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Osborne M, Fubara A, Ó Cinnéide E, Coughlan AY, Wolfe KH. WHO elements - A new category of selfish genetic elements at the borderline between homing elements and transposable elements. Semin Cell Dev Biol 2024; 163:2-13. [PMID: 38664119 DOI: 10.1016/j.semcdb.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an 'arms race' between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.
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Affiliation(s)
- Matthieu Osborne
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Athaliah Fubara
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Eoin Ó Cinnéide
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Aisling Y Coughlan
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
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2
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Rybchuk J, Xiao W. Dual activities of a silencing information regulator complex in yeast transcriptional regulation and DNA-damage response. MLIFE 2024; 3:207-218. [PMID: 38948145 PMCID: PMC11211678 DOI: 10.1002/mlf2.12108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/11/2024] [Accepted: 01/28/2024] [Indexed: 07/02/2024]
Abstract
The Saccharomyces cerevisiae silencing information regulator (SIR) complex contains up to four proteins, namely Sir1, Sir2, Sir3, and Sir4. While Sir2 encodes a NAD-dependent histone deacetylase, other SIR proteins mainly function as structural and scaffold components through physical interaction with various proteins. The SIR complex displays different conformation and composition, including Sir2 homotrimer, Sir1-4 heterotetramer, Sir2-4 heterotrimer, and their derivatives, which recycle and relocate to different chromosomal regions. Major activities of the SIR complex are transcriptional silencing through chromosomal remodeling and modulation of DNA double-strand-break repair pathways. These activities allow the SIR complex to be involved in mating-type maintenance and switching, telomere and subtelomere gene silencing, promotion of nonhomologous end joining, and inhibition of homologous recombination, as well as control of cell aging. This review explores the potential link between epigenetic regulation and DNA damage response conferred by the SIR complex under various conditions aiming at understanding its roles in balancing cell survival and genomic stability in response to internal and environmental stresses. As core activities of the SIR complex are highly conserved in eukaryotes from yeast to humans, knowledge obtained in the yeast may apply to mammalian Sirtuin homologs and related diseases.
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Affiliation(s)
- Josephine Rybchuk
- Department of Biochemistry, Microbiology and ImmunologyUniversity of SaskatchewanSaskatoonSaskatchewanCanada
- Toxicology ProgramUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Wei Xiao
- Department of Biochemistry, Microbiology and ImmunologyUniversity of SaskatchewanSaskatoonSaskatchewanCanada
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3
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Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024; 384:eadj4503. [PMID: 38662846 PMCID: PMC11298794 DOI: 10.1126/science.adj4503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
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Affiliation(s)
- Dana A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 Research Campus Drive, Kannapolis, NC 28081, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Chao Liu
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Yonglin Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hayley R. Stoneman
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jenna VanDenAvond
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Caroline R. Miller
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Emily J. Ubbelohde
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kelly V. Buh
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Max A. B. Haase
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Neža Čadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Jeremy H. DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
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4
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Chavez CM, Groenewald M, Hulfachor AB, Kpurubu G, Huerta R, Hittinger CT, Rokas A. The cell morphological diversity of Saccharomycotina yeasts. FEMS Yeast Res 2024; 24:foad055. [PMID: 38142225 PMCID: PMC10804222 DOI: 10.1093/femsyr/foad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/04/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023] Open
Abstract
The ∼1 200 known species in subphylum Saccharomycotina are a highly diverse clade of unicellular fungi. During its lifecycle, a typical yeast exhibits multiple cell types with various morphologies; these morphologies vary across Saccharomycotina species. Here, we synthesize the evolutionary dimensions of variation in cellular morphology of yeasts across the subphylum, focusing on variation in cell shape, cell size, type of budding, and filament production. Examination of 332 representative species across the subphylum revealed that the most common budding cell shapes are ovoid, spherical, and ellipsoidal, and that their average length and width is 5.6 µm and 3.6 µm, respectively. 58.4% of yeast species examined can produce filamentous cells, and 87.3% of species reproduce asexually by multilateral budding, which does not require utilization of cell polarity for mitosis. Interestingly, ∼1.8% of species examined have not been observed to produce budding cells, but rather only produce filaments of septate hyphae and/or pseudohyphae. 76.9% of yeast species examined have sexual cycle descriptions, with most producing one to four ascospores that are most commonly hat-shaped (37.4%). Systematic description of yeast cellular morphological diversity and reconstruction of its evolution promises to enrich our understanding of the evolutionary cell biology of this major fungal lineage.
