1
|
Nakazawa T, Yamaguchi I, Zhang Y, Saka C, Wu H, Kayama K, Kawauchi M, Sakamoto M, Honda Y. Experimental evidence that lignin-modifying enzymes are essential for degrading plant cell wall lignin by Pleurotus ostreatus using CRISPR/Cas9. Environ Microbiol 2023; 25:1909-1924. [PMID: 37218079 DOI: 10.1111/1462-2920.16427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Lignin-modifying enzymes (LMEs), which include laccases (Lacs), manganese peroxidases (MnPs), versatile peroxidases (VPs), and lignin peroxidases (LiPs), have been considered key factors in lignin degradation by white-rot fungi because they oxidize lignin model compounds and depolymerize synthetic lignin in vitro. However, it remains unclear whether these enzymes are essential/important in the actual degradation of natural lignin in plant cell walls. To address this long-standing issue, we examined the lignin-degrading abilities of multiple mnp/vp/lac mutants of Pleurotus ostreatus. One vp2/vp3/mnp3/mnp6 quadruple-gene mutant was generated from a monokaryotic wild-type strain PC9 using plasmid-based CRISPR/Cas9. Also, two vp2/vp3/mnp2/mnp3/mnp6, two vp2/vp3/mnp3/mnp6/lac2 quintuple-gene mutants, and two vp2/vp3/mnp2/mnp3/mnp6/lac2 sextuple-gene mutants were generated. The lignin-degrading abilities of the sextuple and vp2/vp3/mnp2/mnp3/mnp6 quintuple-gene mutants on the Beech wood sawdust medium reduced drastically, but not so much for those of the vp2/vp3/mnp3/mnp6/lac2 mutants and the quadruple mutant strain. The sextuple-gene mutants also barely degraded lignin in Japanese Cedar wood sawdust and milled rice straw. Thus, this study presented evidence that the LMEs, especially MnPs and VPs, play a crucial role in the degradation of natural lignin by P. ostreatus for the first time.
Collapse
Affiliation(s)
| | - Iori Yamaguchi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yufan Zhang
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Chinami Saka
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hongli Wu
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Keita Kayama
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| |
Collapse
|
2
|
Agnestisia R, Suzuki T, Ono A, Nakamura L, Nezu I, Tanaka Y, Aiso H, Ishiguri F, Yokota S. Lignin-degrading enzymes from a pathogenic canker-rot fungus Inonotus obliquus strain IO-B2. AMB Express 2023; 13:59. [PMID: 37302091 DOI: 10.1186/s13568-023-01566-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/02/2023] [Indexed: 06/13/2023] Open
Abstract
Inonotus obliquus is a pathogenic fungus found in living trees and has been widely used as a traditional medicine for cancer therapy. Although lignocellulose-degrading enzymes are involved in the early stages of host infection, the parasitic life cycle of this fungus has not been fully understood. In this study, we aimed to investigate the activities of laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) from I. obliquus cultivated in Kirk's medium. The fungus was subjected to genome sequencing, and genes related to wood degradation were identified. The draft genome sequence of this fungus comprised 21,203 predicted protein-coding genes, of which 134 were estimated to be related to wood degradation. Among these, 47 genes associated with lignin degradation were found to have the highest number of mnp genes. Furthermore, we cloned the cDNA encoding a putative MnP, referred to as IoMnP1, and characterized its molecular structure. The results show that IoMnP1 has catalytic properties analogous to MnP. Phylogenetic analysis also confirmed that IoMnP1 was closely related to the MnPs from Pyrrhoderma noxium, Fomitiporia mediterranea, and Sanghuangporus baumii, which belong to the same family of Hymenochaetaceae. From the above results, we suggest that IoMnP1 is a member of MnPs.
Collapse
Affiliation(s)
- Retno Agnestisia
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
- Faculty of Mathematics and Natural Sciences, Universitas Palangka Raya, Palangka Raya, 73111, Indonesia
| | - Tomohiro Suzuki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
| | - Akiko Ono
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Luna Nakamura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Ikumi Nezu
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yuki Tanaka
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Haruna Aiso
- Faculty of Agricultural Production and Management, Shizuoka Professional University of Agriculture, Iwata, Shizuoka, 438-0803, Japan
| | - Futoshi Ishiguri
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Shinso Yokota
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
| |
Collapse
|
3
|
Biochemical and molecular characterization of a new heme peroxidase from Aspergillus niger CTM10002, and its application in textile reactive dye decolorization. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
4
|
Atiwesh G, Parrish CC, Banoub J, Le TAT. Lignin degradation by microorganisms: A review. Biotechnol Prog 2021; 38:e3226. [PMID: 34854261 DOI: 10.1002/btpr.3226] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/19/2021] [Accepted: 11/28/2021] [Indexed: 11/09/2022]
Abstract
Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.
Collapse
Affiliation(s)
- Ghada Atiwesh
- Environmental Science Program, Memorial University of Newfoundland. St. John's, St. John's, Newfoundland, Canada
| | - Christopher C Parrish
- Chemistry Department, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada.,Department of Ocean Sciences, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada
| | - Joseph Banoub
- Chemistry Department, Memorial University of Newfoundland St. John's, St. John's, Newfoundland, Canada.,Fisheries and Oceans Canada, Science Branch, Special Projects, St John's, Newfoundland, Canada
| | - Tuyet-Anh T Le
- School of Science and the Environment, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Environmental Policy Institute, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Forestry Economics Research Centre, Vietnamese Academy of Forest Sciences, Hanoi, Vietnam
| |
Collapse
|
5
|
Mushroom Ligninolytic Enzymes―Features and Application of Potential Enzymes for Conversion of Lignin into Bio-Based Chemicals and Materials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11136161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mushroom ligninolytic enzymes are attractive biocatalysts that can degrade lignin through oxido-reduction. Laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase are the main enzymes that depolymerize highly complex lignin structures containing aromatic or aliphatic moieties and oxidize the subunits of monolignol associated with oxidizing agents. Among these enzymes, mushroom laccases are secreted glycoproteins, belonging to a polyphenol oxidase family, which have a powerful oxidizing capability that catalyzes the modification of lignin using synthetic or natural mediators by radical mechanisms via lignin bond cleavage. The high redox potential laccase within mediators can catalyze the oxidation of a wide range of substrates and the polymerization of lignin derivatives for value-added chemicals and materials. The chemoenzymatic process using mushroom laccases has been applied effectively for lignin utilization and the degradation of recalcitrant chemicals as an eco-friendly technology. Laccase-mediated grafting has also been employed to modify lignin and other polymers to obtain novel functional groups able to conjugate small and macro-biomolecules. In this review, the biochemical features of mushroom ligninolytic enzymes and their potential applications in catalytic reactions involving lignin and its derivatives to obtain value-added chemicals and novel materials in lignin valorization are discussed.
