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Watanabe N, Mitsukuni K, Sato T, Zhang J, Ono A, Suzuki T. RNA-Seq analysis of the fruiting bodies and mycelia of angel-wing mushroom Pleurocybella porrigens that cause acute encephalopathy. BMC Res Notes 2024; 17:204. [PMID: 39049055 PMCID: PMC11270884 DOI: 10.1186/s13104-024-06860-2] [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: 05/04/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
OBJECTIVE In 2004, after consuming angel-wing mushrooms, Pleurocybella porrigens, 59 incidents of food poisoning were reported in Japan. Consequently, 17 individuals died of acute encephalopathy. In 2023, we proved that a lectin, pleurocybelline, and pleurocybellaziridine from this mushroom caused damage to the brains of mice. Although we reported genomic and transcriptomic data of P. porrigens in 2013, the assembly quality of the transcriptomic data was inadequate for accurate functional annotation. Thus, we obtained detailed transcriptomic data on the fruiting bodies and mycelia of this mushroom using Illumina NovaSeq 6000. RESULTS De novo assembly data indicated that the N50 lengths for the fruiting bodies and mycelia were improved compared with those previously reported. The differential expression analysis between the fruiting bodies and the mycelia revealed that 1,937 and 1,555 genes were significantly up-regulated in the fruiting bodies and the mycelia, respectively. The biological functions of P. porrigens transcripts, including PA biosynthetic pathways, were investigated using BLAST search, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The obtained results revealed L-valine, a predicted precursor of PA, is biosynthesized in the fruiting bodies and mycelia. Furthermore, real-time RT-PCR was performed to evaluate the accuracy of the results of differential expression analysis.
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Affiliation(s)
- Nozomu Watanabe
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Keisuke Mitsukuni
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Takumi Sato
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Jili Zhang
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Akiko Ono
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
- Faculty of Global Interdisciplinary Science and Innovation, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan.
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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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de Almeida AP, Macrae A, Ribeiro BD, do Nascimento RP. Decolorization and detoxification of different azo dyes by Phanerochaete chrysosporium ME-446 under submerged fermentation. Braz J Microbiol 2021; 52:727-738. [PMID: 33694059 PMCID: PMC8105446 DOI: 10.1007/s42770-021-00458-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/23/2021] [Indexed: 11/28/2022] Open
Abstract
Azo dyes are widely used in the textile industry due to their resistance to light, moisture, and oxidants. They are also an important class of environmental contaminant because of the amount of dye that reaches natural water resources and because they can be toxic, mutagenic, and carcinogenic. Different technologies are used for the decolorization of wastewater containing dyes; among them, the biological processes are the most promising environmentally. The aim of this study was to evaluate the potential of Phanerochaete chrysosporium strain ME-446 to safely decolorize three azo dyes: Direct Yellow 27 (DY27), Reactive Black 5 (RB5), and Reactive Red 120 (RR120). Decolorization efficiency was determined by ultraviolet-visible spectrophotometry and the phytotoxicity of the solutions before and after the fungal treatment was analyzed using Lactuca sativa seeds. P. chrysosporium ME-446 was highly efficient in decolorizing DY27, RB5, and RR120 at 50 mg L-1, decreasing their colors by 82%, 89%, and 94% within 10 days. Removal of dyes was achieved through adsorption on the fungal mycelium as well as biodegradation, inferred by the changes in the dyes' spectral peaks. The intensive decolorization of DY27 and RB5 corresponded to a decrease in phytotoxicity. However, phytotoxicity increased during the removal of color for the dye RR120. The ecotoxicity tests showed that the absence of color does not necessarily translate to an absence of toxicity.
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Affiliation(s)
- Alana Pereira de Almeida
- Laboratório de Ecologia e Processos Microbianos, Departamento de Engenharia Bioquímica, Escola de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149, Rio de Janeiro, RJ, 21941-909, Brazil.
