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Ristinmaa AS, Korotkova E, Arntzen MØ, G H Eijsink V, Xu C, Sundberg A, Hasani M, Larsbrink J. Analyses of long-term fungal degradation of spruce bark reveals varying potential for catabolism of polysaccharides and extractive compounds. BIORESOURCE TECHNOLOGY 2024; 402:130768. [PMID: 38697367 DOI: 10.1016/j.biortech.2024.130768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The bark represents the outer protective layer of trees. It contains high concentrations of antimicrobial extractives, in addition to regular wood polymers. It represents a huge underutilized side stream in forestry, but biotechnological valorization is hampered by a lack of knowledge on microbial bark degradation. Many fungi are efficient lignocellulose degraders, and here, spruce bark degradation by five species, Dichomitus squalens, Rhodonia placenta, Penicillium crustosum, Trichoderma sp. B1, and Trichoderma reesei, was mapped, by continuously analyzing chemical changes in the bark over six months. The study reveals how fungi from different phyla degrade bark using diverse strategies, regarding both wood polymers and extractives, where toxic resin acids were degraded by Basidiomycetes but unmodified/tolerated by Ascomycetes. Proteome analyses of the white-rot D. squalens revealed several proteins, with both known and unknown functions, that were specifically upregulated during growth on bark. This knowledge can accelerate improved utilization of an abundant renewable resource.
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Affiliation(s)
- Amanda S Ristinmaa
- Chalmers University of Technology, Department of Life Sciences, Division of Industrial Biotechnology, SE-412 96 Gothenburg, Sweden
| | - Ekaterina Korotkova
- Åbo Akademi University, Laboratory of Natural Materials Technology, FI-20500 Åbo, Finland
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1433 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1433 Ås, Norway
| | - Chunlin Xu
- Åbo Akademi University, Laboratory of Natural Materials Technology, FI-20500 Åbo, Finland
| | - Anna Sundberg
- Åbo Akademi University, Laboratory of Natural Materials Technology, FI-20500 Åbo, Finland
| | - Merima Hasani
- Department Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Johan Larsbrink
- Chalmers University of Technology, Department of Life Sciences, Division of Industrial Biotechnology, SE-412 96 Gothenburg, Sweden; Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
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2
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Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Exoproteomic Study and Transcriptional Responses of Laccase and Ligninolytic Peroxidase Genes of White-Rot Fungus Trametes hirsuta LE-BIN 072 Grown in the Presence of Monolignol-Related Phenolic Compounds. Int J Mol Sci 2023; 24:13115. [PMID: 37685920 PMCID: PMC10487439 DOI: 10.3390/ijms241713115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Being an abundant renewable source of aromatic compounds, lignin is an important component of future bio-based economy. Currently, biotechnological processing of lignin through low molecular weight compounds is one of the conceptually promising ways for its valorization. To obtain lignin fragments suitable for further inclusion into microbial metabolism, it is proposed to use a ligninolytic system of white-rot fungi, which mainly comprises laccases and peroxidases. However, laccase and peroxidase genes are almost always represented by many non-allelic copies that form multigene families within the genome of white-rot fungi, and the contributions of exact family members to the overall process of lignin degradation has not yet been determined. In this article, the response of the Trametes hirsuta LE-BIN 072 ligninolytic system to the presence of various monolignol-related phenolic compounds (veratryl alcohol, p-coumaric acid, vanillic acid, and syringic acid) in culture media was monitored at the level of gene transcription and protein secretion. By showing which isozymes contribute to the overall functioning of the ligninolytic system of the T. hirsuta LE-BIN 072, the data obtained in this study will greatly contribute to the possible application of this fungus and its ligninolytic enzymes in lignin depolymerization processes.
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Affiliation(s)
| | - Olga A. Glazunova
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia; (K.V.M.); (O.S.S.); (T.V.F.)
