1
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Nowrousian M. The Role of Chromatin and Transcriptional Control in the Formation of Sexual Fruiting Bodies in Fungi. Microbiol Mol Biol Rev 2022; 86:e0010422. [PMID: 36409109 PMCID: PMC9769939 DOI: 10.1128/mmbr.00104-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fungal fruiting bodies are complex, three-dimensional structures that arise from a less complex vegetative mycelium. Their formation requires the coordinated action of many genes and their gene products, and fruiting body formation is accompanied by major changes in the transcriptome. In recent years, numerous transcription factor genes as well as chromatin modifier genes that play a role in fruiting body morphogenesis were identified, and through research on several model organisms, the underlying regulatory networks that integrate chromatin structure, gene expression, and cell differentiation are becoming clearer. This review gives a summary of the current state of research on the role of transcriptional control and chromatin structure in fruiting body development. In the first part, insights from transcriptomics analyses are described, with a focus on comparative transcriptomics. In the second part, examples of more detailed functional characterizations of the role of chromatin modifiers and/or transcription factors in several model organisms (Neurospora crassa, Aspergillus nidulans, Sordaria macrospora, Coprinopsis cinerea, and Schizophyllum commune) that have led to a better understanding of regulatory networks at the level of chromatin structure and transcription are discussed.
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Affiliation(s)
- Minou Nowrousian
- Department of Molecular and Cellular Botany, Ruhr University Bochum, Bochum, Germany
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2
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Wilson AM, Wingfield MJ, Wingfield BD. Truncation of MAT1-2-7 Deregulates Developmental Pathways Associated with Sexual Reproduction in Huntiella omanensis. Microbiol Spectr 2022; 10:e0142522. [PMID: 36154282 PMCID: PMC9602353 DOI: 10.1128/spectrum.01425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/07/2022] [Indexed: 12/30/2022] Open
Abstract
The MAT1-1-1 and MAT1-2-1 genes are thought to be the master regulators of sexual development in most ascomycete fungi, and they are often essential for this process. In contrast, it has been suggested that the secondary mating-type genes act to calibrate the sexual cycle and can be dispensable. Recent functional characterization of genes such as Aspergillus fumigatus MAT1-2-4, Huntiella omanensis MAT1-2-7, and Botrytis cinerea MAT1-1-5 has, however, shown that these secondary genes may play more central roles in the sexual pathway and are essential for the production of mature fruiting structures. We used a comparative transcriptome sequencing (RNA-seq) experiment to show that the truncation of MAT1-2-7 in the wood inhabiting H. omanensis residing in the Ceratocystidaceae is associated with the differential expression of approximately 25% of all the genes present in the genome, including the transcriptional regulators ste12, wc-2, sub1, VeA, HMG8, and pro1. This suggests that MAT1-2-7 may act as a transcription factor and that ΔMAT1-2-7 mutant sterility is the result of layered deregulation of a variety of signaling and developmental pathways. This study is one of only a few that details the functional characterization of a secondary MAT gene in a nonmodel species. Given that this gene is present in other Ceratocystidaceae species and that there are diverse secondary MAT genes present throughout the Pezizomycotina, further investigation into this gene and others like it will provide a clearer understanding of sexual development in these eukaryotes. IMPORTANCE Secondary mating-type genes are being described almost as quickly as new fungal genomes are being sequenced. Understanding the functions of these genes has lagged behind their description, in part due to limited taxonomic distribution, lack of conserved functional domains, and difficulties with regard to genetic manipulation protocols. This study aimed to address this by investigating a novel mating-type gene, MAT1-2-7, for which two independent mutant strains were generated in a previous study. We characterized the molecular response to the truncation of this gene in a nonmodel, wood-infecting fungus and showed that it resulted in widespread differential expression throughout the transcriptome of this fungus. This suggests that secondary MAT genes may play a more important role than previously thought. This study also emphasizes the need for further research into the life cycles of nonmodel fungi, which often exhibit unique features that are very different from the systems understood from model species.
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Affiliation(s)
- A. M. Wilson
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
| | - M. J. Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
| | - B. D. Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
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3
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Wilson AM, Wilken PM, Wingfield MJ, Wingfield BD. Genetic Networks That Govern Sexual Reproduction in the Pezizomycotina. Microbiol Mol Biol Rev 2021; 85:e0002021. [PMID: 34585983 PMCID: PMC8485983 DOI: 10.1128/mmbr.00020-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Sexual development in filamentous fungi is a complex process that relies on the precise control of and interaction between a variety of genetic networks and pathways. The mating-type (MAT) genes are the master regulators of this process and typically act as transcription factors, which control the expression of genes involved at all stages of the sexual cycle. In many fungi, the sexual cycle typically begins when the mating pheromones of one mating type are recognized by a compatible partner, followed by physical interaction and fertilization. Subsequently, highly specialized sexual structures are formed, within which the sexual spores develop after rounds of meiosis and mitosis. These spores are then released and germinate, forming new individuals that initiate new cycles of growth. This review provides an overview of the known genetic networks and pathways that are involved in each major stage of the sexual cycle in filamentous ascomycete fungi.
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Affiliation(s)
- Andi M. Wilson
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - P. Markus Wilken
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Michael J. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Brenda D. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Benites LF, Bucchini F, Sanchez-Brosseau S, Grimsley N, Vandepoele K, Piganeau G. Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage. Genome Biol Evol 2021; 13:6380139. [PMID: 34599324 PMCID: PMC8557840 DOI: 10.1093/gbe/evab216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2021] [Indexed: 12/11/2022] Open
Abstract
Although sex is now accepted as a ubiquitous and ancestral feature of eukaryotes, direct observation of sex is still lacking in most unicellular eukaryotic lineages. Evidence of sex is frequently indirect and inferred from the identification of genes involved in meiosis from whole genome data and/or the detection of recombination signatures from genetic diversity in natural populations. In haploid unicellular eukaryotes, sex-related chromosomes are named mating-type (MTs) chromosomes and generally carry large genomic regions where recombination is suppressed. These regions have been characterized in Fungi and Chlorophyta and determine gamete compatibility and fusion. Two candidate MT+ and MT− alleles, spanning 450–650 kb, have recently been described in Ostreococcus tauri, a marine phytoplanktonic alga from the Mamiellophyceae class, an early diverging branch in the green lineage. Here, we investigate the architecture and evolution of these candidate MT+ and MT− alleles. We analyzed the phylogenetic profile and GC content of MT gene families in eight different genomes whose divergence has been previously estimated at up to 640 Myr, and found evidence that the divergence of the two MT alleles predates speciation in the Ostreococcus genus. Phylogenetic profiles of MT trans-specific polymorphisms in gametologs disclosed candidate MTs in two additional species, and possibly a third. These Mamiellales MT candidates are likely to be the oldest mating-type loci described to date, which makes them fascinating models to investigate the evolutionary mechanisms of haploid sex determination in eukaryotes.
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Affiliation(s)
- Luis Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Sophie Sanchez-Brosseau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Belgium
| | - Gwenaël Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, Banyuls-sur-Mer, France
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Abstract
True morels (Morchella spp., Morchellaceae, Ascomycota) are widely regarded as a highly prized delicacy and are of great economic and scientific value. Recently, the rapid development of cultivation technology and expansion of areas for artificial morel cultivation have propelled morel research into a hot topic. Many studies have been conducted in various aspects of morel biology, but despite this, cultivation sites still frequently report failure to fruit or only low production of fruiting bodies. Key problems include the gap between cultivation practices and basic knowledge of morel biology. In this review, in an effort to highlight the mating systems, evolution, and life cycle of morels, we summarize the current state of knowledge of morel sexual reproduction, the structure and evolution of mating-type genes, the sexual process itself, and the influence of mating-type genes on the asexual stages and conidium production. Understanding of these processes is critical for improving technology for the cultivation of morels and for scaling up their commercial production. Morel species may well be good candidates as model species for improving sexual development research in ascomycetes in the future.
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Wilken SE, Seppälä S, Lankiewicz TS, Saxena M, Henske JK, Salamov AA, Grigoriev IV, O’Malley MA. Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi. Metab Eng Commun 2020; 10:e00107. [PMID: 31799118 PMCID: PMC6883316 DOI: 10.1016/j.mec.2019.e00107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022] Open
Abstract
Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi.
