1
|
Földi C, Merényi Z, Balázs B, Csernetics Á, Miklovics N, Wu H, Hegedüs B, Virágh M, Hou Z, Liu XB, Galgóczy L, Nagy LG. Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes). mSystems 2024; 9:e0120823. [PMID: 38334416 PMCID: PMC10949477 DOI: 10.1128/msystems.01208-23] [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: 11/10/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded program. Fruiting bodies reached the highest complexity levels in the Agaricomycetes; yet, the underlying genetics is currently poorly known. In this work, we functionally characterized a highly conserved gene termed snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologs of snb1 are present in almost all agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. snb1 deletion mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes, and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed differentially regulated genes and gene families that, based on wild-type RNA-Seq data, were upregulated early during development and showed tissue-specific expression, suggesting a potential role in differentiation. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying developmental patterning in the Agaricomycetes. IMPORTANCE Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development.
Collapse
Affiliation(s)
- Csenge Földi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Bálint Balázs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Árpád Csernetics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Nikolett Miklovics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Hongli Wu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Zhihao Hou
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Xiao-Bin Liu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - László Galgóczy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László G. Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| |
Collapse
|
2
|
Quiroz LF, Ciosek T, Grogan H, McKeown PC, Spillane C, Brychkova G. Unravelling the Transcriptional Response of Agaricus bisporus under Lecanicillium fungicola Infection. Int J Mol Sci 2024; 25:1283. [PMID: 38279283 PMCID: PMC10815960 DOI: 10.3390/ijms25021283] [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: 12/15/2023] [Revised: 01/14/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Mushrooms are a nutritionally rich and sustainably-produced food with a growing global market. Agaricus bisporus accounts for 11% of the total world mushroom production and it is the dominant species cultivated in Europe. It faces threats from pathogens that cause important production losses, including the mycoparasite Lecanicillium fungicola, the causative agent of dry bubble disease. Through quantitative real-time polymerase chain reaction (qRT-PCR), we determine the impact of L. fungicola infection on the transcription patterns of A. bisporus genes involved in key cellular processes. Notably, genes related to cell division, fruiting body development, and apoptosis exhibit dynamic transcriptional changes in response to infection. Furthermore, A. bisporus infected with L. fungicola were found to accumulate increased levels of reactive oxygen species (ROS). Interestingly, the transcription levels of genes involved in the production and scavenging mechanisms of ROS were also increased, suggesting the involvement of changes to ROS homeostasis in response to L. fungicola infection. These findings identify potential links between enhanced cell proliferation, impaired fruiting body development, and ROS-mediated defence strategies during the A. bisporus (host)-L. fungicola (pathogen) interaction, and offer avenues for innovative disease control strategies and improved understanding of fungal pathogenesis.
Collapse
Affiliation(s)
- Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Tessa Ciosek
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Helen Grogan
- Teagasc, Horticulture Development Department, Ashtown Research Centre, D15 KN3K Dublin, Ireland;
| | - Peter C. McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| | - Galina Brychkova
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland; (L.F.Q.); (C.S.)
| |
Collapse
|
3
|
Wu J, Nong Y, Chen B, Jiang Y, Chen Y, Wei C, Tao Y, Xie B. Flammutoxin, a Degradation Product of Transepithelial Electrical Resistance-Decreasing Protein, Induces Reactive Oxygen Species and Apoptosis in HepG2 Cells. Foods 2023; 13:66. [PMID: 38201094 PMCID: PMC10778570 DOI: 10.3390/foods13010066] [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: 11/09/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Proteins from Flammulina filiformis were prepared by sodium chloride extraction and fractionated by ammonium sulfate precipitation with increasing saturation degrees to obtain the protein fractions Ffsp-30, Ffsp-50, Ffsp-70, Ffsp-90, and Ffp-90. Among these protein fractions, Ffsp-50 possessed the most significant cytotoxic effect against three human gastrointestinal cancer cell lines, viz. HT-29, SGC-7901, and HepG2. SDS-PAGE and MALDI-TOF/TOF MS/MS analyses revealed that flammutoxin (FTX) was present as a dominating protein in Ffsp-50, which was further evidenced by HPLC-MS/MS determination. Furthermore, native FTX was purified from Ffsp-50 with a molecular weight of 26.78 kDa, exhibiting notable cytotoxicity against gastrointestinal cancer cell lines. Both Ffsp-50 and FTX exposure could enhance intercellular reactive oxygen species (ROS) generation and induce significant apoptosis in HepG2 cells. FTX was identified to be relatively conserved in basidiomycetes according to phylogenetic analysis, and its expression was highly upregulated in the primordium as well as the pileus of the fruiting body from the elongation and maturation stages, as compared with that in mycelium. Taken together, FTX could remarkably inhibit cell growth and induce ROS and apoptosis in HepG2 cells, potentially participating in the growth and development of the fruiting body. These findings from our investigation provided insight into the antigastrointestinal cancer activity of FTX, which could serve as a biological source of health-promoting and biomedical applications.