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Affiliation(s)
- Christina M Chavez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, United States
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Amanda B Hulfachor
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726, United States
| | - Gideon Kpurubu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, United States
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Rene Huerta
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, United States
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, WI 53726, United States
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, United States
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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5
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Wang JJT, Steenwyk JL, Brem RB. Natural trait variation across Saccharomycotina species. FEMS Yeast Res 2024; 24:foae002. [PMID: 38218591 PMCID: PMC10833146 DOI: 10.1093/femsyr/foae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 01/15/2024] Open
Abstract
Among molecular biologists, the group of fungi called Saccharomycotina is famous for its yeasts. These yeasts in turn are famous for what they have in common-genetic, biochemical, and cell-biological characteristics that serve as models for plants and animals. But behind the apparent homogeneity of Saccharomycotina species lie a wealth of differences. In this review, we discuss traits that vary across the Saccharomycotina subphylum. We describe cases of bright pigmentation; a zoo of cell shapes; metabolic specialties; and species with unique rules of gene regulation. We discuss the genetics of this diversity and why it matters, including insights into basic evolutionary principles with relevance across Eukarya.
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Affiliation(s)
- Johnson J -T Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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6
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Wilson AM, Coetzee MPA, Wingfield MJ, Wingfield BD. Needles in fungal haystacks: Discovery of a putative a-factor pheromone and a unique mating strategy in the Leotiomycetes. PLoS One 2023; 18:e0292619. [PMID: 37824487 PMCID: PMC10569646 DOI: 10.1371/journal.pone.0292619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
The Leotiomycetes is a hugely diverse group of fungi, accommodating a wide variety of important plant and animal pathogens, ericoid mycorrhizal fungi, as well as producers of antibiotics. Despite their importance, the genetics of these fungi remain relatively understudied, particularly as they don't include model taxa. For example, sexual reproduction and the genetic mechanisms that underly this process are poorly understood in the Leotiomycetes. We exploited publicly available genomic and transcriptomic resources to identify genes of the mating-type locus and pheromone response pathway in an effort to characterize the mating strategies and behaviors of 124 Leotiomycete species. Our analyses identified a putative a-factor mating pheromone in these species. This significant finding represents the first identification of this gene in Pezizomycotina species outside of the Sordariomycetes. A unique mating strategy was also discovered in Lachnellula species that appear to have lost the need for the primary MAT1-1-1 protein. Ancestral state reconstruction enabled the identification of numerous transitions between homothallism and heterothallism in the Leotiomycetes and suggests a heterothallic ancestor for this group. This comprehensive catalog of mating-related genes from such a large group of fungi provides a rich resource from which in-depth, functional studies can be conducted in these economically and ecologically important species.
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Affiliation(s)
- Andi M. Wilson
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin P. A. Coetzee
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J. Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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7
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Srikant S, Gaudet R, Murray AW. Extending the reach of homology by using successive computational filters to find yeast pheromone genes. Curr Biol 2023; 33:4098-4110.e3. [PMID: 37699395 PMCID: PMC10592104 DOI: 10.1016/j.cub.2023.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/04/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
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Affiliation(s)
- Sriram Srikant
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA.
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8
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Balarezo-Cisneros LN, Timouma S, Hanak A, Currin A, Valle F, Delneri D. High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries. Commun Biol 2023; 6:918. [PMID: 37679437 PMCID: PMC10484914 DOI: 10.1038/s42003-023-05285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Kazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals including organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing long read sequencing we report a high-quality phased genome assembly for three strains of K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14 Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array and mating type locus. This high-quality reference genome provides a resource to advance our fundamental knowledge of biotechnologically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts in biotechnological processes.