Collapse
|
6
|
A Multiomic Approach to Understand How Pleurotus eryngii Transforms Non-Woody Lignocellulosic Material. J Fungi (Basel) 2021; 7:jof7060426. [PMID: 34071235 PMCID: PMC8227661 DOI: 10.3390/jof7060426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Pleurotus eryngii is a grassland-inhabiting fungus of biotechnological interest due to its ability to colonize non-woody lignocellulosic material. Genomic, transcriptomic, exoproteomic, and metabolomic analyses were combined to explain the enzymatic aspects underlaying wheat–straw transformation. Up-regulated and constitutive glycoside–hydrolases, polysaccharide–lyases, and carbohydrate–esterases active on polysaccharides, laccases active on lignin, and a surprisingly high amount of constitutive/inducible aryl–alcohol oxidases (AAOs) constituted the suite of extracellular enzymes at early fungal growth. Higher enzyme diversity and abundance characterized the longer-term growth, with an array of oxidoreductases involved in depolymerization of both cellulose and lignin, which were often up-regulated since initial growth. These oxidative enzymes included lytic polysaccharide monooxygenases (LPMOs) acting on crystalline polysaccharides, cellobiose dehydrogenase involved in LPMO activation, and ligninolytic peroxidases (mainly manganese-oxidizing peroxidases), together with highly abundant H2O2-producing AAOs. Interestingly, some of the most relevant enzymes acting on polysaccharides were appended to a cellulose-binding module. This is potentially related to the non-woody habitat of P. eryngii (in contrast to the wood habitat of many basidiomycetes). Additionally, insights into the intracellular catabolism of aromatic compounds, which is a neglected area of study in lignin degradation by basidiomycetes, were also provided. The multiomic approach reveals that although non-woody decay does not result in dramatic modifications, as revealed by detailed 2D-NMR and other analyses, it implies activation of the complete set of hydrolytic and oxidative enzymes characterizing lignocellulose-decaying basidiomycetes.
Collapse
|
7
|
Ilić Đurđić K, Ostafe R, Đurđević Đelmaš A, Popović N, Schillberg S, Fischer R, Prodanović R. Saturation mutagenesis to improve the degradation of azo dyes by versatile peroxidase and application in form of VP-coated yeast cell walls. Enzyme Microb Technol 2020; 136:109509. [DOI: 10.1016/j.enzmictec.2020.109509] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/25/2019] [Accepted: 01/11/2020] [Indexed: 11/26/2022]
|
8
|
Improvement in oxidative stability of versatile peroxidase by flow cytometry-based high-throughput screening system. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
9
|
Hou L, Ji D, Dong W, Yuan L, Zhang F, Li Y, Zang L. The Synergistic Action of Electro-Fenton and White-Rot Fungi in the Degradation of Lignin. Front Bioeng Biotechnol 2020; 8:99. [PMID: 32226782 PMCID: PMC7080661 DOI: 10.3389/fbioe.2020.00099] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/03/2020] [Indexed: 11/13/2022] Open
Abstract
White-rot fungus is a common lignin-degrading fungus. However, compared with those of microorganisms that biodegrade lignin alone, synergistic systems of electro-Fenton processes and white-rot fungi are superior because of their high efficiency, mild conditions, and environmental friendliness. To investigate the details of lignin degradation by a synergistic system comprising electro-Fenton processes and white-rot fungi, lignin degradation was studied at different voltages with three lignin-degrading fungi (Phanerochaete chrysosporium, Lentinula edodes, and Trametes versicolor). The lignin degradation efficiency (82∼89%) of the synergistic systems at 4 V was higher than that of a control at 96 h post inoculation. Furthermore, the H2O2 produced and phenolic lignin converted in the system can significantly enhance the efficiency of ligninolytic enzymes, so a considerably increased enzyme activity was obtained by the synergistic action of electro-Fenton processes and white-rot fungi. 13C NMR spectroscopy revealed that aromatic structure units (103-162 ppm) were effectively degraded by the three fungi. This study shows that the combination of electro-Fenton processes and white-rot fungi treatment significantly improved the lignin degradation efficiency, which established a promising strategy for lignin degradation and valorization.
Collapse
Affiliation(s)
- Lipeng Hou
- College of Environmental Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, China
| | - Dandan Ji
- College of Environmental Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, China.,Huatai Group Corp. Ltd., Dongying, China.,Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, China
| | - Weifang Dong
- College of Environmental Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, China
| | - Lin Yuan
- College of Environmental Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, China
| | | | - Yan Li
- Langfang Meihua Biotechnology Development Co. Ltd., Langfang, China
| | - Lihua Zang
- College of Environmental Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan, China
| |
Collapse
|
10
|
Kumar A, Chandra R. Ligninolytic enzymes and its mechanisms for degradation of lignocellulosic waste in environment. Heliyon 2020; 6:e03170. [PMID: 32095645 PMCID: PMC7033530 DOI: 10.1016/j.heliyon.2020.e03170] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/04/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Ligninolytic enzymes play a key role in degradation and detoxification of lignocellulosic waste in environment. The major ligninolytic enzymes are laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase. The activities of these enzymes are enhanced by various mediators as well as some other enzymes (feruloyl esterase, aryl-alcohol oxidase, quinone reductases, lipases, catechol 2, 3-dioxygenase) to facilitate the process for degradation and detoxification of lignocellulosic waste in environment. The structurally laccase is isoenzymes with monomeric or dimeric and glycosylation levels (10–45%). This contains four copper ions of three different types. The enzyme catalyzes the overall reaction: 4 benzenediol + O2 to 4 benzosemiquinone + 2H2O. While, lignin peroxidase is a glycoprotein molecular mass of 38–46 kDa containing one mole of iron protoporphyrin IX per one mol of protein, catalyzes the H2O2 dependent oxidative depolymerization of lignin. The manganese peroxidase is a glycosylated heme protein with molecular mass of 40–50kDa. It depolymerizes the lignin molecule in the presence of manganese ion. The versatile peroxidase has broad range substrate sharing typical features of the manganese and lignin peroxidase families. Although ligninolytic enzymes have broad range of industrial application specially the degradation and detoxification of lignocellulosic waste discharged from various industrial activities, its large scale application is still limited due to lack of limited production. Further, the extremophilic properties of ligninolytic enzymes indicated their broad prospects in varied environmental conditions. Therefore it needs more extensive research for understanding its structure and mechanisms for broad range commercial applications.
Collapse
Affiliation(s)
- Adarsh Kumar
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| |
Collapse
|
11
|
Gopalakrishnan RM, Manavalan T, Ramesh J, Thangavelu KP, Heese K. Improvement of Saccharification and Delignification Efficiency of Trichoderma reesei Rut-C30 by Genetic Bioengineering. Microorganisms 2020; 8:microorganisms8020159. [PMID: 31979278 PMCID: PMC7074786 DOI: 10.3390/microorganisms8020159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 11/16/2022] Open
Abstract
Trichoderma reesei produces various saccharification enzymes required for biomass degradation. However, the lack of an effective lignin-degrading enzyme system reduces the species’ efficiency in producing fermentable sugars and increases the pre-treatment costs for biofuel production. In this study, we heterologously expressed the Ganoderma lucidum RMK1 versatile peroxidase gene (vp1) in the Rut-C30 strain of T. reesei. The expression of purified 6×His-tag–containing recombinant G. lucidum-derived protein (rVP1) was confirmed through western blot, which exhibited a single band with a relative molecular weight of 39 kDa. In saccharification and delignification studies using rice straw, the transformant (tVP7, T. reesei Rut-C30 expressing G. lucidum-derived rVP1) showed significant improvement in the yield of total reducing sugar and delignification, compared with that of the parent T. reesei Rut-C30 strain. Scanning electron microscopy (SEM) of tVP7-treated paddy straw showed extensive degradation of several layers of its surface compared with the parent strain due to the presence of G. lucidum-derived rVP1. Our results suggest that the expression of ligninolytic enzymes in cellulase hyperproducing systems helps to integrate the pre-treatment and saccharification steps that may ultimately reduce the costs of bioethanol production.