Collapse
Affiliation(s)
- Jianguo Wu
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.W.); (Y.N.); (Y.C.); (C.W.); (Y.T.)
| | - Yu Nong
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.W.); (Y.N.); (Y.C.); (C.W.); (Y.T.)
| | - Bingzhi Chen
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (B.C.); (Y.J.)
| | - Yuji Jiang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (B.C.); (Y.J.)
| | - Yuanhao Chen
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.W.); (Y.N.); (Y.C.); (C.W.); (Y.T.)
| | - Chuanzheng Wei
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.W.); (Y.N.); (Y.C.); (C.W.); (Y.T.)
| | - Yongxin Tao
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.W.); (Y.N.); (Y.C.); (C.W.); (Y.T.)
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baogui Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.W.); (Y.N.); (Y.C.); (C.W.); (Y.T.)
| |
Collapse
|
4
|
Yang Y, Pian Y, Li J, Xu L, Lu Z, Dai Y, Li Q. Integrative analysis of genome and transcriptome reveal the genetic basis of high temperature tolerance in pleurotus giganteus (Berk. Karun & Hyde). BMC Genomics 2023; 24:552. [PMID: 37723428 PMCID: PMC10506213 DOI: 10.1186/s12864-023-09669-8] [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: 03/29/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Pleurotus giganteus is a commonly cultivated mushroom with notable high temperature resistance, making it significant for the growth of the edible fungi industry in the tropics. Despite its practical importance,, the genetic mechanisms underlying its ability to withstand high temperature tolerance remain elusive. RESULTS In this study, we performed high-quality genome sequencing of a monokaryon isolated from a thermotolerant strain of P. giganteus. The genome size was found to be 40.11 Mb, comprising 17 contigs and 13,054 protein-coding genes. Notably, some genes related to abiotic stress were identified in genome, such as genes regulating heat shock protein, protein kinase activity and signal transduction. These findings provide valuable insights into the genetic basis of P. giganteus' high temperature resistance. Furthermore, the phylogenetic tree showed that P. giganteus was more closely related to P. citrinopileatus than other Pleurotus species. The divergence time between Pleurotus and Lentinus was estimated as 153.9 Mya, and they have a divergence time with Panus at 168.3 Mya, which proved the taxonomic status of P. giganteus at the genome level. Additionally, a comparative transcriptome analysis was conducted between mycelia treated with 40 °C heat shock for 18 h (HS) and an untreated control group (CK). Among the 2,614 differentially expressed genes (DEGs), 1,303 genes were up-regulated and 1,311 were down-regulated in the HS group. The enrichment analysis showed that several genes related to abiotic stress, including heat shock protein, DnaJ protein homologue, ubiquitin protease, transcription factors, DNA mismatch repair proteins, and zinc finger proteins, were significantly up-regulated in the HS group. These genes may play important roles in the high temperature adaptation of P. giganteus. Six DEGs were selected according to fourfold expression changes and were validated by qRT-PCR, laying a good foundation for further gene function analysis. CONCLUSION Our study successfully reported a high-quality genome of P. giganteus and identified genes associated with high-temperature tolerance through an integrative analysis of the genome and transcriptome. This study lays a crucial foundation for understanding the high-temperature tolerance mechanism of P. giganteus, providing valuable insights for genetic modification of P. giganteus strains and the development of high-temperature strains for the edible fungus industry, particularly in tropical regions.