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Decania, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, 21941-902, RJ, Brazil.
| | - Andrew Macrae
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Decania, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, 21941-902, RJ, Brazil
- Laboratório de Biotecnologia Sustentável e Bioinformática Microbiana, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, 21941-902, RJ, Brazil
| | - Bernardo Dias Ribeiro
- Escola de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149, Rio de Janeiro, 21941-909, RJ, Brazil
| | - Rodrigo Pires do Nascimento
- Laboratório de Ecologia e Processos Microbianos, Departamento de Engenharia Bioquímica, Escola de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, 149, Rio de Janeiro, RJ, 21941-909, Brazil
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Decania, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, 21941-902, RJ, Brazil
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Ligninolytic Enzyme Production and Decolorization Capacity of Synthetic Dyes by Saprotrophic White Rot, Brown Rot, and Litter Decomposing Basidiomycetes. J Fungi (Basel) 2020; 6:jof6040301. [PMID: 33228232 PMCID: PMC7711621 DOI: 10.3390/jof6040301] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 01/18/2023] Open
Abstract
An extensive screening of saprotrophic Basidiomycetes causing white rot (WR), brown rot (BR), or litter decomposition (LD) for the production of laccase and Mn-peroxidase (MnP) and decolorization of the synthetic dyes Orange G and Remazol Brilliant Blue R (RBBR) was performed. The study considered in total 150 strains belonging to 77 species. The aim of this work was to compare the decolorization and ligninolytic capacity among different ecophysiological and taxonomic groups of Basidiomycetes. WR strains decolorized both dyes most efficiently; high decolorization capacity was also found in some LD fungi. The enzyme production was recorded in all three ecophysiology groups, but to a different extent. All WR and LD fungi produced laccase, and the majority of them also produced MnP. The strains belonging to BR lacked decolorization capabilities. None of them produced MnP and the production of laccase was either very low or absent. The most efficient decolorization of both dyes and the highest laccase production was found among the members of the orders Polyporales and Agaricales. The strains with high MnP activity occurred across almost all fungal orders (Polyporales, Agaricales, Hymenochaetales, and Russulales). Synthetic dye decolorization by fungal strains was clearly related to their production of ligninolytic enzymes and both properties were determined by the interaction of their ecophysiology and taxonomy, with a more relevant role of ecophysiology. Our screening revealed 12 strains with high decolorization capacity (9 WR and 3 LD), which could be promising for further biotechnological utilization.
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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: 31] [Impact Index Per Article: 7.8] [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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Li Y, Liu J, Wang G, Yang M, Yang X, Li T, Chen G. De novo transcriptome analysis of Pleurotus djamor to identify genes encoding CAZymes related to the decomposition of corn stalk lignocellulose. J Biosci Bioeng 2019; 128:529-536. [PMID: 31147217 DOI: 10.1016/j.jbiosc.2019.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 03/06/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022]
Abstract
CAZymes play a very important role in the biotransformation of corn stalk biomass, which is an important resource for sustainable development. Pleurotus djamor can produce CAZymes related to the decomposition of corn stalk lignocellulose biomass in sole corn stalk substrate; however, little is known about their encoding genes. In order to identify CAZymes encoding genes, RNA high-throughput sequencing of P. djamor was performed in this study. The results showed that a core set of 70 upregulated genes encoding putative CAZymes were revealed. They encode 19 kinds of CAZymes in total, of which there are 4 EGLs, 8 CBHs, 5 BGLs, and 12 LPMOs related to cellulose degradation, 8 XYNs, 1 XYL, 2 AGUs, 3 ABFs, 2 AGLs, and 2 AXEs related to hemicellulose degradation, and 5 LACCs, 2 MnPs, 5 VPs, 3 CDHs, 1 AAO, 1 GOX, 1 AOX, 2 GAOXs, and 3 GLOXs related to lignin degradation. This variety suggests that CAZymes may play a very important role in decomposing the lignocellulose biomass of corn stalk. This is the first study to report the de novo transcriptome sequencing of P. djamor, which will produce a dataset of genes encoding CAZymes, thereby laying the foundation to elucidate the degradation mechanism of corn stalk biomass and boost the biotransformation of corn stalk biomass resources.
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Affiliation(s)
- Yanli Li
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Science, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China; Innovation Platform of Jilin Province for Straw Comprehensive Utilization Technology, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China; Engineering Research Center of the Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China.