Collapse
Affiliation(s)
- Raja Mohan Gopalakrishnan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India; (R.M.G.); (T.M.)
| | - Tamilvendan Manavalan
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India; (R.M.G.); (T.M.)
| | - Janani Ramesh
- Department of Medical Biochemistry, Dr ALM Postgraduate Institute of Biomedical Sciences, University of Madras, Chennai, Tamil Nadu 600 113, India;
| | - Kalaichelvan Puthupalayam Thangavelu
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India; (R.M.G.); (T.M.)
- Correspondence: (K.P.T.); (K.H.)
| | - Klaus Heese
- Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 133-791, Korea
- Correspondence: (K.P.T.); (K.H.)
| |
Collapse
|
12
|
Chan JC, Paice M, Zhang X. Enzymatic Oxidation of Lignin: Challenges and Barriers Toward Practical Applications. ChemCatChem 2019. [DOI: 10.1002/cctc.201901480] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jou C. Chan
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
| | - Michael Paice
- FPInnovations Pulp Paper & Bioproducts 2665 East Mall Vancouver BC V6T 1Z4 Canada
| | - Xiao Zhang
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
- Pacific Northwest National Laboratory 520 Battelle Boulevard P.O. Box 999, MSIN P8-60 Richland WA-99352 USA
| |
Collapse
|
13
|
Romero JO, Fernández-Fueyo E, Avila-Salas F, Recabarren R, Alzate-Morales J, Martínez AT. Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study. Comput Struct Biotechnol J 2019; 17:1066-1074. [PMID: 31452859 PMCID: PMC6700493 DOI: 10.1016/j.csbj.2019.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/03/2019] [Accepted: 07/07/2019] [Indexed: 11/30/2022] Open
Abstract
Lignin peroxidase (LiP) and its natural substrate veratryl alcohol (VA) play a crucial role in lignin degradation by white-rot fungi. Understanding the molecular determinants for the interaction of this enzyme with its substrates is essential in the rational design of engineered peroxidases for biotechnological application. Here, we combine computational and experimental approaches to analyze the interaction of Phanerochaete chrysosporium LiP (isoenzyme H8) with VA and its radical cation (VA•+, resulting from substrate oxidation by the enzyme). Interaction energy calculations at semiempirical quantum mechanical level (SQM) between LiP and VA/VA•+ enabled to identify those residues at the acidic environment of catalytic Trp171 involved in the main interactions. Then, a battery of variants, with single and multiple mutations at these residues (Glu168, Asp165, Glu250, Asp264, and Phe267), was generated by directed mutagenesis, and their kinetics parameters were estimated on VA and two additional substrates. The experimental results show that Glu168 and Glu250 are crucial for the binding of VA, with Glu250 also contributing to the turnover of the enzyme. The experimental results were further rationalized through new calculations of interaction energies between VA/VA•+ and LiP with each of the single mutations. Finally, the delocalization of spin density was determined with quantum mechanics/molecular mechanics calculations (QM/MM), further supporting the contribution of Glu250 to VA oxidation at Trp171.
Collapse
Affiliation(s)
- Jefferson O Romero
- Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.,Doctorado en Ciencias Mencion Investigacion y Desarrollo de Productos Bioactivos, Instituto de Química de Recursos Naturales, Universidad de Talca, 2 Norte 685, Casilla 747, Talca, Chile
| | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain.,Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Fabián Avila-Salas
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Chile.,Escuela de Agronomía, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Chile
| | - Rodrigo Recabarren
- Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulacion y Modelado (CBSM), Departamento de Bioinformática, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain
| |
Collapse
|
14
|
Lee YJ, Shin KS. Isolation and characterization of the second extracellular peroxidase of the white-rot fungus Coriolus hirsutus. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Yeo Jin Lee
- Department of Microbiology, College of Sciences, Taejon University, Taejon, 300-716, Republic of Korea
| | - Kwang Soo Shin
- Department of Microbiology, College of Sciences, Taejon University, Taejon, 300-716, Republic of Korea
| |
Collapse
|
15
|
Evaluation of Versatile Peroxidase’s Activity and Conformation in the Presence of a Hydrated Urea Based Deep Eutectic Solvent. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00881-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
16
|
Endophytic Fungi: Biodiversity, Ecological Significance, and Potential Industrial Applications. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-10480-1_1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
17
|
Rekik H, Zaraî Jaouadi N, Bouacem K, Zenati B, Kourdali S, Badis A, Annane R, Bouanane-Darenfed A, Bejar S, Jaouadi B. Physical and enzymatic properties of a new manganese peroxidase from the white-rot fungus Trametes pubescens strain i8 for lignin biodegradation and textile-dyes biodecolorization. Int J Biol Macromol 2018; 125:514-525. [PMID: 30528991 DOI: 10.1016/j.ijbiomac.2018.12.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/25/2022]
Abstract
A new manganese peroxidase-producing white-rot basidiomycete fungus was isolated from symptomatic wood of the camphor trees Cinnamomum camphora (L.) at the Hamma Botanical Garden (Algeria) and identified as Trametes pubescens strain i8. The enzyme was purified (MnP TP55) to apparent electrophoretic homogeneity and biochemically characterized. The specific activity and Reinheitzahl value of the purified enzyme were 221 U/mg and 2.25, respectively. MALDI-TOF/MS analysis revealed that the purified enzyme was a monomer with a molecular mass of 55.2 kDa. The NH2-terminal sequence of the first 26 amino acid residues of MnP TP55 showed high similarity with those of white-rot fungal peroxidases. It revealed optimal activity at pH 5 and 40 °C. This peroxidase was completely inhibited by sodium azide and potassium cyanide, suggesting the presence of heme-components in its tertiary structure. Interestingly, MnP TP55 showed higher catalytic efficiency, organic solvent-tolerance, dye-decolorization ability, and detergent-compatibility than that of horseradish peroxidase (HRP) from roots of Armoracia rustanica, manganese peroxidase from Bjerkandera adusta strain CX-9 (MnP BA30), and manganese peroxidase from Phanerochaete chrysosporium (MnP PC). Overall, the findings provide strong support for the potential candidacy of MnP TP55 for environmental applications, mainly the development of enzyme-based technologies for lignin biodegradation, textile-dyes biodecolorization, and detergent formulations.
