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Magaña-Ortiz D, López-Castillo LM, Amezquita-Novelo R. White-rot fungus Phlebia floridensis ITM 12: Laccase production, oxidoreductase profile, and hydrogen-peroxide independent activity. J Basic Microbiol 2024; 64:106-118. [PMID: 37840353 DOI: 10.1002/jobm.202300462] [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: 08/10/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
Phlebia genus is a relevant group of fungi with a crucial role in numerous ecosystems. In tropical and subtropical areas this genus allows the efficient degradation of lignin and carbon recovery; however, the majority of these fungal species remain undiscovered. The main purpose of this work was to determine the enzymatic activity of extracellular proteins of a novel Phlebia floridensis strain isolated in Yucatan Peninsula, Mexico. The results that are reported here demonstrate that the soluble protein extract of P. floridensis can degrade a broad spectrum of recalcitrant compounds. This induced protein extract is able to modify not only phenolic and nonphenolic compounds, but also anthroquinone dyes, even without the addition of exogenous hydrogen peroxide. Using liquid chromatography-mass spectrometry (LC-MS), we were able to identify a novel chloroperoxidase in enzymatic extract. As far as we know, this is the first report about the presence of this type of enzyme in the Phlebia genus.
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Affiliation(s)
- Denis Magaña-Ortiz
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I. T. Mérida, Mérida, Yucatán, México
| | - Laura M López-Castillo
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Monterrey, Nuevo Léon, Mexico
| | - Roberto Amezquita-Novelo
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I. T. Mérida, Mérida, Yucatán, México
- Departamento de Ingeniería Química y Bioquímica, Tecnólogico Nacional de México/I. T. Morelia, Col. Lomas de Santiaguito, Morelia, Michoacán, México
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2
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Mali T, Laine K, Hamberg L, Lundell T. Metabolic activities and ultrastructure imaging at late-stage of wood decomposition in interactive brown rot - white rot fungal combinations. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Optimization and Implementation of Fed-Batch Strategy to Produce Ligninolytic Enzyme from the White-Rot Basidiomycete Pycnoporus sanguineus in Bubble Column Reactor. FERMENTATION 2022. [DOI: 10.3390/fermentation8090418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The current work evaluates the production of ligninolytic enzyme optimization via response surface methodology using different inducers: acid cellulignin (CA); MnSO4 (Mn2+); CuSO4·5H2O (Cu2+); veratryl (3, 4-dimethoxybenzyl); alcohol (VA); Tween 80% (T80); and the carbon-to-nitrogen ratio (C/N). A further goal was implementing a fed-batch strategy to produce ligninolytic enzyme extracts from P. sanguineus 2512 using a bubble column reactor (BCR). The best optimized experimental condition in the shake flasks was a 7.5 C/N ratio, 0.025 g/L Cu2+, 1.5 mM Mn2+, 3.0 mM VA and 0.025 mM T80, resulting in 64,580, 9.10 and 80.72 U/L for Laccase (Lac), Manganese (MnP) and Lignin peroxidase (LiP) activities, respectively. In the BCR, three feedings were performed at 24 h intervals on the 6th, 7th and 8th days with a significant increase in Lac (99,600 U/L) and MnP (47.53 U/L) activities on the 8th day and a reduction on the 9th day of cultivation. The LiP activity peak was achieved on the 5th day (416 U/L) of cultivation, decreasing thereafter. Enzyme cocktails concentrated in hollow fiber in the third cultivation batch showed contents of 4 × 105 U/L, 220 U/L and 2.5 g/L for Lac, MnP and total proteins, respectively. The enzymatic cocktail with the highest LiP activity (1200 U/L) was obtained in the first batch. The results showed that the optimization of the biosynthesis of the ligninolytic enzymes provided satisfactory improvement in terms of Lac and MnP production per run.
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4
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Draft Genome Sequences of 19 Clinical Isolates of Candida auris from Hong Kong. Microbiol Resour Announc 2021; 10:10/1/e00308-20. [PMID: 33414279 PMCID: PMC8407681 DOI: 10.1128/mra.00308-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Candida auris is an emerging human pathogen associated with multidrug resistance and nosocomial outbreaks. We report the draft genome sequences of 19 C. auris isolates that were associated with a cluster of cases in a hospital in Hong Kong. Candida auris is an emerging human pathogen associated with multidrug resistance and nosocomial outbreaks. We report the draft genome sequences of 19 C. auris isolates that were associated with a cluster of cases in a hospital in Hong Kong.
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Mali T, Mäki M, Hellén H, Heinonsalo J, Bäck J, Lundell T. Decomposition of spruce wood and release of volatile organic compounds depend on decay type, fungal interactions and enzyme production patterns. FEMS Microbiol Ecol 2020; 95:5554004. [PMID: 31494677 PMCID: PMC6736282 DOI: 10.1093/femsec/fiz135] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 08/22/2019] [Indexed: 01/18/2023] Open
Abstract
Effect of three wood-decaying fungi on decomposition of spruce wood was studied in solid-state cultivation conditions for a period of three months. Two white rot species (Trichaptum abietinum and Phlebia radiata) were challenged by a brown rot species (Fomitopsis pinicola) in varying combinations. Wood decomposition patterns as determined by mass loss, carbon to nitrogen ratio, accumulation of dissolved sugars and release of volatile organic compounds (VOCs) were observed to depend on both fungal combinations and growth time. Similar dependence of fungal species combination, either white or brown rot dominated, was observed for secreted enzyme activities on spruce wood. Fenton chemistry suggesting reduction of Fe3+ to Fe2+ was detected in the presence of F. pinicola, even in co-cultures, together with substantial degradation of wood carbohydrates and accumulation of oxalic acid. Significant correlation was perceived with two enzyme activity patterns (oxidoreductases produced by white rot fungi; hydrolytic enzymes produced by the brown rot fungus) and wood degradation efficiency. Moreover, emission of four signature VOCs clearly grouped the fungal combinations. Our results indicate that fungal decay type, either brown or white rot, determines the loss of wood mass and decomposition of polysaccharides as well as the pattern of VOCs released upon fungal growth on spruce wood.
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Affiliation(s)
- Tuulia Mali
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland
| | - Mari Mäki
- Department of Forest Sciences, University of Helsinki, Viikki Campus, P.O.Box 27, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland
| | - Heidi Hellén
- Finnish Meteorological Institute, P.O.Box 503, FI-00101 Helsinki, Finland
| | - Jussi Heinonsalo
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland.,Finnish Meteorological Institute, P.O.Box 503, FI-00101 Helsinki, Finland
| | - Jaana Bäck
- Department of Forest Sciences, University of Helsinki, Viikki Campus, P.O.Box 27, FI-00014 Helsinki, Finland.,Institute for Atmospheric and Earth System Research, University of Helsinki, FI-00014 Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, University of Helsinki, Viikki Campus, P.O.Box 56, FI-00014 Helsinki, Finland
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6
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Mäkinen M, Kuuskeri J, Laine P, Smolander OP, Kovalchuk A, Zeng Z, Asiegbu FO, Paulin L, Auvinen P, Lundell T. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics 2019; 20:430. [PMID: 31138126 PMCID: PMC6540522 DOI: 10.1186/s12864-019-5817-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol from various waste lignocellulose substrates. Thus, P. radiata is a promising organism for biotechnological applications aiming at sustainable utilization of plant biomass. Here we report the genome sequence of P. radiata isolate 79 originally isolated from decayed alder wood in South Finland. To better understand the evolution of wood decay mechanisms in this fungus and the Polyporales phlebioid clade, gene content and clustering of genes encoding specific carbohydrate-active enzymes (CAZymes) in seven closely related fungal species was investigated. In addition, other genes encoding proteins reflecting the fungal lifestyle including peptidases, transporters, small secreted proteins and genes involved in secondary metabolism were identified in the genome assembly of P. radiata. RESULTS The PACBio sequenced nuclear genome of P. radiata was assembled to 93 contigs with 72X sequencing coverage and annotated, revealing a dense genome of 40.4 Mbp with approximately 14 082 predicted protein-coding genes. According to functional annotation, the genome harbors 209 glycoside hydrolase, 27 carbohydrate esterase, 8 polysaccharide lyase, and over 70 auxiliary redox enzyme-encoding genes. Comparisons with the genomes of other phlebioid fungi revealed shared and specific properties among the species with seemingly similar saprobic wood-decay lifestyles. Clustering of especially GH10 and AA9 enzyme-encoding genes according to genomic localization was discovered to be conserved among the phlebioid species. In P. radiata genome, a rich repertoire of genes involved in the production of secondary metabolites was recognized. In addition, 49 genes encoding predicted ABC proteins were identified in P. radiata genome together with 336 genes encoding peptidases, and 430 genes encoding small secreted proteins. CONCLUSIONS The genome assembly of P. radiata contains wide array of carbohydrate polymer attacking CAZyme and oxidoreductase genes in a composition identifiable for phlebioid white rot lifestyle in wood decomposition, and may thus serve as reference for further studies. Comparative genomics also contributed to enlightening fungal decay mechanisms in conversion and cycling of recalcitrant organic carbon in the forest ecosystems.
