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Beijen EPW, van Maanen MH, Marian IM, Klusener JX, van Roosmalen E, Herman KC, Koster MC, Ohm RA. Transcriptomics reveals the regulation of the immune system of the mushroom-forming fungus Schizophyllum commune during interaction with four competitors. Microbiol Res 2024; 289:127929. [PMID: 39413670 DOI: 10.1016/j.micres.2024.127929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/23/2024] [Accepted: 10/06/2024] [Indexed: 10/18/2024]
Abstract
Mushroom-forming fungi frequently encounter competitors during their lifecycle, but their defense mechanisms remain largely unexplored. We studied the response of the mushroom-forming fungus Schizophyllum commune during interaction with the fungal competitors Trichoderma harzianum, Trichoderma aggressivum and Purpureocillium lilacinum and the bacterial competitor Serratia quinivorans. Transcriptomics revealed 632 up-regulated genes in the direct interaction zone, which were enriched in small secreted proteins and transporters. A set of 26 genes were up-regulated during all interactions, indicating a core transcriptomic defense response. In the non-interacting edge of the mycelium of S. commune, there were 154 up-regulated genes, suggesting that there is a systemic response due to a signal that reaches unaffected areas. The GATA zinc finger transcription factor gene gat1 was up-regulated during interaction and a Δgat1 strain displayed increased colonization by T. harzianum. Previously linked to mushroom development, this transcription factor apparently has a dual role. Moreover, 138 genes were up-regulated during both interaction and mushroom development, indicating priming of the defense response during development to prepare the fruiting body for future interactions. Overall, we unveiled a defensive response of S. commune during interaction with fungal and bacterial competitors and identified a regulator of this response.
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Affiliation(s)
- Erik P W Beijen
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Marieke H van Maanen
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Ioana M Marian
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Janieke X Klusener
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Emmeline van Roosmalen
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Koen C Herman
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Margot C Koster
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Robin A Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands.
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Marian IM, Valdes ID, Hayes RD, LaButti K, Duffy K, Chovatia M, Johnson J, Ng V, Lugones LG, Wösten HAB, Grigoriev IV, Ohm RA. High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune. Fungal Genet Biol 2024; 173:103913. [PMID: 39004162 DOI: 10.1016/j.fgb.2024.103913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Schizophyllum commune is a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains for aspects of mushroom development and 18 monokaryotic strains for lignocellulose degradation. There was considerable heterogeneity among the strains regarding these phenotypes. The majority of the strains developed mushrooms with varying morphologies, although some strains only grew vegetatively under the tested conditions. Growth on various carbon sources showed strain-specific profiles. The genomes of seven monokaryotic strains were sequenced and analyzed together with six previously published genome sequences. Moreover, the related species Schizophyllum fasciatum was sequenced. Although there was considerable genetic variation between the genome assemblies, the genes related to mushroom formation and lignocellulose degradation were well conserved. These sequenced genomes, in combination with the high phenotypic diversity, will provide a solid basis for functional genomics analyses of the strains of S. commune.
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Affiliation(s)
- Ioana M Marian
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ivan D Valdes
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Richard D Hayes
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kecia Duffy
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mansi Chovatia
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jenifer Johnson
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Luis G Lugones
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Robin A Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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Wang C, Zhang X, Wu K, Liu S, Li X, Zhu C, Xiao Y, Fang Z, Liu J. Two Zn 2Cys 6-type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta. Appl Environ Microbiol 2024; 90:e0054524. [PMID: 38899887 PMCID: PMC11267944 DOI: 10.1128/aem.00545-24] [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: 03/22/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
White-rot fungi differentially express laccases when they encounter aromatic compounds. However, the underlying mechanisms are still being explored. Here, proteomics analysis revealed that in addition to increased laccase activity, proteins involved in sphingolipid metabolism and toluene degradation as well as some cytochrome P450s (CYP450s) were differentially expressed and significantly enriched during 48 h of o-toluidine exposure, in Trametes hirsuta AH28-2. Two Zn2Cys6-type transcription factors (TFs), TH8421 and TH4300, were upregulated. Bioinformatics docking and isothermal titration calorimetry assays showed that each of them could bind directly to o-toluidine and another aromatic monomer, guaiacol. Binding to aromatic compounds promoted the formation of TH8421/TH4300 heterodimers. TH8421 and TH4300 silencing in T. hirsuta AH28-2 led to decreased transcriptional levels and activities of LacA and LacB upon o-toluidine and guaiacol exposure. EMSA and ChIP-qPCR analysis further showed that TH8421 and TH4300 bound directly with the promoter regions of lacA and lacB containing CGG or CCG motifs. Furthermore, the two TFs were involved in direct and positive regulation of the transcription of some CYP450s. Together, TH8421 and TH4300, two key regulators found in T. hirsuta AH28-2, function as heterodimers to simultaneously trigger the expression of downstream laccases and intracellular enzymes. Monomeric aromatic compounds act as ligands to promote heterodimer formation and enhance the transcriptional activities of the two TFs.IMPORTANCEWhite-rot fungi differentially express laccase isoenzymes when exposed to aromatic compounds. Clarification of the molecular mechanisms underlying differential laccase expression is essential to elucidate how white-rot fungi respond to the environment. Our study shows that two Zn2Cys6-type transcription factors form heterodimers, interact with the promoters of laccase genes, and positively regulate laccase transcription in Trametes hirsuta AH28-2. Aromatic monomer addition induces faster heterodimer formation and rate of activity. These findings not only identify two new transcription factors involved in fungal laccase transcription but also deepen our understanding of the mechanisms underlying the response to aromatics exposure in white-rot fungi.