| | - Jiahao Liu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Science, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China; Innovation Platform of Jilin Province for Straw Comprehensive Utilization Technology, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China
| | - Gang Wang
- Innovation Platform of Jilin Province for Straw Comprehensive Utilization Technology, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China
| | - Meiying Yang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Science, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China
| | - Xue Yang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Science, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China
| | - Tongbing Li
- Innovation Platform of Jilin Province for Straw Comprehensive Utilization Technology, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China
| | - Guang Chen
- Innovation Platform of Jilin Province for Straw Comprehensive Utilization Technology, Jilin Agricultural University, Xincheng Street 2888, Nanguan District, Changchun 130118, Jilin, China
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Evaluation of Versatile Peroxidase’s Activity and Conformation in the Presence of a Hydrated Urea Based Deep Eutectic Solvent. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00881-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wang X, Yao B, Su X. Linking Enzymatic Oxidative Degradation of Lignin to Organics Detoxification. Int J Mol Sci 2018; 19:ijms19113373. [PMID: 30373305 PMCID: PMC6274955 DOI: 10.3390/ijms19113373] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/25/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022] Open
Abstract
The major enzymes involved in lignin degradation are laccase, class II peroxidases (lignin peroxidase, manganese peroxidase, and versatile peroxidase) and dye peroxidase, which use an oxidative or peroxidative mechanism to deconstruct the complex and recalcitrant lignin. Laccase and manganese peroxidase directly oxidize phenolic lignin components, while lignin peroxidase and versatile peroxidase can act on the more recalcitrant non-phenolic lignin compounds. Mediators or co-oxidants not only increase the catalytic ability of these enzymes, but also largely expand their substrate scope to those with higher redox potential or more complicated structures. Neither laccase nor the peroxidases are stringently selective of substrates. The promiscuous nature in substrate preference can be employed in detoxification of a range of organics.
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Affiliation(s)
- Xiaolu Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Efficient transformation of Pleurotus eryngii with a safe selective marker mutated from the Pesdi1 gene. J Microbiol Methods 2018; 152:7-9. [PMID: 30017848 DOI: 10.1016/j.mimet.2018.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 11/21/2022]
Abstract
We introduced a site-directed mutation in the sdi1 gene and used it as a selective marker for the polyethylene glycol-mediated transformation of Pleurotus eryngii monokaryon protoplasts. The transformants displayed obvious and stable resistance to the fungicide carboxin indicating that the mutant Pesdi1 gene is an efficient selective marker.
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Yoav S, Salame TM, Feldman D, Levinson D, Ioelovich M, Morag E, Yarden O, Bayer EA, Hadar Y. Effects of cre1 modification in the white-rot fungus Pleurotus ostreatus PC9: altering substrate preference during biological pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:212. [PMID: 30065786 PMCID: PMC6062969 DOI: 10.1186/s13068-018-1209-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 07/18/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND During the process of bioethanol production, cellulose is hydrolyzed into its monomeric soluble units. For efficient hydrolysis, a chemical and/or mechanical pretreatment step is required. Such pretreatment is designed to increase enzymatic digestibility of the cellulose chains inter alia by de-crystallization of the cellulose chains and by removing barriers, such as lignin from the plant cell wall. Biological pretreatment, in which lignin is decomposed or modified by white-rot fungi, has also been considered. One disadvantage in biological pretreatment, however, is the consumption of the cellulose by the fungus. Thus, fungal species that attack lignin with only minimal cellulose loss are advantageous. The secretomes of white-rot fungi contain carbohydrate-active enzymes (CAZymes) including lignin-modifying enzymes. Thus, modification of secretome composition can alter the ratio of lignin/cellulose degradation. RESULTS Pleurotus ostreatus PC9 was genetically modified to either overexpress or eliminate (by gene replacement) the transcriptional regulator CRE1, known to act as a repressor in the process of carbon catabolite repression. The cre1-overexpressing transformant demonstrated lower secreted cellulolytic activity and slightly increased selectivity (based on the chemical composition of pretreated wheat straw), whereas the knockout transformant demonstrated increased cellulolytic activity and significantly reduced residual cellulose, thereby displaying lower selectivity. Pretreatment of wheat straw using the wild-type PC9 resulted in 2.8-fold higher yields of soluble sugar compared to untreated wheat straw. The overexpression transformant showed similar yields (2.6-fold), but the knockout transformant exhibited lower yields (1.2-fold) of soluble sugar. Based on proteomic secretome analysis, production of numerous CAZymes was affected by modification of the expression level of cre1. CONCLUSIONS The gene cre1 functions as a regulator for expression of fungal CAZymes active against plant cell wall lignocelluloses, hence altering the substrate preference of the fungi tested. While the cre1 knockout resulted in a less efficient biological pretreatment, i.e., less saccharification of the treated biomass, the converse manipulation of cre1 (overexpression) failed to improve efficiency. Despite the inverse nature of the two genetic alterations, the expected "mirror image" (i.e., opposite regulatory response) was not observed, indicating that the secretion level of CAZymes, was not exclusively dependent on CRE1 activity.