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Affiliation(s)
- Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.,Present address: VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Jaana Kuuskeri
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland
| | - Pia Laine
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland.,Present address: Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Zhen Zeng
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.
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7
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Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens. Microbiol Resour Announc 2019; 8:8/18/e00264-19. [PMID: 31048399 PMCID: PMC6498232 DOI: 10.1128/mra.00264-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Here, we report the draft genome sequences of three isolates of the wood-decaying white-rot basidiomycete fungus Dichomitus squalens. The genomes of these monokaryons were sequenced to provide more information on the intraspecies genomic diversity of this fungus and were compared to the previously sequenced genome of D. squalens LYAD-421 SS1. Here, we report the draft genome sequences of three isolates of the wood-decaying white-rot basidiomycete fungus Dichomitus squalens. The genomes of these monokaryons were sequenced to provide more information on the intraspecies genomic diversity of this fungus and were compared to the previously sequenced genome of D. squalens LYAD-421 SS1.
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8
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Upscale and characterization of lignin-modifying enzymes from Marasmiellus palmivorus VE111 in a bioreactor under parameter optimization and the effect of inducers. J Biotechnol 2019; 295:1-8. [DOI: 10.1016/j.jbiotec.2019.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 11/22/2022]
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9
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Sekan AS, Myronycheva OS, Karlsson O, Gryganskyi AP, Blume Y. Green potential of Pleurotus spp. in biotechnology. PeerJ 2019; 7:e6664. [PMID: 30967974 PMCID: PMC6446892 DOI: 10.7717/peerj.6664] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/22/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The genus Pleurotus is most exploitable xylotrophic fungi, with valuable biotechnological, medical, and nutritional properties. The relevant features of the representatives of this genus to provide attractive low-cost industrial tools have been reported in numerous studies to resolve the pressure of ecological issues. Additionally, a number of Pleurotus species are highly adaptive, do not require any special conditions for growth, and possess specific resistance to contaminating diseases and pests. The unique properties of Pleurotus species widely used in many environmental technologies, such as organic solid waste recycling, chemical pollutant degradation, and bioethanol production. METHODOLOGY The literature study encompasses peer-reviewed journals identified by systematic searches of electronic databases such as Google Scholar, NCBI, Springer, ResearchGate, ScienceDirect, and ISI Web of Knowledge. The search scheme was divided into several steps, as described below. RESULTS In this review, we describe studies examining the biotechnological feasibility of Pleurotus spp. to elucidate the importance of this genus for use in green technology. Here, we review areas of application of the genus Pleurotus as a prospective biotechnological tool. CONCLUSION The incomplete description of some fungal biochemical pathways emphasises the future research goals for this fungal culture.
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Affiliation(s)
- Alona S. Sekan
- Institute of Food Biotechnology and Genomics, National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Olena S. Myronycheva
- Division of Wood Science and Engineering, Department of Engineering Sciences and Mathematics, Lulea University of Technology, Skelleftea, Sweden
| | - Olov Karlsson
- Division of Wood Science and Engineering, Department of Engineering Sciences and Mathematics, Lulea University of Technology, Skelleftea, Sweden
| | | | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Science of Ukraine, Kyiv, Ukraine
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Reina R, Kellner H, Hess J, Jehmlich N, García-Romera I, Aranda E, Hofrichter M, Liers C. Genome and secretome of Chondrostereum purpureum correspond to saprotrophic and phytopathogenic life styles. PLoS One 2019; 14:e0212769. [PMID: 30822315 PMCID: PMC6396904 DOI: 10.1371/journal.pone.0212769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/09/2019] [Indexed: 11/28/2022] Open
Abstract
The basidiomycete Chondrostereum purpureum (Silverleaf fungus) is a saprotroph and plant pathogen commercially used for combatting forest "weed" trees in vegetation management. However, little is known about its lignocellulose-degrading capabilities and the enzymatic machinery that is responsible for the degradative potential, and it is not yet clear to which group of wood-rot fungi it actually belongs. Here, we sequenced and analyzed the draft genome of C. purpureum (41.2 Mbp) and performed a quantitative proteomic approach during growth in submerged and solid-state cultures based on soybean meal suspension or containing beech wood supplemented with phenol-rich olive mill residues, respectively. The fungus harbors characteristic lignocellulolytic hydrolases (GH6 and GH7) and oxidoreductases (e.g. laccase, heme peroxidases). High abundance of some of these genes (e.g. 45 laccases, nine GH7) can be explained by gene expansion, e.g. identified for the laccase orthogroup ORTHOMCL11 that exhibits a total of 18 lineage-specific duplications. Other expanded genes families encode for proteins more related to a pathogenic lifestyle (e.g. protease and cytochrome P450s). The fungus responds to the presence of complex growth substrates (lignocellulose, phenolic residues) by the secretion of most of these lignocellulolytic and lignin-modifying enzymes (e.g. alcohol and aryl alcohol oxidases, laccases, GH6, GH7). Based on the genetic and enzymatic constitution, we consider the 'marasmioid' fungus C. purpureum as a 'phytopathogenic' white-rot fungus (WRF) that possesses a complex extracellular enzyme machinery to accomplish efficient lignocellulose degradation during both saprotrophic and phytopathogenic life phases.
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Affiliation(s)
- Rocio Reina
- Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Harald Kellner
- Unit of Environmental Biotechnology, Dresden University of Technology, International Institute Zittau, Zittau, Germany
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Immaculada García-Romera
- Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Elisabet Aranda
- Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Martin Hofrichter
- Unit of Environmental Biotechnology, Dresden University of Technology, International Institute Zittau, Zittau, Germany
| | - Christiane Liers
- Unit of Environmental Biotechnology, Dresden University of Technology, International Institute Zittau, Zittau, Germany
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11
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Varriale S, Houbraken J, Granchi Z, Pepe O, Cerullo G, Ventorino V, Chin-A-Woeng T, Meijer M, Riley R, Grigoriev IV, Henrissat B, de Vries RP, Faraco V. Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion. Mycologia 2018; 110:316-324. [PMID: 29843575 DOI: 10.1080/00275514.2018.1456835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A novel fungal species able to synthesize enzymes with potential synergistic actions in lignocellulose conversion was isolated from the biomass of Arundo donax during biodegradation under natural conditions in the Gussone Park of the Royal Palace of Portici (Naples, Italy). In this work, this species was subjected to morphological and phylogenetic analyses. Sequencing of its genome was performed, resulting in 28 scaffolds that were assembled into 27.05 Mb containing 9744 predicted genes, among which 396 belong to carbohydrate-active enzyme (CAZyme)-encoding genes. Here we describe and illustrate this previously unknown species, which was named Talaromyces borbonicus, by a polyphasic approach combining phenotypic, physiological, and sequence data.