Collapse
Affiliation(s)
- Hatem Rekik
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia; Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Nadia Zaraî Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia; Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Khelifa Bouacem
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia; Laboratory of Cellular and Molecular Biology, Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene (USTHB), PO Box 32, El Alia, Bab Ezzouar, 16111, Algiers, Algeria
| | - Bilal Zenati
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA), 11, Bd Amirouche PO Box 67, Bou Ismaïl 42415, Tipaza, Algeria
| | - Sidali Kourdali
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA), 11, Bd Amirouche PO Box 67, Bou Ismaïl 42415, Tipaza, Algeria
| | - Abdelmalek Badis
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA), 11, Bd Amirouche PO Box 67, Bou Ismaïl 42415, Tipaza, Algeria; Laboratory of Natural Products Chemistry and Biomolecules (LNPC-BioM), Faculty of Sciences, University of Blida 1, Road of Soumaâ, PO Box 270, 09000 Blida, Algeria
| | - Rachid Annane
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA), 11, Bd Amirouche PO Box 67, Bou Ismaïl 42415, Tipaza, Algeria
| | - Amel Bouanane-Darenfed
- Laboratory of Cellular and Molecular Biology, Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene (USTHB), PO Box 32, El Alia, Bab Ezzouar, 16111, Algiers, Algeria
| | - Samir Bejar
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia; Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Bassem Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia; Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia.
| |
Collapse
|
18
|
Falade AO, Mabinya LV, Okoh AI, Nwodo UU. Ligninolytic enzymes: Versatile biocatalysts for the elimination of endocrine-disrupting chemicals in wastewater. Microbiologyopen 2018; 7:e00722. [PMID: 30328673 PMCID: PMC6291825 DOI: 10.1002/mbo3.722] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/11/2022] Open
Abstract
Direct municipal wastewater effluent discharge from treatment plants has been identified as the major source of endocrine‐disrupting chemicals (EDC) in freshwaters. Consequently, efficient elimination of EDC in wastewater is significant to good water quality. However, conventional wastewater treatment approaches have been deficient in the complete removal of these contaminants. Hence, the exploration of new and more efficient methods for elimination of EDC in wastewater is imperative. Enzymatic treatment approach has been suggested as a suitable option. Nonetheless, ligninolytic enzymes seem to be the most promising group of enzymes for EDC elimination, perhaps, owing to their unique catalytic properties and characteristic high redox potentials for oxidation of a wide spectrum of organic compounds. Therefore, this paper discusses the potential of some ligninolytic enzymes (laccase, manganese peroxidase, and versatile peroxidase) in the elimination of EDC in wastewater and proposes a new scheme of wastewater treatment process for EDC removal.
Collapse
Affiliation(s)
- Ayodeji O Falade
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Leonard V Mabinya
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Anthony I Okoh
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Uchechukwu U Nwodo
- SA-MRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape, South Africa.,Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, Eastern Cape, South Africa
| |
Collapse
|
19
|
Mir-Tutusaus JA, Baccar R, Caminal G, Sarrà M. Can white-rot fungi be a real wastewater treatment alternative for organic micropollutants removal? A review. WATER RESEARCH 2018; 138:137-151. [PMID: 29579480 DOI: 10.1016/j.watres.2018.02.056] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 05/20/2023]
Abstract
Micropollutants are a diverse group of compounds that are detected at trace concentrations and may have a negative effect on the environment and/or human health. Most of them are unregulated contaminants, although they have raised a concern in the scientific and global community and future regulation might be written in the near future. Several approaches have been tested to remove micropollutants from wastewater streams. In this manuscript, a focus is placed in reactor biological treatments that use white-rot fungi. A critical review of white-rot fungal-based technologies for micropollutant removal from wastewater has been conducted, several capabilities and limitations of such approaches have been identified and a range of solutions to overcome most of the limitations have been reviewed and/or proposed. Overall, this review argues that white-rot fungal reactors could be an efficient technology to remove micropollutants from specific wastewater streams.
Collapse
Affiliation(s)
- Josep Anton Mir-Tutusaus
- Departament d'Enginyeria Química Biològica i Ambiental, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Rim Baccar
- ENIS Laboratory of Environmental Engineering and Eco Technology, University of Sfax, BP 1173-3038, Sfax, Tunisia
| | - Glòria Caminal
- Institut de Química Avançada de Catalunya (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Montserrat Sarrà
- Departament d'Enginyeria Química Biològica i Ambiental, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| |
Collapse
|
20
|
Ayuso-Fernández I, Ruiz-Dueñas FJ, Martínez AT. Evolutionary convergence in lignin-degrading enzymes. Proc Natl Acad Sci U S A 2018; 115:6428-6433. [PMID: 29866821 PMCID: PMC6016776 DOI: 10.1073/pnas.1802555115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.
Collapse
Affiliation(s)
- Iván Ayuso-Fernández
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid, Spain
| | - Francisco J Ruiz-Dueñas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid, Spain
| |
Collapse
|
21
|
Sista Kameshwar AK, Qin W. Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi. Mycology 2017; 9:93-105. [PMID: 30123665 PMCID: PMC6059041 DOI: 10.1080/21501203.2017.1419296] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022] Open
Abstract
We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.
Collapse
Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, Canada
| |
Collapse
|
22
|
Affiliation(s)
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain
| |
Collapse
|
23
|
Bouacem K, Rekik H, Jaouadi NZ, Zenati B, Kourdali S, El Hattab M, Badis A, Annane R, Bejar S, Hacene H, Bouanane-Darenfed A, Jaouadi B. Purification and characterization of two novel peroxidases from the dye-decolorizing fungus Bjerkandera adusta strain CX-9. Int J Biol Macromol 2017; 106:636-646. [PMID: 28813685 DOI: 10.1016/j.ijbiomac.2017.08.061] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023]
Abstract
Two extracellular peroxidases from Bjerkandera adusta strain CX-9, namely a lignin peroxidase (called LiP BA45) and manganese peroxidase (called MnP BA30), were purified simultaneously by applying successively, ammonium sulfate precipitation-dialysis, Mono-S Sepharose anion-exchange and Sephacryl S-200 gel filtration and biochemically characterized. The sequence of their NH2-terminal amino acid residues showed high homology with those of fungi peroxidases. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis revealed that the purified enzymes MnP BA30 and LiP BA45 were a monomers with a molecular masses 30125.16 and 45221.10Da, respectively. While MnP BA30 was optimally active at pH 3 and 70°C, LiP BA45 showed optimum activity at pH 4 and 50°C. The two enzymes were inhibited by sodium azide and potassium cyanide, suggesting the presence of heme-components in their tertiary structures. The Km and Vmax for LiP BA45 toward 2,4-Dichlorolphenol (2,4-DCP) were 0.099mM and 9.12U/mg, respectively and for MnP BA30 toward 2,6-Dimethylphenol (2,6-DMP), they were 0.151mM and 18.60U/mg, respectively. Interestingly, MnP BA30 and LiP BA45 demonstrated higher catalytic efficiency than that of other tested peroxidases (MnP, LiP, HaP4, and LiP-SN) and marked organic solvent-stability and dye-decolorization efficiency. Data suggest that these peroxidases may be considered as potential candidates for future applications in distaining synthetic-dyes.