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Affiliation(s)
| | - Soukaina Timouma
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Alistair Hanak
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew Currin
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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9
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Arcangioli B, Gangloff S. The Fission Yeast Mating-Type Switching Motto: "One-for-Two" and "Two-for-One". Microbiol Mol Biol Rev 2023; 87:e0000821. [PMID: 36629411 PMCID: PMC10029342 DOI: 10.1128/mmbr.00008-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Schizosaccharomyces pombe is an ascomycete fungus that divides by medial fission; it is thus commonly referred to as fission yeast, as opposed to the distantly related budding yeast Saccharomyces cerevisiae. The reproductive lifestyle of S. pombe relies on an efficient genetic sex determination system generating a 1:1 sex ratio and using alternating haploid/diploid phases in response to environmental conditions. In this review, we address how one haploid cell manages to generate two sister cells with opposite mating types, a prerequisite to conjugation and meiosis. This mating-type switching process depends on two highly efficient consecutive asymmetric cell divisions that rely on DNA replication, repair, and recombination as well as the structure and components of heterochromatin. We pay special attention to the intimate interplay between the genetic and epigenetic partners involved in this process to underscore the importance of basic research and its profound implication for a better understanding of chromatin biology.
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Affiliation(s)
- Benoît Arcangioli
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
| | - Serge Gangloff
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
- UMR3525, Genetics of Genomes, CNRS-Pasteur Institute, Paris, France
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10
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Yadav V, Sun S, Heitman J. On the evolution of variation in sexual reproduction through the prism of eukaryotic microbes. Proc Natl Acad Sci U S A 2023; 120:e2219120120. [PMID: 36867686 PMCID: PMC10013875 DOI: 10.1073/pnas.2219120120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/23/2023] [Indexed: 03/05/2023] Open
Abstract
Almost all eukaryotes undergo sexual reproduction to generate diversity and select for fitness in their population pools. Interestingly, the systems by which sex is defined are highly diverse and can even differ between evolutionarily closely related species. While the most commonly known form of sex determination involves males and females in animals, eukaryotic microbes can have as many as thousands of different mating types for the same species. Furthermore, some species have found alternatives to sexual reproduction and prefer to grow clonally and yet undergo infrequent facultative sexual reproduction. These organisms are mainly invertebrates and microbes, but several examples are also present among vertebrates suggesting that alternative modes of sexual reproduction evolved multiple times throughout evolution. In this review, we summarize the sex-determination modes and variants of sexual reproduction found across the eukaryotic tree of life and suggest that eukaryotic microbes provide unique opportunities to study these processes in detail. We propose that understanding variations in modes of sexual reproduction can serve as a foundation to study the evolution of sex and why and how it evolved in the first place.
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Affiliation(s)
- Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
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11
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Passer AR, Clancey SA, Shea T, David-Palma M, Averette AF, Boekhout T, Porcel BM, Nowrousian M, Cuomo CA, Sun S, Heitman J, Coelho MA. Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex. eLife 2022; 11:e79114. [PMID: 35713948 PMCID: PMC9296135 DOI: 10.7554/elife.79114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population. Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease. With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility. Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile. Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species. This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.
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Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Terrance Shea
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity InstituteUtrechtNetherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of AmsterdamAmsterdamNetherlands
| | - Betina M Porcel
- Génomique Métabolique, CNRS, University Evry, Université Paris-SaclayEvryFrance
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität BochumBochumGermany
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
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12
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Mating-Type Switching in Budding Yeasts, from Flip/Flop Inversion to Cassette Mechanisms. Microbiol Mol Biol Rev 2022; 86:e0000721. [PMID: 35195440 PMCID: PMC8941940 DOI: 10.1128/mmbr.00007-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mating-type switching is a natural but unusual genetic control process that regulates cell identity in ascomycete yeasts. It involves physically replacing one small piece of genomic DNA by another, resulting in replacement of the master regulatory genes in the mating pathway and hence a switch of cell type and mating behavior. In this review, we concentrate on recent progress that has been made on understanding the origins and evolution of mating-type switching systems in budding yeasts (subphylum Saccharomycotina). Because of the unusual nature and the complexity of the mechanism in Saccharomyces cerevisiae, mating-type switching was assumed until recently to have originated only once or twice during yeast evolution. However, comparative genomics analysis now shows that switching mechanisms arose many times independently-at least 11 times in budding yeasts and once in fission yeasts-a dramatic example of convergent evolution. Most of these lineages switch mating types by a flip/flop mechanism that inverts a section of a chromosome and is simpler than the well-characterized 3-locus cassette mechanism (MAT/HML/HMR) used by S. cerevisiae. Mating-type switching (secondary homothallism) is one of the two possible mechanisms by which a yeast species can become self-fertile. The other mechanism (primary homothallism) has also emerged independently in multiple evolutionary lineages of budding yeasts, indicating that homothallism has been favored strongly by natural selection. Recent work shows that HO endonuclease, which makes the double-strand DNA break that initiates switching at the S. cerevisiae MAT locus, evolved from an unusual mobile genetic element that originally targeted a glycolytic gene, FBA1.