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Affiliation(s)
- Simona Varriale
- a Department of Chemical Sciences , University of Naples Federico II, Complesso Universitario Monte S. Angelo , via Cintia, 4 80126 Naples , Italy
| | - Jos Houbraken
- b Department of Applied and Industrial Mycology , Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
| | - Zoraide Granchi
- c GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden , The Netherlands
| | - Olimpia Pepe
- d Department of Agricultural Sciences , University of Naples Federico II , Via Università 100, 80055 Portici (NA) , Italy
| | - Gabriella Cerullo
- a Department of Chemical Sciences , University of Naples Federico II, Complesso Universitario Monte S. Angelo , via Cintia, 4 80126 Naples , Italy
| | - Valeria Ventorino
- d Department of Agricultural Sciences , University of Naples Federico II , Via Università 100, 80055 Portici (NA) , Italy
| | | | - Martin Meijer
- b Department of Applied and Industrial Mycology , Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
| | - Robert Riley
- f US Department of Energy Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek , California 94598
| | - Igor V Grigoriev
- f US Department of Energy Joint Genome Institute , 2800 Mitchell Drive, Walnut Creek , California 94598
| | - Bernard Henrissat
- g Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS , Université Aix-Marseille , 163 Avenue de Luminy, 13288 , Marseille , France.,h INRA, USC 1408 AFMB, 13288 , Marseille , France.,i Department of Biological Sciences , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Ronald P de Vries
- j Department of Fungal Physiology , Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands.,k Department of Fungal Molecular Physiology , Utrecht University , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands
| | - Vincenza Faraco
- a Department of Chemical Sciences , University of Naples Federico II, Complesso Universitario Monte S. Angelo , via Cintia, 4 80126 Naples , Italy
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12
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Mäkinen MA, Risulainen N, Mattila H, Lundell TK. Transcription of lignocellulose-decomposition associated genes, enzyme activities and production of ethanol upon bioconversion of waste substrate by Phlebia radiata. Appl Microbiol Biotechnol 2018; 102:5657-5672. [PMID: 29728725 DOI: 10.1007/s00253-018-9045-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/17/2018] [Accepted: 04/21/2018] [Indexed: 12/30/2022]
Abstract
Previously identified twelve plant cell wall degradation-associated genes of the white rot fungus Phlebia radiata were studied by RT-qPCR in semi-aerobic solid-state cultures on lignocellulose waste material, and on glucose-containing reference medium. Wood-decay-involved enzyme activities and ethanol production were followed to elucidate both the degradative and fermentative processes. On the waste lignocellulose substrate, P. radiata carbohydrate-active enzyme (CAZy) genes encoding cellulolytic and hemicellulolytic activities were significantly upregulated whereas genes involved in lignin modification displayed a more complex response. Two lignin peroxidase genes were differentially expressed on waste lignocellulose compared to glucose medium, whereas three manganese peroxidase-encoding genes were less affected. On the contrary, highly significant difference was noticed for three cellulolytic genes (cbhI_1, eg1, bgl1) with higher expression levels on the lignocellulose substrate than on glucose. This indicates expression of the wood-attacking degradative enzyme system by the fungus also on the recycled, waste core board material. During the second week of cultivation, ethanol production increased on the core board to 0.24 g/L, and extracellular activities against cellulose, xylan, and lignin were detected. Sugar release from the solid lignocellulose resulted with concomitant accumulation of ethanol as fermentation product. Our findings confirm that the fungus activates its white rot decay system also on industrially processed lignocellulose adopted as growth substrate, and under semi-aerobic cultivation conditions. Thus, P. radiata is a good candidate for lignocellulose-based renewable biotechnology to make biofuels and biocompounds from materials with less value for recycling or manufacturing.
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Affiliation(s)
- Mari A Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland.
| | - Netta Risulainen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Hans Mattila
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Taina K Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
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13
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Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga. GENOME ANNOUNCEMENTS 2018; 6:6/14/e01414-17. [PMID: 29622620 PMCID: PMC5887033 DOI: 10.1128/genomea.01414-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the genome sequence of wood-decaying white-rot fungus Phlebia centrifuga strain FBCC195, isolated from Norway spruce (Picea abies) in Finnish Lapland. The 34.66-Mb genome containing 13,785 gene models is similar to the genome length reported for other saprobic white-rot species.
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14
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Abstract
Here we present the draft genome sequence of the fungus Talaromyces adpressus A-T1C-84X (=CBS 142503). This strain was isolated from lignocellulosic biomass of Arundo donax during biodegradation under natural conditions in the Gussone Park of the Royal Palace of Portici, Naples, Italy.
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15
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Reina R, García-Sánchez M, Liers C, García-Romera I, Aranda E. An Overview of Fungal Applications in the Valorization of Lignocellulosic Agricultural By-Products: The Case of Two-Phase Olive Mill Wastes. Fungal Biol 2018. [DOI: 10.1007/978-3-319-77386-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Tanaka Y, Suzuki T, Kurokura T, Iigo M, Toyama F, Habu N, Dohra H, Konno N. The complete genome sequence and phylogenetic analysis of the mitochondrial DNA of the wood-decaying fungus Fomitopsis palustris. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0603-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mali T, Kuuskeri J, Shah F, Lundell TK. Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes. PLoS One 2017; 12:e0185171. [PMID: 28953947 PMCID: PMC5617175 DOI: 10.1371/journal.pone.0185171] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/07/2017] [Indexed: 12/21/2022] Open
Abstract
Fomitopsis pinicola is a species of Polyporales frequently encountered in Nordic temperate and boreal forests. In nature, the fungus causes destructive brown rot in wood, colonizing tree trunks often occupied by other Basidiomycota species. We mimicked these species-species interactions by introducing F. pinicola to five white rot species, all common saprotrophs of Norway spruce. Hyphal interactions and mycelial growth in various combinations were recorded, while activities of lignocellulose-acting CAZymes and oxidoreductases were followed in co-cultures on two different carbon-source media. Of the species, Phlebia radiata and Trichaptum abietinum were the strongest producers of lignin-modifying oxidoreductases (laccase, manganese peroxidase) when evaluated alone, as well as in co-cultures, on the two different growth media (low-nitrogen liquid medium containing ground coniferous wood, and malt extract broth). F. pinicola was an outstanding producer of oxalic acid (up to 61 mM), whereas presence of P. radiata prevented acidification of the growth environment in the liquid malt-extract cultures. When enzyme profiles of the species combinations were clustered, time-dependent changes were observed on wood-supplemented medium during the eight weeks of growth. End-point acidity and production of mycelium, oxalic acid and oxidoreductase activities, in turn clustered the fungal combinations into three distinct functional groups, determined by the presence of F. pinicola and P. radiata, by principal component analysis. Our findings indicate that combinations of wood-decay fungi have dramatic dynamic effects on the production of lignocellulose-active enzymes, which may lead to divergent degradative processes of dead wood and forest litter.
