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Agnestisia R, Suzuki T, Ono A, Nakamura L, Nezu I, Tanaka Y, Aiso H, Ishiguri F, Yokota S. Lignin-degrading enzymes from a pathogenic canker-rot fungus Inonotus obliquus strain IO-B2. AMB Express 2023; 13:59. [PMID: 37302091 DOI: 10.1186/s13568-023-01566-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 06/02/2023] [Indexed: 06/13/2023] Open
Abstract
Inonotus obliquus is a pathogenic fungus found in living trees and has been widely used as a traditional medicine for cancer therapy. Although lignocellulose-degrading enzymes are involved in the early stages of host infection, the parasitic life cycle of this fungus has not been fully understood. In this study, we aimed to investigate the activities of laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) from I. obliquus cultivated in Kirk's medium. The fungus was subjected to genome sequencing, and genes related to wood degradation were identified. The draft genome sequence of this fungus comprised 21,203 predicted protein-coding genes, of which 134 were estimated to be related to wood degradation. Among these, 47 genes associated with lignin degradation were found to have the highest number of mnp genes. Furthermore, we cloned the cDNA encoding a putative MnP, referred to as IoMnP1, and characterized its molecular structure. The results show that IoMnP1 has catalytic properties analogous to MnP. Phylogenetic analysis also confirmed that IoMnP1 was closely related to the MnPs from Pyrrhoderma noxium, Fomitiporia mediterranea, and Sanghuangporus baumii, which belong to the same family of Hymenochaetaceae. From the above results, we suggest that IoMnP1 is a member of MnPs.
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Affiliation(s)
- Retno Agnestisia
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
- Faculty of Mathematics and Natural Sciences, Universitas Palangka Raya, Palangka Raya, 73111, Indonesia
| | - Tomohiro Suzuki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
| | - Akiko Ono
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Luna Nakamura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Ikumi Nezu
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yuki Tanaka
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Haruna Aiso
- Faculty of Agricultural Production and Management, Shizuoka Professional University of Agriculture, Iwata, Shizuoka, 438-0803, Japan
| | - Futoshi Ishiguri
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Shinso Yokota
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
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Moretti S, Goddard ML, Puca A, Lalevée J, Di Marco S, Mugnai L, Gelhaye E, Goodell B, Bertsch C, Farine S. First Description of Non-Enzymatic Radical-Generating Mechanisms Adopted by Fomitiporia mediterranea: An Unexplored Pathway of the White Rot Agent of the Esca Complex of Diseases. J Fungi (Basel) 2023; 9:jof9040498. [PMID: 37108951 PMCID: PMC10143301 DOI: 10.3390/jof9040498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Fomitiporia mediterranea (Fmed) is the primary Basidiomycota species causing white rot in European vineyards affected by the Esca complex of diseases (ECD). In the last few years, an increasing number of studies have highlighted the importance of reconsidering the role of Fmed in ECD etiology, justifying an increase in research interest related to Fmed's biomolecular pathogenetic mechanisms. In the context of the current re-evaluation of the binary distinction (brown vs. white rot) between biomolecular decay pathways induced by Basidiomycota species, our research aims to investigate the potential for non-enzymatic mechanisms adopted by Fmed, which is typically described as a white rot fungus. Our results demonstrate how, in liquid culture reproducing nutrient restriction conditions often found in wood, Fmed can produce low molecular weight compounds, the hallmark of the non-enzymatic "chelator-mediated Fenton" (CMF) reaction, originally described for brown rot fungi. CMF reactions can redox cycle with ferric iron, generating hydrogen peroxide and ferrous iron, necessary reactants leading to hydroxyl radical (•OH) production. These observations led to the conclusion that a non-enzymatic radical-generating CMF-like mechanism may be utilized by Fmed, potentially together with an enzymatic pool, to contribute to degrading wood constituents; moreover, indicating significant variability between strains.
