department of Biotechnology, University of North Bengal
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25
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Guo WJ, Xu JK, Wu ST, Gao SQ, Wen GB, Tan X, Lin YW. Design and Engineering of an Efficient Peroxidase Using Myoglobin for Dye Decolorization and Lignin Bioconversion. Int J Mol Sci 2021; 23:ijms23010413. [PMID: 35008837 PMCID: PMC8745427 DOI: 10.3390/ijms23010413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
The treatment of environmental pollutants such as synthetic dyes and lignin has received much attention, especially for biotechnological treatments using both native and artificial metalloenzymes. In this study, we designed and engineered an efficient peroxidase using the O2 carrier myoglobin (Mb) as a protein scaffold by four mutations (F43Y/T67R/P88W/F138W), which combines the key structural features of natural peroxidases such as the presence of a conserved His-Arg pair and Tyr/Trp residues close to the heme active center. Kinetic studies revealed that the quadruple mutant exhibits considerably enhanced peroxidase activity, with the catalytic efficiency (kcat/Km) comparable to that of the most efficient natural enzyme, horseradish peroxidase (HRP). Moreover, the designed enzyme can effectively decolorize a variety of synthetic organic dyes and catalyze the bioconversion of lignin, such as Kraft lignin and a model compound, guaiacylglycerol-β-guaiacyl ether (GGE). As analyzed by HPLC and ESI-MS, we identified several bioconversion products of GGE, as produced via bond cleavage followed by dimerization or trimerization, which illustrates the mechanism for lignin bioconversion. This study indicates that the designed enzyme could be exploited for the decolorization of textile wastewater contaminated with various dyes, as well as for the bioconversion of lignin to produce more value-added products.
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Affiliation(s)
- Wen-Jie Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
| | - Jia-Kun Xu
- Key Laboratory of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts of Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China;
| | - Sheng-Tao Wu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
| | - Shu-Qin Gao
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
| | - Ge-Bo Wen
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China;
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (W.-J.G.); (S.-T.W.)
- Key Laboratory of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China; (S.-Q.G.); (G.-B.W.)
- Correspondence: ; Tel.: +86-734-8282375
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26
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Dhankhar P, Dalal V, Singh V, Sharma AK, Kumar P. Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol. Int J Biol Macromol 2021; 193:601-608. [PMID: 34687768 DOI: 10.1016/j.ijbiomac.2021.10.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s-1, followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (kcat) of 0.07 s-1 and 0.07 s-1, respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.
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Affiliation(s)
- Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India.
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27
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Scocozza MF, Martins LO, Murgida DH. Direct Electrochemical Generation of Catalytically Competent Oxyferryl Species of Classes I and P Dye Decolorizing Peroxidases. Int J Mol Sci 2021; 22:12532. [PMID: 34830413 PMCID: PMC8653965 DOI: 10.3390/ijms222212532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/14/2022] Open
Abstract
This work introduces a novel way to obtain catalytically competent oxyferryl species for two different dye-decolorizing peroxidases (DyPs) in the absence of H2O2 or any other peroxide by simply applying a reductive electrochemical potential under aerobic conditions. UV-vis and resonance Raman spectroscopies show that this method yields long-lived compounds II and I for the DyPs from Bacillus subtilis (BsDyP; Class I) and Pseudomonas putida (PpDyP; Class P), respectively. Both electrochemically generated high valent intermediates are able to oxidize ABTS at both acidic and alkaline pH. Interestingly, the electrocatalytic efficiencies obtained at pH 7.6 are very similar to the values recorded for regular catalytic ABTS/H2O2 assays at the optimal pH of the enzymes, ca. 3.7. These findings pave the way for the design of DyP-based electrocatalytic reactors operable in an extended pH range without the need of harmful reagents such as H2O2.