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Tomer M. Salame
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Daria Feldman
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Dana Levinson
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | | | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
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Vos AM, Jurak E, Pelkmans JF, Herman K, Pels G, Baars JJ, Hendrix E, Kabel MA, Lugones LG, Wösten HAB. H 2O 2 as a candidate bottleneck for MnP activity during cultivation of Agaricus bisporus in compost. AMB Express 2017. [PMID: 28629207 PMCID: PMC5474230 DOI: 10.1186/s13568-017-0424-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Degradation of lignin by fungi enhances availability of cellulose and hemicellulose in plant waste and thereby increases the amount of carbon source available to these microorganisms. The button mushroom Agaricus bisporus degrades only about half of the lignin in compost and about 40% of the carbohydrates remain unutilized during mushroom cultivation. Here it was assessed whether over-expression of the manganese peroxidase gene mnp1 improves lignin degradation and, as a consequence, carbohydrate breakdown by A. bisporus. Transformants expressing mnp1 under the control of actin regulatory sequences produced MnP activity in malt extract medium, while the parental strain A15 did not. MnP activity was increased 0.3- and 3-fold at casing and after the 2nd flush of a semi-commercial cultivation, respectively, when compared to strain A15. Pyrolysis-GC-MS showed that overexpression of MnP decreased phenylmethane and phenylethane type lignin relative to the phenylpropane type after the 2nd flush. However, it neither affected the syringyl/guaiacyl derived residue ratio nor the ratio of oxidized to non-oxidized lignin residues. Moreover, the carbohydrate content and accessibility was not affected in compost. Notably, the capacity of compost extract to consume the MnP co-factor H2O2 was 4- to 8-fold higher than its production. This may well explain why over-expression of mnp1 did not improve carbohydrate degradation in compost. In fact, availability of H2O2 may limit lignin degradation by wild-type A. bisporus.
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Feldman D, Kowbel DJ, Glass NL, Yarden O, Hadar Y. A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus. Sci Rep 2017; 7:14553. [PMID: 29109463 PMCID: PMC5674062 DOI: 10.1038/s41598-017-15112-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/20/2017] [Indexed: 12/12/2022] Open
Abstract
Small secreted proteins (SSPs), along with lignocellulose degrading enzymes, are integral components of the secretome of Pleurotus ostreatus, a white rot fungus. In this study, we identified 3 genes (ssp1, 2 and 3) encoding proteins that are annotated as SSPs and that exhibited of ~4,500- fold expression, 24 hr following exposure to the toxic compound 5-hydroxymethylfurfural (HMF). Homologues to genes encoding these SSPs are present in the genomes of other basidiomycete fungi, however the role of SSPs is not yet understood. SSPs, aryl-alcohol oxidases (AAO) and the intracellular aryl-alcohol dehydrogenases (AAD) were also produced after exposure to other aryl-alcohols, known substrates and inducers of AAOs, and during idiophase (after the onset of secondary metabolism). A knockdown strain of ssp1 exhibited reduced production of AAO-and AAD-encoding genes after HMF exposure. Conversely, a strain overexpressing ssp1 exhibited elevated expression of genes encoding AAOs and ADD, resulting in a 3-fold increase in enzymatic activity of AAOs, as well as increased expression and protein abundance of versatile peroxidase 1, which directly degrades lignin. We propose that in addition to symbionts and pathogens, SSPs also have roles in saprophytes and function in P. ostreatus as components of the ligninolytic system.
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Affiliation(s)
- Daria Feldman
- The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Department of Plant Pathology and Microbiology, Rehovot, 76100, Israel
| | - David J Kowbel
- University of California at Berkeley UC Berkeley, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, California, 94720, USA
| | - N Louise Glass
- University of California at Berkeley UC Berkeley, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, California, 94720, USA
| | - Oded Yarden
- The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Department of Plant Pathology and Microbiology, Rehovot, 76100, Israel
| | - Yitzhak Hadar
- The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Department of Plant Pathology and Microbiology, Rehovot, 76100, Israel.
