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Cho Y, Kim JS, Dai YC, Gafforov Y, Lim YW. Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank. PeerJ 2021; 9:e12625. [PMID: 34966599 PMCID: PMC8667721 DOI: 10.7717/peerj.12625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised multiple times over the years. However, the emendations were poorly reflected in studies and public sequence databases. In the present study, the genus Xylodon in Korea was evaluated using molecular and morphological analyses of 172 specimens collected in the period of 2011 to 2018. The host types and geographical distributions were also determined for species delimitation. Furthermore, public sequences that correspond to the Xylodon species in Korea were assessed to validate their identities. Nine Xylodon species were identified in Korea, with three species new to the country. Morphological differentiation and identification of some species were challenging, but all nine species were clearly divided into well-resolved clades in the phylogenetic analyses. Detailed species descriptions, phylogeny, and a key to Xylodon species in Korea are provided in the present study. A total of 646 public ITS and nrLSU sequences corresponding to the nine Xylodon species were found, each with 404 (73.1%) and 57 (61.3%) misidentified or labeled with synonymous names. In many cases, sequences released before the report of new names have not been revised or updated. Revisions of these sequences are arranged in the present study. These amendments may be used to avoid the misidentification of future sequence-based identifications and concurrently prevent the accumulation of misidentified sequences in GenBank.
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Affiliation(s)
- Yoonhee Cho
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Ji Seon Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Yu-Cheng Dai
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yusufjon Gafforov
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
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2
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Wu B, Gaskell J, Held BW, Toapanta C, Vuong TV, Ahrendt S, Lipzen A, Zhang J, Schilling JS, Master E, Grigoriev IV, Blanchette RA, Cullen D, Hibbett DS. Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola". Appl Environ Microbiol 2021; 87:e0032921. [PMID: 34313495 PMCID: PMC8353965 DOI: 10.1128/aem.00329-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species—aspen, pine, and spruce—under various culture conditions. We found that F. pinicola is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.
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Affiliation(s)
- Baojun Wu
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Jill Gaskell
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - Benjamin W. Held
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Cristina Toapanta
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Thu V. Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Steven Ahrendt
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Jiwei Zhang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jonathan S. Schilling
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Emma Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Igor V. Grigoriev
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Robert A. Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - David S. Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
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3
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Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers. J Fungi (Basel) 2021; 7:jof7030185. [PMID: 33807546 PMCID: PMC7998857 DOI: 10.3390/jof7030185] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO2) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO2 emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO2 assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO2 emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.
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Brischke C, Alfredsen G. Wood-water relationships and their role for wood susceptibility to fungal decay. Appl Microbiol Biotechnol 2020; 104:3781-3795. [PMID: 32144473 PMCID: PMC8326242 DOI: 10.1007/s00253-020-10479-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022]
Abstract
Wood in service is sequestering carbon, but it is principally prone to deterioration where different fungi metabolize wood, and carbon dioxide is released back to the atmosphere. A key prerequisite for fungal degradation of wood is the presence of moisture. Conversely, keeping wood dry is the most effective way to protect wood from wood degradation and for long-term binding of carbon. Wood is porous and hygroscopic; it can take up water in liquid and gaseous form, and water is released from wood through evaporation following a given water vapour pressure gradient. During the last decades, the perception of wood-water relationships changed significantly and so did the view on moisture-affected properties of wood. Among the latter is its susceptibility to fungal decay. This paper reviews findings related to wood-water relationships and their role for fungal wood decomposition. These are complex interrelationships not yet fully understood, and current knowledge gaps are therefore identified. Studies with chemically and thermally modified wood are included as examples of fungal wood substrates with altered moisture properties. Quantification and localization of capillary and cell wall water - especially in the over-hygroscopic range - is considered crucial for determining minimum moisture thresholds (MMThr) of wood-decay fungi. The limitations of the various methods and experimental set-ups to investigate wood-water relationships and their role for fungal decay are manifold. Hence, combining techniques from wood science, mycology, biotechnology and advanced analytics is expected to provide new insights and eventually a breakthrough in understanding the intricate balance between fungal decay and wood-water relations. KEY POINTS: • Susceptibility to wood-decay fungi is closely linked to their physiological needs. • Content, state and distribution of moisture in wood are keys for fungal activity. • Quantification and localization of capillary and cell wall water in wood is needed. • New methodological approaches are expected to provide new insights.