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13
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Qazi MA, Wang Q, Dai Z. Sophorolipids bioproduction in the yeast Starmerella bombicola: Current trends and perspectives. BIORESOURCE TECHNOLOGY 2022; 346:126593. [PMID: 34942344 DOI: 10.1016/j.biortech.2021.126593] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Sophorolipids are highly active green surfactants (glycolipid biosurfactants) getting tremendous appreciation worldwide due to their low toxicity, biodegradability, broad spectrum of applications, and significant biotechnological potential. Sophorolipids are mainly produced by an oleaginous budding yeast Starmerella bombicola using low-cost substrates. Therefore, the recent state-of-art literature information about S. bombicola yeast is hereby provided, especially the underlying production pathways, biosynthetic gene cluster, and regulatory enzymes. Moreover, the S. bombicola offers flexibility for regulating the structural diversity of sophorolipids, either genetically or by varying fermentative conditions. The emergence of advanced technologies like 'Omics and CRISPR/Cas have certainly boosted rational engineering research for designing high-performing platform strains. Therefore, currently available genetic engineering tools in S. bombicola were reviewed, thereby opening up exciting new possibilities for improving the overall bioproduction titers, structural variability, and stability of sophorolipids. Finally, some technical perspectives to address the current challenges were discussed.
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Affiliation(s)
- Muneer Ahmed Qazi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, PR China; Institute of Microbiology, Faculty of Natural Science, Shah Abdul Latif University, Khairpur, 66020 Sindh, Pakistan
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, PR China
| | - Zongjie Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, PR China.
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14
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Bai FY, Han DY, Duan SF, Wang QM. The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae. Genes (Basel) 2022; 13:genes13020230. [PMID: 35205274 PMCID: PMC8871604 DOI: 10.3390/genes13020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/01/2023] Open
Abstract
The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.
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Affiliation(s)
- Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
- Correspondence: ; Tel.: +86-10-6480-7406
| | - Da-Yong Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China; (D.-Y.H.); (S.-F.D.)
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China;
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15
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Rueda-Mejia MP, Nägeli L, Lutz S, Ortiz-Merino RA, Frei D, Frey JE, Wolfe KH, Ahrens CH, Freimoser FM. Genome sequence data of the antagonistic soil-borne yeast Cyberlindnera sargentensis (SHA 17.2). Data Brief 2022; 40:107799. [PMID: 35071701 PMCID: PMC8762083 DOI: 10.1016/j.dib.2022.107799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 10/26/2022] Open
Abstract
Cyberlindnera sargentensis strain SHA 17.2, isolated from a Swiss soil sample, exhibited strong antagonistic activity against several plant pathogenic fungi in vitro and was highly competitive against other yeasts in soil. As a basis for identifying the mechanisms underlying its strong antagonistic activity, we have sequenced the genome of C. sargentensis (SHA 17.2) by long- and short read sequencing, de novo assembled them into seven contigs/chromosomes and a mitogenome (total genome size 11.4 Mbp), and annotated 5455 genes. This high-quality genome is the reference for transcriptome and proteome analyses aiming at elucidating the mode of action of C. sargentensis against fungal plant pathogens. It will thus serve as a resource for identifying potential biocontrol genes and performing comparative genomics analyses of yeast genomes.