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Affiliation(s)
- St. Elmo Wilken
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
- Department of Evolution Ecology and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Mohan Saxena
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - John K. Henske
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Asaf A. Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
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7
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Schoch CL, Crous PW, Witthuhn RC, Cronwright G, El-Gholl NE, Wingfield BD. Recombination in Calonectria morganii and phylogeny with other heterothallic small-spored Calonectria species. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Conrad L. Schoch
- Department of Plant Pathology, University of Stellenbosch, P. Bag XI, Matieland 7602, South Africa
| | - Pedro W. Crous
- Department of Plant Pathology, University of Stellenbosch, P. Bag XI, Matieland 7602, South Africa
| | - R. Corlia Witthuhn
- Department of Plant Pathology, University of Stellenbosch, P. Bag XI, Matieland 7602, South Africa
| | - Garth Cronwright
- Department of Genetics, University of Stellenbosch, P. Bag XI, Matieland 7602, South Africa
| | - Nabih E. El-Gholl
- Florida Department of Agricultural Consumer Services, Division of Plant Industry, P.O. Box 147100, Gainesville, Florida, USA 32614-7100
| | - Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
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8
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It's All in the Genes: The Regulatory Pathways of Sexual Reproduction in Filamentous Ascomycetes. Genes (Basel) 2019; 10:genes10050330. [PMID: 31052334 PMCID: PMC6562746 DOI: 10.3390/genes10050330] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 12/23/2022] Open
Abstract
Sexual reproduction in filamentous ascomycete fungi results in the production of highly specialized sexual tissues, which arise from relatively simple, vegetative mycelia. This conversion takes place after the recognition of and response to a variety of exogenous and endogenous cues, and relies on very strictly regulated gene, protein, and metabolite pathways. This makes studying sexual development in fungi an interesting tool in which to study gene-gene, gene-protein, and protein-metabolite interactions. This review provides an overview of some of the most important genes involved in this process; from those involved in the conversion of mycelia into sexually-competent tissue, to those involved in the development of the ascomata, the asci, and ultimately, the ascospores.
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9
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Almeida-Silva F, Barbedo LS, Taylor ML, Muniz MDM, Guimarães AJ, Zancopé-Oliveira RM. Multiplex polymerase chain reaction as an improved method for screening Histoplasma capsulatum mating types. Mem Inst Oswaldo Cruz 2018; 113:e180340. [PMID: 30231112 PMCID: PMC6140378 DOI: 10.1590/0074-02760180340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/17/2018] [Indexed: 12/04/2022] Open
Abstract
Histoplasmosis is a systemic mycosis infection caused by Histoplasma capsulatum, a heterothallic ascomycete. The sexual reproduction of this fungus is regulated by the mating type (MAT1) locus that contains MAT1-1 and MAT1-2 idiomorphs, which were identified by uniplex polymerase chain reaction (PCR). This study aimed to optimise single-step multiplex PCR for the accurate detection of the distinct mating types of H. capsulatum. Among the 26 isolates tested, 20 had MAT1-1 genotype, while six showed MAT1-2 genotype, in agreement with the uniplex PCR results. These results suggest that multiplex PCR is a fast and specific tool for screening H. capsulatum mating types.
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Affiliation(s)
- Fernando Almeida-Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil
| | - Leonardo Silva Barbedo
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil.,Universidade Federal do Amazonas, Instituto de Saúde e Biotecnologia, Coari, AM, Brasil
| | - Maria Lucia Taylor
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Microbiología-Parasitología, DF, México
| | - Mauro de Medeiros Muniz
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil
| | - Allan Jefferson Guimarães
- Universidade Federal Fluminense, Instituto Biomédico, Departamento de Microbiologia e Parasitologia, Niterói, RJ, Brasil
| | - Rosely Maria Zancopé-Oliveira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Micologia, Setor de Imunodiagnóstico, Rio de Janeiro, RJ, Brasil
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10
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Wallen RM, Perlin MH. An Overview of the Function and Maintenance of Sexual Reproduction in Dikaryotic Fungi. Front Microbiol 2018; 9:503. [PMID: 29619017 PMCID: PMC5871698 DOI: 10.3389/fmicb.2018.00503] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Sexual reproduction likely evolved as protection from environmental stresses, specifically, to repair DNA damage, often via homologous recombination. In higher eukaryotes, meiosis and the production of gametes with allelic combinations different from parental type provides the side effect of increased genetic variation. In fungi it appears that while the maintenance of meiosis is paramount for success, outcrossing is not a driving force. In the subkingdom Dikarya, fungal members are characterized by existence of a dikaryon for extended stages within the life cycle. Such fungi possess functional or, in some cases, relictual, loci that govern sexual reproduction between members of their own species. All mating systems identified so far in the Dikarya employ a pheromone/receptor system for haploid organisms to recognize a compatible mating partner, although the paradigm in the Ascomycota, e.g., Saccharomyces cerevisiae, is that genes for the pheromone precursor and receptor are not found in the mating-type locus but rather are regulated by its products. Similarly, the mating systems in the Ascomycota are bipolar, with two non-allelic idiomorphs expressed in cells of opposite mating type. In contrast, for the Basidiomycota, both bipolar and tetrapolar mating systems have been well characterized; further, at least one locus directly encodes the pheromone precursor and the receptor for the pheromone of a different mating type, while a separate locus encodes proteins that may regulate the first locus and/or additional genes required for downstream events. Heterozygosity at both of two unlinked loci is required for cells to productively mate in tetrapolar systems, whereas in bipolar systems the two loci are tightly linked. Finally, a trade-off exists in wild fungal populations between sexual reproduction and the associated costs, with adverse conditions leading to mating. For fungal mammal pathogens, the products of sexual reproduction can be targets for the host immune system. The opposite appears true for phytopathogenic fungi, where mating and pathogenicity are inextricably linked. Here, we explore, compare, and contrast different strategies used among the Dikarya, both saprophytic and pathogenic fungi, and highlight differences between pathogens of mammals and pathogens of plants, providing context for selective pressures acting on this interesting group of fungi.
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Affiliation(s)
| | - Michael H. Perlin
- Department of Biology, University of Louisville, Louisville, KY, United States
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Wilken PM, Steenkamp ET, van der Nest MA, Wingfield MJ, de Beer ZW, Wingfield BD. Unexpected placement of the MAT1-1-2 gene in the MAT1-2 idiomorph of Thielaviopsis. Fungal Genet Biol 2018; 113:32-41. [PMID: 29409964 DOI: 10.1016/j.fgb.2018.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 01/20/2018] [Accepted: 01/29/2018] [Indexed: 01/24/2023]
Abstract
Sexual reproduction in the Ascomycota is controlled by genes encoded at the mating-type or MAT1 locus. The two allelic versions of this locus in heterothallic species, referred to as idiomorphs, are defined by the MAT1-1-1 (for the MAT1-1 idiomorph) and MAT1-2-1 (for the MAT1-2 idiomorph) genes. Both idiomorphs can contain additional genes, although the contents of each is typically specific to and conserved within particular Pezizomycotina lineages. Using full genome sequences, complemented with conventional PCR and Sanger sequencing, we compared the mating-type idiomorphs in heterothallic species of Thielaviopsis (Ceratocystidaceae). The analyses showed that the MAT1-1 idiomorph of T. punctulata, T. paradoxa, T. euricoi, T. ethacetica and T. musarum harboured only the expected MAT1-1-1 gene. In contrast, the MAT1-2 idiomorph of T. punctulata, T. paradoxa and T. euricoi encoded the MAT1-2-1, MAT1-2-7 and MAT1-1-2 genes. Of these, MAT1-2-1 and MAT1-2-7 are genes previously reported in this idiomorph, while MAT1-1-2 is known only in the MAT1-1 idiomorph. Phylogenetic analysis showed that the Thielaviopsis MAT1-1-2 groups with the known homologues of this gene in other Microascales, thus confirming its annotation. Previous work suggests that MAT1-1-2 is involved in fruiting body development, a role that would be unaffected by its idiomorphic position. This notion is supported by our findings for the MAT1 locus structure in Thielaviopsis species. This also serves as the first example of a MAT1-1-specific gene restricted to only the MAT1-2 idiomorph.
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Affiliation(s)
- P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa.
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Magriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
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12
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Wilken PM, Steenkamp ET, Wingfield MJ, de Beer ZW, Wingfield BD. Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2017.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Genetic Variation and Its Reflection on Posttranslational Modifications in Frequency Clock and Mating Type a-1 Proteins in Sordaria fimicola. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1268623. [PMID: 28717646 PMCID: PMC5499255 DOI: 10.1155/2017/1268623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/24/2017] [Accepted: 04/05/2017] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) occur in all essential proteins taking command of their functions. There are many domains inside proteins where modifications take place on side-chains of amino acids through various enzymes to generate different species of proteins. In this manuscript we have, for the first time, predicted posttranslational modifications of frequency clock and mating type a-1 proteins in Sordaria fimicola collected from different sites to see the effect of environment on proteins or various amino acids pickings and their ultimate impact on consensus sequences present in mating type proteins using bioinformatics tools. Furthermore, we have also measured and walked through genomic DNA of various Sordaria strains to determine genetic diversity by genotyping the short sequence repeats (SSRs) of wild strains of S. fimicola collected from contrasting environments of two opposing slopes (harsh and xeric south facing slope and mild north facing slope) of Evolution Canyon (EC), Israel. Based on the whole genome sequence of S. macrospora, we targeted 20 genomic regions in S. fimicola which contain short sequence repeats (SSRs). Our data revealed genetic variations in strains from south facing slope and these findings assist in the hypothesis that genetic variations caused by stressful environments lead to evolution.