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Affiliation(s)
- Christian Brischke
- Department of Wood Biology and Wood Products, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Buesgenweg 4, D-37077, Goettingen, Germany.
| | - Gry Alfredsen
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Forest and Forest Resources, Wood Technology, Høgskoleveien 8, 1433, Ås, Norway
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Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation. Biotechnol Adv 2019; 37:107361. [PMID: 30825514 DOI: 10.1016/j.biotechadv.2019.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 12/26/2022]
Abstract
Fungal strain engineering is commonly used in many areas of biotechnology, including the production of plant biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of plant biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.
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Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi. ISME JOURNAL 2019; 13:1391-1403. [PMID: 30718807 DOI: 10.1038/s41396-019-0359-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 02/07/2023]
Abstract
Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts.
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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8
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Jurak E, Suzuki H, van Erven G, Gandier JA, Wong P, Chan K, Ho CY, Gong Y, Tillier E, Rosso MN, Kabel MA, Miyauchi S, Master ER. Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. BMC Genomics 2018; 19:815. [PMID: 30424733 PMCID: PMC6234650 DOI: 10.1186/s12864-018-5210-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/30/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition. RESULTS Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi. CONCLUSIONS The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.
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Affiliation(s)
- E Jurak
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.,Department of Aquatic Biotechnology and Bioproduct Engineering, Groningen, The Netherlands
| | - H Suzuki
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - G van Erven
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - J A Gandier
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - P Wong
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - K Chan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - C Y Ho
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Y Gong
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - E Tillier
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - M-N Rosso
- Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - M A Kabel
- Wageningen University, Laboratory of Food Chemistry, Bornse Weilanden 9, 6708, WG, Wageningen, The Netherlands
| | - S Miyauchi
- Laboratory of Excellence ARBRE, INRA, Nancy, Lorraine, France.,Aix-Marseille Université, INRA, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - E R Master
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.
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Wu B, Gaskell J, Held BW, Toapanta C, Vuong T, Ahrendt S, Lipzen A, Zhang J, Schilling JS, Master E, Grigoriev IV, Blanchette RA, Cullen D, Hibbett DS. Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola. Appl Environ Microbiol 2018; 84:e00991-18. [PMID: 29884757 PMCID: PMC6070754 DOI: 10.1128/aem.00991-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/03/2018] [Indexed: 12/20/2022] Open
Abstract
Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression and RNA editing were observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression and RNA editing encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. pinicola with independent mechanisms for responding to different conditions. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi.IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that enable fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species, aspen, pine, and spruce, under various culture conditions. We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can potentially yield different proteins from the same gene). We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.
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Affiliation(s)
- Baojun Wu
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Jill Gaskell
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - Benjamin W Held
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Cristina Toapanta
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Thu Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Steven Ahrendt
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Jiwei Zhang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Emma Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, Wisconsin, USA
| | - David S Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
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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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11
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Qin X, Su X, Luo H, Ma R, Yao B, Ma F. Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:58. [PMID: 29507610 PMCID: PMC5833081 DOI: 10.1186/s13068-018-1060-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/23/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Irpex lacteus is one of the most potent white rot fungi for biological pretreatment of lignocellulose for second biofuel production. To elucidate the underlying molecular mechanism involved in lignocellulose deconstruction, genomic and transcriptomic analyses were carried out for I. lacteus CD2 grown in submerged fermentation using ball-milled corn stover as the carbon source. RESULTS Irpex lacteus CD2 efficiently decomposed 74.9% lignin, 86.3% cellulose, and 83.5% hemicellulose in corn stover within 9 days. Manganese peroxidases were rapidly induced, followed by accumulation of cellulase and hemicellulase. Genomic analysis revealed that I. lacteus CD2 possessed a complete set of lignocellulose-degrading enzyme system composed mainly of class II peroxidases, dye-decolorizing peroxidases, auxiliary enzymes, and 182 glycoside hydrolases. Comparative transcriptomic analysis substantiated the notion of a selection mode of degradation. These analyses also suggested that free radicals, derived either from MnP-organic acid interplay or from Fenton reaction involving Fe2+ and H2O2, could play an important role in lignocellulose degradation. CONCLUSIONS The selective strategy employed by I. lacteus CD2, in combination with low extracellular glycosidases cleaving plant cell wall polysaccharides into fermentable sugars, may account for high pretreatment efficiency of I. lacteus. Our study also hints the importance of free radicals for future designing of novel, robust lignocellulose-degrading enzyme cocktails.