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Affiliation(s)
- Samuele Moretti
- Laboratoire Vigne, Biotechnologies et Environnement UPR-3991, Université de Haute-Alsace, 33 rue de Herrlisheim, 68000 Colmar, France
| | - Mary-Lorène Goddard
- Laboratoire Vigne, Biotechnologies et Environnement UPR-3991, Université de Haute-Alsace, 33 rue de Herrlisheim, 68000 Colmar, France
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA, UMR 7042, CEDEX, 68093 Mulhouse, France
| | - Alessandro Puca
- Laboratoire Vigne, Biotechnologies et Environnement UPR-3991, Université de Haute-Alsace, 33 rue de Herrlisheim, 68000 Colmar, France
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, P.le delle Cascine, 28, 50144 Firenze, Italy
| | - Jacques Lalevée
- Institut de Science des Materiaux IS2M, Université de Haute-Alsace, CNRS, IS2M UMR 7361, F-68100 Mulhouse, France
| | - Stefano Di Marco
- Institute of Bioeconomy, CNR, Via Gobetti, 101, 40129 Bologna, Italy
| | - Laura Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, P.le delle Cascine, 28, 50144 Firenze, Italy
| | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Barry Goodell
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Christophe Bertsch
- Laboratoire Vigne, Biotechnologies et Environnement UPR-3991, Université de Haute-Alsace, 33 rue de Herrlisheim, 68000 Colmar, France
| | - Sibylle Farine
- Laboratoire Vigne, Biotechnologies et Environnement UPR-3991, Université de Haute-Alsace, 33 rue de Herrlisheim, 68000 Colmar, France
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3
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Pacetti A, Moretti S, Perrin C, Gelhaye E, Bieler E, Kassemeyer HH, Mugnai L, Farine S, Bertsch C. Grapevine Wood-Degrading Activity of Fomitiporia mediterranea M. Fisch.: A Focus on the Enzymatic Pathway Regulation. Front Microbiol 2022; 13:844264. [PMID: 35369524 PMCID: PMC8971955 DOI: 10.3389/fmicb.2022.844264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Fomitiporia mediterranea is a Basidiomycetes fungus associated with some of the Esca complex diseases and responsible for decay in grapevine wood. Its role in the onset of foliar symptoms has recently been reconsidered, mainly after evidence showing a reduction in foliar symptom expression after removal of rotten wood. The study of its degradation pathways has already been approached by other authors, and with this study much information is consolidated. A microscopic observation of degraded wood provides a first approach to the characterization of F. mediterranea modalities of wood cellular structure degradation. The decay of grapevine wood was reproduced in vitro, and the measurement of each wood-forming polymer loss highlighted characteristics of F. mediterranea common to selective white rot and showed how fungal strain and vine variety are factors determining the wood degradation. All these observations were supported by the analysis of the laccase and manganese peroxidase enzyme activity, as well as by the expression of the genes coding 6 putative laccase isoforms and 3 manganese peroxidase isoforms, thereby highlighting substantial intraspecific variability.
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Affiliation(s)
- Andrea Pacetti
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Florence, Italy
| | - Samuele Moretti
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Célia Perrin
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Eric Gelhaye
- Faculté des Sciences et Technologies Boulevard des Aiguillettes, UMR IAM - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Evi Bieler
- Swiss Nanoscience Institute (SNI) – Nano Imaging, University of Basel, Basel, Switzerland
| | - Hanns-Heinz Kassemeyer
- Swiss Nanoscience Institute (SNI) – Nano Imaging, University of Basel, Basel, Switzerland
- State Institute for Viticulture, Plant Pathology & Diagnostics, Freiburg, Germany
- Faculty of Biology, Plant Biomechanics Group and Botanic Garden, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Laura Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Florence, Italy
| | - Sibylle Farine
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Christophe Bertsch
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
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The Manganese Peroxidase Gene Family of Trametes trogii: Gene Identification and Expression Patterns Using Various Metal Ions under Different Culture Conditions. Microorganisms 2021; 9:microorganisms9122595. [PMID: 34946196 PMCID: PMC8704794 DOI: 10.3390/microorganisms9122595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Manganese peroxidases (MnPs), gene family members of white-rot fungi, are necessary extracellular enzymes that degrade lignocellulose and xenobiotic aromatic pollutants. However, very little is known about the diversity and expression patterns of the MnP gene family in white-rot fungi, especially in contrast to laccases. Here, the gene and protein sequences of eight unique MnP genes of T. trogii S0301 were characterized. Based on the characteristics of gene sequence, all TtMnPs here belong to short-type hybrid MnP (type I) with an average protein length of 363 amino acids, 5–6 introns, and the presence of conserved cysteine residues. Furthermore, analysis of MnP activity showed that metal ions (Mn2+ and Cu2+) and static liquid culture significantly influenced MnP activity. A maximum MnP activity (>14.0 U/mL) toward 2,6-DMP was observed in static liquid culture after the addition of Mn2+ (1 mM) or Cu2+ (0.2 or 2 mM). Moreover, qPCR analysis showed that Mn2+ obviously upregulated the Group I MnP subfamily (T_trogii_09901, 09904, 09903, and 09906), while Cu2+ and H2O2, along with changing temperatures, mainly induced the Group II MnP subfamily (T_trogii_11984, 11971, 11985, and 11983), suggesting diverse functions of fungal MnPs in growth and development, stress response, etc. Our studies here systematically analyzed the gene structure, expression, and regulation of the TtMnP gene family in T. trogii, one of the important lignocellulose-degrading fungi, and these results extended our understanding of the diversity of the MnP gene family and helped to improve MnP production and appilications of Trametes strains and other white-rot fungi.
