1
|
Regulatory basis for reproductive flexibility in a meningitis-causing fungal pathogen. Nat Commun 2022; 13:7938. [PMID: 36566249 PMCID: PMC9790007 DOI: 10.1038/s41467-022-35549-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/09/2022] [Indexed: 12/25/2022] Open
Abstract
Pathogenic fungi of the genus Cryptococcus can undergo two sexual cycles, involving either bisexual diploidization (after fusion of haploid cells of different mating type) or unisexual diploidization (by autodiploidization of a single cell). Here, we construct a gene-deletion library for 111 transcription factor genes in Cryptococcus deneoformans, and explore the roles of these regulatory networks in the two reproductive modes. We show that transcription factors crucial for bisexual syngamy induce the expression of known mating determinants as well as other conserved genes of unknown function. Deletion of one of these genes, which we term FMP1, leads to defects in bisexual reproduction in C. deneoformans, its sister species Cryptococcus neoformans, and the ascomycete Neurospora crassa. Furthermore, we show that a recently evolved regulatory cascade mediates pre-meiotic unisexual autodiploidization, supporting that this reproductive process is a recent evolutionary innovation. Our findings indicate that genetic circuits with different evolutionary ages govern hallmark events distinguishing unisexual and bisexual reproduction in Cryptococcus.
Collapse
|
2
|
Wu B, Hao W, Cox MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biol 2022; 20:144. [PMID: 35706021 PMCID: PMC9202105 DOI: 10.1186/s12915-022-01346-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom’s evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown. Results By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways. Conclusions The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01346-8.
Collapse
Affiliation(s)
- Baojun Wu
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4410, New Zealand.
| |
Collapse
|
3
|
Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation. Nat Commun 2019; 10:5068. [PMID: 31699975 PMCID: PMC6838127 DOI: 10.1038/s41467-019-12927-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/03/2019] [Indexed: 01/04/2023] Open
Abstract
Parasexuality contributes to diversity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt, with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic diversity and facilitate the emergence of new lineages in asexual fungal populations.
Collapse
|
4
|
Ghosh AK, Wangsanut T, Fonzi WA, Rolfes RJ. The GRF10 homeobox gene regulates filamentous growth in the human fungal pathogen Candida albicans. FEMS Yeast Res 2015; 15:fov093. [PMID: 26472755 PMCID: PMC4705307 DOI: 10.1093/femsyr/fov093] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/14/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022] Open
Abstract
Candida albicans is the most common human fungal pathogen and can cause life-threatening infections. Filamentous growth is critical in the pathogenicity of C. albicans, as the transition from yeast to hyphal forms is linked to virulence and is also a pivotal process in fungal biofilm development. Homeodomain-containing transcription factors have been linked to developmental processes in fungi and other eukaryotes. We report here on GRF10, a homeobox transcription factor-encoding gene that plays a role in C. albicans filamentation. Deletion of the GRF10 gene, in both C. albicans SN152 and BWP17 strain backgrounds, results in mutants with strongly decreased hyphal growth. The mutants are defective in chlamydospore and biofilm formation, as well as showing dramatically attenuated virulence in a mouse infection model. Expression of the GRF10 gene is highly induced during stationary phase and filamentation. In summary, our study emphasizes a new role for the homeodomain-containing transcription factor in morphogenesis and pathogenicity of C. albicans.
Collapse
Affiliation(s)
- Anup K Ghosh
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | | | - William A Fonzi
- Department of Microbiology and Immunology, Georgetown University, Washington, DC 20057, USA
| | - Ronda J Rolfes
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| |
Collapse
|
5
|
Bennett RJ, Forche A, Berman J. Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harb Perspect Med 2014; 4:cshperspect.a019604. [PMID: 25081629 DOI: 10.1101/cshperspect.a019604] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Human fungal pathogens can exist in a variety of ploidy states, including euploid and aneuploid forms. Ploidy change has a major impact on phenotypic properties, including the regulation of interactions with the human host. In addition, the rapid emergence of drug-resistant isolates is often associated with the formation of specific supernumerary chromosomes. Pathogens such as Candida albicans and Cryptococcus neoformans appear particularly well adapted for propagation in multiple ploidy states with novel pathways driving ploidy variation. In both species, heterozygous cells also readily undergo loss of heterozygosity (LOH), leading to additional phenotypic changes such as altered drug resistance. Here, we examine the sexual and parasexual cycles that drive ploidy variation in human fungal pathogens and discuss ploidy and LOH events with respect to their far-reaching roles in fungal adaptation and pathogenesis.
Collapse
Affiliation(s)
- Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, Maine 04011
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| |
Collapse
|
6
|
Abstract
Sexual reproduction is a pervasive attribute of eukaryotic species and is now recognized to occur in many clinically important human fungal pathogens. These fungi use sexual or parasexual strategies for various purposes that can have an impact on pathogenesis, such as the formation of drug-resistant isolates, the generation of strains with increased virulence or the modulation of interactions with host cells. In this Review, we examine the mechanisms regulating fungal sex and the consequences of these programmes for human disease.