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Affiliation(s)
- Xing Qin
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Fuying Ma
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
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12
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Miyauchi S, Navarro D, Grisel S, Chevret D, Berrin JG, Rosso MN. The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. PLoS One 2017; 12:e0175528. [PMID: 28394946 PMCID: PMC5386290 DOI: 10.1371/journal.pone.0175528] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/27/2017] [Indexed: 01/22/2023] Open
Abstract
Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.
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Affiliation(s)
- Shingo Miyauchi
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - David Navarro
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Sacha Grisel
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Didier Chevret
- PAPPSO, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Guy Berrin
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noelle Rosso
- Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
- * E-mail:
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13
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Rytioja J, Hildén K, Di Falco M, Zhou M, Aguilar-Pontes MV, Sietiö OM, Tsang A, de Vries RP, Mäkelä MR. The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses. Environ Microbiol 2017; 19:1237-1250. [PMID: 28028889 DOI: 10.1111/1462-2920.13652] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/16/2016] [Accepted: 12/18/2016] [Indexed: 12/27/2022]
Abstract
The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.
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Affiliation(s)
- Johanna Rytioja
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marcos Di Falco
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Outi-Maaria Sietiö
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Ronald P de Vries
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands
| | - Miia R Mäkelä
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
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14
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Álvarez C, Reyes-Sosa FM, Díez B. Enzymatic hydrolysis of biomass from wood. Microb Biotechnol 2016; 9:149-56. [PMID: 26833542 PMCID: PMC4767290 DOI: 10.1111/1751-7915.12346] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/25/2015] [Accepted: 12/03/2015] [Indexed: 01/10/2023] Open
Abstract
Current research and development in cellulosic ethanol production has been focused mainly on agricultural residues and dedicated energy crops such as corn stover and switchgrass; however, woody biomass remains a very important feedstock for ethanol production. The precise composition of hemicellulose in the wood is strongly dependent on the plant species, therefore different types of enzymes are needed based on hemicellulose complexity and type of pretreatment. In general, hardwood species have much lower recalcitrance to enzymes than softwood. For hardwood, xylanases, beta‐xylosidases and xyloglucanases are the main hemicellulases involved in degradation of the hemicellulose backbone, while for softwood the effect of mannanases and beta‐mannosidases is more relevant. Furthermore, there are different key accessory enzymes involved in removing the hemicellulosic fraction and increasing accessibility of cellulases to the cellulose fibres improving the hydrolysis process. A diversity of enzymatic cocktails has been tested using from low to high densities of biomass (2–20% total solids) and a broad range of results has been obtained. The performance of recently developed commercial cocktails on hardwoods and softwoods will enable a further step for the commercialization of fuel ethanol from wood.
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Affiliation(s)
- Consolación Álvarez
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar no. 1, Seville, 41014, Spain
| | - Francisco Manuel Reyes-Sosa
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar no. 1, Seville, 41014, Spain
| | - Bruno Díez
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar no. 1, Seville, 41014, Spain
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15
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Hori C, Cullen D. Prospects for Bioprocess Development Based on Recent Genome Advances in Lignocellulose Degrading Basidiomycetes. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Patyshakuliyeva A, Post H, Zhou M, Jurak E, Heck AJR, Hildén KS, Kabel MA, Mäkelä MR, Altelaar MAF, de Vries RP. Uncovering the abilities ofAgaricus bisporusto degrade plant biomass throughout its life cycle. Environ Microbiol 2015; 17:3098-109. [DOI: 10.1111/1462-2920.12967] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/18/2015] [Accepted: 06/20/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Aleksandrina Patyshakuliyeva
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Centre; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Edita Jurak
- Laboratory of Food Chemistry; Wageningen University; Bornse Weilanden 9 6708 WG Wageningen The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Centre; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Kristiina S. Hildén
- Department of Food and Environmental Sciences; University of Helsinki; P. O. Box 56 00014 Helsinki Finland
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry; Wageningen University; Bornse Weilanden 9 6708 WG Wageningen The Netherlands
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences; University of Helsinki; P. O. Box 56 00014 Helsinki Finland
| | - Maarten A. F. Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
- Netherlands Proteomics Centre; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
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17
