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Marinovíc M, Di Falco M, Aguilar Pontes MV, Gorzsás A, Tsang A, de Vries RP, Mäkelä MR, Hildén K. Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora. Biomolecules 2022; 12:biom12081017. [PMID: 35892327 PMCID: PMC9330253 DOI: 10.3390/biom12081017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them indispensable organisms in the global carbon cycle. In this study, we analyzed the proteomes of two closely related white rot fungi, Obba rivulosa and Gelatoporia subvermispora, during eight-week cultivation on solid spruce wood. Plant cell wall degrading carbohydrate-active enzymes (CAZymes) represented approximately 5% of the total proteins in both species. A core set of orthologous plant cell wall degrading CAZymes was shared between these species on spruce suggesting a conserved plant biomass degradation approach in this clade of basidiomycete fungi. However, differences in time-dependent production of plant cell wall degrading enzymes may be due to differences among initial growth rates of these species on solid spruce wood. The obtained results provide insight into specific enzymes and enzyme sets that are produced during the degradation of solid spruce wood in these fungi. These findings expand the knowledge on enzyme production in nature-mimicking conditions and may contribute to the exploitation of white rot fungi and their enzymes for biotechnological applications.
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Affiliation(s)
- Mila Marinovíc
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada; (M.D.F.); (A.T.)
| | - Maria Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (M.V.A.P.); (R.P.d.V.)
| | - András Gorzsás
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden;
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada; (M.D.F.); (A.T.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (M.V.A.P.); (R.P.d.V.)
| | - Miia R. Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
| | - Kristiina Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland; (M.M.); (M.R.M.)
- Correspondence:
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2
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Sun YF, Lebreton A, Xing JH, Fang YX, Si J, Morin E, Miyauchi S, Drula E, Ahrendt S, Cobaugh K, Lipzen A, Koriabine M, Riley R, Kohler A, Barry K, Henrissat B, Grigoriev IV, Martin FM, Cui BK. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. J Fungi (Basel) 2022; 8:jof8030311. [PMID: 35330313 PMCID: PMC8955403 DOI: 10.3390/jof8030311] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.
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Affiliation(s)
- Yi-Fei Sun
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Annie Lebreton
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jia-Hui Xing
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Yu-Xuan Fang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829 Cologne, Germany
| | - Elodie Drula
- INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France;
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Kelly Cobaugh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
- Department of Biological Sciences, King Abdulaziz University, Jeddah 999088, Saudi Arabia
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
- Department of Microbial and Plant Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Francis M. Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
| | - Bao-Kai Cui
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
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3
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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4
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Biocatalytic potential of basidiomycetes: Relevance, challenges and research interventions in industrial processes. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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5
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Hage H, Miyauchi S, Virágh M, Drula E, Min B, Chaduli D, Navarro D, Favel A, Norest M, Lesage-Meessen L, Bálint B, Merényi Z, de Eugenio L, Morin E, Martínez AT, Baldrian P, Štursová M, Martínez MJ, Novotny C, Magnuson JK, Spatafora JW, Maurice S, Pangilinan J, Andreopoulos W, LaButti K, Hundley H, Na H, Kuo A, Barry K, Lipzen A, Henrissat B, Riley R, Ahrendt S, Nagy LG, Grigoriev IV, Martin F, Rosso MN. Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay. Environ Microbiol 2021; 23:5716-5732. [PMID: 33538380 PMCID: PMC8596683 DOI: 10.1111/1462-2920.15423] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/16/2022]
Abstract
Because they comprise some of the most efficient wood‐decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin‐like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.
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Affiliation(s)
- Hayat Hage
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
| | - Shingo Miyauchi
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Köln, Germany
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Elodie Drula
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, USC1408, AFMB, Marseille, 13009, France
| | - Byoungnam Min
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Delphine Chaduli
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - David Navarro
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Anne Favel
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Manon Norest
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
| | - Laurence Lesage-Meessen
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France.,INRAE, Aix Marseille Univ, CIRM-CF, UMR1163, Marseille, 13009, France
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary
| | - Laura de Eugenio
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, 28040, Spain
| | - Cenek Novotny
- Institute of Microbiology of the Czech Academy of Sciences, Praha 4, 142 20, Czech Republic.,University of Ostrava, Ostrava, 701 03, Czech Republic
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joey W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Sundy Maurice
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, 0316, Norway
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Willian Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hope Hundley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, 6726, Hungary.,Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Francis Martin
- Université de Lorraine, INRAE, UMR1136, Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | - Marie-Noëlle Rosso
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, 13009, France
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6
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Kontro J, Maltari R, Mikkilä J, Kähkönen M, Mäkelä MR, Hildén K, Nousiainen P, Sipilä J. Applicability of Recombinant Laccases From the White-Rot Fungus Obba rivulosa for Mediator-Promoted Oxidation of Biorefinery Lignin at Low pH. Front Bioeng Biotechnol 2020; 8:604497. [PMID: 33392170 PMCID: PMC7773891 DOI: 10.3389/fbioe.2020.604497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/11/2020] [Indexed: 11/18/2022] Open
Abstract
Utilization of lignin-rich side streams has been a focus of intensive studies recently. Combining biocatalytic methods with chemical treatments is a promising approach for sustainable modification of lignocellulosic waste streams. Laccases are catalysts in lignin biodegradation with proven applicability in industrial scale. Laccases directly oxidize lignin phenolic components, and their functional range can be expanded using low-molecular-weight compounds as mediators to include non-phenolic lignin structures. In this work, we studied in detail recombinant laccases from the selectively lignin-degrading white-rot fungus Obba rivulosa for their properties and evaluated their potential as industrial biocatalysts for the modification of wood lignin and lignin-like compounds. We screened and optimized various laccase mediator systems (LMSs) using lignin model compounds and applied the optimized reaction conditions to biorefinery-sourced technical lignin. In the presence of both N-OH-type and phenolic mediators, the O. rivulosa laccases were shown to selectively oxidize lignin in acidic reaction conditions, where a cosolvent is needed to enhance lignin solubility. In comparison to catalytic iron(III)-(2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) oxidation systems, the syringyl-type lignin units were preferred in mediated biocatalytic oxidation systems.