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Affiliation(s)
- Magalí F. Scocozza
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina;
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal;
| | - Daniel H. Murgida
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina;
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
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28
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Cordas CM, Nguyen GS, Valério GN, Jønsson M, Söllner K, Aune IH, Wentzel A, Moura JJG. Discovery and characterization of a novel Dyp-type peroxidase from a marine actinobacterium isolated from Trondheim fjord, Norway. J Inorg Biochem 2021; 226:111651. [PMID: 34740038 DOI: 10.1016/j.jinorgbio.2021.111651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 12/21/2022]
Abstract
A new dye-decolorizing peroxidase (DyP) was discovered through a data mining workflow based on HMMER software and profile Hidden Markov Model (HMM) using a dataset of 1200 genomes originated from a Actinobacteria strain collection isolated from Trondheim fjord. Instead of the conserved GXXDG motif known for Dyp-type peroxidases, the enzyme contains a new conserved motif EXXDG which has been not reported before. The enzyme can oxidize an anthraquinone dye Remazol Brilliant Blue R (Reactive Blue 19) and other phenolic compounds such as ferulic acid, sinapic acid, caffeic acid, 3-methylcatechol, dopamine hydrochloride, and tannic acid. The acidic pH optimum (3 to 4) and the low temperature optimum (25 °C) were confirmed using both biochemical and electrochemical assays. Kinetic and thermodynamic parameters associated with the catalytic redox center were attained by electrochemistry.
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Affiliation(s)
- Cristina M Cordas
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| | - Giang-Son Nguyen
- Sustainable Biotechnology and Bioprospecting, Department of Biotechnology and Nanomedicine, SINTEF Industry, Norway.
| | - Gabriel N Valério
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Malene Jønsson
- Sustainable Biotechnology and Bioprospecting, Department of Biotechnology and Nanomedicine, SINTEF Industry, Norway
| | - Katharina Söllner
- Sustainable Biotechnology and Bioprospecting, Department of Biotechnology and Nanomedicine, SINTEF Industry, Norway
| | - Ingvild H Aune
- Sustainable Biotechnology and Bioprospecting, Department of Biotechnology and Nanomedicine, SINTEF Industry, Norway
| | - Alexander Wentzel
- Sustainable Biotechnology and Bioprospecting, Department of Biotechnology and Nanomedicine, SINTEF Industry, Norway
| | - José J G Moura
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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29
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Pi Q, Zhu Z, Tang L. Transformation of Reactive Blue 19 by a recombinant peroxidase DyP. Bioprocess Biosyst Eng 2021; 45:425-429. [PMID: 34739595 DOI: 10.1007/s00449-021-02660-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
Wastewater containing recalcitrant dyes causes environmental problems. A new superfamily of heme-containing peroxidases, dye-decolorizing peroxidases (DyPs), has been found to decolorize different kinds of dyes, especial anthraquinone dyes efficiently. However, the mechanism of dyes degradation by DyPs has not been fully understood and the toxicity of dye degradation intermediates by DyPs catalysis to microbes is unclear. In this study, a purified recombinant Thermobifida fusca DyP (TfuDyP) in E. coli BL21(DE3) was used to treat Reactive Blue 19 (RB19), an anthraquinone dye. The reaction intermediates analyzed by ultra performance liquid chromatography/mass spectroscopy (UPLC-MS) indicated the initial site of TfuDyP attack on RB19. In addition, it was found that both RB19 and its incomplete degradation products inhibited the growth of Bacillus subtilis. These findings provided a novel understanding of DyPs catalysis to anthraquinone dyes.
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Affiliation(s)
- Qian Pi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, No 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China
| | - Zhubing Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, No 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China
| | - Lei Tang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, No 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China. .,School of Biotechnology, Jiangnan University, No 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China.
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30
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Garber AI, Ramírez GA, McAllister SM, Orsi W, D'Hondt S. Cryptic metabolisms in anoxic subseafloor sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:696-701. [PMID: 34184398 PMCID: PMC8518782 DOI: 10.1111/1758-2229.12983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/06/2021] [Indexed: 06/13/2023]
Abstract
Microbial gene expression in anoxic subseafloor sediment was recently explored in the Baltic Sea and the Peru Margin. Our analysis of these data reveals diverse transcripts encoding proteins associated with neutralization of reactive oxygen species, including catalase, which may provide an in situ source of oxygen. We also detect transcripts associated with oxidation of iron and sulfur, and with reduction of arsenate, selenate and nitrate. Given limited input of electron acceptors from outside the system, these results suggest that the microbial communities use an unexpectedly diverse variety of electron acceptors. Products of water radiolysis and their interactions with sediment continuously provide diverse electron acceptors and hydrogen. Cryptic microbial utilization of these oxidized substrates and H2 may be an important mechanism for multi-million-year survival under the extreme energy limitation in subseafloor sediment.