Collapse
Affiliation(s)
- Yang Yang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
| | - Yongru Pian
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Jingyi Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Lin Xu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Zhu Lu
- Jilin Academy of Vegetables and Flowers Sciences, Changchun, China
| | - Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.
| | - Qinfen Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China.
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China.
| |
Collapse
|
5
|
Yuan H, Liu Z, Guo L, Hou L, Meng J, Chang M. Function of Transcription Factors PoMYB12, PoMYB15, and PoMYB20 in Heat Stress and Growth of Pleurotus ostreatus. Int J Mol Sci 2023; 24:13559. [PMID: 37686365 PMCID: PMC10487880 DOI: 10.3390/ijms241713559] [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: 07/15/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
MYB transcription factors (TFs) have been extensively studied in plant abiotic stress responses and growth and development. However, the role of MYB TFs in the heat stress response and growth and development of Pleurotus ostreatus remains unclear. To investigate the function of PoMYB12, PoMYB15, and PoMYB20 TFs in P. ostreatus, mutant strains of PoMYB12, PoMYB15, and PoMYB20 were generated using RNA interference (RNAi) and overexpression (OE) techniques. The results indicated that the mycelia of OE-PoMYB12, OE-PoMYB20, and RNAi-PoMYB15 mutant strains exhibited positive effects under heat stress at 32 °C, 36 °C, and 40 °C. Compared to wild-type strains, the OE-PoMYB12, OE-PoMYB20, and RNAi-PoMYB15 mutant strains promoted the growth and development of P. ostreatus. These mutant strains also facilitated the recovery of growth and development of P. ostreatus after 24 h of 36 °C heat stress. In conclusion, the expression of PoMYB12 and PoMYB20 supports the mycelium's response to heat stress and enhances the growth and development of P. ostreatus, whereas PoMYB15 produces the opposite effect.
Collapse
Affiliation(s)
- Hui Yuan
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (H.Y.); (Z.L.); (J.M.)
| | - Zongqi Liu
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (H.Y.); (Z.L.); (J.M.)
| | - Lifeng Guo
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (H.Y.); (Z.L.); (J.M.)
| | - Ludan Hou
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (H.Y.); (Z.L.); (J.M.)
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (H.Y.); (Z.L.); (J.M.)
- Shanxi Engineering Research Center of Edible Fungi, Jinzhong 030801, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (H.Y.); (Z.L.); (J.M.)
- Shanxi Engineering Research Center of Edible Fungi, Jinzhong 030801, China
| |
Collapse
|
6
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
7
|
Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
Collapse
Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| |
Collapse
|
8
|
Cai M, Wu X, Liang X, Hu H, Liu Y, Yong T, Li X, Xiao C, Gao X, Chen S, Xie Y, Wu Q. Comparative proteomic analysis of two divergent strains provides insights into thermotolerance mechanisms of Ganoderma lingzhi. Fungal Genet Biol 2023; 167:103796. [PMID: 37146899 DOI: 10.1016/j.fgb.2023.103796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/18/2023] [Accepted: 04/03/2023] [Indexed: 05/07/2023]
Abstract
Heat stress (HS) is a major abiotic factor influencing fungal growth and metabolism. However, the genetic basis of thermotolerance in Ganoderma lingzhi (G. lingzhi) remains largely unknown. In this study, we investigated the thermotolerance capacities of 21 G. lingzhi strains and screened the thermo-tolerant (S566) and heat-sensitive (Z381) strains. The mycelia of S566 and Z381 were collected and subjected to a tandem mass tag (TMT)-based proteome assay. We identified 1493 differentially expressed proteins (DEPs), with 376 and 395 DEPs specific to the heat-tolerant and heat-susceptible genotypes, respectively. In the heat-tolerant genotype, upregulated proteins were linked to stimulus regulation and response. Proteins related to oxidative phosphorylation, glycosylphosphatidylinositol-anchor biosynthesis, and cell wall macromolecule metabolism were downregulated in susceptible genotypes. After HS, the mycelial growth of the heat-sensitive Z381 strain was inhibited, and mitochondrial cristae and cell wall integrity of this strain were severely impaired, suggesting that HS may inhibit mycelial growth of Z381 by damaging the cell wall and mitochondrial structure. Furthermore, thermotolerance-related regulatory pathways were explored by analyzing the protein-protein interaction network of DEPs considered to participate in the controlling the thermotolerance capacity. This study provides insights into G. lingzhi thermotolerance mechanisms and a basis for breeding a thermotolerant germplasm bank for G. lingzhi and other fungi.