Collapse
Affiliation(s)
- Khelifa Bouacem
- Laboratory of Cellular and Molecular Biology, Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene (USTHB), PO Box 32, El Alia, Bab Ezzouar, 16111 Algiers, Algeria; Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia.
| | - Hatem Rekik
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Nadia Zaraî Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Bilal Zenati
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA) 11, Bd Amirouche PO Box 67, Bou Ismaïl, 42415, Tipaza, Algeria
| | - Sidali Kourdali
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA) 11, Bd Amirouche PO Box 67, Bou Ismaïl, 42415, Tipaza, Algeria
| | - Mohamed El Hattab
- Laboratory of Natural Products Chemistry and Biomolecules (LNPC-BioM), Faculty of Sciences, University of Blida 1, Road of Soumaâ, PO Box 270, 09000 Blida, Algeria
| | - Abdelmalek Badis
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA) 11, Bd Amirouche PO Box 67, Bou Ismaïl, 42415, Tipaza, Algeria; Laboratory of Natural Products Chemistry and Biomolecules (LNPC-BioM), Faculty of Sciences, University of Blida 1, Road of Soumaâ, PO Box 270, 09000 Blida, Algeria
| | - Rachid Annane
- National Centre for Research and Development of Fisheries and Aquaculture (CNRDPA) 11, Bd Amirouche PO Box 67, Bou Ismaïl, 42415, Tipaza, Algeria
| | - Samir Bejar
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia
| | - Hocine Hacene
- Laboratory of Cellular and Molecular Biology, Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene (USTHB), PO Box 32, El Alia, Bab Ezzouar, 16111 Algiers, Algeria
| | - Amel Bouanane-Darenfed
- Laboratory of Cellular and Molecular Biology, Microbiology Team, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene (USTHB), PO Box 32, El Alia, Bab Ezzouar, 16111 Algiers, Algeria
| | - Bassem Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, PO Box 1177, Sfax 3018, Tunisia.
| |
Collapse
|
24
|
Afrin S, Karim Z. Isolation and Surface Modification of Nanocellulose: Necessity of Enzymes over Chemicals. CHEMBIOENG REVIEWS 2017. [DOI: 10.1002/cben.201600001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Sadaf Afrin
- Aligarh Muslim University; Faculty of Science; Department of Chemistry; 202002 Aligarh India
| | - Zoheb Karim
- MoRe Research Örnsköldsvik AB; Box 70 891 22 Örnsköldsvik Sweden
| |
Collapse
|
25
|
Laccases as a Potential Tool for the Efficient Conversion of Lignocellulosic Biomass: A Review. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3020017] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
26
|
Glyoxal oxidases: their nature and properties. World J Microbiol Biotechnol 2017; 33:87. [DOI: 10.1007/s11274-017-2254-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/29/2017] [Indexed: 01/30/2023]
|
27
|
Maijala P, Harrington TC, Raudaskoski M. A peroxidase gene family and gene trees inHeterobasidionand related genera. Mycologia 2017. [DOI: 10.1080/15572536.2004.11833106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Pekka Maijala
- Department of Applied Chemistry and Microbiology, P.O. Box 56, 00014 University of Helsinki, Finland
| | - Thomas C. Harrington
- Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, Iowa 50011, USA
| | - Marjatta Raudaskoski
- Department of Biosciences, Division of Plant Physiology, P.O. Box 56, 00014 University of Helsinki, Finland
| |
Collapse
|
28
|
Ayuso-Fernández I, Martínez AT, Ruiz-Dueñas FJ. Experimental recreation of the evolution of lignin-degrading enzymes from the Jurassic to date. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:67. [PMID: 28331543 PMCID: PMC5356311 DOI: 10.1186/s13068-017-0744-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/28/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Floudas et al. (Science 336: 1715) established that lignin-degrading fungi appeared at the end of Carboniferous period associated with the production of the first ligninolytic peroxidases. Here, the subsequent evolution of these enzymes in Polyporales, where most wood-rotting fungi are included, is experimentally recreated using genomic information. RESULTS With this purpose, we analyzed the evolutionary pathway leading to the most efficient lignin-degrading peroxidases characterizing Polyporales species. After sequence reconstruction from 113 genes of ten sequenced genomes, the main enzyme intermediates were resurrected and characterized. Biochemical changes were analyzed together with predicted sequences and structures, to understand how these enzymes acquired the ability to degrade lignin and how this ability changed with time. The most probable first peroxidase in Polyporales would be a manganese peroxidase (Mn3+ oxidizing phenolic lignin) that did not change substantially until the appearance of an exposed tryptophan (oxidizing nonphenolic lignin) originating an ancestral versatile peroxidase. Later, a quick evolution, with loss of the Mn2+-binding site, generated the first lignin peroxidase that evolved to the extant form by improving the catalytic efficiency. Increased stability at acidic pH, which strongly increases the oxidizing power of these enzymes, was observed paralleling the appearance of the exposed catalytic tryptophan. CONCLUSIONS We show how the change in peroxidase catalytic activities meant an evolutionary exploration for more efficient ways of lignin degradation by fungi, a key step for carbon recycling in land ecosystems. The study provides ancestral enzymes with a potential biotechnological interest for the sustainable production of fuels and chemicals in a biomass-based economy.
Collapse
Affiliation(s)
- Iván Ayuso-Fernández
- IPSBB unit, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Angel T. Martínez
- IPSBB unit, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | |
Collapse
|
29
|
Characterization of a novel manganese peroxidase from white-rot fungus Echinodontium taxodii 2538, and its use for the degradation of lignin-related compounds. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.01.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
30
|
Sáez-Jiménez V, Rencoret J, Rodríguez-Carvajal MA, Gutiérrez A, Ruiz-Dueñas FJ, Martínez AT. Role of surface tryptophan for peroxidase oxidation of nonphenolic lignin. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:198. [PMID: 28616078 PMCID: PMC5467052 DOI: 10.1186/s13068-016-0615-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/09/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Despite claims as key enzymes in enzymatic delignification, very scarce information on the reaction rates between the ligninolytic versatile peroxidase (VP) and lignin peroxidase (LiP) and the lignin polymer is available, due to methodological difficulties related to lignin heterogeneity and low solubility. RESULTS Two water-soluble sulfonated lignins (from Picea abies and Eucalyptus grandis) were chemically characterized and used to estimate single electron-transfer rates to the H2O2-activated Pleurotus eryngii VP (native enzyme and mutated variant) transient states (compounds I and II bearing two- and one-electron deficiencies, respectively). When the rate-limiting reduction of compound II was quantified by stopped-flow rapid spectrophotometry, from fourfold (softwood lignin) to over 100-fold (hardwood lignin) lower electron-transfer efficiencies (k3app values) were observed for the W164S variant at surface Trp164, compared with the native VP. These lignosulfonates have ~20-30 % phenolic units, which could be responsible for the observed residual activity. Therefore, methylated (and acetylated) samples were used in new stopped-flow experiments, where negligible electron transfer to the W164S compound II was found. This revealed that the residual reduction of W164S compound II by native lignin was due to its phenolic moiety. Since both native lignins have a relatively similar phenolic moiety, the higher W164S activity on the softwood lignin could be due to easier access of its mono-methoxylated units for direct oxidation at the heme channel in the absence of the catalytic tryptophan. Moreover, the lower electron transfer rates from the derivatized lignosulfonates to native VP suggest that peroxidase attack starts at the phenolic lignin moiety. In agreement with the transient-state kinetic data, very low structural modification of lignin, as revealed by size-exclusion chromatography and two-dimensional nuclear magnetic resonance, was obtained during steady-state treatment (up to 24 h) of native lignosulfonates with the W164S variant compared with native VP and, more importantly, this activity disappeared when nonphenolic lignosulfonates were used. CONCLUSIONS We demonstrate for the first time that the surface tryptophan conserved in most LiPs and VPs (Trp164 of P. eryngii VPL) is strictly required for oxidation of the nonphenolic moiety, which represents the major and more recalcitrant part of the lignin polymer.