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Garcia JF, Lawrence DP, Morales-Cruz A, Travadon R, Minio A, Hernandez-Martinez R, Rolshausen PE, Baumgartner K, Cantu D. Phylogenomics of Plant-Associated Botryosphaeriaceae Species. Front Microbiol 2021; 12:652802. [PMID: 33815343 PMCID: PMC8012773 DOI: 10.3389/fmicb.2021.652802] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/25/2021] [Indexed: 11/29/2022] Open
Abstract
The Botryosphaeriaceae is a fungal family that includes many destructive vascular pathogens of woody plants (e.g., Botryosphaeria dieback of grape, Panicle blight of pistachio). Species in the genera Botryosphaeria, Diplodia, Dothiorella, Lasiodiplodia, Neofusicoccum, and Neoscytalidium attack a range of horticultural crops, but they vary in virulence and their abilities to infect their hosts via different infection courts (flowers, green shoots, woody twigs). Isolates of seventeen species, originating from symptomatic apricot, grape, pistachio, and walnut were tested for pathogenicity on grapevine wood after 4 months of incubation in potted plants in the greenhouse. Results revealed significant variation in virulence in terms of the length of the internal wood lesions caused by these seventeen species. Phylogenomic comparisons of the seventeen species of wood-colonizing fungi revealed clade-specific expansion of gene families representing putative virulence factors involved in toxin production and mobilization, wood degradation, and nutrient uptake. Statistical analyses of the evolution of the size of gene families revealed expansions of secondary metabolism and transporter gene families in Lasiodiplodia and of secreted cell wall degrading enzymes (CAZymes) in Botryosphaeria and Neofusicoccum genomes. In contrast, Diplodia, Dothiorella, and Neoscytalidium generally showed a contraction in the number of members of these gene families. Overall, species with expansions of gene families, such as secreted CAZymes, secondary metabolism, and transporters, were the most virulent (i.e., were associated with the largest lesions), based on our pathogenicity tests and published reports. This study represents the first comparative phylogenomic investigation into the evolution of possible virulence factors from diverse, cosmopolitan members of the Botryosphaeriaceae.
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Affiliation(s)
- Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Daniel P Lawrence
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | | | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
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6
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Dual Purpose of ligninolytic- basidiomycetes: mycoremediation of bioethanol distillation vinasse coupled to sustainable bio-based compounds production. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Mathé C, Fawal N, Roux C, Dunand C. In silico definition of new ligninolytic peroxidase sub-classes in fungi and putative relation to fungal life style. Sci Rep 2019; 9:20373. [PMID: 31889110 PMCID: PMC6937255 DOI: 10.1038/s41598-019-56774-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/02/2019] [Indexed: 12/02/2022] Open
Abstract
Ligninolytic peroxidases are microbial enzymes involved in depolymerisation of lignin, a plant cell wall polymer found in land plants. Among fungi, only Dikarya were found to degrade lignin. The increase of available fungal genomes allows performing an expert annotation of lignin-degrading peroxidase encoding sequences with a particular focus on Class II peroxidases (CII Prx). In addition to the previously described LiP, MnP and VP classes, based on sequence similarity, six new sub-classes have been defined: three found in plant pathogen ascomycetes and three in basidiomycetes. The presence of CII Prxs could be related to fungal life style. Typically, necrotrophic or hemibiotrophic fungi, either ascomycetes or basidiomycetes, possess CII Prxs while symbiotic, endophytic or biotrophic fungi do not. CII Prxs from ascomycetes are rarely subjected to duplications unlike those from basidiomycetes, which can form large recent duplicated families. Even if these CII Prxs classes form two well distinct clusters with divergent gene structures (intron numbers and positions), they share the same key catalytic residues suggesting that they evolved independently from similar ancestral sequences with few or no introns. The lack of CII Prxs encoding sequences in early diverging fungi, together with the absence of duplicated class I peroxidase (CcP) in fungi containing CII Prxs, suggests the potential emergence of an ancestral CII Prx sequence from the duplicated CcP after the separation between ascomycetes and basidiomycetes. As some ascomycetes and basidiomycetes did not possess CII Prx, late gene loss could have occurred.