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3
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Peng M, Bervoets S, Chin-A-Woeng T, Granchi Z, Hildén K, Mäkelä MR, de Vries RP. The transcriptomic response of two basidiomycete fungi to plant biomass is modulated by temperature to a different extent. Microbiol Res 2023; 270:127333. [PMID: 36804127 DOI: 10.1016/j.micres.2023.127333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Many fungi show a strong preference for specific habitats and growth conditions. Investigating the molecular mechanisms of fungal adaptation to varying environmental conditions is of great interest to biodiversity research and is important for many industrial applications. In this study, we compared the transcriptome profiles of two previously genome-sequenced white-rot wood-decay fungi, Trametes pubescens and Phlebia centrifuga, during their growth on two common plant biomass substrates (wheat straw and spruce) at two temperatures (15 °C and 25 °C). The results showed that both fungi partially tailored their molecular responses to different types of carbon sources, differentially expressing genes encoding polysaccharide degrading enzymes, transporters, proteases and monooxygenases. Notably, more lignin modification related AA2 genes and cellulose degradation related AA9 genes were differentially expressed in the tested conditions of T. pubescens than P. centrifuga. In addition, we detected more remarkable transcriptome changes to different growth temperature in P. centrifuga than in T. pubescens, which reflected their different ability to adapt to the temperature fluctuations. In P. centrifuga, differentially expressed genes (DEGs) related to temperature response mainly encode protein kinases, trehalose metabolism, carbon metabolic enzymes and glycoside hydrolases, while the main temperature-related DEGs identified in T. pubescens are only the carbon metabolic enzymes and glycoside hydrolases. Our study revealed both conserved and species-specific transcriptome changes during fungal adaptation to a changing environment, improving our understanding of the molecular mechanisms underlying fungal plant biomass conversion at varying temperatures.
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Affiliation(s)
- Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Sander Bervoets
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | | | - Zoraide Granchi
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, the Netherlands
| | - Kristiina Hildén
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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4
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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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Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
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6
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Basinas P, Rusín J, Chamrádová K, Malachová K, Rybková Z, Novotný Č. Fungal pretreatment parameters for improving methane generation from anaerobic digestion of corn silage. BIORESOURCE TECHNOLOGY 2022; 345:126526. [PMID: 34896537 DOI: 10.1016/j.biortech.2021.126526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Corn silage was treated by white rot fungi (WRF) to investigate the effect of pretreatment on material's ability to produce methane in anaerobic digestion (AD). The selective fungi Pleurotus ostreatus and Dichomitus squalens promoted biogas generation, whereas the non-selective Trametes versicolor and Irpex lacteus had negative effect. Cumulative methane production after 10-day pretreatment with P. ostreatus at 28 °C rose 1.55-fold. The longer pretreatments of 30 and 60-days had smaller effect. When the pretreatment with P. ostreatus was carried out at 40 °C a high H2S release affected the AD process. Effect of WRF action dependent on the type of corn silage. With typical corn silage, the lignin depolymerisation raised the methane generation from 0.301 to 0.465 m3kgVS-1. In contrast, extensive decomposition of hemicellulose in hybrid corn silage deteriorated the effect of pretreatment on methane production.
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Affiliation(s)
- Panagiotis Basinas
- Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, 17. Listopadu 15/2172, Ostrava - Poruba 708 00, Czech Republic
| | - Jiří Rusín
- Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, 17. Listopadu 15/2172, Ostrava - Poruba 708 00, Czech Republic
| | - Kateřina Chamrádová
- Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, 17. Listopadu 15/2172, Ostrava - Poruba 708 00, Czech Republic.