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Aylward J, Steenkamp ET, Dreyer LL, Roets F, Wingfield MJ, Wingfield BD. Genetic basis for high population diversity in Protea-associated Knoxdaviesia. Fungal Genet Biol 2016; 96:47-57. [DOI: 10.1016/j.fgb.2016.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/12/2016] [Accepted: 10/04/2016] [Indexed: 11/25/2022]
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15
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Corcoran P, Anderson JL, Jacobson DJ, Sun Y, Ni P, Lascoux M, Johannesson H. Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma. Genome Res 2016; 26:486-98. [PMID: 26893460 PMCID: PMC4817772 DOI: 10.1101/gr.197244.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/16/2016] [Indexed: 01/01/2023]
Abstract
Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of nondegenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes.We found that suppressed recombination extends across at least 6 Mbp (∼ 63%) of the mating-type (mat) chromosome in N. tetrasperma and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six of eight lineages show introgression into one of their mat chromosomes, with multiple Neurospora species acting as donors. The introgressed tracts have been fixed within lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one lineage. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.
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Affiliation(s)
- Pádraic Corcoran
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden; Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jennifer L Anderson
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - David J Jacobson
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Yu Sun
- Department of Cell and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden
| | | | - Martin Lascoux
- Department of Ecology and Genetics, Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
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16
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Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW. Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta. Mol Ecol 2015; 24:5657-75. [PMID: 26453896 DOI: 10.1111/mec.13417] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/30/2022]
Abstract
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.
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Affiliation(s)
- Pierre Gladieux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecologie Systematique Evolution, Université Paris Sud, Batiment 360, 91405, Orsay, France
| | | | - Fanny Perraudeau
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecole Polytechnique, Route de Saclay, 91128, Palaiseau, France
| | - Liliam A Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Monika Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Iman Sylvain
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David J Jacobson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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17
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Alexander WG, Peris D, Pfannenstiel BT, Opulente DA, Kuang M, Hittinger CT. Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces. Fungal Genet Biol 2015; 89:10-17. [PMID: 26555931 DOI: 10.1016/j.fgb.2015.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 01/19/2023]
Abstract
Saccharomyces interspecies hybrids are critical biocatalysts in the fermented beverage industry, including in the production of lager beers, Belgian ales, ciders, and cold-fermented wines. Current methods for making synthetic interspecies hybrids are cumbersome and/or require genome modifications. We have developed a simple, robust, and efficient method for generating allotetraploid strains of prototrophic Saccharomyces without sporulation or nuclear genome manipulation. S. cerevisiae×S. eubayanus, S. cerevisiae×S. kudriavzevii, and S. cerevisiae×S. uvarum designer hybrid strains were created as synthetic lager, Belgian, and cider strains, respectively. The ploidy and hybrid nature of the strains were confirmed using flow cytometry and PCR-RFLP analysis, respectively. This method provides an efficient means for producing novel synthetic hybrids for beverage and biofuel production, as well as for constructing tetraploids to be used for basic research in evolutionary genetics and genome stability.
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Affiliation(s)
- William G Alexander
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Brandon T Pfannenstiel
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Meihua Kuang
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, United States; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, United States; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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18
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Wilson AM, Wilken PM, van der Nest MA, Steenkamp ET, Wingfield MJ, Wingfield BD. Homothallism: an umbrella term for describing diverse sexual behaviours. IMA Fungus 2015. [PMID: 26203424 PMCID: PMC4500084 DOI: 10.5598/imafungus.2015.06.01.13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sexual reproduction is notoriously complex in fungi with species able to produce sexual progeny by utilizing a variety of different mechanisms. This is even more so for species employing multiple sexual strategies, which is a surprisingly common occurrence. While heterothallism is relatively well understood in terms of its physiological and molecular underpinnings, homothallism remains greatly understudied. This can be attributed to it involving numerous genetically distinct mechanisms that all result in self-fertility; including primary homothallism, pseudohomothallism, mating type switching, and unisexual reproduction. This review highlights the need to classify these homothallic mechanisms based on their molecular determinants and illustrates what is currently known about the multifaceted behaviours associated with homothallism.
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Affiliation(s)
- Andrea M Wilson
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, South Africa, 0028
| | - P Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, South Africa, 0028
| | - Magriet A van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, South Africa, 0028
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, South Africa, 0028
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria, South Africa, 0028
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19
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Wilson AM, Godlonton T, van der Nest MA, Wilken PM, Wingfield MJ, Wingfield BD. Unisexual reproduction in Huntiella moniliformis. Fungal Genet Biol 2015; 80:1-9. [PMID: 25910452 DOI: 10.1016/j.fgb.2015.04.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/10/2015] [Accepted: 04/11/2015] [Indexed: 01/08/2023]
Abstract
Sexual reproduction in fungi is controlled by genes present at the mating type (MAT) locus, which typically harbors transcription factors that influence the expression of many sex-related genes. The MAT locus exists as two alternative idiomorphs in ascomycetous fungi and sexual reproduction is initiated when genes from both idiomorphs are expressed. Thus, the gene content of this locus determines whether a fungus is heterothallic (self-sterile) or homothallic (self-fertile). Recently, a unique sub-class of homothallism has been described in fungi, where individuals possessing a single MAT idiomorph can reproduce sexually in the absence of a partner. Using various mycological, molecular and bioinformatic techniques, we investigated the sexual strategies and characterized the MAT loci in two tree wound-infecting fungi, Huntiella moniliformis and Huntiella omanensis. H. omanensis was shown to exhibit a typically heterothallic sexual reproductive cycle, with isolates possessing either the MAT1-1 or MAT1-2 idiomorph. This was in contrast to the homothallism via unisexual reproduction that was shown in H. moniliformis, where only the MAT1-2-1 gene was present in sexually reproducing cultures. While the evolutionary benefit and mechanisms underpinning a unisexual mating strategy remain unknown, it could have evolved to minimize the costs, while retaining the benefits, of normal sexual reproduction.
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Affiliation(s)
- A M Wilson
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - T Godlonton
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - M A van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - P M Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - M J Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa
| | - B D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa.
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20
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Böhm J, Dahlmann TA, Gümüşer H, Kück U. A MAT1-2 wild-type strain from Penicillium chrysogenum: functional mating-type locus characterization, genome sequencing and mating with an industrial penicillin-producing strain. Mol Microbiol 2015; 95:859-74. [PMID: 25521009 PMCID: PMC4357460 DOI: 10.1111/mmi.12909] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2014] [Indexed: 01/07/2023]
Abstract
In heterothallic ascomycetes, mating is controlled by two nonallelic idiomorphs that determine the 'sex' of the corresponding strains. We recently discovered mating-type loci and a sexual life cycle in the penicillin-producing fungus, Penicillium chrysogenum. All industrial penicillin production strains worldwide are derived from a MAT1-1 isolate. No MAT1-2 strain has been investigated in detail until now. Here, we provide the first functional analysis of a MAT1-2 locus from a wild-type strain. Similar to MAT1-1, the MAT1-2 locus has functions beyond sexual development. Unlike MAT1-1, the MAT1-2 locus affects germination and surface properties of conidiospores and controls light-dependent asexual sporulation. Mating of the MAT1-2 wild type with a MAT1-1 high penicillin producer generated sexual spores. We determined the genomic sequences of parental and progeny strains using next-generation sequencing and found evidence for genome-wide recombination. SNP calling showed that derived industrial strains had an uneven distribution of point mutations compared with the wild type. We found evidence for meiotic recombination in all chromosomes. Our results point to a strategy combining the use of mating-type genes, genetics, and next-generation sequencing to optimize conventional strain improvement methods.
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Affiliation(s)
- Julia Böhm
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Tim A Dahlmann
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Hendrik Gümüşer
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Ulrich Kück
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
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21
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Vegetative incompatibility loci with dedicated roles in allorecognition restrict mycovirus transmission in chestnut blight fungus. Genetics 2014; 197:701-14. [PMID: 24690544 DOI: 10.1534/genetics.114.164574] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vegetative incompatibility (vic), a form of nonself allorecognition, operates widely in filamentous fungi and restricts transmission of virulence-attenuating hypoviruses in the chestnut blight fungus Cryphonectria parasitica. We report here the use of a polymorphism-based comparative genomics approach to complete the molecular identification of the genetically defined C. parasitica vic loci with the identification of vic1 and vic3. The vic1 locus in the C. parasitica reference strain EP155 consists of a polymorphic HET-domain-containing 771-aa ORF designated vic1a-2, which shares 91% identity with the corresponding vic1a-1 allele, and a small (172 aa) idiomorphic DUF1909-domain-containing ORF designated vic1b-2 that is absent at the vic1-1 locus. Gene disruption of either vic1a-2 or vic1b-2 in strain EP155 eliminated restrictions on virus transmission when paired with a vic1 heteroallelic strain; however, only disruption of vic1a-2 abolished the incompatible programmed cell death (PCD) reaction. The vic3 locus of strain EP155 contains two polymorphic ORFs of 599 aa (vic3a-1) and 102 aa (vic3b-1) that shared 46 and 85% aa identity with the corresponding vic3a-2 and vic3b-2 alleles, respectively. Disruption of either vic3a-1 or vic3b-1 resulted in increased virus transmission. However, elimination of PCD required disruption of both vic3a and vic3b. Additional allelic heterogeneity included a sequence inversion and a 8.5-kb insertion containing a LTR retrotransposon sequence and an adjacent HET-domain gene at the vic1 locus and a 7.7-kb sequence deletion associated with a nonfunctional, pseudo vic locus. Combined gene disruption studies formally confirmed restriction of mycovirus transmission by five C. parasitica vic loci and suggested dedicated roles in allorecognition. The relevance of these results to the acquisition and maintenance of vic genes and the potential for manipulation of vic alleles for enhanced mycovirus transmission are discussed.