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Affiliation(s)
- Chenkai Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xinlei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Kun Wu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Shenglong Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xiang Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Chaona Zhu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
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Harder CB, Miyauchi S, Virágh M, Kuo A, Thoen E, Andreopoulos B, Lu D, Skrede I, Drula E, Henrissat B, Morin E, Kohler A, Barry K, LaButti K, Salamov A, Lipzen A, Merényi Z, Hegedüs B, Baldrian P, Stursova M, Weitz H, Taylor A, Koriabine M, Savage E, Grigoriev IV, Nagy LG, Martin F, Kauserud H. Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. CELL GENOMICS 2024; 4:100586. [PMID: 38942024 PMCID: PMC11293592 DOI: 10.1016/j.xgen.2024.100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/28/2024] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway; Department of Biology, Microbial Ecology Group, Biology Department, Lund University, Lund, Sweden; University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, 2100 Copenhagen Ø, Denmark.
| | - Shingo Miyauchi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ella Thoen
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dabao Lu
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Inger Skrede
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France; INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Martina Stursova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Hedda Weitz
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Andy Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK; The James Hutton Institute, Aberdeen, UK
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France.
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
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Li W, Zou G, Bao D, Wu Y. Current Advances in the Functional Genes of Edible and Medicinal Fungi: Research Techniques, Functional Analysis, and Prospects. J Fungi (Basel) 2024; 10:311. [PMID: 38786666 PMCID: PMC11121823 DOI: 10.3390/jof10050311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/02/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand adversity, thereby increasing yield and quality and promoting industrial development. With the rapid development of functional gene research technology and the publication of many whole-genome sequences of edible and medicinal fungi, genes related to important biological traits have been mined, located, and functionally analyzed. This paper summarizes the advantages and disadvantages of different functional gene research techniques and application examples for edible and medicinal fungi; systematically reviews the research progress of functional genes of edible and medicinal fungi in biological processes such as mating type, mycelium and fruit growth and development, substrate utilization and nutrient transport, environmental response, and the synthesis and regulation of important active substances; and proposes future research directions for functional gene research for edible and medicinal fungi. The overall aim of this study was to provide a valuable reference for further promoting the molecular breeding of edible and medicinal fungi with high yield and quality and to promote the wide application of edible and medicinal fungi products in food, medicine, and industry.
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Affiliation(s)
- Wenyun Li
- National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (G.Z.)
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Gen Zou
- National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (G.Z.)
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (G.Z.)
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingying Wu
- National Engineering Research Center of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (W.L.); (G.Z.)
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai 201306, China
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Kraisitudomsook N, Ahrendt S, Riley R, LaButti K, Lipzen A, Daum C, Barry K, Grigoriev IV, Rämä T, Martin F, Smith ME. On the origin of bird's nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota). Mol Phylogenet Evol 2024; 193:108010. [PMID: 38195011 DOI: 10.1016/j.ympev.2024.108010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/15/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.
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Affiliation(s)
- Nattapol Kraisitudomsook
- Plant Pathology Department, Institute of Food and Agricultural Sciences (UF-IFAS), University of Florida, Gainesville, FL 32607, USA; Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Ratchaburi 70150, Thailand.
| | - Steven Ahrendt
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Robert Riley
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kerrie Barry
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, 110 Koshland Hall, Berkeley, CA 94720, USA
| | - Teppo Rämä
- The Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Francis Martin
- University of Lorraine, National Research Institute for Agriculture, Food, and Environment (INRAE), Tree-Microbe Interactions Department, Champenoux 54280, France.
| | - Matthew E Smith
- Plant Pathology Department, Institute of Food and Agricultural Sciences (UF-IFAS), University of Florida, Gainesville, FL 32607, USA.