| | - Kateřina Malachová
- Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, 17. Listopadu 15/2172, Ostrava - Poruba 708 00, Czech Republic; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Zuzana Rybková
- Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, 17. Listopadu 15/2172, Ostrava - Poruba 708 00, Czech Republic; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Čeněk Novotný
- Institute of Environmental Technology, CEET, VSB-Technical University of Ostrava, 17. Listopadu 15/2172, Ostrava - Poruba 708 00, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Czech Republic
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7
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Sun P, Li X, Dilokpimol A, Henrissat B, de Vries RP, Kabel MA, Mäkelä MR. Fungal glycoside hydrolase family 44 xyloglucanases are restricted to the phylum Basidiomycota and show a distinct xyloglucan cleavage pattern. iScience 2022; 25:103666. [PMID: 35028537 PMCID: PMC8741620 DOI: 10.1016/j.isci.2021.103666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/23/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022] Open
Abstract
Xyloglucan is a prominent matrix heteropolysaccharide binding to cellulose microfibrils in primary plant cell walls. Hence, the hydrolysis of xyloglucan facilitates the overall lignocellulosic biomass degradation. Xyloglucanases (XEGs) are key enzymes classified in several glycoside hydrolase (GH) families. So far, family GH44 has been shown to contain bacterial XEGs only. Detailed genome analysis revealed GH44 members in fungal species from the phylum Basidiomycota, but not in other fungi, which we hypothesized to also be XEGs. Two GH44 enzymes from Dichomitus squalens and Pleurotus ostreatus were heterologously produced and characterized. They exhibited XEG activity and displayed a hydrolytic cleavage pattern different from that observed in fungal XEGs from other GH families. Specifically, the fungal GH44 XEGs were not hindered by substitution of neighboring glucosyl units and generated various "XXXG-type," "GXXX(G)-type," and "XXX-type" oligosaccharides. Overall, these fungal GH44 XEGs represent a novel class of enzymes for plant biomass conversion and valorization.
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Affiliation(s)
- Peicheng Sun
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Xinxin Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
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8
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Schilling M, Maia-Grondard A, Baltenweck R, Robert E, Hugueney P, Bertsch C, Farine S, Gelhaye E. Wood degradation by Fomitiporia mediterranea M. Fischer: Physiologic, metabolomic and proteomic approaches. FRONTIERS IN PLANT SCIENCE 2022; 13:988709. [PMID: 36226293 PMCID: PMC9549746 DOI: 10.3389/fpls.2022.988709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/16/2022] [Indexed: 05/13/2023]
Abstract
Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called "amadou," one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites (extractives) and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern was demonstrated, and proteomic analysis identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species, and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche. Proteomics data are available via ProteomeXchange with identifier PXD036889.
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Affiliation(s)
- Marion Schilling
- Université de Lorraine, INRAE, IAM, Nancy, France
- *Correspondence: Marion Schilling,
| | | | | | | | | | - Christophe Bertsch
- Laboratoire Vigne Biotechnologies et Environnement UPR-3991, Université de Haute Alsace, Colmar, France
| | - Sibylle Farine
- Laboratoire Vigne Biotechnologies et Environnement UPR-3991, Université de Haute Alsace, Colmar, France
| | - Eric Gelhaye
- Université de Lorraine, INRAE, IAM, Nancy, France
- Eric Gelhaye,
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9
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Kowalczyk JE, Saha S, Mäkelä MR. Application of CRISPR/Cas9 Tools for Genome Editing in the White-Rot Fungus Dichomitus squalens. Biomolecules 2021; 11:1526. [PMID: 34680159 PMCID: PMC8533725 DOI: 10.3390/biom11101526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022] Open
Abstract
Dichomitus squalens is an emerging reference species that can be used to investigate white-rot fungal plant biomass degradation, as it has flexible physiology to utilize different types of biomass as sources of carbon and energy. Recent comparative (post-) genomic studies on D. squalens resulted in an increasingly detailed knowledge of the genes and enzymes involved in the lignocellulose breakdown in this fungus and showed a complex transcriptional response in the presence of lignocellulose-derived compounds. To fully utilize this increasing amount of data, efficient and reliable genetic manipulation tools are needed, e.g., to characterize the function of certain proteins in vivo and facilitate the construction of strains with enhanced lignocellulolytic capabilities. However, precise genome alterations are often very difficult in wild-type basidiomycetes partially due to extremely low frequencies of homology directed recombination (HDR) and limited availability of selectable markers. To overcome these obstacles, we assessed various Cas9-single guide RNA (sgRNA) ribonucleoprotein (RNP) -based strategies for selectable homology and non-homologous end joining (NHEJ) -based gene editing in D. squalens. We also showed an induction of HDR-based genetic modifications by using single-stranded oligodeoxynucleotides (ssODNs) in a basidiomycete fungus for the first time. This paper provides directions for the application of targeted CRISPR/Cas9-based genome editing in D. squalens and other wild-type (basidiomycete) fungi.