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Affiliation(s)
- Catherine Mathé
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nizar Fawal
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France.
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BolaÑOs AC, Bononi VLÚCR, Londoño JM, Castillo A, Vitali VM, Gugliotta ADM, Muñoz JE. Detecting Manganese Peroxidase (MnP) Gene in GanodermaSpecies. CRYPTOGAMIE MYCOL 2018. [DOI: 10.7872/crym/v39.iss3.2018.325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ana Cristina BolaÑOs
- Universidad del Valle, Facultad de Ciencias, Departamento de Biología, calle 13 No. 100 - 00, Cali – Colombia
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Vera LÚCia Ramos Bononi
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Jorge Mario Londoño
- Universidad Nacional de Colombia, Sede Palmira, Colombia, Carrera 32 No 12 - 00 Chapinero, Vía Candelaria, Palmira Valle del Cauca – Colombia
| | - Andrés Castillo
- Universidad del Valle, Facultad de Ciencias, Departamento de Biología, calle 13 No. 100 - 00, Cali – Colombia
| | - Vera MarÍA Vitali
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Adriana De Mello Gugliotta
- Instituto de Botânica, Av. Miguel Stéfano 3687, São Paulo, SP and Universidade Anhanguera/UNIDERP, Campo Grande, MS, Brasil
| | - Jaime Eduardo Muñoz
- Universidad Nacional de Colombia, Sede Palmira, Colombia, Carrera 32 No 12 - 00 Chapinero, Vía Candelaria, Palmira Valle del Cauca – Colombia
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Substrate-based differential expression analysis reveals control of biomass degrading enzymes in Pycnoporus cinnabarinus. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2017.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Kumar S, Arumugam N, Permaul K, Singh S. Chapter 5 Thermostable Enzymes and Their Industrial Applications. Microb Biotechnol 2016. [DOI: 10.1201/9781315367880-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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Oghenekaro AO, Raffaello T, Kovalchuk A, Asiegbu FO. De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood. BMC Genomics 2016; 17:234. [PMID: 26980399 PMCID: PMC4791870 DOI: 10.1186/s12864-016-2574-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/07/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The basidiomycete Rigidoporus microporus is a fungus that causes the white rot disease of the tropical rubber tree, Hevea brasiliensis, the major source of commercial natural rubber. Besides its lifestyle as a pathogen, the fungus is known to switch to saprotrophic growth on wood with the ability to degrade both lignin and cellulose. There is almost no genomic or transcriptomic information on the saprotrophic abilities of this fungus. In this study, we present the fungal transcriptomic profiles during saprotrophic growth on rubber wood. RESULTS A total of 266.6 million RNA-Seq reads were generated from six libraries of the fungus growing either on rubber wood or without wood. De novo assembly produced 34, 518 unigenes with an average length of 2179 bp. Annotation of unigenes using public databases; GenBank, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups (COG) and Gene Ontology (GO) produced 25, 880 annotated unigenes. Transcriptomic profiling analysis revealed that the fungus expressed over 300 genes encoding lignocellulolytic enzymes. Among these, 175 genes were up-regulated in rubber wood. These include three members of the glycoside hydrolase family 43, as well as various glycosyl transferases, carbohydrate esterases and polysaccharide lyases. A large number of oxidoreductases which includes nine manganese peroxidases were also significantly up-regulated in rubber wood. Several genes involved in fatty acid metabolism and degradation as well as natural rubber degradation were expressed in the transcriptome. Four genes (acyl-CoA synthetase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA acetyltransferase) potentially involved in rubber latex degradation pathway were also induced. A number of ATP binding cassette (ABC) transporters and hydrophobin genes were significantly expressed in the transcriptome during saprotrophic growth. Some genes related to energy metabolism were also induced. CONCLUSIONS The analysed data gives an insight into the activation of lignocellulose breakdown machinery of R. microporus. This study also revealed genes with relevance in antibiotic metabolism (e.g. cephalosporin esterase) as well as those with potential applications in fatty acid degradation. This is the first study on the transcriptomic analysis of R. microporus on rubber wood and should serve as a pioneering resource for future studies of the fungus at the genomic or transcriptomic level.