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Affiliation(s)
- Tuulia Mali
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Jaana Kuuskeri
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Firoz Shah
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
| | - Taina Kristina Lundell
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Campus, University of Helsinki, Helsinki, Finland
- * E-mail:
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Torres-Farradá G, Manzano León AM, Rineau F, Ledo Alonso LL, Sánchez-López MI, Thijs S, Colpaert J, Ramos-Leal M, Guerra G, Vangronsveld J. Diversity of Ligninolytic Enzymes and Their Genes in Strains of the Genus Ganoderma: Applicable for Biodegradation of Xenobiotic Compounds? Front Microbiol 2017; 8:898. [PMID: 28588565 PMCID: PMC5440474 DOI: 10.3389/fmicb.2017.00898] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
White-rot fungi (WRF) and their ligninolytic enzymes (laccases and peroxidases) are considered promising biotechnological tools to remove lignin related Persistent Organic Pollutants from industrial wastewaters and contaminated ecosystems. A high diversity of the genus Ganoderma has been reported in Cuba; in spite of this, the diversity of ligninolytic enzymes and their genes remained unexplored. In this study, 13 native WRF strains were isolated from decayed wood in urban ecosystems in Havana (Cuba). All strains were identified as Ganoderma sp. using a multiplex polymerase chain reaction (PCR)-method based on ITS sequences. All Ganoderma sp. strains produced laccase enzymes at higher levels than non-specific peroxidases. Native-PAGE of extracellular enzymatic extracts revealed a high diversity of laccase isozymes patterns between the strains, suggesting the presence of different amino acid sequences in the laccase enzymes produced by these Ganoderma strains. We determined the diversity of genes encoding laccases and peroxidases using a PCR and cloning approach with basidiomycete-specific primers. Between two and five laccase genes were detected in each strain. In contrast, only one gene encoding manganese peroxidase or versatile peroxidase was detected in each strain. The translated laccases and peroxidases amino acid sequences have not been described before. Extracellular crude enzymatic extracts produced by the Ganoderma UH strains, were able to degrade model chromophoric compounds such as anthraquinone and azo dyes. These findings hold promises for the development of a practical application for the treatment of textile industry wastewaters and also for bioremediation of polluted ecosystems by well-adapted native WRF strains.
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Affiliation(s)
- Giselle Torres-Farradá
- Laboratory of Biotechnology, Department of Microbiology and Virology, Faculty of Biology, University of HavanaHavana, Cuba
| | - Ana M Manzano León
- Department of Phytopathology, Research Institute for Tropical Fruit TreesHavana, Cuba
| | - François Rineau
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityHasselt, Belgium
| | - Lucía L Ledo Alonso
- Laboratory of Biotechnology, Department of Microbiology and Virology, Faculty of Biology, University of HavanaHavana, Cuba
| | - María I Sánchez-López
- Laboratory of Biotechnology, Department of Microbiology and Virology, Faculty of Biology, University of HavanaHavana, Cuba
| | - Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityHasselt, Belgium
| | - Jan Colpaert
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityHasselt, Belgium
| | - Miguel Ramos-Leal
- Department of Phytopathology, Research Institute for Tropical Fruit TreesHavana, Cuba
| | - Gilda Guerra
- Laboratory of Biotechnology, Department of Microbiology and Virology, Faculty of Biology, University of HavanaHavana, Cuba
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityHasselt, Belgium
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Vasina DV, Moiseenko KV, Fedorova TV, Tyazhelova TV. Lignin-degrading peroxidases in white-rot fungus Trametes hirsuta 072. Absolute expression quantification of full multigene family. PLoS One 2017; 12:e0173813. [PMID: 28301519 PMCID: PMC5354401 DOI: 10.1371/journal.pone.0173813] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/27/2017] [Indexed: 11/26/2022] Open
Abstract
Ligninolytic heme peroxidases comprise an extensive family of enzymes, which production is characteristic for white-rot Basidiomycota. The majority of fungal heme peroxidases are encoded by multigene families that differentially express closely related proteins. Currently, there were very few attempts to characterize the complete multigene family of heme peroxidases in a single fungus. Here we are focusing on identification and characterization of peroxidase genes, which are transcribed and secreted by basidiomycete Trametes hirsuta 072, an efficient lignin degrader. The T. hirsuta genome contains 18 ligninolytic peroxidase genes encoding 9 putative lignin peroxidases (LiP), 7 putative short manganese peroxidases (MnP) and 2 putative versatile peroxidases (VP). Using ddPCR method we have quantified the absolute expression of the 18 peroxidase genes under different culture conditions and on different growth stages of basidiomycete. It was shown that only two genes (one MnP and one VP) were prevalently expressed as well as secreted into cultural broth under all conditions investigated. However their transcriptome and protein profiles differed in time depending on the effector used. The expression of other peroxidase genes revealed a significant variability, so one can propose the specific roles of these enzymes in fungal development and lifestyle.
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Affiliation(s)
- Daria V. Vasina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
| | - Konstantin V. Moiseenko
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
- * E-mail:
| | - Tatiana V. Fedorova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
| | - Tatiana V. Tyazhelova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, Russia
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20
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Peng M, Dilokpimol A, Mäkelä MR, Hildén K, Bervoets S, Riley R, Grigoriev IV, Hainaut M, Henrissat B, de Vries RP, Granchi Z. The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi. J Biotechnol 2017; 246:1-3. [DOI: 10.1016/j.jbiotec.2017.02.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/10/2017] [Accepted: 02/13/2017] [Indexed: 01/20/2023]
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21
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Xu H, Guo MY, Gao YH, Bai XH, Zhou XW. Expression and characteristics of manganese peroxidase from Ganoderma lucidum in Pichia pastoris and its application in the degradation of four dyes and phenol. BMC Biotechnol 2017; 17:19. [PMID: 28231778 PMCID: PMC5324234 DOI: 10.1186/s12896-017-0338-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 02/10/2017] [Indexed: 11/16/2022] Open
Abstract
Background Manganese peroxidase (MnP) of white rot basidiomycetes, an extracellular heme enzyme, is part of a peroxidase superfamily that is capable of degrading the different phenolic compounds. Ganoderma, a white rot basidiomycete widely distributed worldwide, could secrete lignin-modifying enzymes (LME), including laccase (Lac), lignin peroxidases (LiP) and MnP. Results After the selection of a G. lucidum strain from five Ganoderma strains, the 1092 bp full-length cDNA of the MnP gene, designated as G. lucidum MnP (GluMnP1), was cloned from the selected strain. We subsequently constructed an eukaryotic expression vector, pAO815:: GlMnP, and transferred it into Pichia pastoris SMD116. Recombinant GluMnP1 (rGluMnP1) was with a yield of 126 mg/L and a molecular weight of approximately 37.72 kDa and a specific enzyme activity of 524.61 U/L. The rGluMnP1 could be capable of the decolorization of four types of dyes and the degradation of phenol. Phenol and its principal degradation products including hydroquinone, pyrocatechol, resorcinol, benzoquinone, were detected successfully in the experiments. Conclusions The rGluMnP1 could be effectively expressed in Pichia pastoris and with a higher oxidation activity. We infer that, in the initial stages of the reaction, the catechol-mediated cycle should be the principal route of enzymatic degradation of phenol and its oxidation products. This study highlights the potential industrial applications associated with the production of MnP by genetic engineering methods, and the application of industrial wastewater treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0338-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Xu
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Meng-Yuan Guo
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yan-Hua Gao
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiao-Hui Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Xuan-Wei Zhou
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, and School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Genome Sequence of the Basidiomycete White-Rot Fungus Trametes pubescens FBCC735. GENOME ANNOUNCEMENTS 2017; 5:5/8/e01643-16. [PMID: 28232439 PMCID: PMC5323618 DOI: 10.1128/genomea.01643-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we report the genome sequence of the basidiomycete white-rot fungus Trametes pubescens FBCC735, isolated from Finland. The 39.67-Mb genome containing 14,451 gene models is typical among saprobic wood-rotting species.