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Affiliation(s)
| | | | - Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland; (J.E.K.); (S.S.)
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10
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Daou M, Bisotto A, Haon M, Oliveira Correia L, Cottyn B, Drula E, Garajová S, Bertrand E, Record E, Navarro D, Raouche S, Baumberger S, Faulds CB. A Putative Lignin Copper Oxidase from Trichoderma reesei. J Fungi (Basel) 2021; 7:jof7080643. [PMID: 34436182 PMCID: PMC8400822 DOI: 10.3390/jof7080643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
The ability of Trichoderma reesei, a fungus widely used for the commercial production of hemicellulases and cellulases, to grow and modify technical soda lignin was investigated. By quantifying fungal genomic DNA, T. reesei showed growth and sporulation in solid and liquid cultures containing lignin alone. The analysis of released soluble lignin and residual insoluble lignin was indicative of enzymatic oxidative conversion of phenolic lignin side chains and the modification of lignin structure by cleaving the β-O-4 linkages. The results also showed that polymerization reactions were taking place. A proteomic analysis conducted to investigate secreted proteins at days 3, 7, and 14 of growth revealed the presence of five auxiliary activity (AA) enzymes in the secretome: AA6, AA9, two AA3 enzymes), and the only copper radical oxidase encoded in the genome of T. reesei. This enzyme was heterologously produced and characterized, and its activity on lignin-derived molecules was investigated. Phylogenetic characterization demonstrated that this enzyme belonged to the AA5_1 family, which includes characterized glyoxal oxidases. However, the enzyme displayed overlapping physicochemical and catalytic properties across the AA5 family. The enzyme was remarkably stable at high pH and oxidized both, alcohols and aldehydes with preference to the alcohol group. It was also active on lignin-derived phenolic molecules as well as simple carbohydrates. HPSEC and LC-MS analyses on the reactions of the produced protein on lignin dimers (SS ββ, SS βO4 and GG β5) uncovered the polymerizing activity of this enzyme, which was accordingly named lignin copper oxidase (TrLOx). Polymers of up 10 units were formed by hydroxy group oxidation and radical formation. The activations of lignin molecules by TrLOx along with the co-secretion of this enzyme with reductases and FAD flavoproteins oxidoreductases during growth on lignin suggest a synergistic mechanism for lignin breakdown.
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Affiliation(s)
- Mariane Daou
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - Alexandra Bisotto
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - Mireille Haon
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - Lydie Oliveira Correia
- PAPPSO Platform, INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Betty Cottyn
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (B.C.); (S.B.)
| | - Elodie Drula
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - Soňa Garajová
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - Emmanuel Bertrand
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - Eric Record
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - David Navarro
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
- CIRM-CF BBF, INRAE, Aix Marseille University, 13288 Marseille, France
| | - Sana Raouche
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
| | - Stéphanie Baumberger
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (B.C.); (S.B.)
| | - Craig B. Faulds
- BBF, INRAE, Aix Marseille University, 13288 Marseille, France; (M.D.); (A.B.); (M.H.); (E.D.); (S.G.); (E.B.); (E.R.); (D.N.); (S.R.)
- Correspondence:
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11
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Li F, Zhang J, Ma F, Chen Q, Xiao Q, Zhang X, Xie S, Yu H. Lytic polysaccharide monooxygenases promote oxidative cleavage of lignin and lignin-carbohydrate complexes during fungal degradation of lignocellulose. Environ Microbiol 2021; 23:4547-4560. [PMID: 34169632 DOI: 10.1111/1462-2920.15648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/06/2023]
Abstract
Overcoming lignocellulosic biomass recalcitrance, especially the cleavage of cross-linkages in lignin-carbohydrate complexes (LCCs) and lignin, is essential for both the carbon cycle and industrial biorefinery. Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes that play a key role in fungal polysaccharide oxidative degradation. Nevertheless, comprehensive analysis showed that LPMOs from a white-rot fungus, Pleurotus ostreatus, correlated well with the Fenton reaction and were involved in the degradation of recalcitrant nonpolysaccharide fractions in this research. Thus, LPMOs participated in the extracellular Fenton reaction by enhancing iron reduction in quinone redox cycling. A Fenton reaction system consisting of LPMOs, hydroquinone, and ferric iron can efficiently produce hydroxy radicals and then cleave LCCs or lignin linkages. This finding indicates that LPMOs are underestimated auxiliary enzymes in eliminating biomass recalcitrance.