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Affiliation(s)
- Maria Paula Rueda-Mejia
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland
| | - Lukas Nägeli
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland
| | - Stefanie Lutz
- Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland
| | | | - Daniel Frei
- Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland
| | - Jürg E Frey
- Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland
| | - Kenneth H Wolfe
- Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Christian H Ahrens
- Agroscope, Competence Division Method Development and Analytics, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland.,SIB, Swiss Institute of Bioinformatics, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland
| | - Florian M Freimoser
- Agroscope, Research Division Plant Protection, Müller-Thurgau-Strasse 29, Wädenswil 8820, Switzerland
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16
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Ata Ö, Ergün BG, Fickers P, Heistinger L, Mattanovich D, Rebnegger C, Gasser B. What makes Komagataella phaffii non-conventional? FEMS Yeast Res 2021; 21:6440159. [PMID: 34849756 PMCID: PMC8709784 DOI: 10.1093/femsyr/foab059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the 'conventional' yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Burcu Gündüz Ergün
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Turkey.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium
| | - Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Innovative Immunotherapeutics, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Growth-Decoupled Protein Production in Yeast, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
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17
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Solieri L, Cassanelli S, Huff F, Barroso L, Branduardi P, Louis EJ, Morrissey JP. Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts. FEMS Yeast Res 2021; 21:foab058. [PMID: 34791177 PMCID: PMC8673824 DOI: 10.1093/femsyr/foab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/14/2021] [Indexed: 11/14/2022] Open
Abstract
Evolution has provided a vast diversity of yeasts that play fundamental roles in nature and society. This diversity is not limited to genotypically homogeneous species with natural interspecies hybrids and allodiploids that blur species boundaries frequently isolated. Thus, life cycle and the nature of breeding systems have profound effects on genome variation, shaping heterozygosity, genotype diversity and ploidy level. The apparent enrichment of hybrids in industry-related environments suggests that hybridization provides an adaptive route against stressors and creates interest in developing new hybrids for biotechnological uses. For example, in the Saccharomyces genus where regulatory circuits controlling cell identity, mating competence and meiosis commitment have been extensively studied, this body of knowledge is being used to combine interesting traits into synthetic F1 hybrids, to bypass F1 hybrid sterility and to dissect complex phenotypes by bulk segregant analysis. Although these aspects are less known in other industrially promising yeasts, advances in whole-genome sequencing and analysis are changing this and new insights are being gained, especially in the food-associated genera Zygosaccharomyces and Kluyveromyces. We discuss this new knowledge and highlight how deciphering cell identity circuits in these lineages will contribute significantly to identify the genetic determinants underpinning complex phenotypes and open new avenues for breeding programmes.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Franziska Huff
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Liliane Barroso
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Edward J Louis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John P Morrissey
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
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18
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Takayama Y. Strains and approaches for genetic crosses in the oleaginous yeast Lipomyces starkeyi. Yeast 2021; 38:625-633. [PMID: 34596906 PMCID: PMC9292350 DOI: 10.1002/yea.3671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/05/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022] Open
Abstract
The oleaginous yeast Lipomyces starkeyi is a powerful lipid producer with great industrial potential. Recent studies have reported the isolation of mutant L. starkeyi cells with higher lipid producing capacity. Although genetic engineering strategies have been applied to L. starkeyi, classical genetic approaches are lacking. The development of tools that facilitate genetic crosses in L. starkeyi would not only make it possible to build improved lipid‐producing strains but also facilitate molecular biological analysis of this species. In this study, I report a set of strains and approaches useful for performing genetic crosses with L. starkeyi. The homothallic L. starkeyi reportedly forms an ascus containing two to 20 spores. These spores were resistant to glusulase and could be dissected using a micromanipulator, suggesting that random spore and tetrad (spore dissection) analysis can be adapted for L. starkeyi. Additionally, to isolate a pair of heterothallic strains useful for genetic crosses, the homothallic strain was exposed to UV irradiation, and 10 self‐sterile strains were crossed with one another. One of these combinations, Ls75 and Ls100, sporulated stably. Moreover, to detect genetic recombination, I introduced a different drug resistance marker into each strain and crossed them. The resulting progeny exhibited Mendelian segregation of the resistance markers. Altogether, the work reported here provides a powerful resource for genetic analysis in L. starkeyi.