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7
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Beijen EPW, Ohm RA. Genome annotations for the ascomycete fungi Trichoderma harzianum, Trichoderma aggressivum, and Purpureocillium lilacinum. Microbiol Resour Announc 2024; 13:e0115323. [PMID: 38385672 DOI: 10.1128/mra.01153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
We sequenced and annotated the genomes of the ascomycete fungi Trichoderma harzianum, Trichoderma aggressivum f. europaeum, and Purpureocillium lilacinum. Moreover, we developed a website to allow users to interactively analyze the assemblies, gene predictions, and functional annotations of these species and 70+ previously sequenced fungi.
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Affiliation(s)
- Erik P W Beijen
- Department of Biology, Microbiology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Robin A Ohm
- Department of Biology, Microbiology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
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8
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Sun X, Liu D, Zhao X. Transcription factors: switches for regulating growth and development in macrofungi. Appl Microbiol Biotechnol 2023; 107:6179-6191. [PMID: 37624406 DOI: 10.1007/s00253-023-12726-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/31/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Macrofungi (or mushrooms) act as an extraordinarily important part to human health due to their nutritional and/or medicinal value, but the detailed researches in growth and development mechanisms have yet to be explored further. Transcription factors (TFs) play indispensable roles in signal transduction and affect growth, development, and metabolism of macrofungi. In recent years, increasing research effort has been employed to probe the relationship between the development of macrofungi and TFs. Herein, the present review comprehensively summarized the functional TFs researched in macrofungi, including modulating mycelial growth, fructification, sclerotial formation, sexual reproduction, spore formation, and secondary metabolism. Meanwhile, the possible effect mechanisms of TFs on the growth and development of some macrofungi were also revealed. Specific examples of functional characterizations of TFs in macrofungi (such as Schizophyllum commune and Coprinopsis cinerea) were described to a better comprehension of regulatory effect. Future research prospects in the field of TFs of macrofungi are discussed. We illustrated the functional versatility of the TFs in macrofungi based on specific examples. A systematical realization of the interaction and possible mechanisms between TFs and macrofungi can supply possible solutions to regulate genetic characteristics, which supply novel insights into the regulation of growth, development and metabolism of macrofungi. KEY POINTS: • The functional TFs researched in macrofungi were summarized. • The possible effect mechanisms of TFs in macrofungal were described. • The multiple physiological functions of TFs in macrofungi were discussed.
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Affiliation(s)
- Xueyan Sun
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Dongmei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
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Yu H, Jiang N, Yan M, Cheng X, Zhang L, Zhai D, Liu J, Zhang M, Song C, Yu H, Li Q. Comparative analysis of proteomes and transcriptomes revealed the molecular mechanism of development and nutrition of Pleurotus giganteus at different fruiting body development stages. Front Nutr 2023; 10:1197983. [PMID: 37545588 PMCID: PMC10402744 DOI: 10.3389/fnut.2023.1197983] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 08/08/2023] Open
Abstract
Pleurotus giganteus is a commercially cultivated high-temperature mushroom. Investigating the molecular mechanism of fruiting body development will help us to better understand the regulation of substrates and energy in this process. However, little information has been reported on the development and nutrients of the P. giganteus fruiting body. In the present study, P. giganteus is cultivated in a climate chamber, and comparative transcriptome, proteome, and nutritional analysis of P. giganteus fruiting bodies were performed. Our results revealed that Cytochrome P450 monooxygenases and hydrophobin proteins play important roles during the differentiation in the elongation stage. Later, carbon metabolism dominate the fruiting body metabolism and genes related to the carbohydrate metabolic process, glycolytic process, and gluconeogenesis were up-regulated in the mature fruiting bodies. The up-regulation of carbohydrate substrates utilization CAZymes genes and inconsistent protein expression in pileus indicated a reverse transportation of mRNA from the fruiting body to vegetative mycelia. In addition, protein concentration in the pileus is higher than that in the stem, while the stem is the major nitrogen metabolic and amino acid synthetic location. The integrated transcriptomic, proteomic, and nutritional analysis indicated a two-way transportation of substrates and mRNAs in P. giganteus. Stem synthesizes amino acids and transported them to pileus with reducing sugars, while pileus induces the expression of substrate degradation mRNA according to the needs of growth and development and transports them in the other direction.
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Affiliation(s)
- Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ning Jiang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Miaomiao Yan
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Xuan Cheng
- Agricultural Specialty Industry Development Center, Qujiang, Zhejiang, China
| | - Lujun Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dandan Zhai
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Jianyu Liu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Meiyan Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chunyan Song
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hao Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qiaozhen Li
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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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: 8] [Impact Index Per Article: 4.0] [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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