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Affiliation(s)
- Fei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jialong Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fuying Ma
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qing Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qiuyun Xiao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiaoyu Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shangxian Xie
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongbo Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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12
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From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi. Biotechnol Adv 2021; 50:107770. [PMID: 33989704 DOI: 10.1016/j.biotechadv.2021.107770] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/04/2021] [Accepted: 05/08/2021] [Indexed: 01/21/2023]
Abstract
In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation.
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13
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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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14
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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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15
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Daly P, Peng M, Mitchell HD, Kim Y, Ansong C, Brewer H, de Gijsel P, Lipton MS, Markillie LM, Nicora CD, Orr G, Wiebenga A, Hildén KS, Kabel MA, Baker SE, Mäkelä MR, de Vries RP. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation. Environ Microbiol 2020; 22:1154-1166. [PMID: 31876091 PMCID: PMC7065180 DOI: 10.1111/1462-2920.14907] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/20/2019] [Indexed: 11/27/2022]
Abstract
Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.
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Affiliation(s)
- Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Hugh D. Mitchell
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Young‐Mo Kim
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Charles Ansong
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Heather Brewer
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Peter de Gijsel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Mary S. Lipton
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Lye Meng Markillie
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Carrie D. Nicora
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Galya Orr
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Kristiina S. Hildén
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Mirjam A. Kabel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Scott E. Baker
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Miia R. Mäkelä
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
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16
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Abstract
One of the main aims of the University of Pavia mycology laboratory was to collect wood decay fungal (WDF) strains in order to deepen taxonomic studies, species distribution, officinal properties or to investigate potential applications such as biocomposite material production based on fungi. The Italian Alps, Apennines and wood plains were investigated to collect Basidiomycota basidiomata from living or dead trees. The purpose of this study was to investigate the wood decay strains of the Mediterranean area, selecting sampling sites in North and Central Italy, including forests near the Ligurian and Adriatic seas, or near the Lombardy lakes. The isolation of mycelia in pure culture was performed according to the current methodology and the identity of the strains was confirmed by molecular analyses. The strains are maintained in the Research Culture Collection MicUNIPV of Pavia University (Italy). Among the 500 WDF strains in the collection, the most interesting isolates from the Mediterranean area are: Dichomitus squalens (basidioma collected from Pinus pinea), Hericium erinaceus (medicinal mushroom), Inocutis tamaricis (white-rot agent on Tamarix trees), Perenniporia meridionalis (wood degrader through Mn peroxidase) and P. ochroleuca. In addition, strains of species related to the Mediterranean climate (e.g., Fomitiporia mediterranea and Cellulariella warnieri) were obtained from sites with a continental-temperate climate.
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17
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Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens. J Biotechnol 2020; 308:35-39. [PMID: 31778732 DOI: 10.1016/j.jbiotec.2019.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/18/2019] [Accepted: 11/23/2019] [Indexed: 11/23/2022]
Abstract
Heterologous production of fungal ligninolytic cocktails is challenging due to the low yields of catalytically active lignin modifying peroxidases. Production using a natural system, such as a wood-rotting fungus, is a promising alternative if specific or preferential induction of the ligninolytic activities could be achieved. Using transcriptomics, gene expression of the white-rot Dichomitus squalens during growth on mixtures of aromatic compounds, with ring structures representing the two major lignin sub-units, was compared to a wood substrate. Most of the genes encoding lignin modifying enzymes (laccases and peroxidases) categorised as highly or moderately expressed on wood were expressed similarly on aromatic compounds. Higher expression levels of a subset of manganese and versatile peroxidases was observed on di- compared to mono-methoxylated aromatics. The expression of polysaccharide degrading enzymes was lower on aromatic compounds compared to wood, demonstrating that the induction of lignin modifying enzymes became more specific. This study suggests potential for aromatic waste streams, e.g. from lignocellulose pretreatment, to produce a lignin-specific enzyme cocktail from D. squalens or other white-rot fungi.