Collapse
Affiliation(s)
- Manjun Cai
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaoxian Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaowei Liang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Huiping Hu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yuanchao Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Tianqiao Yong
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiangmin Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Chun Xiao
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiong Gao
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shaodan Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yizhen Xie
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Guangdong Yuewei Edible Fungi Technology Co. Ltd., Guangzhou 510663, China.
| | - Qingping Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.
| |
Collapse
|
9
|
Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis. J Fungi (Basel) 2022; 9:jof9010064. [PMID: 36675885 PMCID: PMC9862757 DOI: 10.3390/jof9010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
Stipe gradient elongation is an important and remarkable feature in the development of most mushroom fruiting bodies. However, its molecular mechanism has rarely been described. Here, the decreasing trend of stipe elongation and increasing trend of cell length in a gradient from the top to the base of the stipe were determined in a model basidiomycete mushroom: Flammulina filiformis. According to RNA-seq results, 1409 differentially expressed genes (DEGs) were identified among elongation region (ER), transition region (TR), and stable region (SR) samples, including 26 transcription factors (TFs). Based on Short Time-series Expression Miner (STEM) clustering of DEGs, clusters 1 and 3, with obvious expression trends that were consistent with or in contrast to the elongation rate, were screened. The cluster 1 DEGs were mainly involved in the GO cellular component category and KEGG genetic information processing class; however, the cluster 3 DEGs were mainly involved in metabolic processes. Furthermore, qRT-PCR confirmed that key genes of the long-chain fatty acid synthesis pathway were involved in stipe gradient elongation and regulated by NADPH oxidase-derived ROS signaling molecules. These findings provide an essential basis for understanding the molecular mechanism of stipe gradient elongation.
Collapse
|
10
|
Barh A, Sharma K, Bhatt P, Annepu SK, Nath M, Shirur M, Kumari B, Kaundal K, Kamal S, Sharma VP, Gupta S, Sharma A, Gupta M, Dutta U. Identification of Key Regulatory Pathways of Basidiocarp Formation in Pleurotus spp. Using Modeling, Simulation and System Biology Studies. J Fungi (Basel) 2022; 8:jof8101073. [PMID: 36294638 PMCID: PMC9604897 DOI: 10.3390/jof8101073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/21/2022] Open
Abstract
Pleurotus (Oyster mushroom) is an important cultivated edible mushroom across the world. It has several therapeutic effects as it contains various useful bio-molecules. The cultivation and crop management of these basidiomycete fungi depends on many extrinsic and intrinsic factors such as substrate composition, growing environment, enzymatic properties, and the genetic makeup, etc. Moreover, for efficient crop production, a comprehensive understanding of the fundamental properties viz. intrinsic–extrinsic factors and genotype-environment interaction analysis is required. The present study explores the basidiocarp formation biology in Pleurotus mushroom using an in silico response to the environmental factors and involvement of the major regulatory genes. The predictive model developed in this study indicates involvement of the key regulatory pathways in the pinhead to fruit body development process. Notably, the major regulatory pathways involved in the conversion of mycelium aggregation to pinhead formation and White Collar protein (PoWC1) binding flavin-chromophore (FAD) to activate respiratory enzymes. Overall, cell differentiation and higher expression of respiratory enzymes are the two important steps for basidiocarp formation. PoWC1 and pofst genes were participate in the structural changes process. Besides this, the PoWC1 gene is also involved in the respiratory requirement, while the OLYA6 gene is the triggering point of fruiting. The findings of the present study could be utilized to understand the detailed mechanism associated with the basidiocarp formation and to cultivate mushrooms at a sustainable level.