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Seppälä S, Wilken SE, Knop D, Solomon KV, O’Malley MA. The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown. Metab Eng 2017; 44:45-59. [DOI: 10.1016/j.ymben.2017.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/16/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
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14
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15
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Stajić M, Vukojević J, Milovanović I, Ćilerdžić J, Knežević A. Role of Mushroom Mn-Oxidizing Peroxidases in Biomass Conversion. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-43679-1_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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16
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Qu J, Zhao M, Hsiang T, Feng X, Zhang J, Huang C. Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2503023. [PMID: 27703969 PMCID: PMC5040776 DOI: 10.1155/2016/2503023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022]
Abstract
Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) of Pleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs in P. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved in P. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs of P. ostreatus were not conserved across Agaricomycotina fungi.
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Affiliation(s)
- Jibin Qu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Mengran Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Xiaoxing Feng
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Micro & Nano Research Institute of IC and System Applications, Shenzhen, Guangdong, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
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Chmelová D, Ondrejovič M. Purification and characterization of extracellular laccase produced byCeriporiopsis subvermisporaand decolorization of triphenylmethane dyes. J Basic Microbiol 2016; 56:1173-1182. [DOI: 10.1002/jobm.201600152] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/06/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Daniela Chmelová
- Faculty of Natural Sciences; Department of Biotechnologies; University of SS. Cyril and Methodius; Trnava Slovak Republic
| | - Miroslav Ondrejovič
- Faculty of Natural Sciences; Department of Biotechnologies; University of SS. Cyril and Methodius; Trnava Slovak Republic
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Toyokawa C, Shobu M, Tsukamoto R, Okamura S, Honda Y, Kamitsuji H, Izumitsu K, Suzuki K, Irie T. Effects of overexpression of PKAc genes on expressions of lignin-modifying enzymes by Pleurotus ostreatus. Biosci Biotechnol Biochem 2016; 80:1759-67. [PMID: 26979984 DOI: 10.1080/09168451.2016.1158630] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We studied the role of genes encoding the cAMP-dependent protein kinase A catalytic subunit (PKAc) in the ligninolytic system in Pleurotus ostreatus. The wild-type P. ostreatus strain PC9 has two PKAc-encoding genes: PKAc1 and PKAc2 (protein ID 114122 and 85056). In the current study, PKAc1 and PKAc2 were fused with a β-tubulin promoter and introduced into strain PC9 to produce the overexpression strains PKAc1-97 and PKAc2-69. These strains showed significantly higher transcription levels of isozyme genes encoding lignin-modifying enzymes than strain PC9, but the specific gene expression patterns differed between the two recombinant strains. Both recombinants showed 2.05-2.10-fold faster degradation of beechwood lignin than strain PC9. These results indicate that PKAc plays an important role in inducing the wood degradation system in P. ostreatus.
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Affiliation(s)
- Chihana Toyokawa
- a School of Environmental Science , University of Shiga Prefecture , Hikone , Japan
| | - Misaki Shobu
- a School of Environmental Science , University of Shiga Prefecture , Hikone , Japan
| | - Rie Tsukamoto
- a School of Environmental Science , University of Shiga Prefecture , Hikone , Japan
| | - Saki Okamura
- a School of Environmental Science , University of Shiga Prefecture , Hikone , Japan
| | - Yoichi Honda
- b Graduate School of Agriculture , Kyoto University , Kyoto , Japan
| | | | - Kousuke Izumitsu
- a School of Environmental Science , University of Shiga Prefecture , Hikone , Japan
| | - Kazumi Suzuki
- a School of Environmental Science , University of Shiga Prefecture , Hikone , Japan
| | - Toshikazu Irie
- a School of Environmental Science , University of Shiga Prefecture , Hikone , Japan
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19
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Qu J, Huang C, Zhang J. Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus. Gene 2016; 575:524-530. [DOI: 10.1016/j.gene.2015.09.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 11/16/2022]
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20
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Hori C, Cullen D. Prospects for Bioprocess Development Based on Recent Genome Advances in Lignocellulose Degrading Basidiomycetes. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Dai Y, Si M, Chen Y, Zhang N, Zhou M, Liao Q, Shi D, Liu Y. Combination of biological pretreatment with NaOH/Urea pretreatment at cold temperature to enhance enzymatic hydrolysis of rice straw. BIORESOURCE TECHNOLOGY 2015; 198:725-731. [PMID: 26452179 DOI: 10.1016/j.biortech.2015.09.091] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
A stepwise pretreatment of combination of bacterial treatment with NaOH/Urea (NU) treatment was conducted to enhance enzymatic hydrolysis of rice straw (RS). The results showed that the composition of RS changed significantly, the lignin and hemicellulose decreased while cellulose increased. The biological treatment with a bacterium Sphingobacterium sp. LD-1 achieved mild conditions for the sequential NU treatment, reducing the concentration of the NU solution from 7%/12% to 4%/6% and increasing the temperature from -20°C to -10°C. The saccharification of rice straw co-treated with bacterium Sphingobacterium sp. LD-1 and 4%/6% NU at -10°C resulted in 1.396-fold and 1.372-fold increase of reducing sugar and glucose yield respectively than that of sole NU treatment.