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18
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Mäkelä MR, Hildén K, Kowalczyk JE, Hatakka A. Progress and Research Needs of Plant Biomass Degradation by Basidiomycete Fungi. GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens. Appl Environ Microbiol 2019; 85:AEM.01828-19. [PMID: 31585998 DOI: 10.1128/aem.01828-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/22/2019] [Indexed: 12/15/2022] Open
Abstract
The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of plant biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant biomass utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.
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20
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Kowalczyk JE, Peng M, Pawlowski M, Lipzen A, Ng V, Singan V, Wang M, Grigoriev IV, Mäkelä MR. The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds. Front Bioeng Biotechnol 2019; 7:229. [PMID: 31616664 PMCID: PMC6763618 DOI: 10.3389/fbioe.2019.00229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/05/2019] [Indexed: 11/13/2022] Open
Abstract
Lignocellulosic plant biomass is an important feedstock for bio-based economy. In particular, it is an abundant renewable source of aromatic compounds, which are present as part of lignin, as side-groups of xylan and pectin, and in other forms, such as tannins. As filamentous fungi are the main organisms that modify and degrade lignocellulose, they have developed a versatile metabolism to convert the aromatic compounds that are toxic at relatively low concentrations to less toxic ones. During this process, fungi form metabolites some of which represent high-value platform chemicals or important chemical building blocks, such as benzoic, vanillic, and protocatechuic acid. Especially basidiomycete white-rot fungi with unique ability to degrade the recalcitrant lignin polymer are expected to perform highly efficient enzymatic conversions of aromatic compounds, thus having huge potential for biotechnological exploitation. However, the aromatic metabolism of basidiomycete fungi is poorly studied and knowledge on them is based on the combined results of studies in variety of species, leaving the overall picture in each organism unclear. Dichomitus squalens is an efficiently wood-degrading white-rot basidiomycete that produces a diverse set of extracellular enzymes targeted for lignocellulose degradation, including oxidative enzymes that act on lignin. Our recent study showed that several intra- and extracellular aromatic compounds were produced when D. squalens was cultivated on spruce wood, indicating also versatile aromatic metabolic abilities for this species. In order to provide the first molecular level systematic insight into the conversion of plant biomass derived aromatic compounds by basidiomycete fungi, we analyzed the transcriptomes of D. squalens when grown with 10 different lignocellulose-related aromatic monomers. Significant differences for example with respect to the expression of lignocellulose degradation related genes, but also putative genes encoding transporters and catabolic pathway genes were observed between the cultivations supplemented with the different aromatic compounds. The results demonstrate that the transcriptional response of D. squalens is highly dependent on the specific aromatic compounds present suggesting that instead of a common regulatory system, fine-tuned regulation is needed for aromatic metabolism.
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Affiliation(s)
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Megan Pawlowski
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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21
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Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens. Microbiol Resour Announc 2019; 8:8/18/e00264-19. [PMID: 31048399 PMCID: PMC6498232 DOI: 10.1128/mra.00264-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Here, we report the draft genome sequences of three isolates of the wood-decaying white-rot basidiomycete fungus Dichomitus squalens. The genomes of these monokaryons were sequenced to provide more information on the intraspecies genomic diversity of this fungus and were compared to the previously sequenced genome of D. squalens LYAD-421 SS1. Here, we report the draft genome sequences of three isolates of the wood-decaying white-rot basidiomycete fungus Dichomitus squalens. The genomes of these monokaryons were sequenced to provide more information on the intraspecies genomic diversity of this fungus and were compared to the previously sequenced genome of D. squalens LYAD-421 SS1.
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22
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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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