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Affiliation(s)
- Abbot O Oghenekaro
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland.
| | - Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
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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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13
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Park JW, Kang HW, Ha BS, Kim SI, Kim S, Ro HS. Strain-dependent response to Cu2+ in the expression of laccase in Pycnoporus coccineus. Arch Microbiol 2015; 197:589-96. [DOI: 10.1007/s00203-015-1090-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 01/30/2015] [Accepted: 02/05/2015] [Indexed: 10/24/2022]
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14
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Levasseur A, Lomascolo A, Chabrol O, Ruiz-Dueñas FJ, Boukhris-Uzan E, Piumi F, Kües U, Ram AFJ, Murat C, Haon M, Benoit I, Arfi Y, Chevret D, Drula E, Kwon MJ, Gouret P, Lesage-Meessen L, Lombard V, Mariette J, Noirot C, Park J, Patyshakuliyeva A, Sigoillot JC, Wiebenga A, Wösten HAB, Martin F, Coutinho PM, de Vries RP, Martínez AT, Klopp C, Pontarotti P, Henrissat B, Record E. The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics 2014; 15:486. [PMID: 24942338 PMCID: PMC4101180 DOI: 10.1186/1471-2164-15-486] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology. RESULTS The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases. CONCLUSIONS With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass.
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Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.
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Fungal accumulation of metals from building materials during brown rot wood decay. Arch Microbiol 2014; 196:565-74. [PMID: 24859913 DOI: 10.1007/s00203-014-0993-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/30/2014] [Accepted: 05/10/2014] [Indexed: 10/25/2022]
Abstract
This study analyzes the accumulation and translocation of metal ions in wood during the degradation performed by one strain of each of the three brown rot fungi; Serpula lacrymans, Meruliporia incrassata and Coniophora puteana. These fungi species are inhabitants of the built environment where the prevention and understanding of fungal decay is of high priority. This study focuses on the influence of various building materials in relation to fungal growth and metal uptake. Changes in the concentration of iron, manganese, calcium and copper ions in the decayed wood were analyzed by induced coupled plasma spectroscopy and related to wood weight loss and oxalic acid accumulation. Metal transport into the fungal inoculated wood was found to be dependent on the individual strain/species. The S. lacrymans strain caused a significant increase in total iron whereas the concentration of copper ions in the wood appeared decreased after 10 weeks of decay. Wood inoculated with the M. incrassata isolate showed the contrary tendency with high copper accumulation and low iron increase despite similar weight losses for the two strains. However, significantly lower oxalic acid accumulation was recorded in M. incrassata degraded wood. The addition of a building material resulted in increased weight loss in wood degraded by C. puteana in the soil-block test; however, this could not be directly linked specifically to the accumulation of any of the four metals recorded. The accumulation of oxalic acid seemed to influence the iron uptake. The study assessing the influence of the presence of soil and glass in the soil-block test revealed that soil contributed the majority of the metals for uptake by the fungi and contributed to increased weight loss. The varying uptake observed among the three brown rot fungi strains toward the four metals analyzed may be related to the specific non-enzymatic and enzymatic properties including bio-chelators employed by each of the species during wood decay.
