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Magaña-Ortiz D, López-Castillo LM, Amezquita-Novelo R. White-rot fungus Phlebia floridensis ITM 12: Laccase production, oxidoreductase profile, and hydrogen-peroxide independent activity. J Basic Microbiol 2024; 64:106-118. [PMID: 37840353 DOI: 10.1002/jobm.202300462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
Phlebia genus is a relevant group of fungi with a crucial role in numerous ecosystems. In tropical and subtropical areas this genus allows the efficient degradation of lignin and carbon recovery; however, the majority of these fungal species remain undiscovered. The main purpose of this work was to determine the enzymatic activity of extracellular proteins of a novel Phlebia floridensis strain isolated in Yucatan Peninsula, Mexico. The results that are reported here demonstrate that the soluble protein extract of P. floridensis can degrade a broad spectrum of recalcitrant compounds. This induced protein extract is able to modify not only phenolic and nonphenolic compounds, but also anthroquinone dyes, even without the addition of exogenous hydrogen peroxide. Using liquid chromatography-mass spectrometry (LC-MS), we were able to identify a novel chloroperoxidase in enzymatic extract. As far as we know, this is the first report about the presence of this type of enzyme in the Phlebia genus.
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Affiliation(s)
- Denis Magaña-Ortiz
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I. T. Mérida, Mérida, Yucatán, México
| | - Laura M López-Castillo
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Monterrey, Nuevo Léon, Mexico
| | - Roberto Amezquita-Novelo
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I. T. Mérida, Mérida, Yucatán, México
- Departamento de Ingeniería Química y Bioquímica, Tecnólogico Nacional de México/I. T. Morelia, Col. Lomas de Santiaguito, Morelia, Michoacán, México
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2
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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3
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Hirakawa MP, Rodriguez A, Tran-Gyamfi MB, Light YK, Martinez S, Diamond-Pott H, Simmons BA, Sale KL. Phenothiazines Rapidly Induce Laccase Expression and Lignin-Degrading Properties in the White-Rot Fungus Phlebia radiata. J Fungi (Basel) 2023; 9:jof9030371. [PMID: 36983539 PMCID: PMC10053029 DOI: 10.3390/jof9030371] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Phlebia radiata is a widespread white-rot basidiomycete fungus with significance in diverse biotechnological applications due to its ability to degrade aromatic compounds, xenobiotics, and lignin using an assortment of oxidative enzymes including laccase. In this work, a chemical screen with 480 conditions was conducted to identify chemical inducers of laccase expression in P. radiata. Among the chemicals tested, phenothiazines were observed to induce laccase activity in P. radiata, with promethazine being the strongest laccase inducer of the phenothiazine-derived compounds examined. Secretomes produced by promethazine-treated P. radiata exhibited increased laccase protein abundance, increased enzymatic activity, and an enhanced ability to degrade phenolic model lignin compounds. Transcriptomics analyses revealed that promethazine rapidly induced the expression of genes encoding lignin-degrading enzymes, including laccase and various oxidoreductases, showing that the increased laccase activity was due to increased laccase gene expression. Finally, the generality of promethazine as an inducer of laccases in fungi was demonstrated by showing that promethazine treatment also increased laccase activity in other relevant fungal species with known lignin conversion capabilities including Trametes versicolor and Pleurotus ostreatus.
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Affiliation(s)
- Matthew P. Hirakawa
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
- Correspondence: (M.P.H.); (K.L.S.)
| | - Alberto Rodriguez
- Biomaterials and Biomanufacturing Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Mary B. Tran-Gyamfi
- Bioresource and Environmental Security Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Yooli K. Light
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Salvador Martinez
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Henry Diamond-Pott
- Bioresource and Environmental Security Department, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Blake A. Simmons
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Kenneth L. Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Computational Biology and Biophysics Department, Sandia National Laboratories, Livermore, CA 94550, USA
- Correspondence: (M.P.H.); (K.L.S.)