Collapse
Affiliation(s)
- Anupam Barh
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
- Correspondence: (A.B.); (S.K.A.)
| | - Kanika Sharma
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | - Pankaj Bhatt
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Sudheer Kumar Annepu
- ICAR-Indian Institute of Soil and Water Conservation, Research Center, Udhagamandalam 643 006, India
- Correspondence: (A.B.); (S.K.A.)
| | - Manoj Nath
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | - Mahantesh Shirur
- National Institute of Agricultural Extension Management (MANAGE), Hyderabad 500 030, India
| | - Babita Kumari
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | - Kirti Kaundal
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | - Shwet Kamal
- ICAR-Directorate of Mushroom Research, Solan 173 213, India
| | | | - Sachin Gupta
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu 180 009, India
| | - Annu Sharma
- Department of Plant Pathology, College of Horticulture, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan 173 230, India
| | - Moni Gupta
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu 180 009, India
| | - Upma Dutta
- Division of Plant Pathology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu 180 009, India
| |
Collapse
|
11
|
Liu Y, Ma X, Long Y, Yao S, Wei C, Han X, Gan B, Yan J, Xie B. Effects of β-1,6-Glucan Synthase Gene ( FfGS6) Overexpression on Stress Response and Fruit Body Development in Flammulina filiformis. Genes (Basel) 2022; 13:1753. [PMID: 36292637 PMCID: PMC9601887 DOI: 10.3390/genes13101753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2023] Open
Abstract
β-1, 6-glucan synthase is a key enzyme of β-1, 6-glucan synthesis, which plays a vital role in the cell wall cross-linking of fungi. However, the role of the β-1, 6-glucan synthase gene in the development of the fruiting body and the stress response of macrofungi is largely unknown. In this study, four overexpression transformants of the β-1, 6-glucan synthase gene (FfGS6) were successfully obtained, and gene function was studied in Flammulina filiformis. The overexpression of FfGS6 can increase the width of mycelium cells and improve the tolerance ability under mechanical injury and oxidative stress. Moreover, FfGS6 gene expression fluctuated in up-regulation during the recovery process of mycelium injury but showed a negative correlation with H2O2 concentration. Fruiting body phenotype tests showed that mycelia's recovery ability after scratching improved when the FfGS6 gene was overexpressed. However, primordia formation and the stipe elongation ability were significantly inhibited. Our findings indicate that FfGS6 is involved in regulating mycelial cell morphology, the mycelial stress response, and fruit body development in F. filiformis.
Collapse
Affiliation(s)
- Yuanyuan Liu
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinbin Ma
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Long
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sen Yao
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chuanzheng Wei
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Han
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Bingcheng Gan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Junjie Yan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
| | - Baogui Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
12
|
De Novo Assembly Transcriptome Analysis Reveals the Preliminary Molecular Mechanism of Primordium Formation in Pleurotus tuoliensis. Genes (Basel) 2022; 13:genes13101747. [PMID: 36292631 PMCID: PMC9601356 DOI: 10.3390/genes13101747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Primordium formation is extremely important for yield of Pleurotus tuoliensis. However, the molecular mechanism underlying primordium formation is largely unknown. This study investigated the transcriptional properties during primordium formation of P. tuoliensis by comparing transcriptome. Clean reads were assembled into 57,075 transcripts and 6874 unigenes. A total of 1397 differentially expressed genes were identified (26 DEGs altered in all stages). GO and KEGG enrichment analysis showed that these DEGs were involved in “oxidoreductase activity”, “glycolysis/gluconeogenesis”, “MAPK signaling pathways”, and “ribosomes”. Our results support further understanding of the transcriptional changes and molecular processes underlying primordium formation and differentiation of P. tuoliensis.
Collapse
|
13
|
Comparative transcriptome analysis revealed candidate genes involved in fruiting body development and sporulation in Ganoderma lucidum. Arch Microbiol 2022; 204:514. [PMID: 35867171 DOI: 10.1007/s00203-022-03088-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/20/2022] [Indexed: 11/02/2022]
Abstract
Ganoderma lucidum is an edible mushroom highly regarded in the traditional Chinese medicine. To better understand the molecular mechanisms underlying fruiting body development in G. lucidum, transcriptome analysis based on RNA sequencing was carried out on different developmental stages: mycelium (G1); primordium (G2); young fruiting body (G3); mature fruiting body (G4); fruiting body in post-sporulation stage (G5). In total, 26,137 unigenes with an average length of 1078 bp were de novo assembled. Functional annotation of transcriptomes matched 72.49% of the unigenes to known proteins available in at least one database. Differentially expressed genes (DEGs) were identified between the evaluated stages: 3135 DEGs in G1 versus G2; 120 in G2 versus G3; 3919 in G3 versus G4; and 1012 in G4 versus G5. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs identified in G1 versus G2 revealed that, in addition to global and overview maps, enriched pathways were related to amino acid metabolism and carbohydrate metabolism. In contrast, DEGs identified in G2 versus G3 were mainly assigned to the category of metabolism of amino acids and their derivatives, comprising mostly upregulated unigenes. In addition, highly expressed unigenes associated with the transition between different developmental stages were identified, including those encoding hydrophobins, cytochrome P450s, extracellular proteases, and several transcription factors. Meanwhile, highly expressed unigenes related to meiosis such as DMC1, MSH4, HOP1, and Mek1 were also analyzed. Our study provides important insights into the molecular mechanisms underlying fruiting body development and sporulation in G. lucidum.