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Affiliation(s)
| | - Gustavo A. Ramírez
- Graduate School of Oceanography, University of Rhode IslandNarragansettRIUSA
- Department of Marine Sciences, University of North CarolinaChapel HillNCUSA
- College of Veterinary Medicine, Western University of Health SciencesPomonaCAUSA
| | - Sean M. McAllister
- Joint Institute for the Study of the Atmosphere and Ocean, University of WashingtonSeattleWAUSA
- Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - William Orsi
- Department of Earth & Environmental Sciences, Paleontology and GeobiologyLudwig‐Maximilians‐Universität MünchenMunich80333Germany
| | - Steven D'Hondt
- Graduate School of Oceanography, University of Rhode IslandNarragansettRIUSA
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31
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Lučić M, Wilson MT, Svistunenko DA, Owen RL, Hough MA, Worrall JAR. Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of Fe IV = O formation in bacterial dye-decolorizing peroxidases. J Biol Inorg Chem 2021; 26:743-761. [PMID: 34477969 PMCID: PMC8463360 DOI: 10.1007/s00775-021-01896-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (FeIV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Michael T Wilson
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Dimitri A Svistunenko
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, Oxfordshire, UK
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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Efficient Degradation of Zearalenone by Dye-Decolorizing Peroxidase from Streptomyces thermocarboxydus Combining Catalytic Properties of Manganese Peroxidase and Laccase. Toxins (Basel) 2021; 13:toxins13090602. [PMID: 34564606 PMCID: PMC8473283 DOI: 10.3390/toxins13090602] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
Ligninolytic enzymes, including laccase, manganese peroxidase, and dye-decolorizing peroxidase (DyP), have attracted much attention in the degradation of mycotoxins. Among these enzymes, the possible degradation pathway of mycotoxins catalyzed by DyP is not yet clear. Herein, a DyP-encoding gene, StDyP, from Streptomyces thermocarboxydus 41291 was identified, cloned, and expressed in Escherichia coli BL21/pG-Tf2. The recombinant StDyP was capable of catalyzing the oxidation of the peroxidase substrate 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), phenolic lignin compounds 2,6-dimethylphenol, and guaiacol, non-phenolic lignin compound veratryl alcohol, Mn2+, as well as anthraquinone dye reactive blue 19. Moreover, StDyP was able to slightly degrade zearalenone (ZEN). Most importantly, we found that StDyP combined the catalytic properties of manganese peroxidase and laccase, and could significantly accelerate the enzymatic degradation of ZEN in the presence of their corresponding substrates Mn2+ and 1-hydroxybenzotriazole. Furthermore, the biological toxicities of the main degradation products 15-OH-ZEN and 13-OH-ZEN-quinone might be remarkably removed. These findings suggested that DyP might be a promising candidate for the efficient degradation of mycotoxins in food and feed.
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Dye Decoloring Peroxidase Structure, Catalytic Properties and Applications: Current Advancement and Futurity. Catalysts 2021. [DOI: 10.3390/catal11080955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Dye decoloring peroxidases (DyPs) were named after their high efficiency to decolorize and degrade a wide range of dyes. DyPs are a type of heme peroxidase and are quite different from known heme peroxidases in terms of amino acid sequences, protein structure, catalytic residues, and physical and chemical properties. DyPs oxidize polycyclic dyes and phenolic compounds. Thus they find high application potentials in dealing with environmental problems. The structure and catalytic characteristics of DyPs of different families from the amino acid sequence, protein structure, and enzymatic properties, and analyzes the high-efficiency degradation ability of some DyPs in dye and lignin degradation, which vary greatly among DyPs classes. In addition, application prospects of DyPs in biomedicine and other fields are also discussed briefly. At the same time, the research strategy based on genetic engineering and synthetic biology in improving the stability and catalytic activity of DyPs are summarized along with the important industrial applications of DyPs and associated challenges. Moreover, according to the current research findings, bringing DyPs to the industrial level may require improving the catalytic efficiency of DyP, increasing production, and enhancing alkali resistance and toxicity.