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4
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Mali T, Laine K, Hamberg L, Lundell T. Metabolic activities and ultrastructure imaging at late-stage of wood decomposition in interactive brown rot - white rot fungal combinations. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Pareek M, Hegedüs B, Hou Z, Csernetics Á, Wu H, Virágh M, Sahu N, Liu XB, Nagy L. Preassembled Cas9 Ribonucleoprotein-Mediated Gene Deletion Identifies the Carbon Catabolite Repressor and Its Target Genes in Coprinopsis cinerea. Appl Environ Microbiol 2022; 88:e0094022. [PMID: 36374019 PMCID: PMC9746306 DOI: 10.1128/aem.00940-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. The cre1 gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota species remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. We used a rapid and efficient gene deletion approach based on PCR-amplified split-marker DNA cassettes together with in vitro assembled Cas9-guide RNA ribonucleoproteins (Cas9 RNPs) to generate C. cinerea cre1 gene deletion strains. Gene expression profiling of two independent C. cinerea cre1 mutants showed significant deregulation of carbohydrate metabolism, plant cell wall degrading enzymes (PCWDEs), plasma membrane transporter-related and several transcription factor-encoding genes, among others. Our results support the notion that, like reports in the ascomycetes, Cre1 of C. cinerea orchestrates CCR through a combined regulation of diverse genes, including PCWDEs, transcription factors that positively regulate PCWDEs, and membrane transporters which could import simple sugars that can induce the expression of PWCDEs. Somewhat paradoxically, though in accordance with other Agaricomycetes, genes related to lignin degradation were mostly downregulated in cre1 mutants, indicating they fall under different regulation than other PCWDEs. The gene deletion approach and the data presented here will expand our knowledge of CCR in the Basidiomycota and provide functional hypotheses on genes related to plant biomass degradation. IMPORTANCE Mushroom-forming fungi include some of the most efficient lignocellulosic plant biomass degraders. They degrade dead plant materials by a battery of lignin-, cellulose-, hemicellulose-, and pectin-degrading enzymes, the encoding genes of which are under tight transcriptional control. One of the highest-level regulations of these metabolic enzymes is known as carbon catabolite repression, which is orchestrated by the transcription factor Cre1, and ensures that costly lignocellulose-degrading enzyme genes are expressed only when simple carbon sources (e.g., glucose) are not available. Here, we identified the Cre1 ortholog in a litter decomposer Agaricomycete, Coprinopsis cinerea, knocked it out, and characterized transcriptional changes in the mutants. We identified several dozen lignocellulolytic enzyme genes as well as membrane transporters and other transcription factors as putative target genes of C. cinerea cre1. These results extend knowledge on carbon catabolite repression to litter decomposer Basidiomycota.
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Affiliation(s)
- Manish Pareek
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Botond Hegedüs
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Zhihao Hou
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Árpád Csernetics
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Hongli Wu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Máté Virágh
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Neha Sahu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - László Nagy
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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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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Yuan Z, Wu Q, Xu L, Druzhinina IS, Stukenbrock EH, Nieuwenhuis BPS, Zhong Z, Liu ZJ, Wang X, Cai F, Kubicek CP, Shan X, Wang J, Shi G, Peng L, Martin FM. Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism. THE ISME JOURNAL 2022; 16:1294-1305. [PMID: 34916613 PMCID: PMC9038928 DOI: 10.1038/s41396-021-01176-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022]
Abstract
Comparative and pan-genomic analyses of the endophytic fungus Pezicula neosporulosa (Helotiales, Ascomycota) from needles of the relict fir, Abies beshanzuensis, showed expansions of carbohydrate metabolism and secondary metabolite biosynthetic genes characteristic for unrelated plant-beneficial helotialean, such as dark septate endophytes and ericoid mycorrhizal fungi. The current species within the relatively young Pliocene genus Pezicula are predominantly saprotrophic, while P. neosporulosa lacks such features. To understand the genomic background of this putatively convergent evolution, we performed population analyses of 77 P. neosporulosa isolates. This revealed a mosaic structure of a dozen non-recombining and highly genetically polymorphic subpopulations with a unique mating system structure. We found that one idiomorph of a probably duplicated mat1-2 gene was found in putatively heterothallic isolates, while the other co-occurred with mat1-1 locus suggesting homothallic reproduction for these strains. Moreover, 24 and 81 genes implicated in plant cell-wall degradation and secondary metabolite biosynthesis, respectively, showed signatures of the balancing selection. These findings highlight the evolutionary pattern of the two gene families for allowing the fungus a rapid adaptation towards endophytism and facilitating diverse symbiotic interactions.