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Affiliation(s)
- Youzhi Dai
- Department of Environmental Science and Engineering, Xiangtan University, Xiangtan City 411105, China
| | - Mengying Si
- Department of Environmental Science and Engineering, Xiangtan University, Xiangtan City 411105, China
| | - Yuehui Chen
- Department of Environmental Science and Engineering, Xiangtan University, Xiangtan City 411105, China.
| | - Nianlei Zhang
- Department of Environmental Science and Engineering, Xiangtan University, Xiangtan City 411105, China
| | - Mo Zhou
- Department of Environmental Science and Engineering, Xiangtan University, Xiangtan City 411105, China
| | - Qi Liao
- Department of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Centre for Control and Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Deqiang Shi
- Guangxi Academy of Sciences, Nanning City, Guangxi Zhuang Autonomous Region 530007, China
| | - Yine Liu
- Department of Environmental Science and Engineering, Xiangtan University, Xiangtan City 411105, China
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22
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Chen SH, Yien Ting AS. Biodecolorization and biodegradation potential of recalcitrant triphenylmethane dyes by Coriolopsis sp. isolated from compost. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 150:274-280. [PMID: 25527986 DOI: 10.1016/j.jenvman.2014.09.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/01/2014] [Accepted: 09/09/2014] [Indexed: 06/04/2023]
Abstract
Triphenylmethane dyes (TPM) are recalcitrant colorants brought into the environment. In this study, a lesser-known white rot fungus Coriolopsis sp. (1c3), isolated from compost of Empty Fruit Bunch (EFB) of oil palm, was explored for its decolorization potential of TPM dyes. The isolate 1c3 demonstrated good decolorization efficiencies in the treatment of Crystal Violet (CV; 100 mg l(-1)), Methyl Violet (MV; 100 mg l(-1)) and Cotton Blue (CB; 50 mg(-1)), with 94%, 97% and 91%, within 7, 7 and 1 day(s), respectively. Malachite Green (MG; 100 mg l(-1)) was the most recalcitrant dye, with 52% decolorization after 9 days. Dye removal by 1c3 was presumably via biosorption, whereby the process was determined to be influenced by fungal biomass, initial dye concentrations and oxygen requirements. Biodegradation was also a likely mechanism responsible for dye removal by 1c3, occurred as indicated by the reduction of dye spectra peaks. Detection of laccase, lignin peroxidase and NADH-DCIP reductase activities further substantiate the possible occurrence of biodegradation of TPM dyes by 1c3.
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Affiliation(s)
- Si Hui Chen
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia
| | - Adeline Su Yien Ting
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia.
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23
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Knop D, Yarden O, Hadar Y. The ligninolytic peroxidases in the genus Pleurotus: divergence in activities, expression, and potential applications. Appl Microbiol Biotechnol 2014; 99:1025-38. [PMID: 25503316 DOI: 10.1007/s00253-014-6256-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 11/29/2022]
Abstract
Mushrooms of the genus Pleurotus are comprised of cultivated edible ligninolytic fungi with medicinal properties and a wide array of biotechnological and environmental applications. Like other white-rot fungi (WRF), they are able to grow on a variety of lignocellulosic biomass substrates and degrade both natural and anthropogenic aromatic compounds. This is due to the presence of the non-specific oxidative enzymatic systems, which are mainly consisted of lacasses, versatile peroxidases (VPs), and short manganese peroxidases (short-MnPs). Additional, less studied, peroxidase are dye-decolorizing peroxidases (DyPs) and heme-thiolate peroxidases (HTPs). During the past two decades, substantial information has accumulated concerning the biochemistry, structure and function of the Pleurotus ligninolytic peroxidases, which are considered to play a key role in many biodegradation processes. The production of these enzymes is dependent on growth media composition, pH, and temperature as well as the growth phase of the fungus. Mn(2+) concentration differentially affects the expression of the different genes. It also severs as a preferred substrate for these preoxidases. Recently, sequencing of the Pleurotus ostreatus genome was completed, and a comprehensive picture of the ligninolytic peroxidase gene family, consisting of three VPs and six short-MnPs, has been established. Similar enzymes were also discovered and studied in other Pleurotus species. In addition, progress has been made in the development of molecular tools for targeted gene replacement, RNAi-based gene silencing and overexpression of genes of interest. These advances increase the fundamental understanding of the ligninolytic system and provide the opportunity for harnessing the unique attributes of these WRF for applied purposes.