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22
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Van der Nest MA, Olson A, Lind M, Vélëz H, Dalman K, Brandström Durling M, Karlsson M, Stenlid J. Distribution and evolution of het gene homologs in the basidiomycota. Fungal Genet Biol 2013; 64:45-57. [PMID: 24380733 DOI: 10.1016/j.fgb.2013.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/04/2013] [Accepted: 12/20/2013] [Indexed: 12/24/2022]
Abstract
In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.
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Affiliation(s)
- M A Van der Nest
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden.
| | - A Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Lind
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - H Vélëz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - K Dalman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - M Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - J Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
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23
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Muniz MM, Sousa CN, Evangelista Oliveira MM, Pizzini CV, Almeida MA, Rodríguez-Arellanes G, Taylor ML, Zancopé-Oliveira RM. Sexual variability in Histoplasma capsulatum and its possible distribution: what is going on? Rev Iberoam Micol 2013; 31:7-10. [PMID: 24262630 DOI: 10.1016/j.riam.2013.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/01/2013] [Indexed: 11/16/2022] Open
Abstract
Histoplasma capsulatum is a dimorphic fungal pathogen naturally found in the soil. Inhalation of conidia can result in pulmonary histoplasmosis and, in some cases, causes severe disseminated disease and death. This fungus is an ascomycete that has an anamorphic or asexual stage and a teleomorphic or sexual stage, known as Ajellomyces capsulatus, which results from (+) and (-) mating types. Sexual reproduction is regulated by a specialized genomic region known as the mating-type (MAT1) locus. The mating process in this heterothallic species is represented by isolates that contain only one of the two different MAT1 locus idiomorphs (MAT1-1 or MAT1-2) that have unrelated sequences encoding different transcription factors. In medically important dimorphic pathogens and in most ascomycete molds, one MAT locus idiomorph encodes a high-mobility-group (HMG) box-domain transcription factor, and the other idiomorph encodes an alpha-box domain transcription factor. There is scarce molecular information about H. capsulatum mating type although recombinant population structures have been reported that could occur in nature and this process has been documented in distinct models such as parasites and other fungi. In this review, we shall focus on published studies on H. capsulatum sexuality, and outline the distribution of the two H. capsulatum mating types in Latin America. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012).
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Affiliation(s)
- Mauro Medeiros Muniz
- Instituto de Pesquisa Clínica Evandro Chagas, IPEC/FIOCRUZ, Rio de Janeiro, Brazil.
| | | | | | - Claudia Vera Pizzini
- Instituto de Pesquisa Clínica Evandro Chagas, IPEC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Marcos Abreu Almeida
- Instituto de Pesquisa Clínica Evandro Chagas, IPEC/FIOCRUZ, Rio de Janeiro, Brazil
| | - Gabriela Rodríguez-Arellanes
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), México D.F., Mexico
| | - Maria Lucia Taylor
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), México D.F., Mexico
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24
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Ait Benkhali J, Coppin E, Brun S, Peraza-Reyes L, Martin T, Dixelius C, Lazar N, van Tilbeurgh H, Debuchy R. A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina. PLoS Genet 2013; 9:e1003642. [PMID: 23935511 PMCID: PMC3730723 DOI: 10.1371/journal.pgen.1003642] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 06/03/2013] [Indexed: 12/14/2022] Open
Abstract
High-mobility group (HMG) B proteins are eukaryotic DNA-binding proteins characterized by the HMG-box functional motif. These transcription factors play a pivotal role in global genomic functions and in the control of genes involved in specific developmental or metabolic pathways. The filamentous ascomycete Podospora anserina contains 12 HMG-box genes. Of these, four have been previously characterized; three are mating-type genes that control fertilization and development of the fruit-body, whereas the last one encodes a factor involved in mitochondrial DNA stability. Systematic deletion analysis of the eight remaining uncharacterized HMG-box genes indicated that none were essential for viability, but that seven were involved in the sexual cycle. Two HMG-box genes display striking features. PaHMG5, an ortholog of SpSte11 from Schizosaccharomyces pombe, is a pivotal activator of mating-type genes in P. anserina, whereas PaHMG9 is a repressor of several phenomena specific to the stationary phase, most notably hyphal anastomoses. Transcriptional analyses of HMG-box genes in HMG-box deletion strains indicated that PaHMG5 is at the hub of a network of several HMG-box factors that regulate mating-type genes and mating-type target genes. Genetic analyses revealed that this network also controls fertility genes that are not regulated by mating-type transcription factors. This study points to the critical role of HMG-box members in sexual reproduction in fungi, as 11 out of 12 members were involved in the sexual cycle in P. anserina. PaHMG5 and SpSte11 are conserved transcriptional regulators of mating-type genes, although P. anserina and S. pombe diverged 550 million years ago. Two HMG-box genes, SOX9 and its upstream regulator SRY, also play an important role in sex determination in mammals. The P. anserina and S. pombe mating-type genes and their upstream regulatory factor form a module of HMG-box genes analogous to the SRY/SOX9 module, revealing a commonality of sex regulation in animals and fungi. Podospora anserina, a coprophilous fungus, is used extensively as a model organism to address questions of sexual development and mating-type functions. Its mating-type locus contains three HMGB genes that encode transcription factors involved in fertilization and fruit-body development. We present the functional characterization of the remaining HMGB genes, which revealed that 11 of 12 HMGB genes were involved in sexual development. An analysis of the relationships between these genes uncovered a regulatory network governing the expression of mating-type genes. PaHMG5 is a key transcription factor that operates upstream of mating-type genes in this network. A homolog of PaHMG5 performs a similar function in the fission yeast Schizosaccharomyces pombe, which diverged from P. anserina 550 million years ago. The conservation of a regulatory circuit over such a prolonged timeframe is a striking exception to the general observation that sex developmental pathways are highly variable, even across closely related lineages. A module consisting of two HMGB transcription factors (Sry and Sox9) is a key regulator of sex determination in mammals. We propose that the module containing PaHMG5 and mating-type HMGB genes is the fungal counterpart of the mammalian module, revealing a commonality of sex regulation in animals and fungi.
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Affiliation(s)
- Jinane Ait Benkhali
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Evelyne Coppin
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Sylvain Brun
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- Université Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), Paris, France
| | - Leonardo Peraza-Reyes
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Tom Martin
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Noureddine Lazar
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Herman van Tilbeurgh
- Université Paris-Sud, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Orsay, France
| | - Robert Debuchy
- Université Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- * E-mail:
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Gioti A, Mushegian AA, Strandberg R, Stajich JE, Johannesson H. Unidirectional Evolutionary Transitions in Fungal Mating Systems and the Role of Transposable Elements. Mol Biol Evol 2012; 29:3215-26. [DOI: 10.1093/molbev/mss132] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Zaffarano PL, Queloz V, Duò A, Grünig CR. Sex in the PAC: a hidden affair in dark septate endophytes? BMC Evol Biol 2011; 11:282. [PMID: 21961933 PMCID: PMC3199270 DOI: 10.1186/1471-2148-11-282] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 09/30/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungi are asexually and sexually reproducing organisms that can combine the evolutionary advantages of the two reproductive modes. However, for many fungi the sexual cycle has never been observed in the field or in vitro and it remains unclear whether sexual reproduction is absent or cryptic. Nevertheless, there are indirect approaches to assess the occurrence of sex in a species, such as population studies, expression analysis of genes involved in mating processes and analysis of their selective constraints. The members of the Phialocephala fortinii s. l. - Acephala applanata species complex (PAC) are ascomycetes and the predominant dark septate endophytes that colonize woody plant roots. Despite their abundance in many ecosystems of the northern hemisphere, no sexual state has been identified to date and little is known about their reproductive biology, and how it shaped their evolutionary history and contributes to their ecological role in forest ecosystems. We therefore aimed at assessing the importance of sexual reproduction by indirect approaches that included molecular analyses of the mating type (MAT) genes involved in reproductive processes. RESULTS The study included 19 PAC species and > 3, 000 strains that represented populations from different hosts, continents and ecosystems. Whereas A. applanata had a homothallic (self-fertile) MAT locus structure, all other species were structurally heterothallic (self-sterile). Compatible mating types were observed to co-occur more frequently than expected by chance. Moreover, in > 80% of the populations a 1:1 mating type ratio and gametic equilibrium were found. MAT genes were shown to evolve under strong purifying selection. CONCLUSIONS The signature of sex was found in worldwide populations of PAC species and functionality of MAT genes is likely preserved by purifying selection. We hypothesize that cryptic sex regularely occurs in the PAC and that further field studies and in vitro crosses will lead to the discovery of the sexual state. Although structurally heterothallic species prevail, it cannot be excluded that homothallism represents the ancestral breeding system in the PAC.