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Affiliation(s)
- Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China. .,Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
| | - Qi Wu
- grid.458488.d0000 0004 0627 1442State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Liangxiong Xu
- grid.411411.00000 0004 0644 5457School of Life Sciences, Huizhou University, Huizhou, 516007 China
| | - Irina S. Druzhinina
- grid.27871.3b0000 0000 9750 7019Key Laboratory of Plant Immunity, Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China ,grid.5329.d0000 0001 2348 4034Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, A1060 Austria
| | - Eva H. Stukenbrock
- grid.9764.c0000 0001 2153 9986Botanical Institute, Christian-Albrechts Universität zu Kiel, 24118 Kiel, Germany ,grid.419520.b0000 0001 2222 4708Environmental Genomics Research Group, Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Bart P. S. Nieuwenhuis
- grid.5252.00000 0004 1936 973XDivision of Evolutionary Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Zhenhui Zhong
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Zhong-Jian Liu
- grid.256111.00000 0004 1760 2876Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xinyu Wang
- grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Feng Cai
- grid.27871.3b0000 0000 9750 7019Key Laboratory of Plant Immunity, Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Christian P. Kubicek
- grid.5329.d0000 0001 2348 4034Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, A1060 Austria
| | - Xiaoliang Shan
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091 Beijing, China ,grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Jieyu Wang
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Guohui Shi
- grid.458488.d0000 0004 0627 1442State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Long Peng
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091 Beijing, China ,grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Francis M. Martin
- grid.29172.3f0000 0001 2194 6418Université de Lorraine, INRAe, UMR 1136 Interactions Arbres/Microorganismes, INRAe-Grand Est-Nancy, 54280 Champenoux, France
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Mattila H, Österman-Udd J, Mali T, Lundell T. Basidiomycota Fungi and ROS: Genomic Perspective on Key Enzymes Involved in Generation and Mitigation of Reactive Oxygen Species. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:837605. [PMID: 37746164 PMCID: PMC10512322 DOI: 10.3389/ffunb.2022.837605] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/21/2022] [Indexed: 09/26/2023]
Abstract
Our review includes a genomic survey of a multitude of reactive oxygen species (ROS) related intra- and extracellular enzymes and proteins among fungi of Basidiomycota, following their taxonomic classification within the systematic classes and orders, and focusing on different fungal lifestyles (saprobic, symbiotic, pathogenic). Intra- and extracellular ROS metabolism-involved enzymes (49 different protein families, summing 4170 protein models) were searched as protein encoding genes among 63 genomes selected according to current taxonomy. Extracellular and intracellular ROS metabolism and mechanisms in Basidiomycota are illustrated in detail. In brief, it may be concluded that differences between the set of extracellular enzymes activated by ROS, especially by H2O2, and involved in generation of H2O2, follow the differences in fungal lifestyles. The wood and plant biomass degrading white-rot fungi and the litter-decomposing species of Agaricomycetes contain the highest counts for genes encoding various extracellular peroxidases, mono- and peroxygenases, and oxidases. These findings further confirm the necessity of the multigene families of various extracellular oxidoreductases for efficient and complete degradation of wood lignocelluloses by fungi. High variations in the sizes of the extracellular ROS-involved gene families were found, however, among species with mycorrhizal symbiotic lifestyle. In addition, there are some differences among the sets of intracellular thiol-mediation involving proteins, and existence of enzyme mechanisms for quenching of intracellular H2O2 and ROS. In animal- and plant-pathogenic species, extracellular ROS enzymes are absent or rare. In these fungi, intracellular peroxidases are seemingly in minor role than in the independent saprobic, filamentous species of Basidiomycota. Noteworthy is that our genomic survey and review of the literature point to that there are differences both in generation of extracellular ROS as well as in mechanisms of response to oxidative stress and mitigation of ROS between fungi of Basidiomycota and Ascomycota.