Collapse
Affiliation(s)
- Verónica Sáez-Jiménez
- CSIC, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Jorge Rencoret
- CSIC, Instituto de Recursos Naturales y Agrobiología de Sevilla, Avenida Reina Mercedes 10, 41012 Seville, Spain
| | | | - Ana Gutiérrez
- CSIC, Instituto de Recursos Naturales y Agrobiología de Sevilla, Avenida Reina Mercedes 10, 41012 Seville, Spain
| | | | - Angel T. Martínez
- CSIC, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| |
Collapse
|
31
|
Tang X, Dong S, Shi W, Gao N, Zuo L, Xu H. Fates of nickel and fluoranthene during the bioremediation byPleurotus eryngiiin three different soils. J Basic Microbiol 2016; 56:1194-1202. [DOI: 10.1002/jobm.201600171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/15/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Xia Tang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education); College of Life Science; Sichuan University; Chengdu Sichuan P. R. China
| | - Shunwen Dong
- Industrial Crop Research Institute of Sichuan Academy of Agricultural Sciences; Chengdu Sichuan P. R. China
| | - Wenjin Shi
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education); College of Life Science; Sichuan University; Chengdu Sichuan P. R. China
| | - Ni Gao
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education); College of Life Science; Sichuan University; Chengdu Sichuan P. R. China
| | - Lei Zuo
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education); College of Life Science; Sichuan University; Chengdu Sichuan P. R. China
| | - Heng Xu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education); College of Life Science; Sichuan University; Chengdu Sichuan P. R. China
| |
Collapse
|
32
|
Unveiling the basis of alkaline stability of an evolved versatile peroxidase. Biochem J 2016; 473:1917-28. [DOI: 10.1042/bcj20160248] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022]
Abstract
A variant of high biotechnological interest (called 2-1B) was obtained by directed evolution of the Pleurotus eryngii VP (versatile peroxidase) expressed in Saccharomyces cerevisiae [García-Ruiz, González-Pérez, Ruiz-Dueñas, Martínez and Alcalde (2012) Biochem. J. 441, 487–498]. 2-1B shows seven mutations in the mature protein that resulted in improved functional expression, activity and thermostability, along with a remarkable stronger alkaline stability (it retains 60% of the initial activity after 120 h of incubation at pH 9 compared with complete inactivation of the native enzyme after only 1 h). The latter is highly demanded for biorefinery applications. In the present study we investigate the structural basis behind the enhanced alkaline stabilization of this evolved enzyme. In order to do this, several VP variants containing one or several of the mutations present in 2-1B were expressed in Escherichia coli, and their alkaline stability and biochemical properties were determined. In addition, the crystal structures of 2-1B and one of the intermediate variants were solved and carefully analysed, and molecular dynamics simulations were carried out. We concluded that the introduction of three basic residues in VP (Lys-37, Arg-39 and Arg-330) led to new connections between haem and helix B (where the distal histidine residue is located), and formation of new electrostatic interactions, that avoided the hexa-co-ordination of the haem iron. These new structural determinants stabilized the haem and its environment, helping to maintain the structural enzyme integrity (with penta-co-ordinated haem iron) under alkaline conditions. Moreover, the reinforcement of the solvent-exposed area around Gln-305 in the proximal side, prompted by the Q202L mutation, further enhanced the stability.
Collapse
|
33
|
Sánchez-Alejandro F, Juarez-Moreno K, Baratto MC, Basosi R, Vazquez-Duhalt R. Tryptophan-surface modification of versatile peroxidase from Bjerkandera adusta enhances its catalytic performance. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
34
|
Kameshwar AKS, Qin W. Lignin Degrading Fungal Enzymes. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
35
|
Potential of White-Rot Fungi to Treat Xenobiotic-Containing Wastewater. FUNGAL APPLICATIONS IN SUSTAINABLE ENVIRONMENTAL BIOTECHNOLOGY 2016. [DOI: 10.1007/978-3-319-42852-9_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
36
|
Sáez-Jiménez V, Fernández-Fueyo E, Medrano FJ, Romero A, Martínez AT, Ruiz-Dueñas FJ. Improving the pH-stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase. PLoS One 2015; 10:e0140984. [PMID: 26496708 PMCID: PMC4619715 DOI: 10.1371/journal.pone.0140984] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/04/2015] [Indexed: 11/18/2022] Open
Abstract
Versatile peroxidase (VP) from the white-rot fungus Pleurotus eryngii is a high redox potential peroxidase of biotechnological interest able to oxidize a wide range of recalcitrant substrates including lignin, phenolic and non-phenolic aromatic compounds and dyes. However, the relatively low stability towards pH of this and other fungal peroxidases is a drawback for their industrial application. A strategy based on the comparative analysis of the crystal structures of VP and the highly pH-stable manganese peroxidase (MnP4) from Pleurotus ostreatus was followed to improve the VP pH stability. Several interactions, including hydrogen bonds and salt bridges, and charged residues exposed to the solvent were identified as putatively contributing to the pH stability of MnP4. The eight amino acid residues responsible for these interactions and seven surface basic residues were introduced into VP by directed mutagenesis. Furthermore, two cysteines were also included to explore the effect of an extra disulfide bond stabilizing the distal Ca2+ region. Three of the four designed variants were crystallized and new interactions were confirmed, being correlated with the observed improvement in pH stability. The extra hydrogen bonds and salt bridges stabilized the heme pocket at acidic and neutral pH as revealed by UV-visible spectroscopy. They led to a VP variant that retained a significant percentage of the initial activity at both pH 3.5 (61% after 24 h) and pH 7 (55% after 120 h) compared with the native enzyme, which was almost completely inactivated. The introduction of extra solvent-exposed basic residues and an additional disulfide bond into the above variant further improved the stability at acidic pH (85% residual activity at pH 3.5 after 24 h when introduced separately, and 64% at pH 3 when introduced together). The analysis of the results provides a rational explanation to the pH stability improvement achieved.