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Zuccarello L, Barbosa C, Galdino E, Lončar N, Silveira CM, Fraaije MW, Todorovic S. SERR Spectroelectrochemistry as a Guide for Rational Design of DyP-Based Bioelectronics Devices. Int J Mol Sci 2021; 22:7998. [PMID: 34360763 PMCID: PMC8348443 DOI: 10.3390/ijms22157998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
Immobilised dye-decolorizing peroxidases (DyPs) are promising biocatalysts for the development of biotechnological devices such as biosensors for the detection of H2O2. To this end, these enzymes have to preserve native, solution properties upon immobilisation on the electrode surface. In this work, DyPs from Cellulomonas bogoriensis (CboDyP), Streptomyces coelicolor (ScoDyP) and Thermobifida fusca (TfuDyP) are immobilised on biocompatible silver electrodes functionalized with alkanethiols. Their structural, redox and catalytic properties upon immobilisation are evaluated by surface-enhanced resonance Raman (SERR) spectroelectrochemistry and cyclic voltammetry. Among the studied electrode/DyP constructs, only CboDyP shows preserved native structure upon attachment to the electrode. However, a comparison of the redox potentials of the enzyme in solution and immobilised states reveals a large discrepancy, and the enzyme shows no electrocatalytic activity in the presence of H2O2. While some immobilised DyPs outperform existing peroxidase-based biosensors, others fail to fulfil the essential requirements that guarantee their applicability in the immobilised state. The capacity of SERR spectroelectrochemistry for fast screening of the performance of immobilised heme enzymes places it in the front-line of experimental approaches that can advance the search for promising DyP candidates.
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Affiliation(s)
- Lidia Zuccarello
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Catarina Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Edilson Galdino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Nikola Lončar
- Gecco Biotech, Nijenborgh 4, 9747AG Groningen, The Netherlands;
| | - Célia M. Silveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
| | - Marco W. Fraaije
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands;
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (L.Z.); (C.B.); (E.G.); (C.M.S.)
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Stravoravdis S, Shipway JR, Goodell B. How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes. Front Microbiol 2021; 12:665001. [PMID: 34322098 PMCID: PMC8312274 DOI: 10.3389/fmicb.2021.665001] [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: 03/02/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.
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Affiliation(s)
- Stefanos Stravoravdis
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - J Reuben Shipway
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Barry Goodell
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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36
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Qin X, Su X, Tu T, Zhang J, Wang X, Wang Y, Wang Y, Bai Y, Yao B, Luo H, Huang H. Enzymatic Degradation of Multiple Major Mycotoxins by Dye-Decolorizing Peroxidase from Bacillus subtilis. Toxins (Basel) 2021; 13:toxins13060429. [PMID: 34205294 PMCID: PMC8235724 DOI: 10.3390/toxins13060429] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 12/28/2022] Open
Abstract
The co-occurrence of multiple mycotoxins, including aflatoxin B1 (AFB1), zearalenone (ZEN) and deoxynivalenol (DON), widely exists in cereal-based animal feed and food. At present, most reported mycotoxins degrading enzymes target only a certain type of mycotoxins. Therefore, it is of great significance for mining enzymes involved in the simultaneous degradation of different types of mycotoxins. In this study, a dye-decolorizing peroxidase-encoding gene BsDyP from Bacillus subtilis SCK6 was cloned and expressed in Escherichia coli BL21/pG-Tf2. The purified recombinant BsDyP was capable of oxidizing various substrates, including lignin phenolic model compounds 2,6-dimethylphenol and guaiacol, the substrate 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid), anthraquinone dye reactive blue 19 and azo dye reactive black 5, as well as Mn2+. In addition, BsDyP could efficiently degrade different types of mycotoxins, including AFB1, ZEN and DON, in presence of Mn2+. More important, the toxicities of their corresponding enzymatic degradation products AFB1-diol, 15-OH-ZEN and C15H18O8 were significantly lower than AFB1, ZEN and DON. In summary, these results proved that BsDyP was a promising candidate for the simultaneous degradation of multiple mycotoxins in animal feed and food.