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Lee S, J. Mitchell R. Perspectives on the use of transcriptomics to advance biofuels. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.4.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Couturier M, Navarro D, Chevret D, Henrissat B, Piumi F, Ruiz-Dueñas FJ, Martinez AT, Grigoriev IV, Riley R, Lipzen A, Berrin JG, Master ER, Rosso MN. Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:216. [PMID: 26692083 PMCID: PMC4683735 DOI: 10.1186/s13068-015-0407-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/03/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND White-rot basidiomycete fungi are potent degraders of plant biomass, with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. The Polyporale fungus Pycnoporus coccineus BRFM310 grows well on both coniferous and deciduous wood. In the present study, we analyzed the early response of the fungus to softwood (pine) and hardwood (aspen) feedstocks and tested the effect of the secreted enzymes on lignocellulose deconstruction. RESULTS Transcriptomic and proteomic analyses revealed that P. coccineus grown separately on pine and aspen displayed similar sets of transcripts and enzymes implicated in lignin and polysaccharide degradation. In particular, the expression of lignin-targeting oxidoreductases, such as manganese peroxidases, increased upon cultivation on both woods. The sets of enzymes secreted during growth on both pine and aspen were more efficient in saccharide release from pine than from aspen, and characterization of the residual solids revealed polysaccharide conversion on both pine and aspen fiber surfaces. CONCLUSION The combined analysis of soluble sugars and solid residues showed the suitability of P. coccineus secreted enzymes for softwood degradation. Analyses of solubilized products and residual surface chemistries of enzyme-treated wood samples pointed to differences in fiber penetration by different P. coccineus secretomes. Accordingly, beyond the variety of CAZymes identified in P. coccineus genome, transcriptome and secretome, we discuss several parameters such as the abundance of manganese peroxidases and the potential role of cytochrome P450s and pectin degradation on the efficacy of fungi for softwood conversion.
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Affiliation(s)
- Marie Couturier
- />Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />Polytech’Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada
| | - David Navarro
- />Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />Polytech’Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
| | - Didier Chevret
- />INRA, UMR1319 Micalis, Plateforme d’Analyse Protéomique de Paris Sud-Ouest, 78352 Jouy-En-Josas, France
| | - Bernard Henrissat
- />Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 13288 Marseille, France
- />Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- />INRA, USC 1408 AFMB, 13288 Marseille, France
| | - François Piumi
- />Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />Polytech’Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
| | | | | | - Igor V. Grigoriev
- />US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - Robert Riley
- />US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - Anna Lipzen
- />US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA
| | - Jean-Guy Berrin
- />Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />Polytech’Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
| | - Emma R. Master
- />Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada
| | - Marie-Noëlle Rosso
- />Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
- />Polytech’Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France
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19
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Kolbusz MA, Di Falco M, Ishmael N, Marqueteau S, Moisan MC, Baptista CDS, Powlowski J, Tsang A. Transcriptome and exoproteome analysis of utilization of plant-derived biomass by Myceliophthora thermophila. Fungal Genet Biol 2014; 72:10-20. [PMID: 24881579 DOI: 10.1016/j.fgb.2014.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 11/29/2022]
Abstract
Myceliophthora thermophila is a thermophilic fungus whose genome encodes a wide range of carbohydrate-active enzymes (CAZymes) involved in plant biomass degradation. Such enzymes have potential applications in turning different kinds of lignocellulosic feedstock into sugar precursors for biofuels and chemicals. The present study examined and compared the transcriptomes and exoproteomes of M. thermophila during cultivation on different types of complex biomass to gain insight into how its secreted enzymatic machinery varies with different sources of lignocellulose. In the transcriptome analysis three monocot (barley, oat, triticale) and three dicot (alfalfa, canola, flax) plants were used whereas in the proteome analysis additional substrates, i.e. wood and corn stover pulps, were included. A core set of 59 genes encoding CAZymes was up-regulated in response to both monocot and dicot straws, including nine polysaccharide monooxygenases and GH10, but not GH11, xylanases. Genes encoding additional xylanolytic enzymes were up-regulated during growth on monocot straws, while genes encoding additional pectinolytic enzymes were up-regulated in response to dicot biomass. Exoproteome analysis was generally consistent with the conclusions drawn from transcriptome analysis, but additional CAZymes that accumulated to high levels were identified. Despite the wide variety of biomass sources tested some CAZy family members were not expressed under any condition. The results of this study provide a comprehensive view from both transcriptome and exoproteome levels, of how M. thermophila responds to a wide range of biomass sources using its genomic resources.