Collapse
Affiliation(s)
| | | | - Francisco Javier Medrano
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- * E-mail: (FJM, for questions related to obtaining X-ray crystal structures); (ATM); (FJR-D)
| | - Antonio Romero
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- * E-mail: (FJM, for questions related to obtaining X-ray crystal structures); (ATM); (FJR-D)
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- * E-mail: (FJM, for questions related to obtaining X-ray crystal structures); (ATM); (FJR-D)
| |
Collapse
|
37
|
Palma C, Lloret L, Sepúlveda L, Contreras E. Production of versatile peroxidase from Pleurotus eryngii by solid-state fermentation using agricultural residues and evaluation of its catalytic properties. Prep Biochem Biotechnol 2015; 46:200-7. [PMID: 26444982 DOI: 10.1080/10826068.2015.1084513] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Interest in production of ligninolytic enzymes has been growing over recent years for their use in various applications such as recalcitrant pollutants bioremediation; specifically, versatile peroxidase (VP) presents a great potential due to its catalytic versatility. The proper selection of the fermentation mode and the culture medium should be an imperative to ensure a successful production by an economic and available medium that favors the process viability. VP was produced by solid-state fermentation (SSF) of Pleurotus eryngii, using the agricultural residue banana peel as growth medium; an enzymatic activity of 10,800 U L(-1) (36 U g(-1) of substrate) was detected after 18 days, whereas only 1800 U L(-1) was reached by conventional submerged fermentation (SF) with glucose-based medium. The kinetic parameters were determined by evaluating the H2O2 and Mn(2+) concentration effects on the Mn(3+)-tartrate complex formation. The results indicated that although the H2O2 inhibitory effect was observed for the enzyme produced by both media, the reaction rates for VP obtained by SSF were less impacted. This outcome suggests the presence of substances released from banana peel during the fermentation, which might exhibit a protective effect resulting in an improved kinetic behavior of the enzyme.
Collapse
Affiliation(s)
- C Palma
- a Departamento de Ingeniería Química y Ambiental , Universidad Técnica Federico Santa María , Santiago , Chile
| | - L Lloret
- a Departamento de Ingeniería Química y Ambiental , Universidad Técnica Federico Santa María , Santiago , Chile
| | - L Sepúlveda
- b Departamento de Ingeniería Química , Universidad de Santiago de Chile , Santiago , Chile
| | - E Contreras
- b Departamento de Ingeniería Química , Universidad de Santiago de Chile , Santiago , Chile
| |
Collapse
|
38
|
Sáez-Jiménez V, Baratto MC, Pogni R, Rencoret J, Gutiérrez A, Santos JI, Martínez AT, Ruiz-Dueñas FJ. Demonstration of Lignin-to-Peroxidase Direct Electron Transfer: A TRANSIENT-STATE KINETICS, DIRECTED MUTAGENESIS, EPR, AND NMR STUDY. J Biol Chem 2015; 290:23201-13. [PMID: 26240145 PMCID: PMC4645588 DOI: 10.1074/jbc.m115.665919] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Indexed: 11/23/2022] Open
Abstract
Versatile peroxidase (VP) is a high redox-potential peroxidase of biotechnological interest that is able to oxidize phenolic and non-phenolic aromatics, Mn2+, and different dyes. The ability of VP from Pleurotus eryngii to oxidize water-soluble lignins (softwood and hardwood lignosulfonates) is demonstrated here by a combination of directed mutagenesis and spectroscopic techniques, among others. In addition, direct electron transfer between the peroxidase and the lignin macromolecule was kinetically characterized using stopped-flow spectrophotometry. VP variants were used to show that this reaction strongly depends on the presence of a solvent-exposed tryptophan residue (Trp-164). Moreover, the tryptophanyl radical detected by EPR spectroscopy of H2O2-activated VP (being absent from the W164S variant) was identified as catalytically active because it was reduced during lignosulfonate oxidation, resulting in the appearance of a lignin radical. The decrease of lignin fluorescence (excitation at 355 nm/emission at 400 nm) during VP treatment under steady-state conditions was accompanied by a decrease of the lignin (aromatic nuclei and side chains) signals in one-dimensional and two-dimensional NMR spectra, confirming the ligninolytic capabilities of the enzyme. Simultaneously, size-exclusion chromatography showed an increase of the molecular mass of the modified residual lignin, especially for the (low molecular mass) hardwood lignosulfonate, revealing that the oxidation products tend to recondense during the VP treatment. Finally, mutagenesis of selected residues neighboring Trp-164 resulted in improved apparent second-order rate constants for lignosulfonate reactions, revealing that changes in its protein environment (modifying the net negative charge and/or substrate accessibility/binding) can modulate the reactivity of the catalytic tryptophan.
Collapse
Affiliation(s)
- Verónica Sáez-Jiménez
- From the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Maria Camilla Baratto
- the Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, I-53100 Siena, Italy
| | - Rebecca Pogni
- the Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro, I-53100 Siena, Italy
| | - Jorge Rencoret
- the Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, P. O. Box 1052, E-41080 Seville, Spain, and
| | - Ana Gutiérrez
- the Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, P. O. Box 1052, E-41080 Seville, Spain, and
| | - José Ignacio Santos
- the NMR Facility, SGIKER, Universidad del País Vasco, UPV/EHU Donostia, 48940 Leioa, Bizkaia Spain
| | - Angel T Martínez
- From the Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain,
| | | |
Collapse
|
39
|
Characterization and application of a novel class II thermophilic peroxidase from Myceliophthora thermophila in biosynthesis of polycatechol. Enzyme Microb Technol 2015; 75-76:49-56. [DOI: 10.1016/j.enzmictec.2015.04.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 04/24/2015] [Accepted: 04/28/2015] [Indexed: 12/22/2022]
|
40
|
Baratto MC, Juarez-Moreno K, Pogni R, Basosi R, Vazquez-Duhalt R. EPR and LC-MS studies on the mechanism of industrial dye decolorization by versatile peroxidase from Bjerkandera adusta. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:8683-8692. [PMID: 25567062 DOI: 10.1007/s11356-014-4051-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
The mechanisms of industrial dye transformation by versatile peroxidase were elucidated. Purified versatile peroxidase from Bjerkandera adusta was able to decolorize different classes of dyes including azo and phthalocyanines, but unable to transform any of the anthraquinones tested. Kinetic constants for selected dyes were determined and the transformation products were analyzed by EPR spectroscopy and mass spectrometry. The EPR and MS analyses of the enzymatic decolorization products showed the cleavage of the azo bond in azo dyes and the total disruption of the phthalocyaninic ring in phthalocyanine dyes. The EPR analysis on two copper-containing dyes, reactive violet 5 (azo) and reactive blue 72 (phthalocyanine), showed that the transformation can or not break the metal-ion coordination bond according the dye nature. The role of the catalytic Trp172 in the dye transformation by a long-range electron transfer pathway was confirmed and the oxidation mechanisms are proposed and discussed.