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Development of a novel compound microbial agent for degradation of kitchen waste. Braz J Microbiol 2017; 48:442-450. [PMID: 28279600 PMCID: PMC5498451 DOI: 10.1016/j.bjm.2016.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 11/04/2016] [Accepted: 12/26/2016] [Indexed: 11/20/2022] Open
Abstract
Large quantities of kitchen waste are produced in modern society and its disposal poses serious environmental and social problems. The aim of this study was to isolate degradative strains from kitchen waste and to develop a novel and effective microbial agent. One hundred and four strains were isolated from kitchen waste and the 84 dominant strains were used to inoculate protein-, starch-, fat- and cellulose-containing media for detecting their degradability. Twelve dominant strains of various species with high degradability (eight bacteria, one actinomycetes and three fungi) were selected to develop a compound microbial agent “YH” and five strains of these species including H7 (Brevibacterium epidermidis), A3 (Paenibacillus polymyxa), E3 (Aspergillus japonicus), F9 (Aspergillus versicolor) and A5 (Penicillium digitatum), were new for kitchen waste degradation. YH was compared with three commercial microbial agents—“Tiangeng” (TG), “Yilezai” (YLZ) and Effective Microorganisms (EM), by their effects on reduction, maturity and deodorization. The results showed that YH exerted the greatest efficacy on mass loss which decreased about 65.87% after 14 days. The agent inhibited NH3 and H2S emissions significantly during composting process. The concentration of NH3 decreased from 7.1 to 3.2 ppm and that of H2S reduced from 0.7 to 0.2 ppm. Moreover, E4/E6 (Extinction value460nm/Extinction value665nm) of YH decreased from 2.51 to 1.31, which meant YH had an obvious maturity effect. These results highlighted the potential application of YH in composting kitchen waste.
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El Enshasy HA, Hanapi SZ, Abdelgalil SA, Malek RA, Pareek A. Mycoremediation: Decolourization Potential of Fungal Ligninolytic Enzymes. Fungal Biol 2017. [DOI: 10.1007/978-3-319-68957-9_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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25
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Kuuskeri J, Häkkinen M, Laine P, Smolander OP, Tamene F, Miettinen S, Nousiainen P, Kemell M, Auvinen P, Lundell T. Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:192. [PMID: 27602055 PMCID: PMC5011852 DOI: 10.1186/s13068-016-0608-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/30/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The white-rot Agaricomycetes species Phlebia radiata is an efficient wood-decaying fungus degrading all wood components, including cellulose, hemicellulose, and lignin. We cultivated P. radiata in solid state cultures on spruce wood, and extended the experiment to 6 weeks to gain more knowledge on the time-scale dynamics of protein expression upon growth and wood decay. Total proteome and transcriptome of P. radiata were analyzed by peptide LC-MS/MS and RNA sequencing at specific time points to study the enzymatic machinery on the fungus' natural growth substrate. RESULTS According to proteomics analyses, several CAZy oxidoreductase class-II peroxidases with glyoxal and alcohol oxidases were the most abundant proteins produced on wood together with enzymes important for cellulose utilization, such as GH7 and GH6 cellobiohydrolases. Transcriptome additionally displayed expression of multiple AA9 lytic polysaccharide monooxygenases indicative of oxidative cleavage of wood carbohydrate polymers. Large differences were observed for individual protein quantities at specific time points, with a tendency of enhanced production of specific peroxidases on the first 2 weeks of growth on wood. Among the 10 class-II peroxidases, new MnP1-long, characterized MnP2-long and LiP3 were produced in high protein abundances, while LiP2 and LiP1 were upregulated at highest level as transcripts on wood together with the oxidases and one acetyl xylan esterase, implying their necessity as primary enzymes to function against coniferous wood lignin to gain carbohydrate accessibility and fungal growth. Majority of the CAZy encoding transcripts upregulated on spruce wood represented activities against plant cell wall and were identified in the proteome, comprising main activities of white-rot decay. CONCLUSIONS Our data indicate significant changes in carbohydrate-active enzyme expression during the six-week surveillance of P. radiata growing on wood. Response to wood substrate is seen already during the first weeks. The immediate oxidative enzyme action on lignin and wood cell walls is supported by detected lignin substructure sidechain cleavages, release of phenolic units, and visual changes in xylem cell wall ultrastructure. This study contributes to increasing knowledge on fungal genetics and lignocellulose bioconversion pathways, allowing us to head for systems biology, development of biofuel production, and industrial applications on plant biomass utilizing wood-decay fungi.
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Affiliation(s)
- Jaana Kuuskeri
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
| | - Mari Häkkinen
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
| | - Pia Laine
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Fitsum Tamene
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sini Miettinen
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Paula Nousiainen
- Laboratory of Organic Chemistry, Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Marianna Kemell
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Taina Lundell
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
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Lee H, Jang Y, Lee YM, Lee H, Kim GH, Kim JJ. Enhanced removal of PAHs by Peniophora incarnata and ascertainment of its novel ligninolytic enzyme genes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 164:10-8. [PMID: 26342262 DOI: 10.1016/j.jenvman.2015.08.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 07/06/2015] [Accepted: 08/24/2015] [Indexed: 05/24/2023]
Abstract
The hazardous effects of the PAHs should be managed by removal using white rot fungal ligninolytic enzymes. The white rot fungus Peniophora incarnataKUC8836 was stimulated to produce ligninolytic enzymes in a liquid medium by the addition of four substances: 0.5 g L(-1) Tween 80, 70 mg L(-1) CuSO4·5H2O, 10 mg L(-1) MnSO4·H2O, and 0.3 g L(-1) veratryl alcohol. The experiments were carried out in two different media: basal salt and 2% malt extract (ME) liquid medium. Under the experimental conditions, both laccase and manganese-dependent peroxidase (MnP) demonstrated with the highest activities in 2% ME liquid medium following the addition of Tween 80. The biodegradation of anthracene and pyrene was significantly enhanced by the induced ligninolytic enzymes when Tween 80 was added. Tween 80 is a viable co-substrate for P. incarnata, as it enhances the ability of P. incarnata to manage effective biodegradation of PAHs. Most of all, the novel laccase and MnP genes ascertained in this study, showed that the genes were involved in the production of ligninolytic enzymes from P. incarnataKUC8836.
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Affiliation(s)
- Hwanhwi Lee
- Division of Environmental Science & Ecological Engineering, Korea University, Republic of Korea
| | - Yeongseon Jang
- Division of Wood Chemistry & Microbiology, Korea Forest Research Institute, Republic of Korea
| | - Young Min Lee
- Division of Environmental Science & Ecological Engineering, Korea University, Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering, Korea University, Republic of Korea
| | - Gyu-Hyeok Kim
- Division of Environmental Science & Ecological Engineering, Korea University, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, Korea University, Republic of Korea.
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Chen W, Zheng L, Jia R, Wang N. Cloning and expression of a new manganese peroxidase from Irpex lacteus F17 and its application in decolorization of reactive black 5. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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28
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Kuuskeri J, Mäkelä MR, Isotalo J, Oksanen I, Lundell T. Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota). BMC Microbiol 2015; 15:217. [PMID: 26482661 PMCID: PMC4610053 DOI: 10.1186/s12866-015-0538-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Phlebia consists of a number of species that are significant in wood decay. Biotechnological potential of a few species for enzyme production and degradation of lignin and pollutants has been previously studied, when most of the species of this genus are unknown. Therefore, we carried out a wider study on biochemistry and systematics of Phlebia species. METHODS Isolates belonging to the genus Phlebia were subjected to four-gene sequence analysis in order to clarify their phylogenetic placement at species level and evolutionary relationships of the genus among phlebioid Polyporales. rRNA-encoding (5.8S, partial LSU) and two protein-encoding gene (gapdh, rpb2) sequences were adopted for the evolutionary analysis, and ITS sequences (ITS1+5.8S+ITS2) were aligned for in-depth species-level phylogeny. The 49 fungal isolates were cultivated on semi-solid milled spruce wood medium for 21 days in order to follow their production of extracellular lignocellulose-converting oxidoreductases and carbohydrate active enzymes. RESULTS Four-gene phylogenetic analysis confirmed the polyphyletic nature of the genus Phlebia. Ten species-level subgroups were formed, and their lignocellulose-converting enzyme activity profiles coincided with the phylogenetic grouping. The highest enzyme activities for lignin modification (manganese peroxidase activity) were obtained for Phlebia radiata group, which supports our previous studies on the enzymology and gene expression of this species on lignocellulosic substrates. CONCLUSIONS Our study implies that there is a species-level connection of molecular systematics (genotype) to the efficiency in production of both lignocellulose-converting carbohydrate active enzymes and oxidoreductases (enzyme phenotype) on spruce wood. Thus, we may propose a similar phylogrouping approach for prediction of lignocellulose-converting enzyme phenotypes in new fungal species or genetically and biochemically less-studied isolates of the wood-decay Polyporales.