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Affiliation(s)
- Jussi Kontro
- Department of Chemistry, Faculty of Science, Chemicum, University of Helsinki, Helsinki, Finland
| | - Riku Maltari
- Department of Chemistry, Faculty of Science, Chemicum, University of Helsinki, Helsinki, Finland
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Joona Mikkilä
- Department of Chemistry, Faculty of Science, Chemicum, University of Helsinki, Helsinki, Finland
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Mika Kähkönen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Miia R. Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Paula Nousiainen
- Department of Chemistry, Faculty of Science, Chemicum, University of Helsinki, Helsinki, Finland
| | - Jussi Sipilä
- Department of Chemistry, Faculty of Science, Chemicum, University of Helsinki, Helsinki, Finland
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7
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Kölle M, Horta MAC, Nowrousian M, Ohm RA, Benz JP, Pilgård A. Degradative Capacity of Two Strains of Rhodonia placenta: From Phenotype to Genotype. Front Microbiol 2020; 11:1338. [PMID: 32625194 PMCID: PMC7314958 DOI: 10.3389/fmicb.2020.01338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 01/23/2023] Open
Abstract
Brown rot fungi, such as Rhodonia placenta (previously Postia placenta), occur naturally in northern coniferous forest ecosystems and are known to be the most destructive group of decay fungi, degrading wood faster and more effectively than other wood-degrading organisms. It has been shown that brown rot fungi not only rely on enzymatic degradation of lignocellulose, but also use low molecular weight oxidative agents in a non-enzymatic degradation step prior to the enzymatic degradation. R. placenta is used in standardized decay tests in both Europe and North America. However, two different strains are employed (FPRL280 and MAD-698, respectively) for which differences in colonization-rate, mass loss, as well as in gene expression have been observed, limiting the comparability of results. To elucidate the divergence between both strains, we investigated the phenotypes in more detail and compared their genomes. Significant phenotypic differences were found between the two strains, and no fusion was possible. MAD-698 degraded scots pine more aggressively, had a more constant growth rate and produced mycelia faster than FPRL280. After sequencing the genome of FPRL280 and comparing it with the published MAD-698 genome we found 660,566 SNPs, resulting in 98.4% genome identity. Specific analysis of the carbohydrate-active enzymes, encoded by the genome (CAZome) identified differences in many families related to plant biomass degradation, including SNPs, indels, gaps or insertions within structural domains. Four genes belonging to the AA3_2 family could not be found in or amplified from FPRL280 gDNA, suggesting the absence of these genes. Differences in other CAZy encoding genes that could potentially affect the lignocellulolytic activity of the strains were also predicted by comparison of genome assemblies (e.g., GH2, GH3, GH5, GH10, GH16, GH78, GT2, GT15, and CBM13). Overall, these mutations help to explain the phenotypic differences observed between both strains as they could interfere with the enzymatic activities, substrate binding ability or protein folding. The investigation of the molecular reasons that make these two strains distinct contributes to the understanding of the development of this important brown rot reference species and will help to put the data obtained from standardized decay tests across the globe into a better biological context.