Collapse
|
7
|
Pérez-Martín J, de Sena-Tomás C. Dikaryotic cell cycle in the phytopathogenic fungus Ustilago maydis is controlled by the DNA damage response cascade. PLANT SIGNALING & BEHAVIOR 2011; 6:1574-7. [PMID: 21918381 PMCID: PMC3256387 DOI: 10.4161/psb.6.10.17055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 06/27/2011] [Indexed: 05/24/2023]
Abstract
In a large group of fungi, mating results in a dikaryon, a cell in which the two nuclei--one from each parent cell--share a single cytoplasm for a period of time without undergoing nuclear fusion. The dikaryon stage is typical in the life cycles of many fungal species primarily in the Basidiomycota, a large group that includes mushrooms, bracket fungi and many phytopathogenic fungi, such as the corn pathogen Ustilago maydis. Recently, we described that in U. maydis two conserved DNA-damage checkpoint kinases, Chk1 and Atr1, work together to control the dikaryon formation. However, how this pathway is activated during the dikaryon formation and how its activation/deactivation is coordinated with the different cell cycle phases is unknown. Here we propose and discuss several hypothesis to address these questions.
Collapse
Affiliation(s)
- Jose Pérez-Martín
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología CSIC, Madrid, Spain.
| | | |
Collapse
|
8
|
Vollmeister E, Schipper K, Baumann S, Haag C, Pohlmann T, Stock J, Feldbrügge M. Fungal development of the plant pathogen Ustilago maydis. FEMS Microbiol Rev 2011; 36:59-77. [PMID: 21729109 DOI: 10.1111/j.1574-6976.2011.00296.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The maize pathogen Ustilago maydis has to undergo various morphological transitions for the completion of its sexual life cycle. For example, haploid cells respond to pheromone by forming conjugation tubes that fuse at their tips. The resulting dikaryon grows filamentously, expanding rapidly at the apex and inserting retraction septa at the basal pole. In this review, we present progress on the underlying mechanisms regulating such defined developmental programmes. The key findings of the postgenomic era are as follows: (1) endosomes function not only during receptor recycling, but also as multifunctional transport platforms; (2) a new transcriptional master regulator for pathogenicity is part of an intricate transcriptional network; (3) determinants for uniparental mitochondrial inheritance are encoded at the a2 mating-type locus; (4) microtubule-dependent mRNA transport is important in determining the axis of polarity; and (5) a battery of fungal effectors encoded in gene clusters is crucial for plant infection. Importantly, most processes are tightly controlled at the transcriptional, post-transcriptional and post-translational levels, resulting in a complex regulatory network. This intricate system is crucial for the timing of the correct order of developmental phases. Thus, new insights from all layers of regulation have substantially advanced our understanding of fungal development.
Collapse
Affiliation(s)
- Evelyn Vollmeister
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
The ability of fungi to transition between unicellular and multicellular growth has a profound impact on our health and the economy. Many important fungal pathogens of humans, animals, and plants are dimorphic, and the ability to switch between morphological states has been associated with their virulence. Cryptococcus neoformans is a human fungal pathogen that causes life-threatening meningoencephalitis in immunocompromised and, in some cases, immunocompetent hosts. Cryptococcus neoformans grows vegetatively as a budding yeast and switches to hyphal growth during the sexual cycle, which is important in the study of cryptococcal pathogenicity because spores resulting from sexual development are infectious propagules and can colonize the lungs of a host. In addition, sexual reproduction contributes to the genotypic variability of Cryptococcus species, which may lead to increased fitness and virulence. Despite significant advances in our understanding of the mechanisms behind the development of C. neoformans, our knowledge is still incomplete. Recent studies have led to the emergence of many intriguing questions and hypotheses. In this review, we describe and discuss the most interesting aspects of C. neoformans development and address their impact on pathogenicity.
Collapse
Affiliation(s)
- Lukasz Kozubowski
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | | |
Collapse
|
10
|
Jones SK, Bennett RJ. Fungal mating pheromones: choreographing the dating game. Fungal Genet Biol 2011; 48:668-76. [PMID: 21496492 PMCID: PMC3100450 DOI: 10.1016/j.fgb.2011.04.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/23/2011] [Accepted: 04/05/2011] [Indexed: 01/11/2023]
Abstract
Pheromones are ubiquitous from bacteria to mammals - a testament to their importance in regulating inter-cellular communication. In fungal species, they play a critical role in choreographing interactions between mating partners during the program of sexual reproduction. Here, we describe how fungal pheromones are synthesized, their interactions with G protein-coupled receptors, and the signals propagated by this interaction, using Saccharomyces cerevisiae as a reference point. Divergence from this model system is compared amongst the ascomycetes and basidiomycetes, which reveals the wealth of information that has been gleaned from studying pheromone-driven processes across a wide spectrum of the fungal kingdom.
Collapse
Affiliation(s)
- Stephen K. Jones
- Graduate Program in Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912
| | - Richard J. Bennett
- Graduate Program in Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912
| |
Collapse
|
11
|
Harris SD. Hyphal morphogenesis: an evolutionary perspective. Fungal Biol 2011; 115:475-84. [PMID: 21640312 DOI: 10.1016/j.funbio.2011.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 01/31/2011] [Accepted: 02/02/2011] [Indexed: 12/20/2022]
Abstract
Two modes of cellular morphogenesis predominate within the fungal kingdom; yeast growth and hyphal growth. The availability of complete genome sequences that span the kingdom has made possible the use of comparative approaches that address important questions regarding the evolution of these growth modes. These comparisons have also emphasized the point that not all hyphae are the same despite outward appearances. Topics considered here include the origins of hyphal growth, as well as the potential causes of and the consequences resulting from the loss of hyphal growth in yeast lineages. The mechanisms that enable distinct morphological outputs (i.e., yeast vs. hyphae) using an essentially identical inventory of gene products are also considered. Finally, processes implicated in the regulation of hyphal tip complexes are addressed from an evolutionary perspective.
Collapse
Affiliation(s)
- Steven D Harris
- Center for Plant Science Innovation and Department of Plant Pathology, University of Nebraska, E126 Beadle Center, Lincoln, NE 68506, USA.
| |
Collapse
|