Collapse
|
14
|
FFGA1 Protein Is Essential for Regulating Vegetative Growth, Cell Wall Integrity, and Protection against Stress in Flammunina filiformis. J Fungi (Basel) 2022; 8:jof8040401. [PMID: 35448632 PMCID: PMC9030616 DOI: 10.3390/jof8040401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 01/25/2023] Open
Abstract
Flammulina filiformis is a popular mushroom which has been regarded as a potential model fungus for mycelium growth, fruiting body development, and stress response studies. Based on a genome-wide search, four genes encoding heterotrimeric G protein α subunits were identified in F. filiformis. The data of conserved domain analysis showed that these genes contain only one subgroup I of Gα subunit (Gαi), similar to many other fungi. To explore the function of Gαi, FfGa1 over-expression (OE) and RNA interference (RNAi) strains were generated using the Agrobacterium tumefaciens-mediated transformation (ATMT) approach. RNAi strains showed remarkably reduced growth on PDA medium and sensitivity to cell wall-perturbing agents, with maximum growth inhibition, but showed better growth in response to hypertonic stress-causing agents, while OE strains exhibited more resistance to thermal stress and mycoparasite Trichoderma as compared to the wild-type and RNAi strains. Taken together, our results indicated that FfGa1 positively regulates hyphal extension, and is crucial for the maintenance of cell wall integrity and protection against biotic and abiotic (hypertonic and thermal) stress.
Collapse
|
15
|
A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor. Microorganisms 2021; 9:microorganisms9122612. [PMID: 34946213 PMCID: PMC8708209 DOI: 10.3390/microorganisms9122612] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 02/05/2023] Open
Abstract
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis.
Collapse
|
16
|
Evolutionary Morphogenesis of Sexual Fruiting Bodies in Basidiomycota: Toward a New Evo-Devo Synthesis. Microbiol Mol Biol Rev 2021; 86:e0001921. [PMID: 34817241 DOI: 10.1128/mmbr.00019-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The development of sexual fruiting bodies is one of the most complex morphogenetic processes in fungi. Mycologists have long been fascinated by the morphological and developmental diversity of fruiting bodies; however, evolutionary developmental biology of fungi still lags significantly behind that of animals or plants. Here, we summarize the current state of knowledge on fruiting bodies of mushroom-forming Basidiomycota, focusing on phylogenetic and developmental biology. Phylogenetic approaches have revealed a complex history of morphological transformations and convergence in fruiting body morphologies. Frequent transformations and convergence is characteristic of fruiting bodies in contrast to animals or plants, where main body plans are highly conserved. At the same time, insights into the genetic bases of fruiting body development have been achieved using forward and reverse genetic approaches in selected model systems. Phylogenetic and developmental studies of fruiting bodies have each yielded major advances, but they have produced largely disjunct bodies of knowledge. An integrative approach, combining phylogenetic, developmental, and functional biology, is needed to achieve a true fungal evolutionary developmental biology (evo-devo) synthesis for fungal fruiting bodies.
