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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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Zhang Y, He Y, Huang J, Chen J, Jia X, Peng X. Dimorphism of Candida tropicalis and its effect on nitrogen and phosphorus removal and sludge settleability. BIORESOURCE TECHNOLOGY 2023; 382:129186. [PMID: 37201869 DOI: 10.1016/j.biortech.2023.129186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/10/2023] [Accepted: 05/14/2023] [Indexed: 05/20/2023]
Abstract
Candida tropicalis PNY, a novel dimorphic strain with the capacity of simultaneous carbon, nitrogen and phosphorus removal in anaerobic and aerobic conditions, was isolated from activated sludge. Dimorphism of C. tropicalis PNY had effect on removing nitrogen and phosphorous and slightly affected COD removal under aerobic condition. Sample with high hypha formation rate (40 ± 5%) had more removal efficiencies of NH4+-N (50 mg/L) and PO43--P (10 mg/L), which could achieve 82.19% and 97.53%, respectively. High hypha cells dosage exhibited good settleability and filamentous overgrowth was not observed. According to label-free quantitative proteomics assays. Up-regulated proteins involved in the mitogen-activated protein kinase (MAPK) pathway indicated the active growth and metabolism process of sample with high hypha formation rate (40 ± 5%). And proteins concerning about glutamate synthetase and SPX domain-contain protein explain for the nutrient removal mechanism including assimilation of ammonia and polyphosphates synthesis.
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Affiliation(s)
- Yaqi Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuzhe He
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingfei Huang
- College of Plant Protection, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China.
| | - Jiejing Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoshan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
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A Special Phenotype of Aconidial Aspergillus niger SH2 and Its Mechanism of Formation via CRISPRi. J Fungi (Basel) 2022; 8:jof8070679. [PMID: 35887436 PMCID: PMC9319794 DOI: 10.3390/jof8070679] [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: 05/24/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
The complex morphological structure of Aspergillus niger influences its production of proteins, metabolites, etc., making the genetic manipulation and clonal purification of this species increasingly difficult, especially in aconidial Aspergillus niger. In this study, we found that N-acetyl-D-glucosamine (GlcNAc) could induce the formation of spore-like propagules in the aconidial Aspergillus niger SH2 strain. The spore-like propagules possessed life activities such as drug resistance, genetic transformation, and germination. Transcriptomic analysis indicated that the spore-like propagules were resting conidia entering dormancy and becoming more tolerant to environmental stresses. The Dac1 gene and the metabolic pathway of GlcNAc converted to glycolysis are related to the formation of the spore-like propagules, as evidenced by the CRISPRi system, qPCR, and semi-quantitative RT-PCR. Moreover, a method based on the CRISPR-Cas9 tool to rapidly recycle screening tags and recover genes was suitable for Aspergillus niger SH2. To sum up, this suggests that the spore-like propagules are resting conidia and the mechanism of their formation is the metabolic pathway of GlcNAc converted to glycolysis, particularly the Dac1 gene. This study can improve our understanding of the critical factors involved in mechanisms of phenotypic change and provides a good model for researching phenotypic change in filamentous fungi.
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Lew SQ, Lin CH. N-acetylglucosamine-mediated morphological transition in Candida albicans and Candida tropicalis. Curr Genet 2021; 67:249-254. [PMID: 33388851 DOI: 10.1007/s00294-020-01138-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
Morphological transitions in Candida species are key factors in facilitating invasion and adapting to environmental changes. N-acetylglucosamine (GlcNAc) is a monosaccharide signalling molecule that can regulate morphological transitions in Candida albicans and Candida tropicalis. Interestingly, although the uptake and metabolic pathways of GlcNAc and GlcNAc-mediated white-to-opaque cell switching are similar between the two Candida species, GlcNAc induces hyphal development in C. albicans, whereas it suppresses hyphal development in C. tropicalis. These findings indicate that the characteristics of C. albicans and C. tropicalis in response to GlcNAc are remarkably different. Here, we compare the conserved and divergent GlcNAc-mediated signalling pathways and catabolism between the two Candida species. Deletion of NGT1, a GlcNAc transportation gene, inhibited hyphal formation in C. albicans but promoted hyphal development in C. tropicalis. To further understand these opposite effects on filamentous growth in response to GlcNAc in the two Candida species, the cyclic adenosine monophosphate/protein kinase A (cAMP/PKA) signalling pathways in both C. albicans and C. tropicalis were compared. Interestingly, GlcNAc activated the cAMP/PKA signalling pathway of the two Candida species, suggesting that the hyphal development-regulated circuit is remarkably diverse between the two species. Indeed, the Ndt80-like gene REP1, which is critical for regulating GlcNAc catabolism, exhibits distinct roles in the hyphal development of C. albicans and C. tropicalis. These data suggest possible reasons for the divergent hyphal growth response in C. albicans and C. tropicalis upon GlcNAc induction.
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Affiliation(s)
- Shi Qian Lew
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ching-Hsuan Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan.
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