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Rai A, Klare JP, Reinke PYA, Englmaier F, Fohrer J, Fedorov R, Taft MH, Chizhov I, Curth U, Plettenburg O, Manstein DJ. Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum. Int J Mol Sci 2021; 22:ijms22126265. [PMID: 34200865 PMCID: PMC8230527 DOI: 10.3390/ijms22126265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/29/2021] [Accepted: 06/05/2021] [Indexed: 12/23/2022] Open
Abstract
A novel cytoplasmic dye-decolorizing peroxidase from Dictyostelium discoideum was investigated that oxidizes anthraquinone dyes, lignin model compounds, and general peroxidase substrates such as ABTS efficiently. Unlike related enzymes, an aspartate residue replaces the first glycine of the conserved GXXDG motif in Dictyostelium DyPA. In solution, Dictyostelium DyPA exists as a stable dimer with the side chain of Asp146 contributing to the stabilization of the dimer interface by extending the hydrogen bond network connecting two monomers. To gain mechanistic insights, we solved the Dictyostelium DyPA structures in the absence of substrate as well as in the presence of potassium cyanide and veratryl alcohol to 1.7, 1.85, and 1.6 Å resolution, respectively. The active site of Dictyostelium DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an activated oxygen or CN- molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from H2O2 during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in Dictyostelium DyPA. Further, we identified two substrate-binding pockets per monomer in Dictyostelium DyPA at the dimer interface. Long-range electron transfer pathways associated with a hydrogen-bonding network that connects the substrate-binding sites with the heme moiety are described.
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Affiliation(s)
- Amrita Rai
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany
| | - Johann P. Klare
- Department of Physics, University of Osnabrueck, Barbarastrasse 7, D-49076 Osnabrück, Germany;
| | - Patrick Y. A. Reinke
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
- Center for Free-Electron Laser Science, German Electron Synchrotron (DESY), Notkestr. 85, D-22607 Hamburg, Germany
| | - Felix Englmaier
- Institute of Medicinal Chemistry, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany; (F.E.); (O.P.)
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
| | - Jörg Fohrer
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
- NMR Department of the Department of Chemistry, Technical University Darmstadt, Clemens Schöpf Institute for Organic Chemistry and Biochemistry, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Roman Fedorov
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Manuel H. Taft
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany; (F.E.); (O.P.)
- Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1b, D-30167 Hannover, Germany;
| | - Dietmar J. Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Fritz Hartmann Centre for Medical Research Carl Neuberg Str. 1, D-30625 Hannover, Germany; (A.R.); (P.Y.A.R.); (M.H.T.); (I.C.); (U.C.)
- Division for Structural Biochemistry, Hannover Medical School, Carl Neuberg Str. 1, D-30625 Hannover, Germany;
- RESiST, Cluster of Excellence 2155, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
- Correspondence: ; Tel.: +49-511-5323700
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Becarelli S, Chicca I, La China S, Siracusa G, Bardi A, Gullo M, Petroni G, Levin DB, Di Gregorio S. A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons. Front Microbiol 2021; 12:647373. [PMID: 34177829 PMCID: PMC8221241 DOI: 10.3389/fmicb.2021.647373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.
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Affiliation(s)
- Simone Becarelli
- Department of Biology, University of Pisa, Pisa, Italy.,BD Biodigressioni, Pisa, Italy
| | - Ilaria Chicca
- Department of Biology, University of Pisa, Pisa, Italy.,Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy
| | | | - Alessandra Bardi
- Department of Civil and Environmental Engineering, University of Florence, Florence, Italy
| | - Maria Gullo
- Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy
| | | | - David Bernard Levin
- BD Biodigressioni, Pisa, Italy.,Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada
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Zitare UA, Habib MH, Rozeboom H, Mascotti ML, Todorovic S, Fraaije MW. Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase. FEBS J 2021; 288:3602-3618. [PMID: 33369202 PMCID: PMC8248431 DOI: 10.1111/febs.15687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process. DATABASE: Structural data are available in the PDB database under the accession number 7ANV.