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Affiliation(s)
- Martina Kölle
- Chair of Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Maria Augusta Crivelente Horta
- Professorship for Wood Bioprocesses, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
| | - Robin A Ohm
- Department of Biology, Microbiology, Utrecht University, Utrecht, Netherlands
| | - J Philipp Benz
- Professorship for Wood Bioprocesses, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Institute of Advanced Study, Technical University of Munich, Garching, Germany
| | - Annica Pilgård
- Chair of Wood Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.,Biobased Materials, Bioeconomy, RISE Research Institutes of Sweden, Borås, Sweden
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8
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Mikkilä J, Trogen M, Koivu KAY, Kontro J, Kuuskeri J, Maltari R, Dekere Z, Kemell M, Mäkelä MR, Nousiainen PA, Hummel M, Sipilä J, Hildén K. Fungal Treatment Modifies Kraft Lignin for Lignin- and Cellulose-Based Carbon Fiber Precursors. ACS OMEGA 2020; 5:6130-6140. [PMID: 32226896 PMCID: PMC7098016 DOI: 10.1021/acsomega.0c00142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 02/28/2020] [Indexed: 05/17/2023]
Abstract
The kraft lignin's low molecular weight and too high hydroxyl content hinder its application in bio-based carbon fibers. In this study, we were able to polymerize kraft lignin and reduce the amount of hydroxyl groups by incubating it with the white-rot fungus Obba rivulosa. Enzymatic radical oxidation reactions were hypothesized to induce condensation of lignin, which increased the amount of aromatic rings connected by carbon-carbon bonds. This modification is assumed to be beneficial when aiming for graphite materials such as carbon fibers. Furthermore, the ratio of remaining aliphatic hydroxyls to phenolic hydroxyls was increased, making the structure more favorable for carbon fiber production. When the modified lignin was mixed together with cellulose, the mixture could be spun into intact precursor fibers by using dry-jet wet spinning. The modified lignin leaked less to the spin bath compared with the unmodified lignin starting material, making the recycling of spin-bath solvents easier. The stronger incorporation of modified lignin in the precursor fibers was confirmed by composition analysis, thermogravimetry, and mechanical testing. This work shows how white-rot fungal treatment can be used to modify the structure of lignin to be more favorable for the production of bio-based fiber materials.
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Affiliation(s)
- Joona Mikkilä
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki FI-00014 Helsinki, Finland
- Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki FI-00014 Helsinki, Finland
- .
Tel.: +358504413086
| | - Mikaela Trogen
- Department
of Bioproducts and Biosystems, Aalto University, Vuorimiehentie 1, Espoo FI-00076 Aalto, Finland
| | - Klaus A. Y. Koivu
- Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki FI-00014 Helsinki, Finland
| | - Jussi Kontro
- Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki FI-00014 Helsinki, Finland
| | - Jaana Kuuskeri
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki FI-00014 Helsinki, Finland
| | - Riku Maltari
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki FI-00014 Helsinki, Finland
- Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki FI-00014 Helsinki, Finland
| | - Zane Dekere
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki FI-00014 Helsinki, Finland
| | - Marianna Kemell
- Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki FI-00014 Helsinki, Finland
| | - Miia R. Mäkelä
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki FI-00014 Helsinki, Finland
| | - Paula A. Nousiainen
- Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki FI-00014 Helsinki, Finland
| | - Michael Hummel
- Department
of Bioproducts and Biosystems, Aalto University, Vuorimiehentie 1, Espoo FI-00076 Aalto, Finland
| | - Jussi Sipilä
- Department
of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki FI-00014 Helsinki, Finland
| | - Kristiina Hildén
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki FI-00014 Helsinki, Finland
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9
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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10
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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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11
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Marinović M, Aguilar-Pontes MV, Zhou M, Miettinen O, de Vries RP, Mäkelä MR, Hildén K. Temporal transcriptome analysis of the white-rot fungus Obba rivulosa shows expression of a constitutive set of plant cell wall degradation targeted genes during growth on solid spruce wood. Fungal Genet Biol 2017; 112:47-54. [PMID: 28754284 DOI: 10.1016/j.fgb.2017.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022]
Abstract
The basidiomycete white-rot fungus Obba rivulosa, a close relative of Gelatoporia (Ceriporiopsis) subvermispora, is an efficient degrader of softwood. The dikaryotic O. rivulosa strain T241i (FBCC949) has been shown to selectively remove lignin from spruce wood prior to depolymerization of plant cell wall polysaccharides, thus possessing potential in biotechnological applications such as pretreatment of wood in pulp and paper industry. In this work, we studied the time-course of the conversion of spruce by the genome-sequenced monokaryotic O. rivulosa strain 3A-2, which is derived from the dikaryon T241i, to get insight into transcriptome level changes during prolonged solid state cultivation. During 8-week cultivation, O. rivulosa expressed a constitutive set of genes encoding putative plant cell wall degrading enzymes. High level of expression of the genes targeted towards all plant cell wall polymers was detected at 2-week time point, after which majority of the genes showed reduced expression. This implicated non-selective degradation of lignin by the O. rivulosa monokaryon and suggests high variation between mono- and dikaryotic strains of the white-rot fungi with respect to their abilities to convert plant cell wall polymers.
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Affiliation(s)
- Mila Marinović
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Maria Victoria Aguilar-Pontes
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Otto Miettinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miia R Mäkelä
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Kristiina Hildén
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland.
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