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Affiliation(s)
- Pascal L Zaffarano
- Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zurich, 8092 Zürich, Switzerland
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Abstract
Sexual reproduction enables genetic exchange in eukaryotic organisms as diverse as fungi, animals, plants, and ciliates. Given its ubiquity, sex is thought to have evolved once, possibly concomitant with or shortly after the origin of eukaryotic organisms themselves. The basic principles of sex are conserved, including ploidy changes, the formation of gametes via meiosis, mate recognition, and cell-cell fusion leading to the production of a zygote. Although the basic tenants are shared, sex determination and sexual reproduction occur in myriad forms throughout nature, including outbreeding systems with more than two mating types or sexes, unisexual selfing, and even examples in which organisms switch mating type. As robust and diverse genetic models, fungi provide insights into the molecular nature of sex, sexual specification, and evolution to advance our understanding of sexual reproduction and its impact throughout the eukaryotic tree of life.
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Affiliation(s)
- Min Ni
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Bidard F, Aït Benkhali J, Coppin E, Imbeaud S, Grognet P, Delacroix H, Debuchy R. Genome-wide gene expression profiling of fertilization competent mycelium in opposite mating types in the heterothallic fungus Podospora anserina. PLoS One 2011; 6:e21476. [PMID: 21738678 PMCID: PMC3125171 DOI: 10.1371/journal.pone.0021476] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 05/29/2011] [Indexed: 12/15/2022] Open
Abstract
Background Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat− mating types are determined by dissimilar allelic sequences. The mat− sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. Methodology/Principal Findings The transcriptomic profiles of the mat+ and mat− strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1− and fpr1− mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat− strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. Conclusions/Significance This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.
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Affiliation(s)
- Frédérique Bidard
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Jinane Aït Benkhali
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Evelyne Coppin
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Sandrine Imbeaud
- CNRS, Centre de Génétique Moléculaire FRE3144, GODMAP, Gif sur Yvette, France
| | - Pierre Grognet
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- UFR des Sciences du Vivant, Université Paris 7-Denis Diderot, Paris, France
| | - Hervé Delacroix
- CNRS, Centre de Génétique Moléculaire FRE3144, GODMAP, Gif sur Yvette, France
- Univ Paris-Sud, Orsay, France
| | - Robert Debuchy
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- * E-mail:
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Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1. EUKARYOTIC CELL 2011; 10:724-33. [PMID: 21515825 DOI: 10.1128/ec.00016-11] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
With the advent of high-throughput DNA sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (SNP) maps. Here we combined high-throughput sequencing with bulk segregant analysis to expedite mutation mapping. The general map location of a mutation can be identified by a single backcross to a strain enriched in SNPs compared to a standard wild-type strain. Bulk segregant analysis simultaneously increases the likelihood of determining the precise nature of the mutation. We present here a high-density SNP map between Neurospora crassa Mauriceville-1-c (FGSC2225) and OR74A (FGSC2489), the strains most typically used by Neurospora researchers to carry out mapping crosses. We further have demonstrated the utility of the Mauriceville sequence and our approach by mapping the mutation responsible for the only existing temperature-sensitive (ts) cell cycle mutation in Neurospora, nuclear division cycle-1 (ndc-1). The single T-to-C point mutation maps to the gene encoding ornithine decarboxylase (ODC), spe-1 (NCU01271), and changes a Phe to a Ser residue within a highly conserved motif next to the catalytic site of the enzyme. By growth on spermidine and complementation with a wild-type spe-1 gene, we showed that the defect in spe-1 is responsible for the ts ndc-1 mutation. Based on our results, we propose changing ndc-1 to spe-1(ndc), which reflects that this mutation results in an ODC with a specific nuclear division defect.
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Martin SH, Wingfield BD, Wingfield MJ, Steenkamp ET. Structure and evolution of the Fusarium mating type locus: new insights from the Gibberellafujikuroi complex. Fungal Genet Biol 2011; 48:731-40. [PMID: 21453780 DOI: 10.1016/j.fgb.2011.03.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Revised: 03/18/2011] [Accepted: 03/21/2011] [Indexed: 11/26/2022]
Abstract
Mating type genes are central to sexual reproduction and compatibility in Ascomycete fungi. However the "MAT" loci experience unique evolutionary pressures that can result in rapid divergence and enhanced inter-specific gene-flow (lateral gene transfer). In this study, molecular evolution of MAT loci was considered using the genus Fusarium (Teleomorph: Gibberella) as a model. Both MAT1-1 and MAT1-2 "idiomorphs" from eleven species of the Gibberellafujikuroi species complex were sequenced. Molecular evolution of the MAT loci from these heterothallic (self-sterile) species was compared with that of the MAT loci from nine homothallic (self-fertile) species in the Fusariumgraminearum species complex. Although Fusarium has previously been thought to have the same complement of four MAT genes that are found in Neurospora, we found evidence of a novel gene, MAT1-2-3, that may be specific to the Hypocreales. All MAT genes share a similar set of cis-regulatory motifs, although homothallic species might have recruited novel regulatory elements, which could potentially facilitate alternate expression of MAT1-1-1 and MAT1-2-1. FusariumMAT loci displayed evidence consistent with historical lateral gene-flow. Most notably, the MAT1-1 idiomorph of Fusariumsacchari appears to be unrelated to those of other species in the G.fujikuroi complex. In general, FusariumMAT genes are highly divergent. Both positive selection and relaxed selective constraint could account for this phenomenon. However, the extent of both recombination and inter-specific gene-flow in the MAT locus also appears to affect the rate of divergence.
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Affiliation(s)
- Simon H Martin
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
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Strandberg R, Nygren K, Menkis A, James TY, Wik L, Stajich JE, Johannesson H. Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Fungal Genet Biol 2010; 47:869-78. [DOI: 10.1016/j.fgb.2010.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 06/12/2010] [Accepted: 06/17/2010] [Indexed: 12/16/2022]
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Functional characterization of MAT1-1-specific mating-type genes in the homothallic ascomycete Sordaria macrospora provides new insights into essential and nonessential sexual regulators. EUKARYOTIC CELL 2010; 9:894-905. [PMID: 20435701 DOI: 10.1128/ec.00019-10] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Mating-type genes in fungi encode regulators of mating and sexual development. Heterothallic ascomycete species require different sets of mating-type genes to control nonself-recognition and mating of compatible partners of different mating types. Homothallic (self-fertile) species also carry mating-type genes in their genome that are essential for sexual development. To analyze the molecular basis of homothallism and the role of mating-type genes during fruiting-body development, we deleted each of the three genes, SmtA-1 (MAT1-1-1), SmtA-2 (MAT1-1-2), and SmtA-3 (MAT1-1-3), contained in the MAT1-1 part of the mating-type locus of the homothallic ascomycete species Sordaria macrospora. Phenotypic analysis of deletion mutants revealed that the PPF domain protein-encoding gene SmtA-2 is essential for sexual reproduction, whereas the alpha domain protein-encoding genes SmtA-1 and SmtA-3 play no role in fruiting-body development. By means of cross-species microarray analysis using Neurospora crassa oligonucleotide microarrays hybridized with S. macrospora targets and quantitative real-time PCR, we identified genes expressed under the control of SmtA-1 and SmtA-2. Both genes are involved in the regulation of gene expression, including that of pheromone genes.
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da Silva CC, Cruz RC, Bucciarelli-Rodriguez M, Vilas-Boas A. Neurospora crassa mat A-2 and mat A-3 proteins weakly interact in the yeast two-hybrid system and affect yeast growth. Genet Mol Biol 2009; 32:354-61. [PMID: 21637691 PMCID: PMC3036917 DOI: 10.1590/s1415-47572009000200023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 02/03/2009] [Indexed: 11/22/2022] Open
Abstract
Mating-type genes control the entry into the sexual cycle, mating identity and sexual development in fungi. The mat A-2 and mat A-3 genes, present in the mat A idiomorph of the filamentous fungus Neurospora crassa, are required for post-fertilization functions but are not essential for mating identity. Their putative roles as transcription factors are based on the similarity of mat A-2 with the Podospora anserina SMR1 gene and an HMG motif present in the mat A-3 gene. In this work the yeast two-hybrid system was used to identify transcriptional activity and protein-protein interaction of N. crassamat A-2 and mat A-3 genes. We observed that the mat A-3 protein alone is capable of weakly activating transcription of yeast reporter genes; it also binds with low specificity to the GAL1 promoter sequence, possibly due to its HMG domain. Our results also indicate that mat A-3 is capable to form homodimers, and interact with mat A-2. Interference on yeast growth was observed on some transformants suggesting a toxic action of the mat A-2 protein. Our data on pattern of interactions of mat proteins contributes towards understanding the control of vegetative and sexual cycles in filamentous fungi.