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Affiliation(s)
- Ulises A. Zitare
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE)Departamento de Química Inorgánica, Analítica y Química FísicaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires and CONICETArgentina
| | - Mohamed H. Habib
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Department of Microbiology and ImmunologyFaculty of PharmacyCairo UniversityEgypt
| | | | - Maria L. Mascotti
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- IMIBIO‐SL CONICETFacultad de Química Bioquímica y FarmaciaUniversidad Nacional de San LuisArgentina
| | - Smilja Todorovic
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
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Guo WJ, Xu JK, Liu JJ, Lang JJ, Gao SQ, Wen GB, Lin YW. Biotransformation of Lignin by an Artificial Heme Enzyme Designed in Myoglobin With a Covalently Linked Heme Group. Front Bioeng Biotechnol 2021; 9:664388. [PMID: 34136471 PMCID: PMC8201792 DOI: 10.3389/fbioe.2021.664388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
The conversion of Kraft lignin in plant biomass into renewable chemicals, aiming at harvesting aromatic compounds, is a challenge process in biorefinery. Comparing to the traditional chemical methods, enzymatic catalysis provides a gentle way for the degradation of lignin. Alternative to natural enzymes, artificial enzymes have been received much attention for potential applications. We herein achieved the biodegradation of Kraft lignin using an artificial peroxidase rationally designed in myoglobin (Mb), F43Y/T67R Mb, with a covalently linked heme cofactor. The artificial enzyme of F43Y/T67R Mb has improved catalytic efficiencies at mild acidic pH for phenolic and aromatic amine substrates, including Kraft lignin and the model lignin dimer guaiacylglycerol-β-guaiacyl ether (GGE). We proposed a possible catalytic mechanism for the biotransformation of lignin catalyzed by the enzyme, based on the results of kinetic UV-Vis studies and UPLC-ESI-MS analysis, as well as molecular modeling studies. With the advantages of F43Y/T67R Mb, such as the high-yield by overexpression in E. coli cells and the enhanced protein stability, this study suggests that the artificial enzyme has potential applications in the biodegradation of lignin to provide sustainable bioresource.
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Affiliation(s)
- Wen-Jie Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao, China
| | - Jing-Jing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Jia Lang
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
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Sugano Y, Yoshida T. DyP-Type Peroxidases: Recent Advances and Perspectives. Int J Mol Sci 2021; 22:5556. [PMID: 34074047 PMCID: PMC8197335 DOI: 10.3390/ijms22115556] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022] Open
Abstract
In this review, we chart the major milestones in the research progress on the DyP-type peroxidase family over the past decade. Though mainly distributed among bacteria and fungi, this family actually exhibits more widespread diversity. Advanced tertiary structural analyses have revealed common and different features among members of this family. Notably, the catalytic cycle for the peroxidase activity of DyP-type peroxidases appears to be different from that of other ubiquitous heme peroxidases. DyP-type peroxidases have also been reported to possess activities in addition to peroxidase function, including hydrolase or oxidase activity. They also show various cellular distributions, functioning not only inside cells but also outside of cells. Some are also cargo proteins of encapsulin. Unique, noteworthy functions include a key role in life-cycle switching in Streptomyces and the operation of an iron transport system in Staphylococcus aureus, Bacillus subtilis and Escherichia coli. We also present several probable physiological roles of DyP-type peroxidases that reflect the widespread distribution and function of these enzymes. Lignin degradation is the most common function attributed to DyP-type peroxidases, but their activity is not high compared with that of standard lignin-degrading enzymes. From an environmental standpoint, degradation of natural antifungal anthraquinone compounds is a specific focus of DyP-type peroxidase research. Considered in its totality, the DyP-type peroxidase family offers a rich source of diverse and attractive materials for research scientists.
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Affiliation(s)
- Yasushi Sugano
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Tokyo 112-8681, Japan;
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42
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Shrestha R, Jia K, Khadka S, Eltis LD, Li P. Mechanistic Insights into DyPB from Rhodococcus jostii RHA1 Via Kinetic Characterization. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Samiksha Khadka
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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43
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Zhang Y, Ren J, Wang Q, Wang S, Li S, Li H. Oxidation characteristics and degradation potential of a dye-decolorizing peroxidase from Bacillus amyloliquefaciens for crystal violet dye. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Uchida T, Omura I, Umetsu S, Ishimori K. Radical transfer but not heme distal residues is essential for pH dependence of dye-decolorizing activity of peroxidase from Vibrio cholerae. J Inorg Biochem 2021; 219:111422. [PMID: 33756393 DOI: 10.1016/j.jinorgbio.2021.111422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/02/2021] [Accepted: 03/07/2021] [Indexed: 02/08/2023]
Abstract
Dye-decolorizing peroxidase (DyP) is a heme-containing enzyme that catalyzes the degradation of anthraquinone dyes. A main feature of DyP is the acidic optimal pH for dye-decolorizing activity. In this study, we constructed several mutant DyP enzymes from Vibrio cholerae (VcDyP), with a view to identifying the decisive factor of the low pH preference of DyP. Initially, distal Asp144, a conserved residue, was replaced with His, which led to significant loss of dye-decolorizing activity. Introduction of His into a position slightly distant from heme resulted in restoration of activity but no shift in optimal pH, indicating that distal residues do not contribute to the pH dependence of catalytic activity. His178, an essential residue for dye decolorization, is located near heme and forms hydrogen bonds with Asp138 and Thr278. While Trp and Tyr mutants of His178 were inactive, the Phe mutant displayed ~35% activity of wild-type VcDyP, indicating that this position is a potential radical transfer route from heme to the active site on the protein surface. The Thr278Val mutant displayed similar enzymatic properties as WT VcDyP, whereas the Asp138Val mutant displayed significantly increased activity at pH 6.5. On the basis of these findings, we propose that neither distal amino acid residues, including Asp144, nor hydrogen bonds between His178 and Thr278 are responsible while the hydrogen bond between His178 and Asp138 plays a key role in the pH dependence of activity.