Collapse
|
17
|
Wan JN, Li Y, Guo T, Ji GY, Luo SZ, Ji KP, Cao Y, Tan Q, Bao DP, Yang RH. Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development. Front Microbiol 2021; 12:732458. [PMID: 34659161 PMCID: PMC8511702 DOI: 10.3389/fmicb.2021.732458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023] Open
Abstract
Phlebopus portentosus (Berk. and Broome) Boedijin, a widely consumed mushroom in China and Thailand, is the first species in the order Boletaceae to have been industrially cultivated on a large scale. However, to date, the lignocellulose degradation system and molecular basis of fruiting body development in P. portentosus have remained cryptic. In the present study, genome and transcriptome sequencing of P. portentosus was performed during the mycelium (S), primordium (P), and fruiting body (F) stages. A genome of 32.74 Mb with a 48.92% GC content across 62 scaffolds was obtained. A total of 9,464 putative genes were predicted from the genome, of which the number of genes related to plant cell wall-degrading enzymes was much lower than that of some saprophytic mushrooms with specific ectomycorrhizal niches. Principal component analysis of RNA-Seq data revealed that the gene expression profiles at all three stages were different. The low expression of plant cell wall-degrading genes also confirmed the limited ability to degrade lignocellulose. The expression profiles also revealed that some conserved and specific pathways were enriched in the different developmental stages of P. portentosus. Starch and sucrose metabolic pathways were enriched in the mycelium stage, while DNA replication, the proteasome and MAPK signaling pathways may be associated with maturation. These results provide a new perspective for understanding the key pathways and hub genes involved in P. portentosus development.
Collapse
Affiliation(s)
- Jia-Ning Wan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ting Guo
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guang-Yan Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Shun-Zhen Luo
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Kai-Ping Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Yang Cao
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Qi Tan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Rui-Heng Yang
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
18
|
Luo L, Zhang S, Wu J, Sun X, Ma A. Heat stress in macrofungi: effects and response mechanisms. Appl Microbiol Biotechnol 2021; 105:7567-7576. [PMID: 34536103 DOI: 10.1007/s00253-021-11574-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022]
Abstract
Temperature is one of the key factors that affects the growth and development of macrofungi. Heat stress not only negatively affects the morphology and growth rate of macrofungi, but also destroys cell structures and influences cell metabolism. Due to loosed structure of cell walls and increased membrane fluidity, which caused by heat stress, the outflow of intracellular nutrients makes macrofungi more vulnerable to invasion by pathogens. Macrofungi accumulate reactive oxygen species (ROS), Ca2+, and nitric oxide (NO) when heat-stressed, which transmit and amplify the heat stimulation signal through intracellular signal transduction pathways. Through regulation of some transcription factors including heat response factors (HSFs), POZCP26 and MYB, macrofungi respond to heat stress by different mechanisms. In this paper, we present mechanisms used by macrofungi to adapt and survive under heat stress conditions, including antioxidant defense systems that eliminate the excess ROS, increase in trehalose levels that prevent enzymes and proteins deformation, and stabilize cell structures and heat shock proteins (HSPs) that repair damaged proteins and synthesis of auxins, which increase the activity of antioxidant enzymes. All of these help macrofungi resist and adapt to heat stress. KEY POINTS: • The effects of heat stress on macrofungal growth and development were described. • The respond mechanisms to heat stress in macrofungi were summarized. • The further research directions of heat stress in macrofungi were discussed.
Collapse
Affiliation(s)
- Lu Luo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuhui Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junyue Wu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueyan Sun
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Agro-Microbial Resources and Utilization, Ministry of Agriculture, Wuhan, 430070, China.
| |
Collapse
|
19
|
Krah F, Hess J, Hennicke F, Kar R, Bässler C. Transcriptional response of mushrooms to artificial sun exposure. Ecol Evol 2021; 11:10538-10546. [PMID: 34367595 PMCID: PMC8328440 DOI: 10.1002/ece3.7862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/18/2021] [Accepted: 06/17/2021] [Indexed: 01/08/2023] Open
Abstract
Climate change causes increased tree mortality leading to canopy loss and thus sun-exposed forest floors. Sun exposure creates extreme temperatures and radiation, with potentially more drastic effects on forest organisms than the current increase in mean temperature. Such conditions might potentially negatively affect the maturation of mushrooms of forest fungi. A failure of reaching maturation would mean no sexual spore release and, thus, entail a loss of genetic diversity. However, we currently have a limited understanding of the quality and quantity of mushroom-specific molecular responses caused by sun exposure. Thus, to understand the short-term responses toward enhanced sun exposure, we exposed mushrooms of the wood-inhabiting forest species Lentinula edodes, while still attached to their mycelium and substrate, to artificial solar light (ca. 30°C and 100,000 lux) for 5, 30, and 60 min. We found significant differentially expressed genes at 30 and 60 min. Eukaryotic Orthologous Groups (KOG) class enrichment pointed to defense mechanisms. The 20 most significant differentially expressed genes showed the expression of heat-shock proteins, an important family of proteins under heat stress. Although preliminary, our results suggest mushroom-specific molecular responses to tolerate enhanced sun exposure as expected under climate change. Whether mushroom-specific molecular responses are able to maintain fungal fitness under opening forest canopies remains to be tested.