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Affiliation(s)
- Carla C da Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
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Kaneko I, Dementhon K, Xiang Q, Glass NL. Nonallelic interactions between het-c and a polymorphic locus, pin-c, are essential for nonself recognition and programmed cell death in Neurospora crassa. Genetics 2009; 172:1545-55. [PMID: 16554411 PMCID: PMC1456284 DOI: 10.1534/genetics.105.051490] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nonself recognition in filamentous fungi is conferred by genetic differences at het (heterokaryon incompatibility) loci. When individuals that differ in het specificity undergo hyphal fusion, the heterokaryon undergoes a programmed cell death reaction or is highly unstable. In Neurospora crassa, three allelic specificities at the het-c locus are conferred by a highly polymorphic domain. This domain shows trans-species polymorphisms indicative of balancing selection, consistent with the role of het loci in nonself recognition. We determined that a locus closely linked to het-c, called pin-c (partner for incompatibility with het-c) was required for het-c nonself recognition and heterokaryon incompatibility (HI). The pin-c alleles in isolates that differ in het-c specificity were extremely polymorphic. Heterokaryon and transformation tests showed that nonself recognition was mediated by synergistic nonallelic interactions between het-c and pin-c, while allelic interactions at het-c increased the severity of the HI phenotype. The pin-c locus encodes a protein containing a HET domain; predicted proteins containing HET domains are frequent in filamentous ascomycete genomes. These data suggest that nonallelic interactions may be important in nonself recognition in filamentous fungi and that proteins containing a HET domain may be a key factor in these interactions.
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Affiliation(s)
- Isao Kaneko
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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The Saccharomyces cerevisiae PRM1 homolog in Neurospora crassa is involved in vegetative and sexual cell fusion events but also has postfertilization functions. Genetics 2008; 181:497-510. [PMID: 19064710 DOI: 10.1534/genetics.108.096149] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell-cell fusion is essential for a variety of developmental steps in many eukaryotic organisms, during both fertilization and vegetative cell growth. Although the molecular mechanisms associated with intracellular membrane fusion are well characterized, the molecular mechanisms of plasma membrane merger between cells are poorly understood. In the filamentous fungus Neurospora crassa, cell fusion events occur during both vegetative and sexual stages of its life cycle, thus making it an attractive model for studying the molecular basis of cell fusion during vegetative growth vs. sexual reproduction. In the unicellular yeast Saccharomyces cerevisiae, one of the few proteins implicated in plasma membrane merger during mating is Prm1p; prm1Delta mutants show an approximately 50% reduction in mating cell fusion. Here we report on the role of the PRM1 homolog in N. crassa. N. crassa strains with deletions of a Prm1-like gene (Prm1) showed an approximately 50% reduction in both vegetative and sexual cell fusion events, suggesting that PRM1 is part of the general cell fusion machinery. However, unlike S. cerevisiae, N. crassa strains carrying a Prm1 deletion exhibited complete sterility as either a male or female mating partner, a phenotype that was not complemented in a heterokaryon with wild type (WT). Crosses with DeltaPrm1 strains were blocked early in sexual development, well before development of ascogenous hyphae. The DeltaPrm1 sexual defect in N. crassa was not suppressed by mutations in Sad-1, which is required for meiotic silencing of unpaired DNA (MSUD). However, mutations in Sad-1 increased the number of progeny obtained in crosses with a DeltaPrm1 (Prm1-gfp) complemented strain. These data indicate multiple roles for PRM1 during sexual development.
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Wik L, Karlsson M, Johannesson H. The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa. BMC Evol Biol 2008; 8:109. [PMID: 18405383 PMCID: PMC2335104 DOI: 10.1186/1471-2148-8-109] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 04/11/2008] [Indexed: 12/23/2022] Open
Abstract
Background Comparative sequencing studies among a wide range of taxonomic groups, including fungi, have led to the discovery that reproductive genes evolve more rapidly than other genes. However, for fungal reproductive genes the question has remained whether the rapid evolution is a result of stochastic or deterministic processes. The mating-type (mat) genes constitute the master regulators of sexual reproduction in filamentous ascomycetes and here we present a study of the molecular evolution of the four mat-genes (mat a-1, mat A-1, mat A-2 and mat A-3) of 20 Neurospora taxa. Results We estimated nonsynonymous and synonymous substitution rates of genes to infer their evolutionary rate, and confirmed that the mat-genes evolve rapidly. Furthermore, the evolutionary trajectories are related to the reproductive modes of the taxa; likelihood methods revealed that positive selection acting on specific codons drives the diversity in heterothallic taxa, while among homothallic taxa the rapid evolution is due to a lack of selective constraint. The latter finding is supported by presence of stop codons and frame shift mutations disrupting the open reading frames of mat a-1, mat A-2 and mat A-3 in homothallic taxa. Lower selective constraints of mat-genes was found among homothallic than heterothallic taxa, and comparisons with non-reproductive genes argue that this disparity is not a nonspecific, genome-wide phenomenon. Conclusion Our data show that the mat-genes evolve rapidly in Neurospora. The rapid divergence is due to either adaptive evolution or lack of selective constraints, depending on the reproductive mode of the taxa. This is the first instance of positive selection acting on reproductive genes in the fungal kingdom, and illustrates how the evolutionary trajectory of reproductive genes can change after a switch in reproductive behaviour of an organism.
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Affiliation(s)
- Lotta Wik
- Uppsala University, Department of Evolutionary Biology, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
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Idnurm A, Walton FJ, Floyd A, Heitman J. Identification of the sex genes in an early diverged fungus. Nature 2008; 451:193-6. [PMID: 18185588 DOI: 10.1038/nature06453] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 11/05/2007] [Indexed: 11/09/2022]
Abstract
Sex determination in fungi is controlled by a small, specialized region of the genome in contrast to the large sex-specific chromosomes of animals and some plants. Different gene combinations reside at these mating-type (MAT) loci and confer sexual identity; invariably they encode homeodomain, alpha-box, or high mobility group (HMG)-domain transcription factors. So far, MAT loci have been characterized from a single monophyletic clade of fungi, the Dikarya (the ascomycetes and basidiomycetes), and the ancestral state and evolutionary history of these loci have remained a mystery. Mating in the basal members of the kingdom has been less well studied, and even their precise taxonomic inter-relationships are still obscure. Here we apply bioinformatic and genetic mapping to identify the sex-determining (sex) region in Phycomyces blakesleeanus (Zygomycota), which represents an early branch within the fungi. Each sex allele contains a single gene that encodes an HMG-domain protein, implicating the HMG-domain proteins as an earlier form of fungal MAT loci. Additionally, one allele also contains a copy of a unique, chromosome-specific repetitive element, suggesting a generalized mechanism for the earliest steps in the evolution of sex determination and sex chromosome structure in eukaryotes.
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Affiliation(s)
- Alexander Idnurm
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Kanematsu S, Adachi Y, Ito T. Mating-type loci of heterothallic Diaporthe spp.: homologous genes are present in opposite mating-types. Curr Genet 2007; 52:11-22. [PMID: 17476509 DOI: 10.1007/s00294-007-0132-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 04/09/2007] [Accepted: 04/11/2007] [Indexed: 10/23/2022]
Abstract
Sexual reproduction of fungi is governed by genes located on the mating-type (MAT) locus. To analyze the MAT locus of the genus Diaporthe (anamorph: Phomopsis), a large genera within the ascomycetous class Sordariomycetes, we cloned and sequenced loci MAT1-1 and MAT1-2 from two heterothallic Diaporthe species, designated as Diaporthe W- and G-types (four isolates in total). The mating-type loci structures of Diaporthe W- and G-types were similar; MAT1-1 isolates had a MAT locus containing three genes, MAT1-1-1, MAT1-1-2 and MAT1-1-3, as was the case with other Sordariomycetes, and in contrast to other Sordariomycetes, MAT1-2 isolates had genes homologous to MAT1-1-2 and MAT1-1-3, in addition to MAT1-2-1. Expression analysis by RT-PCR revealed that all the mating-type genes of Diaporthe W-type were transcriptionally active during vegetative growth. The structure of MAT loci of Diaporthe W- and G-types is distinct from that in other heterothallic filamentous ascomycetes, which have dissimilar gene structure in opposite mating-type loci. This unique structure is informative to discussing the evolutionary history and function of mating-type genes of Sordariomycete fungi.
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Affiliation(s)
- Satoko Kanematsu
- Apple Research Station, National Institute of Fruit Tree Science, NARO, Shimokuriyagawa, Morioka 020-0123, Japan.