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Affiliation(s)
- Yuko Takayama
- Department of Biosciences, School of Science and Engineering, Teikyo University, Utsunomiya, Tochigi, Japan.,Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University Graduate Schools, Utsunomiya, Tochigi, Japan
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19
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Draft Genome Sequence of the Yeast Ogataea degrootiae Strain UCD465, Isolated from Soil in Ireland. Microbiol Resour Announc 2021; 10:e0073621. [PMID: 34591679 PMCID: PMC8483666 DOI: 10.1128/mra.00736-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Ogataea degrootiae is an ascomycete yeast that was first isolated in the Netherlands in 2017. It is a member of the Pichiaceae clade. Here, we present the genome sequence of O. degrootiae UCD465, which was isolated from soil in Ireland. This genome is 14.6 Mb and haploid.
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20
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Hanson SJ, Cinnéide EÓ, Salzberg LI, Wolfe KH, McGowan J, Fitzpatrick DA, Matlin K. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex. G3 (BETHESDA, MD.) 2021; 11:jkab211. [PMID: 34849824 PMCID: PMC8496258 DOI: 10.1093/g3journal/jkab211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022]
Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.
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Affiliation(s)
- Sara J Hanson
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Eoin Ó Cinnéide
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Letal I Salzberg
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Kate Matlin
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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21
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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22
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Maroc L, Fairhead C. Lessons from the Nakaseomyces: mating-type switching, DSB repair and evolution of Ho. Curr Genet 2021; 67:685-693. [PMID: 33830322 DOI: 10.1007/s00294-021-01182-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
This short paper aims to review what our recent studies in the Nakaseomyces yeasts, principally Candida glabrata, reveal about the evolution of the mating-type switching system and its components, as well as about the repair of chromosomal double-strand breaks in this clade. In the model yeast Saccharomyces cerevisiae, the study of mating-type switching has, over the years, led to major discoveries in how cells process chromosomal breaks. Indeed, in this species, switching, which allows every haploid cell to produce cells of opposite mating types that can mate together, is initiated by the Ho endonuclease, linking sexual reproduction to a programmed chromosomal cut. More recently, the availability of other yeasts' genomes from type strains and from populations, and the ability to manipulate and edit the genomes of most yeasts in the laboratory, has enabled scientists to explore mating-type switching in new species, thus enriching our evolutionary perspective on this phenomenon. In this review, we will show how the study of mating-type switching in C. glabrata and Nakaseomyces delphensis has allowed us to reveal possible additional roles for Ho, and also to discover major differences in DSB repair at central and subtelomeric sexual loci. In addition, we report how the study of repair of chromosomal breaks induced by CRISPR-Cas9 reveals that efficient and faithful NHEJ is a major repair pathway in C. glabrata.
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Affiliation(s)
- Laetitia Maroc
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Cécile Fairhead
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France.
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23
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Červenák F, Sepšiová R, Nosek J, Tomáška Ľ. Step-by-Step Evolution of Telomeres: Lessons from Yeasts. Genome Biol Evol 2020; 13:6127219. [PMID: 33537752 PMCID: PMC7857110 DOI: 10.1093/gbe/evaa268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2020] [Indexed: 12/23/2022] Open
Abstract
In virtually every eukaryotic species, the ends of nuclear chromosomes are protected by telomeres, nucleoprotein structures counteracting the end-replication problem and suppressing recombination and undue DNA repair. Although in most cases, the primary structure of telomeric DNA is conserved, there are several exceptions to this rule. One is represented by the telomeric repeats of ascomycetous yeasts, which encompass a great variety of sequences, whose evolutionary origin has been puzzling for several decades. At present, the key questions concerning the driving force behind their rapid evolution and the means of co-evolution of telomeric repeats and telomere-binding proteins remain largely unanswered. Previously published studies addressed mostly the general concepts of the evolutionary origin of telomeres, key properties of telomeric proteins as well as the molecular mechanisms of telomere maintenance; however, the evolutionary process itself has not been analyzed thoroughly. Here, we aimed to inspect the evolution of telomeres in ascomycetous yeasts from the subphyla Saccharomycotina and Taphrinomycotina, with special focus on the evolutionary origin of species-specific telomeric repeats. We analyzed the sequences of telomeric repeats from 204 yeast species classified into 20 families and as a result, we propose a step-by-step model, which integrates the diversity of telomeric repeats, telomerase RNAs, telomere-binding protein complexes and explains a propensity of certain species to generate the repeat heterogeneity within a single telomeric array.