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MESH Headings
- Basidiomycota/classification
- Basidiomycota/enzymology
- Basidiomycota/genetics
- Basidiomycota/metabolism
- Biotransformation
- Cluster Analysis
- Culture Media/chemistry
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/genetics
- Lignin/metabolism
- Microbiological Techniques
- Molecular Sequence Data
- Phylogeny
- RNA Polymerase II/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Jaana Kuuskeri
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
| | - Jarkko Isotalo
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
| | - Ilona Oksanen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
| | - Taina Lundell
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
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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]
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30
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Knop D, Yarden O, Hadar Y. The ligninolytic peroxidases in the genus Pleurotus: divergence in activities, expression, and potential applications. Appl Microbiol Biotechnol 2014; 99:1025-38. [PMID: 25503316 DOI: 10.1007/s00253-014-6256-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 11/29/2022]
Abstract
Mushrooms of the genus Pleurotus are comprised of cultivated edible ligninolytic fungi with medicinal properties and a wide array of biotechnological and environmental applications. Like other white-rot fungi (WRF), they are able to grow on a variety of lignocellulosic biomass substrates and degrade both natural and anthropogenic aromatic compounds. This is due to the presence of the non-specific oxidative enzymatic systems, which are mainly consisted of lacasses, versatile peroxidases (VPs), and short manganese peroxidases (short-MnPs). Additional, less studied, peroxidase are dye-decolorizing peroxidases (DyPs) and heme-thiolate peroxidases (HTPs). During the past two decades, substantial information has accumulated concerning the biochemistry, structure and function of the Pleurotus ligninolytic peroxidases, which are considered to play a key role in many biodegradation processes. The production of these enzymes is dependent on growth media composition, pH, and temperature as well as the growth phase of the fungus. Mn(2+) concentration differentially affects the expression of the different genes. It also severs as a preferred substrate for these preoxidases. Recently, sequencing of the Pleurotus ostreatus genome was completed, and a comprehensive picture of the ligninolytic peroxidase gene family, consisting of three VPs and six short-MnPs, has been established. Similar enzymes were also discovered and studied in other Pleurotus species. In addition, progress has been made in the development of molecular tools for targeted gene replacement, RNAi-based gene silencing and overexpression of genes of interest. These advances increase the fundamental understanding of the ligninolytic system and provide the opportunity for harnessing the unique attributes of these WRF for applied purposes.
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Affiliation(s)
- Doriv Knop
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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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]
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Hildén K, Mäkelä MR, Steffen KT, Hofrichter M, Hatakka A, Archer DB, Lundell TK. Biochemical and molecular characterization of an atypical manganese peroxidase of the litter-decomposing fungus Agrocybe praecox. Fungal Genet Biol 2014; 72:131-136. [DOI: 10.1016/j.fgb.2014.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 11/16/2022]
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Biochemical and molecular characterization of a novel laccase from selective lignin-degrading white-rot fungus Echinodontium taxodii 2538. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.03.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Salavirta H, Oksanen I, Kuuskeri J, Mäkelä M, Laine P, Paulin L, Lundell T. Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events. PLoS One 2014; 9:e97141. [PMID: 24824642 PMCID: PMC4019555 DOI: 10.1371/journal.pone.0097141] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/15/2014] [Indexed: 01/28/2023] Open
Abstract
Mitochondria are eukaryotic organelles supporting individual life-style via generation of proton motive force and cellular energy, and indispensable metabolic pathways. As part of genome sequencing of the white rot Basidiomycota species Phlebia radiata, we first assembled its mitochondrial genome (mtDNA). So far, the 156 348 bp mtDNA is the second largest described for fungi, and of considerable size among eukaryotes. The P. radiata mtDNA assembled as single circular dsDNA molecule containing genes for the large and small ribosomal RNAs, 28 transfer RNAs, and over 100 open reading frames encoding the 14 fungal conserved protein subunits of the mitochondrial complexes I, III, IV, and V. Two genes (atp6 and tRNA-IleGAU) were duplicated within 6.1 kbp inverted region, which is a unique feature of the genome. The large mtDNA size, however, is explained by the dominance of intronic and intergenic regions (sum 80% of mtDNA sequence). The intergenic DNA stretches harness short (≤ 200 nt) repetitive, dispersed and overlapping sequence elements in abundance. Long self-splicing introns of types I and II interrupt eleven of the conserved genes (cox1,2,3; cob; nad1,2,4,4L,5; rnl; rns). The introns embrace a total of 57 homing endonucleases with LAGLIDADGD and GYI-YIG core motifs, which makes P. radiata mtDNA to one of the largest known reservoirs of intron-homing endonucleases. The inverted duplication, intergenic stretches, and intronic features are indications of dynamics and genetic flexibility of the mtDNA, not fully recognized to this extent in fungal mitochondrial genomes previously, thus giving new insights for the evolution of organelle genomes in eukaryotes.
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Affiliation(s)
- Heikki Salavirta
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ilona Oksanen
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jaana Kuuskeri
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Miia Mäkelä
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Taina Lundell
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Mn²⁺-deficiency reveals a key role for the Pleurotus ostreatus versatile peroxidase (VP4) in oxidation of aromatic compounds. Appl Microbiol Biotechnol 2014; 98:6795-804. [PMID: 24737058 DOI: 10.1007/s00253-014-5689-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
Abstract
The manganese peroxidase gene family (mnps) is a part of the ligninolytic system of Pleurotus ostreatus. This gene family is comprised of nine members, mnp1-9, encoding short manganese peroxidases (short-MnPs) or versatile peroxidases (VPs). We show that unlike in Mn(2+)-amended glucose-peptone (GP) medium, where redundancy among mnps was reported, in Mn(2+)-deficient GP medium mnp4 [encoding versatile peroxidase isoenzyme 4 (VP4)] has a key and nonredundant function. The abundance of mnps transcripts at time points corresponding to the tropophase (active growth), early idiophase, and idiophase indicates that mnp4 is the predominantly expressed mnp gene and that its relative predominance is dependent on the age of the culture. In this medium, azo dye, Orange II (OII) decolorization occurs only during the idiophase and a Δmnp4 strain showed a drastic reduction in this decolorization. Three degradation metabolites were identified by liquid chromatography-mass spectroscopy (LC-MS), indicating both asymmetric and symmetric enzymatic cleavage of the azo-bond. In addition, the culture filtrate of Δmnp4 showed negligible values of oxidation capability of four typical VP substrates: Mn(2+), 2,6-dimethoxyphenol, phenol red, and Reactive Black 5 (RB5), compared to the wild-type strain PC9. We concluded that under Mn(2+)-deficient GP culture, VP4 (encoded by mnp4) is the main active ligninolytic enzyme able to oxidize Mn(2+) as well as high and low redox potential aromatic substrate, including dyes. Furthermore, other VPs/MnPs do not compensate for the lack of VP4 activity.