Collapse
Affiliation(s)
- Maria Camilla Baratto
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | | | | | | | | |
Collapse
|
41
|
Sáez-Jiménez V, Acebes S, Guallar V, Martínez AT, Ruiz-Dueñas FJ. Improving the oxidative stability of a high redox potential fungal peroxidase by rational design. PLoS One 2015; 10:e0124750. [PMID: 25923713 PMCID: PMC4414599 DOI: 10.1371/journal.pone.0124750] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/05/2015] [Indexed: 11/19/2022] Open
Abstract
Ligninolytic peroxidases are enzymes of biotechnological interest due to their ability to oxidize high redox potential aromatic compounds, including the recalcitrant lignin polymer. However, different obstacles prevent their use in industrial and environmental applications, including low stability towards their natural oxidizing-substrate H2O2. In this work, versatile peroxidase was taken as a model ligninolytic peroxidase, its oxidative inactivation by H2O2 was studied and different strategies were evaluated with the aim of improving H2O2 stability. Oxidation of the methionine residues was produced during enzyme inactivation by H2O2 excess. Substitution of these residues, located near the heme cofactor and the catalytic tryptophan, rendered a variant with a 7.8-fold decreased oxidative inactivation rate. A second strategy consisted in mutating two residues (Thr45 and Ile103) near the catalytic distal histidine with the aim of modifying the reactivity of the enzyme with H2O2. The T45A/I103T variant showed a 2.9-fold slower reaction rate with H2O2 and 2.8-fold enhanced oxidative stability. Finally, both strategies were combined in the T45A/I103T/M152F/M262F/M265L variant, whose stability in the presence of H2O2 was improved 11.7-fold. This variant showed an increased half-life, over 30 min compared with 3.4 min of the native enzyme, under an excess of 2000 equivalents of H2O2. Interestingly, the stability improvement achieved was related with slower formation, subsequent stabilization and slower bleaching of the enzyme Compound III, a peroxidase intermediate that is not part of the catalytic cycle and leads to the inactivation of the enzyme.
Collapse
Affiliation(s)
- Verónica Sáez-Jiménez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sandra Acebes
- Joint Barcelona Supercomputing Center—Centre for Genomic Regulation, Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Victor Guallar
- Joint Barcelona Supercomputing Center—Centre for Genomic Regulation, Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail:
| |
Collapse
|
42
|
Ligninolytic Enzymes for Water Depollution, Coal Breakdown, and Paper Industry. ENVIRONMENTAL CHEMISTRY FOR A SUSTAINABLE WORLD 2015. [DOI: 10.1007/978-3-319-11906-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
43
|
Microbial enzyme systems for lignin degradation and their transcriptional regulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1336-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
44
|
Nousiainen P, Kontro J, Manner H, Hatakka A, Sipilä J. Phenolic mediators enhance the manganese peroxidase catalyzed oxidation of recalcitrant lignin model compounds and synthetic lignin. Fungal Genet Biol 2014; 72:137-149. [DOI: 10.1016/j.fgb.2014.07.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/18/2014] [Accepted: 07/19/2014] [Indexed: 11/29/2022]
|
45
|
Gonzalez-Perez D, Garcia-Ruiz E, Ruiz-Dueñas FJ, Martinez AT, Alcalde M. Structural Determinants of Oxidative Stabilization in an Evolved Versatile Peroxidase. ACS Catal 2014. [DOI: 10.1021/cs501218v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Gonzalez-Perez
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
| | - Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | | | - Angel T. Martinez
- Biological Research Centre, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
46
|
Kim YH, Lee HS, Kwon HJ, Patnaik BB, Nam KW, Han YS, Bang IS, Han MD. Effects of different selenium levels on growth and regulation of laccase and versatile peroxidase in white-rot fungus, Pleurotus eryngii. World J Microbiol Biotechnol 2014; 30:2101-9. [DOI: 10.1007/s11274-014-1636-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 03/11/2014] [Indexed: 12/17/2022]
|
47
|
Moreno AD, Ibarra D, Alvira P, Tomás-Pejó E, Ballesteros M. A review of biological delignification and detoxification methods for lignocellulosic bioethanol production. Crit Rev Biotechnol 2014; 35:342-54. [DOI: 10.3109/07388551.2013.878896] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
48
|
Fernández-Fueyo E, Ruiz-Dueñas FJ, Martínez MJ, Romero A, Hammel KE, Medrano FJ, Martínez AT. Ligninolytic peroxidase genes in the oyster mushroom genome: heterologous expression, molecular structure, catalytic and stability properties, and lignin-degrading ability. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:2. [PMID: 24387130 PMCID: PMC3902061 DOI: 10.1186/1754-6834-7-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/16/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND The genome of Pleurotus ostreatus, an important edible mushroom and a model ligninolytic organism of interest in lignocellulose biorefineries due to its ability to delignify agricultural wastes, was sequenced with the purpose of identifying and characterizing the enzymes responsible for lignin degradation. RESULTS Heterologous expression of the class II peroxidase genes, followed by kinetic studies, enabled their functional classification. The resulting inventory revealed the absence of lignin peroxidases (LiPs) and the presence of three versatile peroxidases (VPs) and six manganese peroxidases (MnPs), the crystal structures of two of them (VP1 and MnP4) were solved at 1.0 to 1.1 Å showing significant structural differences. Gene expansion supports the importance of both peroxidase types in the white-rot lifestyle of this fungus. Using a lignin model dimer and synthetic lignin, we showed that VP is able to degrade lignin. Moreover, the dual Mn-mediated and Mn-independent activity of P. ostreatus MnPs justifies their inclusion in a new peroxidase subfamily. The availability of the whole POD repertoire enabled investigation, at a biochemical level, of the existence of duplicated genes. Differences between isoenzymes are not limited to their kinetic constants. Surprising differences in their activity T50 and residual activity at both acidic and alkaline pH were observed. Directed mutagenesis and spectroscopic/structural information were combined to explain the catalytic and stability properties of the most interesting isoenzymes, and their evolutionary history was analyzed in the context of over 200 basidiomycete peroxidase sequences. CONCLUSIONS The analysis of the P. ostreatus genome shows a lignin-degrading system where the role generally played by LiP has been assumed by VP. Moreover, it enabled the first characterization of the complete set of peroxidase isoenzymes in a basidiomycete, revealing strong differences in stability properties and providing enzymes of biotechnological interest.
Collapse
Affiliation(s)
- Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Francisco J Ruiz-Dueñas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Antonio Romero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Kenneth E Hammel
- US Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Francisco Javier Medrano
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
| |
Collapse
|
49
|
Bao X, Huang X, Lu X, Li JJ. Improvement of hydrogen peroxide stability of Pleurotus eryngii versatile ligninolytic peroxidase by rational protein engineering. Enzyme Microb Technol 2014; 54:51-8. [DOI: 10.1016/j.enzmictec.2013.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 11/16/2022]
|
50
|
Daniel G. Fungal and Bacterial Biodegradation: White Rots, Brown Rots, Soft Rots, and Bacteria. ACS SYMPOSIUM SERIES 2014. [DOI: 10.1021/bk-2014-1158.ch002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Geoffrey Daniel
- Department of Forest Products/Wood Science, Swedish University of Agricultural Sciences, Box 7008, Uppsala, Sweden
| |
Collapse
|