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Affiliation(s)
- Takeshi Uchida
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan.
| | - Issei Omura
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Sayaka Umetsu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Koichiro Ishimori
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
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45
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Comparing Ligninolytic Capabilities of Bacterial and Fungal Dye-Decolorizing Peroxidases and Class-II Peroxidase-Catalases. Int J Mol Sci 2021; 22:ijms22052629. [PMID: 33807844 PMCID: PMC7961821 DOI: 10.3390/ijms22052629] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 11/17/2022] Open
Abstract
We aim to clarify the ligninolytic capabilities of dye-decolorizing peroxidases (DyPs) from bacteria and fungi, compared to fungal lignin peroxidase (LiP) and versatile peroxidase (VP). With this purpose, DyPs from Amycolatopsis sp., Thermomonospora curvata, and Auricularia auricula-judae, VP from Pleurotus eryngii, and LiP from Phanerochaete chrysosporium were produced, and their kinetic constants and reduction potentials determined. Sharp differences were found in the oxidation of nonphenolic simple (veratryl alcohol, VA) and dimeric (veratrylglycerol-β- guaiacyl ether, VGE) lignin model compounds, with LiP showing the highest catalytic efficiencies (around 15 and 200 s−1·mM−1 for VGE and VA, respectively), while the efficiency of the A. auricula-judae DyP was 1–3 orders of magnitude lower, and no activity was detected with the bacterial DyPs. VP and LiP also showed the highest reduction potential (1.28–1.33 V) in the rate-limiting step of the catalytic cycle (i.e., compound-II reduction to resting enzyme), estimated by stopped-flow measurements at the equilibrium, while the T. curvata DyP showed the lowest value (1.23 V). We conclude that, when using realistic enzyme doses, only fungal LiP and VP, and in much lower extent fungal DyP, oxidize nonphenolic aromatics and, therefore, have the capability to act on the main moiety of the native lignin macromolecule.
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Armylisas AHN, Yeong SK, Maznee TITN, Hoong SS. Effect of Bio‐Based Aldehyde Structure on the Conversion and Selectivity Towards Glycerol Acetal Over Amberlyst‐46 by Using a Solvent‐Free Approach. ChemistrySelect 2021. [DOI: 10.1002/slct.202004215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Abu Hassan Noor Armylisas
- Advanced Oleochemical Technology Division Malaysian Palm Oil Board (MPOB) No. 6, Persiaran Institusi 43000 Kajang Selangor Malaysia
| | - Shoot Kian Yeong
- Advanced Oleochemical Technology Division Malaysian Palm Oil Board (MPOB) No. 6, Persiaran Institusi 43000 Kajang Selangor Malaysia
| | - Tuan Ismail Tuan Noor Maznee
- Advanced Oleochemical Technology Division Malaysian Palm Oil Board (MPOB) No. 6, Persiaran Institusi 43000 Kajang Selangor Malaysia
| | - Seng Soi Hoong
- Advanced Oleochemical Technology Division Malaysian Palm Oil Board (MPOB) No. 6, Persiaran Institusi 43000 Kajang Selangor Malaysia
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47
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Zhu N, Gao J, Liang D, Zhu Y, Li B, Jin H. Thermal pretreatment enhances the degradation and humification of lignocellulose by stimulating thermophilic bacteria during dairy manure composting. BIORESOURCE TECHNOLOGY 2021; 319:124149. [PMID: 32979596 DOI: 10.1016/j.biortech.2020.124149] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
This study investigated the effect of thermal pretreatment (TP) on the lignocellulose degradation and humification during dairy manure composting and the underlying microbial mechanism. The results showed that TP accelerated temperature rise and elevated composting temperature by increasing 26% initial content of simple organics. The degradation of cellulose, hemicellulose and lignin was 78, 10 and 109% higher in thermal pretreatment composting (TPC) than traditional composting (TC), respectively. Moreover, TP significantly improved the humification degree of composts, as indicated by 14 and 38% higher humus content and humification indexes in TPC, respectively. 16S rRNA sequencing showed that TP increased the relative abundance of thermophilic bacteria in TPC, of which Thermobifida, Planifilum, Truepera and Thermomonospora were potentially involved in lignocellulose biodegradation and humification. Canonical correspondence analysis revealed that TP changed the main factor determining the bacterial community evolution from dissolved organic carbon (DOC) in TC to temperature in TPC.