Collapse
Affiliation(s)
- Franz‐Sebastian Krah
- Conservation BiologyInstitute for Ecology, Evolution and DiversityFaculty of Biological SciencesGoethe University FrankfurtFrankfurt am MainGermany
| | - Jaqueline Hess
- Department of Soil EcologyUFZ Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
| | - Florian Hennicke
- Conservation BiologyInstitute for Ecology, Evolution and DiversityFaculty of Biological SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Project Group Genetics and Genomics of FungiChair Evolution of Plants and FungiRuhr‐University Bochum (RUB)BochumGermany
| | - Ritwika Kar
- Centre for Plant Molecular Biology, Developmental GeneticsUniversity of TübingenTübingenGermany
| | - Claus Bässler
- Conservation BiologyInstitute for Ecology, Evolution and DiversityFaculty of Biological SciencesGoethe University FrankfurtFrankfurt am MainGermany
- Bavarian Forest National ParkGrafenauGermany
| |
Collapse
|
20
|
Orban A, Weber A, Herzog R, Hennicke F, Rühl M. Transcriptome of different fruiting stages in the cultivated mushroom Cyclocybe aegerita suggests a complex regulation of fruiting and reveals enzymes putatively involved in fungal oxylipin biosynthesis. BMC Genomics 2021; 22:324. [PMID: 33947322 PMCID: PMC8097960 DOI: 10.1186/s12864-021-07648-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cyclocybe aegerita (syn. Agrocybe aegerita) is a commercially cultivated mushroom. Its archetypal agaric morphology and its ability to undergo its whole life cycle under laboratory conditions makes this fungus a well-suited model for studying fruiting body (basidiome, basidiocarp) development. To elucidate the so far barely understood biosynthesis of fungal volatiles, alterations in the transcriptome during different developmental stages of C. aegerita were analyzed and combined with changes in the volatile profile during its different fruiting stages. RESULTS A transcriptomic study at seven points in time during fruiting body development of C. aegerita with seven mycelial and five fruiting body stages was conducted. Differential gene expression was observed for genes involved in fungal fruiting body formation showing interesting transcriptional patterns and correlations of these fruiting-related genes with the developmental stages. Combining transcriptome and volatilome data, enzymes putatively involved in the biosynthesis of C8 oxylipins in C. aegerita including lipoxygenases (LOXs), dioxygenases (DOXs), hydroperoxide lyases (HPLs), alcohol dehydrogenases (ADHs) and ene-reductases could be identified. Furthermore, we were able to localize the mycelium as the main source for sesquiterpenes predominant during sporulation in the headspace of C. aegerita cultures. In contrast, changes in the C8 profile detected in late stages of development are probably due to the activity of enzymes located in the fruiting bodies. CONCLUSIONS In this study, the combination of volatilome and transcriptome data of C. aegerita revealed interesting candidates both for functional genetics-based analysis of fruiting-related genes and for prospective enzyme characterization studies to further elucidate the so far barely understood biosynthesis of fungal C8 oxylipins.
Collapse
Affiliation(s)
- Axel Orban
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany
| | - Annsophie Weber
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany
| | - Robert Herzog
- International Institute Zittau, Technical University Dresden, 02763, Zittau, Saxony, Germany
| | - Florian Hennicke
- Project Group Genetics and Genomics of Fungi, Ruhr-University Bochum, Chair Evolution of Plants and Fungi, 44780, Bochum, North Rhine-Westphalia, Germany.
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany. .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME Branch for Bioresources, 35392, Giessen, Hesse, Germany.
| |
Collapse
|