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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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Research Status and Application Prospects of the Medicinal Mushroom Armillaria mellea. Appl Biochem Biotechnol 2022; 195:3491-3507. [PMID: 36417110 DOI: 10.1007/s12010-022-04240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
Armillaria is one of the most common diseases underlying chronic root rot in woody plants. Although there is no particularly effective way to prevent it, soil disinfection is a common effective protective measure. However, Armillaria itself has important medicinal value and is a symbiotic fungus in the cultivation of Gastrodia elata and Polyporus umbellatus. Therefore, researching Armillaria is of great practical significance. In this review, the biological characteristics, cultivation methods, chemical components, food and medicinal value and efficacy of Armillaria were all reviewed, and its development and utilization direction were analyzed and discussed.
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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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A First Insight into North American Plant Pathogenic Fungi Armillaria Sinapina Transcriptome. BIOLOGY 2020; 9:biology9070153. [PMID: 32635577 PMCID: PMC7407180 DOI: 10.3390/biology9070153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 12/02/2022]
Abstract
Armillaria sinapina, a fungal pathogen of primary timber species of North American forests, causes white root rot disease that ultimately kills the trees. A more detailed understanding of the molecular mechanisms underlying this illness will support future developments on disease resistance and management, as well as in the decomposition of cellulosic material for further use. In this study, RNA-Seq technology was used to compare the transcriptome profiles of A. sinapina fungal culture grown in yeast malt broth medium supplemented or not with betulin, a natural compound of the terpenoid group found in abundance in white birch bark. This was done to identify enzyme transcripts involved in the metabolism (redox reaction) of betulin into betulinic acid, a potent anticancer drug. De novo assembly and characterization of A. sinapina transcriptome was performed using Illumina technology. A total of 170,592,464 reads were generated, then 273,561 transcripts were characterized. Approximately, 53% of transcripts could be identified using public databases with several metabolic pathways represented. A total of 11 transcripts involved in terpenoid biosynthesis were identified. In addition, 25 gene transcripts that could play a significant role in lignin degradation were uncovered, as well as several redox enzymes of the cytochromes P450 family. To our knowledge, this research is the first transcriptomic study carried out on A. sinapina.
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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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Mäkinen M, Kuuskeri J, Laine P, Smolander OP, Kovalchuk A, Zeng Z, Asiegbu FO, Paulin L, Auvinen P, Lundell T. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics 2019; 20:430. [PMID: 31138126 PMCID: PMC6540522 DOI: 10.1186/s12864-019-5817-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The white rot fungus Phlebia radiata, a type species of the genus Phlebia, is an efficient decomposer of plant cell wall polysaccharides, modifier of softwood and hardwood lignin, and is able to produce ethanol from various waste lignocellulose substrates. Thus, P. radiata is a promising organism for biotechnological applications aiming at sustainable utilization of plant biomass. Here we report the genome sequence of P. radiata isolate 79 originally isolated from decayed alder wood in South Finland. To better understand the evolution of wood decay mechanisms in this fungus and the Polyporales phlebioid clade, gene content and clustering of genes encoding specific carbohydrate-active enzymes (CAZymes) in seven closely related fungal species was investigated. In addition, other genes encoding proteins reflecting the fungal lifestyle including peptidases, transporters, small secreted proteins and genes involved in secondary metabolism were identified in the genome assembly of P. radiata. RESULTS The PACBio sequenced nuclear genome of P. radiata was assembled to 93 contigs with 72X sequencing coverage and annotated, revealing a dense genome of 40.4 Mbp with approximately 14 082 predicted protein-coding genes. According to functional annotation, the genome harbors 209 glycoside hydrolase, 27 carbohydrate esterase, 8 polysaccharide lyase, and over 70 auxiliary redox enzyme-encoding genes. Comparisons with the genomes of other phlebioid fungi revealed shared and specific properties among the species with seemingly similar saprobic wood-decay lifestyles. Clustering of especially GH10 and AA9 enzyme-encoding genes according to genomic localization was discovered to be conserved among the phlebioid species. In P. radiata genome, a rich repertoire of genes involved in the production of secondary metabolites was recognized. In addition, 49 genes encoding predicted ABC proteins were identified in P. radiata genome together with 336 genes encoding peptidases, and 430 genes encoding small secreted proteins. CONCLUSIONS The genome assembly of P. radiata contains wide array of carbohydrate polymer attacking CAZyme and oxidoreductase genes in a composition identifiable for phlebioid white rot lifestyle in wood decomposition, and may thus serve as reference for further studies. Comparative genomics also contributed to enlightening fungal decay mechanisms in conversion and cycling of recalcitrant organic carbon in the forest ecosystems.
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Affiliation(s)
- Mari Mäkinen
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.,Present address: VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Jaana Kuuskeri
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland
| | - Pia Laine
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland.,Present address: Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Zhen Zeng
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikki Campus, FI-00014, Helsinki, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, Viikki Campus, FI-00014, Helsinki, Finland
| | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, FI-00014, Helsinki, Finland.
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Kumar A, Chaturvedi AK, Yadav K, Arunkumar KP, Malyan SK, Raja P, Kumar R, Khan SA, Yadav KK, Rana KL, Kour D, Yadav N, Yadav AN. Fungal Phytoremediation of Heavy Metal-Contaminated Resources: Current Scenario and Future Prospects. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-25506-0_18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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