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Fungal pretreatment of lignocellulosic biomass. Biotechnol Adv 2012; 30:1447-57. [DOI: 10.1016/j.biotechadv.2012.03.003] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/25/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
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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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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: 61] [Impact Index Per Article: 5.1] [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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Lomascolo A, Uzan-Boukhris E, Herpoël-Gimbert I, Sigoillot JC, Lesage-Meessen L. Peculiarities of Pycnoporus species for applications in biotechnology. Appl Microbiol Biotechnol 2011; 92:1129-49. [PMID: 22038244 DOI: 10.1007/s00253-011-3596-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/02/2011] [Accepted: 09/18/2011] [Indexed: 11/24/2022]
Abstract
The genus Pycnoporus forms a cosmopolitan group of four species belonging to the polyporoid white-rot fungi, the most representative group of homobasidiomycetes causing wood decay. Pycnoporus fungi are listed as food- and cosmetic-grade microorganisms and emerged in the early 1990s as a genus whose biochemistry, biodegradation and biotechnological properties have since been progressively detailed. First highlighted for their original metabolic pathways involved in the functionalization of plant cell wall aromatic compounds to yield high-value molecules, e.g. aromas and antioxidants, the Pycnoporus species were later explored for their potential to produce various enzymes of industrial interest, such as hydrolases and oxidases. However, the most noteworthy feature of the genus Pycnoporus is its ability to overproduce high redox potential laccase-a multi-copper extracellular phenoloxidase-as the predominant ligninolytic enzyme. A major potential use of the Pycnoporus fungi is thus to harness their laccases for various applications such as the bioconversion of agricultural by-products and raw plant materials into valuable products, the biopulping and biobleaching of paper pulp and the biodegradation of organopollutants, xenobiotics and industrial contaminants. All the studies performed in the last decade show the genus Pycnoporus to be a strong contender for white biotechnology. In this review, we describe the properties of Pycnoporus fungi in relation to their biotechnological applications and potential.
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Affiliation(s)
- Anne Lomascolo
- UMR INRA de Biotechnologie des Champignons Filamenteux, ESIL, Marseille, France.
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Jeon JR, Baldrian P, Murugesan K, Chang YS. Laccase-catalysed oxidations of naturally occurring phenols: from in vivo biosynthetic pathways to green synthetic applications. Microb Biotechnol 2011; 5:318-32. [PMID: 21791030 PMCID: PMC3821676 DOI: 10.1111/j.1751-7915.2011.00273.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Laccases are oxidases that contain several copper atoms, and catalyse single-electron oxidations of phenolic compounds with concomitant reduction of oxygen to water. The enzymes are particularly widespread in ligninolytic basidiomycetes, but also occur in certain prokaryotes, insects and plants. Depending on the species, laccases are involved in various biosynthetic processes contributing to carbon recycling in land ecosystems and the morphogenesis of biomatrices, wherein low-molecular-weight naturally occurring phenols serve as key enzyme substrates. Studies of these in vivo synthetic pathways have afforded new insights into fungal laccase applicability in green synthetic chemistry. Thus, we here review fungal laccase-catalysed oxidations of naturally occurring phenols that are particularly relevant to the synthesis of fine organic chemicals, and we discuss how the discovered synthetic strategies mimic laccase-involved in vivo pathways, thus enhancing the green nature of such reactions. Laccase-catalysed in vivo processes yield several types of biopolymers, including those of cuticles, lignin, polyflavonoids, humus and the melanin pigments, using natural mono- or poly-phenols as building blocks. The in vivo synthetic pathways involve either phenoxyl radical-mediated coupling or cross-linking reactions, and can be adapted to the design of in vitro oxidative processes involving fungal laccases in organic synthesis; the laccase substrates and the synthetic mechanisms reflect in vivo processes. Notably, such in vitro synthetic pathways can also reproduce physicochemical properties (e.g. those of chromophores, and radical-scavenging, hydration and antimicrobial activities) found in natural biomaterials. Careful study of laccase-associated in vivo metabolic pathways has been rewarded by the discovery of novel green applications for fungal laccases. This review comprehensively summarizes the available data on laccase-catalysed biosynthetic pathways and associated applications in fine chemical syntheses.
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Affiliation(s)
- Jong-Rok Jeon
- Corporate R&D Group, LG Chem Research Park, Daejeon 305-380, Korea
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Liers C, Arnstadt T, Ullrich R, Hofrichter M. Patterns of lignin degradation and oxidative enzyme secretion by different wood- and litter-colonizing basidiomycetes and ascomycetes grown on beech-wood. FEMS Microbiol Ecol 2011; 78:91-102. [DOI: 10.1111/j.1574-6941.2011.01144.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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