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Bubnick M, Smulian AG. The MAT1 locus of Histoplasma capsulatum is responsive in a mating type-specific manner. EUKARYOTIC CELL 2007; 6:616-21. [PMID: 17322347 PMCID: PMC1865664 DOI: 10.1128/ec.00020-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 02/14/2007] [Indexed: 11/20/2022]
Abstract
Recombination events associated with sexual replication in pathogens may generate new strains with altered virulence. Histoplasma capsulatum is a mating-competent, pathogenic fungus with two described phenotypic mating types, + and -. The mating (MAT) locus of H. capsulatum was identified to facilitate molecular studies of mating in this organism. Through syntenic analysis of the H. capsulatum genomic sequence databases, a MAT1-1 idiomorph region was identified in H. capsulatum strains G217B and WU24, and a MAT1-2 idiomorph region was identified in the strain G186AR. A mating type-specific PCR assay was developed, and two clinical isolates of opposite genotypic mating type, UH1 and VA1, were identified. A known--mating type strain, T-3-1 (ATCC 22635), was demonstrated to be of MAT1-2 genotypic mating type. The clinical isolates UH1 and VA1 were found to be mating compatible and also displayed mating-type-dependent regulation of the MAT transcription factors in response to extracts predicted to contain mating pheromones. These studies support a role for the identified MAT1 locus in determining mating type in H. capsulatum.
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Affiliation(s)
- Meggan Bubnick
- Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267-0560, USA
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Prillinger H, Lopandic K, Sugita T, Wuczkowski M. Asterotremella gen. nov. albida, an anamorphic tremelloid yeast isolated from the agarics Asterophora lycoperdoides and Asterophora parasitica. J GEN APPL MICROBIOL 2007; 53:167-75. [PMID: 17726297 DOI: 10.2323/jgam.53.167] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Using a genotypic approach (PCR-fingerprinting, DNA/DNA reassociation, partial sequences of the 26S rDNA gene, complete sequences of the 18S rDNA gene, and sequences of the internal transcribed spacers) five tremelloid yeast isolates from the agarics Asterophora lycoperdoides and A. parasitica were shown to be conspecific with Cryptococcus ramirezgomezianus. It was not possible to distinguish the yeast strains from A. lycoperdoides and A. parasitica using sequences from the intergenic spacer (IGS1). Phylogeny based on the 26S (D1/D2-domain), ITS1-5.8S-ITS2 and complete 18S rDNA demonstrated that C. ramirezgomezianus is closely related to several additional Cryptococcus species (C. humicola, C. longus, C. musci, C. pseudolongus) within the Trichosporonales. A new genus, Asterotremella, and a new family, Asterotremellaceae were introduced for Cryptococcus species clustering within the Trichosporonales having a ubiquinone Q-9. Cryptococcus ramirezgomezianus is a synonym of Asterotremella albida.
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Affiliation(s)
- Hansjörg Prillinger
- University of Natural Resources and Applied Life Sciences, Institute of Applied Microbiology (IAM), Austrian Center of Biological Resources and Applied Mycology (ACBR), Wien, Austria.
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Keszthelyi A, Jeney A, Kerényi Z, Mendes O, Waalwijk C, Hornok L. Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides (Gibberella fujikuroi MP-A). Antonie van Leeuwenhoek 2006; 91:373-91. [PMID: 17124547 DOI: 10.1007/s10482-006-9123-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 10/09/2006] [Indexed: 11/27/2022]
Abstract
Mating type in filamentous ascomycetes is controlled by idiomorphic alleles, named MAT1-1 and MAT1-2, which contain 1-3 genes. Of these genes MAT1-1-1 and MAT1-2-1 encode putative transcription factors and are thus considered to be the major regulators of sexual communication and mating. Fungi with no known sexual stage may also have fully functional mating type genes and therefore it was plausible to hypothesize that the MAT products may also regulate other types of genes not involved directly in the mating process. To identify putative target genes of these transcription factors in Fusarium verticillioides, DeltaMAT1-2-1 knock out mutants were produced and transcript profiles of mutant and wild type were compared by means of differential cDNA hybridization. Clones, either up- or down-regulated in the DeltaMAT1-2-1 mutant were sequenced and a total of 248 sequences were blasted against the NCBI database as well as the Gibberella zeae and Gibberella moniliformis genomes. Fifty-five percent of the clones were down-regulated in the mutant, indicating that the MAT1-2-1 product positively affected these tagged sequences. On the other hand, 45% were found to be up-regulated in the mutant, suggesting that the MAT1-2-1 product also exerted a negative regulatory function on this set of genes. Sequences involved in protein synthesis and metabolism occurred more frequently among the clones up-regulated in the mutant, whereas genes belonging to cell signalling and communication were especially frequently tagged among the sequences down-regulated in the mutant.
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Affiliation(s)
- Anita Keszthelyi
- Agricultural Biotechnology Center, Szent-Györgyi A. u. 4, H-2100, Gödöllo, Hungary
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Kerényi Z, Oláh B, Jeney A, Hornok L, Leslie JF. The homologue of het-c of Neurospora crassa lacks vegetative compatibility function in Fusarium proliferatum. Appl Environ Microbiol 2006; 72:6527-32. [PMID: 17021201 PMCID: PMC1610276 DOI: 10.1128/aem.01543-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For two fungal strains to be vegetatively compatible and capable of forming a stable vegetative heterokaryon they must carry matching alleles at a series of loci variously termed het or vic genes. Cloned het/vic genes from Neurospora crassa and Podospora anserina have no obvious functional similarity and have various cellular functions. Our objective was to identify the homologue of the Neurospora het-c gene in Fusarium proliferatum and to determine if this gene has a vegetative compatibility function in this economically important and widely dispersed fungal pathogen. In F. proliferatum and five other closely related Fusarium species we found a few differences in the DNA sequence, but the changes were silent and did not alter the amino acid sequence of the resulting protein. Deleting the gene altered sexual fertility as the female parent, but it did not alter male fertility or existing vegetative compatibility interactions. Replacement of the allele-specific portion of the coding sequence with the sequence of an alternate allele in N. crassa did not result in a vegetative incompatibility response in transformed strains of F. proliferatum. Thus, the fphch gene in Fusarium appears unlikely to have the vegetative compatibility function associated with its homologue in N. crassa. These results suggest that the vegetative compatibility phenotype may result from convergent evolution. Thus, the genes involved in this process may need to be identified at the species level or at the level of a group of species and could prove to be attractive targets for the development of antifungal agents.
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Affiliation(s)
- Zoltán Kerényi
- Agricultural Biotechnology Center, Szent-Györgyi A u 4, H-2100 Gödöll, Hungary
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43
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Tsong AE, Tuch BB, Li H, Johnson AD. Evolution of alternative transcriptional circuits with identical logic. Nature 2006; 443:415-20. [PMID: 17006507 DOI: 10.1038/nature05099] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 07/21/2006] [Indexed: 11/08/2022]
Abstract
Evolution of gene regulation is an important contributor to the variety of life. Here, we analyse the evolution of a combinatorial transcriptional circuit composed of sequence-specific DNA-binding proteins that are conserved among all eukaryotes. This circuit regulates mating in the ascomycete yeast lineage. We first identify a group of mating genes that was transcriptionally regulated by an activator in a fungal ancestor, but is now transcriptionally regulated by a repressor in modern bakers' yeast. Despite this change in regulatory mechanism, the logical output of the overall circuit remains the same. By examining the regulation of mating in modern yeasts that are related to different extents, we deduce specific, sequential changes in both cis- and trans-regulatory elements that constitute the transition from positive to negative regulation. These changes indicate specific mechanisms by which fitness barriers were traversed during the transition.
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Affiliation(s)
- Annie E Tsong
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, California 94143-2200, USA
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Nolting N, Pöggeler S. A STE12 homologue of the homothallic ascomyceteSordaria macrosporainteracts with the MADS box protein MCM1 and is required for ascosporogenesis. Mol Microbiol 2006; 62:853-68. [PMID: 16999832 DOI: 10.1111/j.1365-2958.2006.05415.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MADS box protein MCM1 controls diverse developmental processes and is essential for fruiting body formation in the homothallic ascomycete Sordaria macrospora. MADS box proteins derive their regulatory specificity from a wide range of different protein interactions. We have recently shown that the S. macrospora MCM1 is able to interact with the alpha-domain mating-type protein SMTA-1. To further evaluate the functional roles of MCM1, we used the yeast two-hybrid approach to identify MCM1-interacting proteins. From this screen, we isolated a protein with a putative N-terminal homeodomain and C-terminal C2/H2-Zn2+ finger domains. The protein is a member of the highly conserved fungal STE12 transcription factor family of proteins and was therefore termed STE12. Furthermore, we demonstrate by means of two-hybrid and far western analysis that in addition to MCM1, the S. macrospora STE12 protein is able to interact with the mating-type protein SMTA-1. Unlike the situation in the closely related heterothallic ascomycete Neurospora crassa, deletion (Delta) of the ste12 gene in S. macrospora neither affects vegetative growth nor fruiting body formation. However, ascus and ascospore development are highly impaired by the Deltaste12 mutation. Our data provide another example of the functional divergence within the fungal STE12 transcription factor family.