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Affiliation(s)
| | | | | | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, Helsinki, Finland
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9
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Tomé LMR, da Silva FF, Fonseca PLC, Mendes-Pereira T, Azevedo VADC, Brenig B, Badotti F, Góes-Neto A. Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown. J Fungi (Basel) 2022; 8:jof8020142. [PMID: 35205897 PMCID: PMC8876698 DOI: 10.3390/jof8020142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.
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Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Felipe Ferreira da Silva
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Paula Luize Camargos Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073 Göttingen, Germany;
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte 30421-169, MG, Brazil;
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
- Correspondence: ; Tel.: +55-31-994130996
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Saini S, Sharma KK. Fungal lignocellulolytic enzymes and lignocellulose: A critical review on their contribution to multiproduct biorefinery and global biofuel research. Int J Biol Macromol 2021; 193:2304-2319. [PMID: 34800524 DOI: 10.1016/j.ijbiomac.2021.11.063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/27/2021] [Accepted: 11/10/2021] [Indexed: 01/15/2023]
Abstract
The continuous increase in the global energy demand has diminished fossil fuel reserves and elevated the risk of environmental deterioration and human health. Biorefinery processes involved in producing bio-based energy-enriched chemicals have paved way to meet the energy demands. Compared to the thermochemical processes, fungal system biorefinery processes seems to be a promising approach for lignocellulose conversion. It also offers an eco-friendly and energy-efficient route for biofuel generation. Essentially, ligninolytic white-rot fungi and their enzyme arsenals degrade the plant biomass into structural constituents with minimal by-products generation. Hemi- or cellulolytic enzymes from certain soft and brown-rot fungi are always favoured to hydrolyze complex polysaccharides into fermentable sugars and other value-added products. However, the cost of saccharifying enzymes remains the major limitation, which hinders their application in lignocellulosic biorefinery. In the past, research has been focused on the role of lignocellulolytic fungi in biofuel production; however, a cumulative study comprising the contribution of the lignocellulolytic enzymes in biorefinery technologies is still lagging. Therefore, the overarching goal of this review article is to discuss the major contribution of lignocellulolytic fungi and their enzyme arsenal in global biofuel research and multiproduct biorefinery.
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Affiliation(s)
- Sonu Saini
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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Bilal M, Qamar SA, Yadav V, Cheng H, Khan M, Adil SF, Taherzadeh MJ, Iqbal HM. Exploring the potential of ligninolytic armory for lignin valorization – A way forward for sustainable and cleaner production. JOURNAL OF CLEANER PRODUCTION 2021. [DOI: 10.1016/j.jclepro.2021.129420] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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12
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Species diversity, taxonomy and multi-gene phylogeny of phlebioid clade (Phanerochaetaceae, Irpicaceae, Meruliaceae) of Polyporales. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00490-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Feldman D, Yarden O, Hadar Y. Seeking the Roles for Fungal Small-Secreted Proteins in Affecting Saprophytic Lifestyles. Front Microbiol 2020; 11:455. [PMID: 32265881 PMCID: PMC7105643 DOI: 10.3389/fmicb.2020.00455] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/03/2020] [Indexed: 11/24/2022] Open
Abstract
Small secreted proteins (SSPs) comprise 40–60% of the total fungal secretome and are present in fungi of all phylogenetic groups, representing the entire spectrum of lifestyles. They are characteristically shorter than 300 amino acids in length and have a signal peptide. The majority of SSPs are coded by orphan genes, which lack known domains or similarities to known protein sequences. Effectors are a group of SSPs that have been investigated extensively in fungi that interact with living hosts, either pathogens or mutualistic systems. They are involved in suppressing the host defense response and altering its physiology. Here, we aim to delineate some of the potential roles of SSPs in saprotrophic fungi, that have been bioinformatically predicted as effectors, and termed in this mini-review as “effector-like” proteins. The effector-like Ssp1 from the white-rot fungus Pleurotus ostreatus is presented as a case study, and its potential role in regulating the ligninolytic system, secondary metabolism, development, and fruiting body initiation are discussed. We propose that deciphering the nature of effector-like SSPs will contribute to our understanding of development and communication in saprophytic fungi, as well as help, to elucidate the origin, regulation, and mechanisms of fungal-host, fungal-fungal, and fungal-bacterial interactions.