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Affiliation(s)
- Magdalena Anna Kolbusz
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Nadeeza Ishmael
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Sandrine Marqueteau
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Marie-Claude Moisan
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Cassio da Silva Baptista
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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20
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Rytioja J, Hildén K, Hatakka A, Mäkelä MR. Transcriptional analysis of selected cellulose-acting enzymes encoding genes of the white-rot fungus Dichomitus squalens on spruce wood and microcrystalline cellulose. Fungal Genet Biol 2014; 72:91-98. [PMID: 24394946 DOI: 10.1016/j.fgb.2013.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 10/25/2022]
Abstract
The recent discovery of oxidative cellulose degradation enhancing enzymes has considerably changed the traditional concept of hydrolytic cellulose degradation. The relative expression levels of ten cellulose-acting enzyme encoding genes of the white-rot fungus Dichomitus squalens were studied on solid-state spruce wood and in microcrystalline Avicel cellulose cultures. From the cellobiohydrolase encoding genes, cel7c was detected at the highest level and showed constitutive expression whereas variable transcript levels were detected for cel7a, cel7b and cel6 in the course of four-week spruce cultivation. The cellulolytic enzyme activities detected in the liquid cultures were consistent with the transcript levels. Interestingly, the selected lytic polysaccharide monooxygenase (LPMO) encoding genes were expressed in both cultures, but showed different transcription patterns on wood compared to those in submerged microcrystalline cellulose cultures. On spruce wood, higher transcript levels were detected for the lpmos carrying cellulose binding module (CBM) than for the lpmos without CBMs. In both cultures, the expression levels of the lpmo genes were generally higher than the levels of cellobiose dehydrogenase (CDH) encoding genes. Based on the results of this work, the oxidative cellulose cleaving enzymes of D. squalens have essential role in cellulose degrading machinery of the fungus.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, Finland.
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21
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Hunt CG, Houtman CJ, Jones DC, Kitin P, Korripally P, Hammel KE. Spatial mapping of extracellular oxidant production by a white rot basidiomycete on wood reveals details of ligninolytic mechanism. Environ Microbiol 2012. [PMID: 23206186 DOI: 10.1111/1462-2920.12039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Oxidative cleavage of the recalcitrant plant polymer lignin is a crucial step in global carbon cycling, and is accomplished most efficiently by fungi that cause white rot of wood. These basidiomycetes secrete many enzymes and metabolites with proposed ligninolytic roles, and it is not clear whether all of these agents are physiologically important during attack on natural lignocellulosic substrates. One new approach to this problem is to infer properties of ligninolytic oxidants from their spatial distribution relative to the fungus on the lignocellulose. We grew Phanerochaete chrysosporium on wood sections in the presence of oxidant-sensing beads based on the ratiometric fluorescent dye BODIPY 581/591. The beads, having fixed locations relative to the fungal hyphae, enabled spatial mapping of cumulative extracellular oxidant distributions by confocal fluorescence microscopy. The results showed that oxidation gradients occurred around the hyphae, and data analysis using a mathematical reaction-diffusion model indicated that the dominant oxidant during incipient white rot had a half-life under 0.1 s. The best available hypothesis is that this oxidant is the cation radical of the secreted P. chrysosporium metabolite veratryl alcohol.
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22
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MacDonald J, Suzuki H, Master ER. Expression and regulation of genes encoding lignocellulose-degrading activity in the genus Phanerochaete. Appl Microbiol Biotechnol 2012; 94:339-51. [PMID: 22391967 DOI: 10.1007/s00253-012-3937-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 10/28/2022]
Abstract
As white-rot basidiomycetes, Phanerochaete species are critical to the cycling of carbon sequestered as woody biomass, and are predicted to encode many enzymes that can be harnessed to promote the conversion of lignocellulose to sugars for fermentation to fuels and chemicals. Advances in genomic, transcriptomic, and proteomic technologies have enabled detailed analyses of different Phanerochaete species and have revealed numerous enzyme families required for lignocellulose utilization, as well as insight into the regulation of corresponding genes. Recent studies of Phanerochaete are also exemplified by molecular analyses following cultivation on different wood preparations, and show substrate-dependent responses that were difficult to predict using model compounds or isolated plant polysaccharides. The aim of this mini-review is to synthesize results from studies that have applied recent advances in molecular tools to evaluate the expression and regulation of proteins that contribute to lignocellulose conversion in Phanerochaete species. The identification of proteins with as yet unknown function are also highlighted and noted as important targets for future investigation of white-rot decay.
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Affiliation(s)
- Jacqueline MacDonald
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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