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Mäkelä MR, Sietiö OM, de Vries RP, Timonen S, Hildén K. Oxalate-metabolising genes of the white-rot fungus Dichomitus squalens are differentially induced on wood and at high proton concentration. PLoS One 2014; 9:e87959. [PMID: 24505339 PMCID: PMC3914892 DOI: 10.1371/journal.pone.0087959] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/03/2014] [Indexed: 11/23/2022] Open
Abstract
Oxalic acid is a prevalent fungal metabolite with versatile roles in growth and nutrition, including degradation of plant biomass. However, the toxicity of oxalic acid makes regulation of its intra- and extracellular concentration crucial. To increase the knowledge of fungal oxalate metabolism, a transcriptional level study on oxalate-catabolising genes was performed with an effective lignin-degrading white-rot fungus Dichomitus squalens, which has demonstrated particular abilities in production and degradation of oxalic acid. The expression of oxalic-acid decomposing oxalate decarboxylase (ODC) and formic-acid decomposing formate dehydrogenase (FDH) encoding genes was followed during the growth of D. squalens on its natural spruce wood substrate. The effect of high proton concentration on the regulation of the oxalate-catabolising genes was determined after addition of organic acid (oxalic acid) and inorganic acid (hydrochloric acid) to the liquid cultures of D. squalens. In order to evaluate the co-expression of oxalate-catabolising and manganese peroxidase (MnP) encoding genes, the expression of one MnP encoding gene, mnp1, of D. squalens was also surveyed in the solid state and liquid cultures. Sequential action of ODC and FDH encoding genes was detected in the studied cultivations. The odc1, fdh2 and fdh3 genes of D. squalens showed constitutive expression, whereas ODC2 and FHD1 most likely are the main responsible enzymes for detoxification of high concentrations of oxalic and formic acids. The results also confirmed the central role of ODC1 when D. squalens grows on coniferous wood. Phylogenetic analysis revealed that fungal ODCs have evolved from at least two gene copies whereas FDHs have a single ancestral gene. As a conclusion, the multiplicity of oxalate-catabolising genes and their differential regulation on wood and in acid-amended cultures of D. squalens point to divergent physiological roles for the corresponding enzymes.
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Affiliation(s)
- Miia R. Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Outi-Maaria Sietiö
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | | | - Sari Timonen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
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Sulej J, Janusz G, Mazur A, Żuber K, Żebracka A, Rogalski J. Cellobiose dehydrogenase from the ligninolytic basidiomycete Phlebia lindtneri. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ruiz-Dueñas FJ, Lundell T, Floudas D, Nagy LG, Barrasa JM, Hibbett DS, Martínez AT. Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes. Mycologia 2013; 105:1428-44. [PMID: 23921235 DOI: 10.3852/13-059] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species representing the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequenced B. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)-oxidation site being at the origin of all the LiP enzymes, which are found only in species of the order Polyporales.
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Yakovlev IA, Hietala AM, Courty PE, Lundell T, Solheim H, Fossdal CG. Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation. Fungal Genet Biol 2013; 56:17-24. [PMID: 23665189 DOI: 10.1016/j.fgb.2013.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 11/15/2022]
Abstract
The pathogenic white-rot basidiomycete Heterobasidion irregulare is able to remove lignin and hemicellulose prior to cellulose during the colonization of root and stem xylem of conifer and broadleaf trees. We identified and followed the regulation of expression of genes belonging to families encoding ligninolytic enzymes. In comparison with typical white-rot fungi, the H. irregulare genome has exclusively the short-manganese peroxidase type encoding genes (6 short-MnPs) and thereby a slight contraction in the pool of class II heme-containing peroxidases, but an expansion of the MCO laccases with 17 gene models. Furthermore, the genome shows a versatile set of other oxidoreductase genes putatively involved in lignin oxidation and conversion, including 5 glyoxal oxidases, 19 quinone-oxidoreductases and 12 aryl-alcohol oxidases. Their genetic multiplicity and gene-specific regulation patterns on cultures based on defined lignin, cellulose or Norway spruce lignocellulose substrates suggest divergent specificities and physiological roles for these enzymes. While the short-MnP encoding genes showed similar transcript levels upon fungal growth on heartwood and reaction zone (RZ), a xylem defense tissue rich in phenolic compounds unique to trees, a subset of laccases showed higher gene expression in the RZ cultures. In contrast, other oxidoreductases depending on initial MnP activity showed generally lower transcript levels on RZ than on heartwood. These data suggest that the rate of fungal oxidative conversion of xylem lignin differs between spruce RZ and heartwood. It is conceivable that in RZ part of the oxidoreductase activities of laccases are related to the detoxification of phenolic compounds involved in host-defense. Expression of the several short-MnP enzymes indicated an important role for these enzymes in effective delignification of wood by H. irregulare.
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Affiliation(s)
- Igor A Yakovlev
- Norwegian Forest and Landscape Institute, PO Box 115, N-1431 Ås, Norway
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Uhrecký R, Moncoľ J, Koman M, Titiš J, Boča R. Structure and magnetism of a Mn(iii)–Mn(ii)–Mn(ii)–Mn(iii) chain complex. Dalton Trans 2013; 42:9490-4. [DOI: 10.1039/c3dt50940k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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41
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Mäkelä MR, Lundell T, Hatakka A, Hildén K. Effect of copper, nutrient nitrogen, and wood-supplement on the production of lignin-modifying enzymes by the white-rot fungus Phlebia radiata. Fungal Biol 2012; 117:62-70. [PMID: 23332834 DOI: 10.1016/j.funbio.2012.11.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 11/06/2012] [Accepted: 11/26/2012] [Indexed: 11/15/2022]
Abstract
Production of the oxidoreductive lignin-modifying enzymes - lignin and manganese peroxidases (MnPs), and laccase - of the white-rot basidiomycete Phlebia radiata was investigated in semi-solid cultures supplemented with milled grey alder or Norway spruce and charcoal. Concentrations of nutrient nitrogen and Cu-supplement varied also in the cultures. According to extracellular activities, production of both lignin peroxidase (LiP) and MnP was significantly promoted with wood as carbon source, with milled alder (MA) and low nitrogen (LN) resulting with the maximal LiP activities (550 nkat l(-1)) and noticeable levels of MnP (3 μkat l(-1)). Activities of LiP and MnP were also elevated on high nitrogen (HN) complex medium when supplemented with spruce and charcoal. Maximal laccase activities (22 and 29 μkat l(-1)) were obtained in extra high nitrogen (eHN) containing defined and complex media supplemented with 1.5 mM Cu(2+). However, the nitrogen source, either peptone or ammonium nitrate and asparagine, caused no stimulation on laccase production without Cu-supplement. This is also the first report to demonstrate a new, on high Cu(2+) amended medium produced extracellular laccase of P. radiata with pI value of 4.9, thereby complementing our previous findings on gene expression, and cloning of a second laccase of this fungus.
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Affiliation(s)
- Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology, Viikki Biocenter 1, FIN-00014 Helsinki, Finland.
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Järvinen J, Taskila S, Isomäki R, Ojamo H. Screening of white-rot fungi manganese peroxidases: a comparison between the specific activities of the enzyme from different native producers. AMB Express 2012. [PMID: 23190610 PMCID: PMC3549895 DOI: 10.1186/2191-0855-2-62] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this study manganese peroxidase (MnP) enzymes from selected white-rot fungi were isolated and compared for potential future recombinant production. White-rot fungi were cultivated in small-scale in liquid media and a simplified process was established for the purification of extracellular enzymes. Five lignin degrading organisms were selected (Bjerkandera sp., Phanerochaete (P.) chrysosporium, Physisporinus (P.) rivulosus, Phlebia (P.) radiata and Phlebia sp. Nf b19) and studied for MnP production in small-scale. Extracellular MnP activity was followed and cultivations were harvested at proximity of the peak activity. The production of MnPs varied in different organisms but was clearly regulated by inducing liquid media components (Mn2+, veratryl alcohol and malonate). In total 8 different MnP isoforms were purified. Results of this study reinforce the conception that MnPs from distinct organisms differ substantially in their properties. Production of the extracellular enzyme in general did not reach a substantial level. This further suggests that these native producers are not suitable for industrial scale production of the enzyme. The highest specific activities were observed with MnPs from P. chrysosporium (200 U mg-1), Phlebia sp. Nf b19 (55 U mg-1) and P. rivulosus (89 U mg-1) and these MnPs are considered as the most potential candidates for further studies. The molecular weight of the purified MnPs was estimated to be between 45–50 kDa.