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Affiliation(s)
- Ning Zhu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Crop and Livestock Integrated Farming, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Jun Gao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Dong Liang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Crop and Livestock Integrated Farming, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China.
| | - Yanyun Zhu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Crop and Livestock Integrated Farming, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China.
| | - Bingqing Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hongmei Jin
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Key Laboratory of Crop and Livestock Integrated Farming, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China.
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48
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation. Angew Chem Int Ed Engl 2020; 59:21656-21662. [PMID: 32780931 PMCID: PMC7756461 DOI: 10.1002/anie.202008622] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 01/06/2023]
Abstract
Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (FeIV =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the FeIII and FeIV =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.
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Affiliation(s)
- Marina Lučić
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | | | - Michael T. Wilson
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Amanda K. Chaplin
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
| | - Bradley Davy
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Ali Ebrahim
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Danny Axford
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | | | | | - Shigeki Owada
- RIKEN Spring-8 Center1-1-1 KoutoSayoHyogo679-5148Japan
- Japan Synchrotron Radiation Research Institute1-1-1 KoutoSayoHyogo679-5198Japan
| | | | - Ivo Tews
- Biological SciencesInstitute for Life SciencesUniversity of SouthamptonUniversity RoadSouthamptonSO17 1BJUK
| | - Robin L. Owen
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOxfordshireOX11 0DEUK
| | - Michael A. Hough
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterEssexCO4 3SQUK
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49
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Lučić M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR. Serial Femtosecond Zero Dose Crystallography Captures a Water‐Free Distal Heme Site in a Dye‐Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe
IV
=O Formation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marina Lučić
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | | | - Michael T. Wilson
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Amanda K. Chaplin
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
| | - Bradley Davy
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Ali Ebrahim
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Danny Axford
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Takehiko Tosha
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Shigeki Owada
- RIKEN Spring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
- Japan Synchrotron Radiation Research Institute 1-1-1 Kouto Sayo Hyogo 679-5198 Japan
| | | | - Ivo Tews
- Biological Sciences Institute for Life Sciences University of Southampton University Road Southampton SO17 1BJ UK
| | - Robin L. Owen
- Diamond Light Source Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - Michael A. Hough
- School of Life Sciences University of Essex Wivenhoe Park Colchester Essex CO4 3SQ UK
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50
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Kont R, Bissaro B, Eijsink VGH, Väljamäe P. Kinetic insights into the peroxygenase activity of cellulose-active lytic polysaccharide monooxygenases (LPMOs). Nat Commun 2020; 11:5786. [PMID: 33188177 PMCID: PMC7666214 DOI: 10.1038/s41467-020-19561-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/13/2020] [Indexed: 01/06/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are widely distributed in Nature, where they catalyze the hydroxylation of glycosidic bonds in polysaccharides. Despite the importance of LPMOs in the global carbon cycle and in industrial biomass conversion, the catalytic properties of these monocopper enzymes remain enigmatic. Strikingly, there is a remarkable lack of kinetic data, likely due to a multitude of experimental challenges related to the insoluble nature of LPMO substrates, like cellulose and chitin, and to the occurrence of multiple side reactions. Here, we employed competition between well characterized reference enzymes and LPMOs for the H2O2 co-substrate to kinetically characterize LPMO-catalyzed cellulose oxidation. LPMOs of both bacterial and fungal origin showed high peroxygenase efficiencies, with kcat/KmH2O2 values in the order of 105-106 M-1 s-1. Besides providing crucial insight into the cellulolytic peroxygenase reaction, these results show that LPMOs belonging to multiple families and active on multiple substrates are true peroxygenases.
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Affiliation(s)
- Riin Kont
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway.,INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, Ås, Norway
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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