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Affiliation(s)
- Daria Feldman
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
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Zhang R. Functional characterization of cellulose-degrading AA9 lytic polysaccharide monooxygenases and their potential exploitation. Appl Microbiol Biotechnol 2020; 104:3229-3243. [PMID: 32076777 DOI: 10.1007/s00253-020-10467-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 12/25/2019] [Accepted: 02/12/2020] [Indexed: 01/05/2023]
Abstract
Cellulose-degrading auxiliary activity family 9 (AA9) lytic polysaccharide monooxygenases (LPMOs) are known to be widely distributed among filamentous fungi and participate in the degradation of lignocellulose via the oxidative cleavage of celluloses, cello-oligosaccharides, or hemicelluloses. AA9 LPMOs have been reported to have extensive interactions with not only cellulases but also oxidases. The addition of AA9 LPMOs can greatly reduce the amount of cellulase needed for saccharification and increase the yield of glucose. The discovery of AA9 LPMOs has greatly changed our understanding of how fungi degrade cellulose. In this review, apart from summarizing the recent discoveries related to their catalytic reaction, functional diversity, and practical applications, the stability, expression system, and protein engineering of AA9 LPMOs are reviewed for the first time. This review may provide a reference value to further broaden the substrate range of AA9 LPMOs, expand the scope of their practical applications, and realize their customization for industrial utilization.Key Points• The stability and expression system of AA9 LPMOs are reviewed for the first time.• The protein engineering of AA9 LPMOs is systematically summarized for the first time.• The latest research results on the catalytic mechanism of AA9 LPMOs are summarized.• The application of AA9 LPMOs and their relationship with other enzymes are reviewed.
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Affiliation(s)
- Ruiqin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, 266237, China.
- Department of Bioengineering, Huainan Normal University, No. 278 Xueyuannan Road, Huainan, 232038, China.
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Mattila HK, Mäkinen M, Lundell T. Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:26. [PMID: 32123543 PMCID: PMC7038570 DOI: 10.1186/s13068-020-01677-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/05/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fungal decomposition of wood is considered as a strictly aerobic process. However, recent findings on wood-decaying fungi to produce ethanol from various lignocelluloses under oxygen-depleted conditions lead us to question this. We designed gene expression study of the white rot fungus Phlebia radiata (isolate FBCC0043) by adopting comparative transcriptomics and functional genomics on solid lignocellulose substrates under varying cultivation atmospheric conditions. RESULTS Switch to fermentative conditions was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides. Changes in the expression profiles of CAZy (carbohydrate-active enzyme) encoding genes upon oxygen depletion, lead into an alternative wood decomposition strategy. Surprisingly, we noticed higher cellulolytic activity under fermentative conditions in comparison to aerobic cultivation. In addition, our results manifest how oxygen depletion affects over 200 genes of fungal primary metabolism including several transcription factors. We present new functions for acetate generating phosphoketolase pathway and its potential regulator, Adr1 transcription factor, in carbon catabolism under oxygen depletion. CONCLUSIONS Physiologically resilient wood-decomposing Basidiomycota species P. radiata is capable of thriving under respirative and fermentative conditions utilizing only untreated lignocellulose as carbon source. Hypoxia-response mechanism in the fungus is, however, divergent from the regulation described for Ascomycota fermenting yeasts or animal-pathogenic species of Basidiomycota.
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Affiliation(s)
- Hans Kristian Mattila
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
| | - Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
- Present Address: VTT Technical Research Centre of Finland Ltd, 02044 VTT Espoo, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, 00014 Helsinki, Finland
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