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Affiliation(s)
- Doriv Knop
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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24
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Microbial enzyme systems for lignin degradation and their transcriptional regulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1336-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Wood and humus decay strategies by white-rot basidiomycetes correlate with two different dye decolorization and enzyme secretion patterns on agar plates. Fungal Genet Biol 2014; 72:106-114. [PMID: 24726546 DOI: 10.1016/j.fgb.2014.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/19/2014] [Accepted: 03/24/2014] [Indexed: 11/24/2022]
Abstract
During several forays for ligninolytic fungi in different Spanish native forests, 35 white-rot basidiomycetes growing on dead wood (16 species from 12 genera) and leaf litter (19 species from 10 genera) were selected for their ability to decolorize two recalcitrant aromatic dyes (Reactive Blue 38 and Reactive Black 5) added to malt extract agar medium. In this study, two dye decolorization patterns were observed and correlated with two ecophysiological groups (wood and humus white-rot basidiomycetes) and three taxonomical groups (orders Polyporales, Hymenochaetales and Agaricales). Depending on the above groups, different decolorization zones were observed on the dye-containing plates, being restricted to the colony area or extending to the surrounding medium, which suggested two different decay strategies. These two strategies were related to the ability to secrete peroxidases and laccases inside (white-rot wood Polyporales, Hymenochaetales and Agaricales) and outside (white-rot humus Agaricales) of the fungal colony, as revealed by enzymatic tests performed directly on the agar plates. Similar oxidoreductases production patterns were observed when fungi were grown in the absence of dyes, although the set of enzyme released was different. All these results suggest that the decolorization patterns observed could be related with the existence of two decay strategies developed by white-rot basidiomycetes adapted to wood and leaf litter decay in the field.
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26
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Fernández-Fueyo E, Castanera R, Ruiz-Dueñas FJ, López-Lucendo MF, Ramírez L, Pisabarro AG, Martínez AT. Ligninolytic peroxidase gene expression by Pleurotus ostreatus: differential regulation in lignocellulose medium and effect of temperature and pH. Fungal Genet Biol 2014; 72:150-161. [PMID: 24560615 DOI: 10.1016/j.fgb.2014.02.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 02/03/2014] [Accepted: 02/09/2014] [Indexed: 11/16/2022]
Abstract
Pleurotus ostreatus is an important edible mushroom and a model lignin degrading organism, whose genome contains nine genes of ligninolytic peroxidases, characteristic of white-rot fungi. These genes encode six manganese peroxidase (MnP) and three versatile peroxidase (VP) isoenzymes. Using liquid chromatography coupled to tandem mass spectrometry, secretion of four of these peroxidase isoenzymes (VP1, VP2, MnP2 and MnP6) was confirmed when P. ostreatus grows in a lignocellulose medium at 25°C (three more isoenzymes were identified by only one unique peptide). Then, the effect of environmental parameters on the expression of the above nine genes was studied by reverse transcription-quantitative PCR by changing the incubation temperature and medium pH of P. ostreatus cultures pre-grown under the above conditions (using specific primers and two reference genes for result normalization). The cultures maintained at 25°C (without pH adjustment) provided the highest levels of peroxidase transcripts and the highest total activity on Mn(2+) (a substrate of both MnP and VP) and Reactive Black 5 (a VP specific substrate). The global analysis of the expression patterns divides peroxidase genes into three main groups according to the level of expression at optimal conditions (vp1/mnp3>vp2/vp3/mnp1/mnp2/mnp6>mnp4/mnp5). Decreasing or increasing the incubation temperature (to 10°C or 37°C) and adjusting the culture pH to acidic or alkaline conditions (pH 3 and 8) generally led to downregulation of most of the peroxidase genes (and decrease of the enzymatic activity), as shown when the transcription levels were referred to those found in the cultures maintained at the initial conditions. Temperature modification produced less dramatic effects than pH modification, with most genes being downregulated during the whole 10°C treatment, while many of them were alternatively upregulated (often 6h after the thermal shock) and downregulated (12h) at 37°C. Interestingly, mnp4 and mnp5 were the only peroxidase genes upregulated under alkaline pH conditions. The differences in the transcription levels of the peroxidase genes when the culture temperature and pH parameters were changed suggest an adaptive expression according to environmental conditions. Finally, the intracellular proteome was analyzed, under the same conditions used in the secretomic analysis, and the protein product of the highly-transcribed gene mnp3 was detected. Therefore, it was concluded that the absence of MnP3 from the secretome of the P. ostreatus lignocellulose cultures was related to impaired secretion.