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Morales M, Mate MJ, Romero A, Martínez MJ, Martínez ÁT, Ruiz-Dueñas FJ. Two oxidation sites for low redox potential substrates: a directed mutagenesis, kinetic, and crystallographic study on Pleurotus eryngii versatile peroxidase. J Biol Chem 2012; 287:41053-67. [PMID: 23071108 DOI: 10.1074/jbc.m112.405548] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Versatile peroxidase shares with manganese peroxidase and lignin peroxidase the ability to oxidize Mn(2+) and high redox potential aromatic compounds, respectively. Moreover, it is also able to oxidize phenols (and low redox potential dyes) at two catalytic sites, as shown by biphasic kinetics. A high efficiency site (with 2,6-dimethoxyphenol and p-hydroquinone catalytic efficiencies of ∼70 and ∼700 s(-1) mM(-1), respectively) was localized at the same exposed Trp-164 responsible for high redox potential substrate oxidation (as shown by activity loss in the W164S variant). The second site, characterized by low catalytic efficiency (∼3 and ∼50 s(-1) mM(-1) for 2,6-dimethoxyphenol and p-hydroquinone, respectively) was localized at the main heme access channel. Steady-state and transient-state kinetics for oxidation of phenols and dyes at the latter site were improved when side chains of residues forming the heme channel edge were removed in single and multiple variants. Among them, the E140G/K176G, E140G/P141G/K176G, and E140G/W164S/K176G variants attained catalytic efficiencies for oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) at the heme channel similar to those of the exposed tryptophan site. The heme channel enlargement shown by x-ray diffraction of the E140G, P141G, K176G, and E140G/K176G variants would allow a better substrate accommodation near the heme, as revealed by the up to 26-fold lower K(m) values (compared with native VP). The resulting interactions were shown by the x-ray structure of the E140G-guaiacol complex, which includes two H-bonds of the substrate with Arg-43 and Pro-139 in the distal heme pocket (at the end of the heme channel) and several hydrophobic interactions with other residues and the heme cofactor.
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Affiliation(s)
- María Morales
- Centro de Investigaciones Biológicas (CIB), CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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Janusz G, Kucharzyk KH, Pawlik A, Staszczak M, Paszczynski AJ. Fungal laccase, manganese peroxidase and lignin peroxidase: gene expression and regulation. Enzyme Microb Technol 2012. [PMID: 23199732 DOI: 10.1016/j.enzmictec.2012.10.003] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extensive research efforts have been dedicated to characterizing expression of laccases and peroxidases and their regulation in numerous fungal species. Much attention has been brought to these enzymes broad substrate specificity resulting in oxidation of a variety of organic compounds which brings about possibilities of their utilization in biotechnological and environmental applications. Research attempts have resulted in increased production of both laccases and peroxidases by the aid of heterologous and homologous expression. Through analysis of promoter regions, protein expression patterns and culture conditions manipulations it was possible to compare and identify common pathways of these enzymes' production and secretion. Although laccase and peroxidase proteins have been crystallized and thoroughly analyzed, there are still a lot of questions remaining about their evolutionary origin and the physiological functions. This review describes the present understanding of promoter sequences and correlation between the observed regulatory effects on laccase, manganese peroxidase and lignin peroxidase genes transcript levels and the presence of specific response elements.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Skłodowska University, Akademicka 19 Street, 20-033 Lublin, Poland.
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Paliwal R, Rawat AP, Rawat M, Rai JPN. Bioligninolysis: recent updates for biotechnological solution. Appl Biochem Biotechnol 2012; 167:1865-89. [PMID: 22639362 DOI: 10.1007/s12010-012-9735-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 05/10/2012] [Indexed: 10/28/2022]
Abstract
Bioligninolysis involves living organisms and/or their products in degradation of lignin, which is highly resistant, plant-originated polymer having three-dimensional network of dimethoxylated (syringyl), monomethoxylated (guaiacyl), and non-methoxylated (p-hydroxyphenyl) phenylpropanoid and acetylated units. As a major repository of aromatic chemical structures on earth, lignin bears paramount significance for its removal owing to potential application of bioligninolytic systems in industrial production. Early reports illustrating the discovery and cloning of ligninolytic biocatalysts in fungi was truly a landmark in the field of enzymatic delignification. However, the enzymology for bacterial delignification is hitherto poorly understood. Moreover, the lignin-degrading bacterial genes are still unknown and need further exploration. This review deals with the current knowledge about ligninolytic enzyme families produced by fungi and bacteria, their mechanisms of action, and genetic regulation and reservations, which render them attractive candidates in biotechnological applications.
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Affiliation(s)
- Rashmi Paliwal
- Ecotechnology Laboratory, Department of Environmental Science, G.B.Pant. University of Agriculture and Technology, Pantnagar 263145, India
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Heterologous expression and structural characterization of two low pH laccases from a biopulping white-rot fungus Physisporinus rivulosus. Appl Microbiol Biotechnol 2012; 97:1589-99. [DOI: 10.1007/s00253-012-4011-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 03/05/2012] [Accepted: 03/06/2012] [Indexed: 11/25/2022]
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Fernández-Fueyo E, Ruiz-Dueñas FJ, Miki Y, Martínez MJ, Hammel KE, Martínez AT. Lignin-degrading peroxidases from genome of selective ligninolytic fungus Ceriporiopsis subvermispora. J Biol Chem 2012; 287:16903-16. [PMID: 22437835 DOI: 10.1074/jbc.m112.356378] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The white-rot fungus Ceriporiopsis subvermispora delignifies lignocellulose with high selectivity, but until now it has appeared to lack the specialized peroxidases, termed lignin peroxidases (LiPs) and versatile peroxidases (VPs), that are generally thought important for ligninolysis. We screened the recently sequenced C. subvermispora genome for genes that encode peroxidases with a potential ligninolytic role. A total of 26 peroxidase genes was apparent after a structural-functional classification based on homology modeling and a search for diagnostic catalytic amino acid residues. In addition to revealing the presence of nine heme-thiolate peroxidase superfamily members and the unexpected absence of the dye-decolorizing peroxidase superfamily, the search showed that the C. subvermispora genome encodes 16 class II enzymes in the plant-fungal-bacterial peroxidase superfamily, where LiPs and VPs are classified. The 16 encoded enzymes include 13 putative manganese peroxidases and one generic peroxidase but most notably two peroxidases containing the catalytic tryptophan characteristic of LiPs and VPs. We expressed these two enzymes in Escherichia coli and determined their substrate specificities on typical LiP/VP substrates, including nonphenolic lignin model monomers and dimers, as well as synthetic lignin. The results show that the two newly discovered C. subvermispora peroxidases are functionally competent LiPs and also suggest that they are phylogenetically and catalytically intermediate between classical LiPs and VPs. These results offer new insight into selective lignin degradation by C. subvermispora.
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Affiliation(s)
- Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E-28040 Madrid, Spain
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Ufot UF, Akpanabiatu MI. An engineered <i>Phlebia radiata</i> manganese peroxidase: expression, refolding, purification and preliminary characterization. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ajmb.2012.24037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ruiz-Dueñas FJ, Fernández E, Martínez MJ, Martínez AT. Pleurotus ostreatus heme peroxidases: An in silico analysis from the genome sequence to the enzyme molecular structure. C R Biol 2011; 334:795-805. [DOI: 10.1016/j.crvi.2011.06.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Purification and characterization of novel manganese peroxidase from Rhizoctonia sp. SYBC-M3. BIOTECHNOL BIOPROC E 2011. [DOI: 10.1007/s12257-010-0130-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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