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Affiliation(s)
- Nicole Nolting
- Department of General and Molecular Botany, Ruhr University of Bochum, 44780 Bochum, Germany
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Paoletti M, Buck KW, Brasier CM. Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote Ophiostoma novo-ulmi. Mol Ecol 2006; 15:249-62. [PMID: 16367844 DOI: 10.1111/j.1365-294x.2005.02728.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Dutch elm disease fungus Ophiostoma novo-ulmi, which has destroyed billions of elm trees worldwide, originally invaded Europe as a series of clonal populations with a single mating type (MAT-2) and a single vegetative incompatibility (vic) type. The populations then rapidly became diverse with the appearance of the MAT-1 type and many vegetative incompatibility types. Here, we have investigated the mechanism using isolates from sites in Portugal at which the rapid evolution of O. novo-ulmi populations from clonality to heterogeneity was well established. We show by genetic mapping of vic and MAT loci with AFLP markers and by sequence analysis of MAT loci that this diversification was due to selective acquisition by O. novo-ulmi of the MAT-1 and vic loci from another species, Ophiostoma ulmi. A global survey showed that interspecies transfer of the MAT-1 locus occurred on many occasions as O. novo-ulmi spread across the world. We discuss the possibility that fixation of the MAT-1 and vic loci occurred in response to spread of deleterious viruses in the originally clonal populations. The process demonstrates the potential of interspecies gene transfer for facilitating rapid adaptation of invasive organisms to a new environment.
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Affiliation(s)
- Mathieu Paoletti
- Department of Biological Sciences, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
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Nolting N, Pöggeler S. A MADS box protein interacts with a mating-type protein and is required for fruiting body development in the homothallic ascomycete Sordaria macrospora. EUKARYOTIC CELL 2006; 5:1043-56. [PMID: 16835449 PMCID: PMC1489284 DOI: 10.1128/ec.00086-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 05/01/2006] [Indexed: 11/20/2022]
Abstract
MADS box transcription factors control diverse developmental processes in plants, metazoans, and fungi. To analyze the involvement of MADS box proteins in fruiting body development of filamentous ascomycetes, we isolated the mcm1 gene from the homothallic ascomycete Sordaria macrospora, which encodes a putative homologue of the Saccharomyces cerevisiae MADS box protein Mcm1p. Deletion of the S. macrospora mcm1 gene resulted in reduced biomass, increased hyphal branching, and reduced hyphal compartment length during vegetative growth. Furthermore, the S. macrospora Deltamcm1 strain was unable to produce fruiting bodies or ascospores during sexual development. A yeast two-hybrid analysis in conjugation with in vitro analyses demonstrated that the S. macrospora MCM1 protein can interact with the putative transcription factor SMTA-1, encoded by the S. macrospora mating-type locus. These results suggest that the S. macrospora MCM1 protein is involved in the transcriptional regulation of mating-type-specific genes as well as in fruiting body development.
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Affiliation(s)
- Nicole Nolting
- Department of General and Molecular Botany, Ruhr University of Bochum, ND6/161, Universitätsstrasse 150, 44780 Bochum, Germany
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Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, Weiss RL, Borkovich KA, Dunlap JC. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 2006; 103:10352-10357. [PMID: 16801547 PMCID: PMC1482798 DOI: 10.1073/pnas.0601456103] [Citation(s) in RCA: 911] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The low rate of homologous recombination exhibited by wild-type strains of filamentous fungi has hindered development of high-throughput gene knockout procedures for this group of organisms. In this study, we describe a method for rapidly creating knockout mutants in which we make use of yeast recombinational cloning, Neurospora mutant strains deficient in nonhomologous end-joining DNA repair, custom-written software tools, and robotics. To illustrate our approach, we have created strains bearing deletions of 103 Neurospora genes encoding transcription factors. Characterization of strains during growth and both asexual and sexual development revealed phenotypes for 43% of the deletion mutants, with more than half of these strains possessing multiple defects. Overall, the methodology, which achieves high-throughput gene disruption at an efficiency >90% in this filamentous fungus, promises to be applicable to other eukaryotic organisms that have a low frequency of homologous recombination.
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Affiliation(s)
- Hildur V Colot
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755
| | - Gyungsoon Park
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Gloria E Turner
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, University of California, Los Angeles, CA 90095
| | - Carol Ringelberg
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755
| | - Christopher M Crew
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Liubov Litvinkova
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Richard L Weiss
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, University of California, Los Angeles, CA 90095
| | | | - Jay C Dunlap
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755;
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Pöggeler S, Nowrousian M, Ringelberg C, Loros JJ, Dunlap JC, Kück U. Microarray and real-time PCR analyses reveal mating type-dependent gene expression in a homothallic fungus. Mol Genet Genomics 2006; 275:492-503. [PMID: 16482473 DOI: 10.1007/s00438-006-0107-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 01/20/2006] [Indexed: 11/26/2022]
Abstract
Sordaria macrospora is a homothallic ascomycete which is able to form fertile fruiting bodies without a mating partner. To analyze the molecular basis of homothallism and the role of mating products during fruiting body development, we have deleted the mating type gene Smta-1 encoding a high-mobility group domain (HMG) protein. The DeltaSmta-1 deletion strain is morphologically wild type during vegetative growth, but it is unable to produce perithecia or ascospores. To identify genes expressed under control of Smta-1, we performed a cross-species microarray analysis using Neurospora crassa cDNA microarrays hybridized with S. macrospora targets. We identified 107 genes that are more than twofold up- or down-regulated in the mutant. Functional classification revealed that 81 genes have homologues with known or putative functions. Comparison of array data from DeltaSmta-1 with those from three phenotypically similar mutants revealed that only a limited set of ten genes is deregulated in all mutants. Remarkably, the ppg2 gene encoding a putative lipopeptide pheromone is 500-fold down-regulated in the DeltaSmta-1 mutant while in all other sterile mutants this gene is up-regulated.
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Affiliation(s)
- S Pöggeler
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780, Bochum, Germany.
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Paoletti M, Buck KW, Brasier CM. Cloning and sequence analysis of the MAT-B (MAT-2) genes from the three Dutch elm disease pathogens, Ophiostoma ulmi, O. novo-ulmi, and O. himal-ulmi. ACTA ACUST UNITED AC 2005; 109:983-91. [PMID: 16209304 DOI: 10.1017/s0953756205003308] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
There were two successive pandemics of Dutch Elm Disease (DED) in Europe, parts of Asia and North America in the last century, caused by two ascomycete fungal species, Ophiostoma ulmi and O. novo-ulmi. A third DED species, O. himal-ulmi, was later discovered in the Himalayas. For each of these three species, we now report on the cloning and analysis of a 2.2 kb sequence containing the coding region and 5' and 3' flanking sequences of the mating type B (MAT-B) gene, which is involved in the control of sexual compatibility. The amino acid sequence of the single protein encoded by the gene for each species contained a conserved DNA-binding motif called the high mobility group (HMG) box which showed significant sequence similarity to corresponding sequences in many ascomycete MAT-2 genes. Phylogenetic trees constructed from the MAT-B (renamed MAT-2) nucleotide and derived amino acid sequences showed distinct clades corresponding to the three Ophiostoma species and a clear separation of the O. novo-ulmi clade into the two subspecies americana and novo-ulmi. The 3' flanking regions have been shown to contain variable numbers of repeated oligonucleotide sequences, the number of which is species-specific and readily distinguished by a simple PCR assay.
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Affiliation(s)
- Mathieu Paoletti
- Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK
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Fleissner A, Sarkar S, Jacobson DJ, Roca MG, Read ND, Glass NL. The so locus is required for vegetative cell fusion and postfertilization events in Neurospora crassa. EUKARYOTIC CELL 2005; 4:920-30. [PMID: 15879526 PMCID: PMC1140088 DOI: 10.1128/ec.4.5.920-930.2005] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The process of cell fusion is a basic developmental feature found in most eukaryotic organisms. In filamentous fungi, cell fusion events play an important role during both vegetative growth and sexual reproduction. We employ the model organism Neurospora crassa to dissect the mechanisms of cell fusion and cell-cell communication involved in fusion processes. In this study, we characterized a mutant with a mutation in the gene so, which exhibits defects in cell fusion. The so mutant has a pleiotropic phenotype, including shortened aerial hyphae, an altered conidiation pattern, and female sterility. Using light microscopy and heterokaryon tests, the so mutant was shown to possess defects in germling and hyphal fusion. Although so produces conidial anastomosis tubes, so germlings did not home toward wild-type germlings nor were wild-type germlings attracted to so germlings. We employed a trichogyne attraction and fusion assay to determine whether the female sterility of the so mutant is caused by impaired communication or fusion failure between mating partners. so showed no defects in attraction or fusion between mating partners, indicating that so is specific for vegetative hyphal fusion and/or associated communication events. The so gene encodes a protein of unknown function, but which contains a WW domain; WW domains are predicted to be involved in protein-protein interactions. Database searches showed that so was conserved in the genomes of filamentous ascomycete fungi but was absent in ascomycete yeast and basidiomycete species.
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Affiliation(s)
- André Fleissner
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720-3102, USA
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