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Affiliation(s)
- Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain
| | - Raul Castanera
- Department of Agrarian Production, Universidad Pública de Navarra, E-31006 Pamplona, Spain
| | | | - María F López-Lucendo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain
| | - Lucía Ramírez
- Department of Agrarian Production, Universidad Pública de Navarra, E-31006 Pamplona, Spain
| | - Antonio G Pisabarro
- Department of Agrarian Production, Universidad Pública de Navarra, E-31006 Pamplona, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28006 Madrid, Spain.
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Salame TM, Knop D, Levinson D, Mabjeesh SJ, Yarden O, Hadar Y. Inactivation of a Pleurotus ostreatus versatile peroxidase-encoding gene (mnp2) results in reduced lignin degradation. Environ Microbiol 2013; 16:265-77. [PMID: 24119015 DOI: 10.1111/1462-2920.12279] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/29/2013] [Accepted: 09/01/2013] [Indexed: 11/27/2022]
Abstract
Lignin biodegradation by white-rot fungi is pivotal to the earth's carbon cycle. Manganese peroxidases (MnPs), the most common extracellular ligninolytic peroxidases produced by white-rot fungi, are considered key in ligninolysis. Pleurotus ostreatus, the oyster mushroom, is a preferential lignin degrader occupying niches rich in lignocellulose such as decaying trees. Here, we provide direct, genetically based proof for the functional significance of MnP to P. ostreatus ligninolytic capacity under conditions mimicking its natural habitat. When grown on a natural lignocellulosic substrate of cotton stalks under solid-state culture conditions, gene and isoenzyme expression profiles of its short MnP and versatile peroxidase (VP)-encoding gene family revealed that mnp2 was predominately expressed. mnp2, encoding the versatile short MnP isoenzyme 2 was disrupted. Inactivation of mnp2 resulted in three interrelated phenotypes, relative to the wild-type strain: (i) reduction of 14% and 36% in lignin mineralization of stalks non-amended and amended with Mn(2+), respectively; (ii) marked reduction of the bioconverted lignocellulose sensitivity to subsequent bacterial hydrolyses; and (iii) decrease in fungal respiration rate. These results may serve as the basis to clarify the roles of the various types of fungal MnPs and VPs in their contribution to white-rot decay of wood and lignocellulose in various ecosystems.
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Affiliation(s)
- Tomer M Salame
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100, Israel
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Abstract
Manganese peroxidases (MnPs) are key players in the ligninolytic system of white rot fungi. In Pleurotus ostreatus (the oyster mushroom) these enzymes are encoded by a gene family comprising nine members, mnp1 to -9 (mnp genes). Mn(2+) amendment to P. ostreatus cultures results in enhanced degradation of recalcitrant compounds (such as the azo dye orange II) and lignin. In Mn(2+)-amended glucose-peptone medium, mnp3, mnp4, and mnp9 were the most highly expressed mnp genes. After 7 days of incubation, the time point at which the greatest capacity for orange II decolorization was observed, mnp3 expression and the presence of MnP3 in the extracellular culture fluids were predominant. To determine the significance of MnP3 for ligninolytic functionality in Mn(2+)-sufficient cultures, mnp3 was inactivated via the Δku80 strain-based P. ostreatus gene-targeting system. In Mn(2+)-sufficient medium, inactivation of mnp3 did not significantly affect expression of nontargeted MnPs or their genes, nor did it considerably diminish the fungal Mn(2+)-mediated orange II decolorization capacity, despite the significant reduction in total MnP activity. Similarly, inactivation of either mnp4 or mnp9 did not affect orange II decolorization ability. These results indicate functional redundancy within the P. ostreatus MnP gene family, enabling compensation upon deficiency of one of its members.
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