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Affiliation(s)
- Filip Červenák
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Regina Sepšiová
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
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24
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Toyomura K, Hisatomi T, Yokoyama N, Miyamoto A. Identification of a novel gene controlling homothallism in the yeast Kazachstania naganishii isolated in Japan. Yeast 2020; 38:72-80. [PMID: 33047808 DOI: 10.1002/yea.3525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/08/2022] Open
Abstract
A novel gene controlling homothallic life cycle was identified in the yeast Kazachstania naganishii isolated in Japan. This gene was isolated by means of complementing a mutation, mti1, which had led to heterothallism from original homothallism in the yeast. The configuration of original mutation in MTI1 gene revealed that a truncated product is formed due to occurrence of a stop codon by a nucleotide insertion. When the gene was disrupted with a marker, the disruptant spore clone was haploid and stably heterothallic. Disfunction of the gene caused inability to self-diploidize due to defect of mating-type interconversion. The gene MTI1 (for Mating Type Interconversion) is a weak homolog of the Saccharomyces cerevisiae VID22/ENV11, which has been reported to function in vacuolar protein processing. K. naganishii has a gene representing significant homology with the HO gene of S. cerevisiae on chromosome V, which has not been clarified to be involved in regulation of life cycle in K. naganishii. The MTI1 gene defined in this study is located on K. naganishii chromosome IV and does not represent significant homology to the above ScHO-like gene and any other genes concerning life cycles of yeasts. From the viewpoint of gene evolution, it is extremely interesting that the MTI1 gene is a new type of gene controlling homothallism in addition to an HO-type gene, leading to discovery of an unknown mechanism regulating life cycles in yeasts.
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Affiliation(s)
- Kousuke Toyomura
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
| | - Taisuke Hisatomi
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
| | - Nanami Yokoyama
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
| | - Akira Miyamoto
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
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25
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Damasceno JD, Marques CA, Black J, Briggs E, McCulloch R. Read, Write, Adapt: Challenges and Opportunities during Kinetoplastid Genome Replication. Trends Genet 2020; 37:21-34. [PMID: 32993968 PMCID: PMC9213392 DOI: 10.1016/j.tig.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
The genomes of all organisms are read throughout their growth and development, generating new copies during cell division and encoding the cellular activities dictated by the genome’s content. However, genomes are not invariant information stores but are purposefully altered in minor and major ways, adapting cellular behaviour and driving evolution. Kinetoplastids are eukaryotic microbes that display a wide range of such read–write genome activities, in many cases affecting critical aspects of their biology, such as host adaptation. Here we discuss the range of read–write genome changes found in two well-studied kinetoplastid parasites, Trypanosoma brucei and Leishmania, focusing on recent work that suggests such adaptive genome variation is linked to novel strategies the parasites use to replicate their unconventional genomes. Polycistronic transcription dominates and shapes kinetoplastid genomes, inevitably leading to clashes with DNA replication. By harnessing the resultant DNA damage for adaptation, kinetoplastids have huge potential for dynamic read–write genome variation. Major origins of DNA replication are confined to the boundaries of polycistronic transcription units in the Trypanosoma brucei and Leishmania genomes, putatively limiting DNA damage. Subtelomeres may lack this arrangement, generating read–write hotspots. In T. brucei, early replication of the highly transcribed subtelomeric variant surface glycoprotein (VSG) expression site may ensure replication-transcription clashes within this site to trigger DNA recombination, an event critical for antigenic variation. Leishmania genomes show extensive aneuploidy and copy number variation. Notably, DNA replication requires recombination factors and relies on post-S phase replication of subtelomeres. Evolution of compartmentalised DNA replication programmes underpin important aspects of genome biology in kinetoplastids, illustrating the consolidation of genome maintenance strategies to promote genome plasticity.
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Affiliation(s)
- Jeziel D Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Jennifer Black
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Emma Briggs
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK; Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
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Zhou Li Y, Boisnard S, Enache-Angoulvant A, Fairhead C. Genome editing in the yeast Nakaseomyces delphensis and description of its complete sexual cycle. Yeast 2020; 38:57-71. [PMID: 32941662 DOI: 10.1002/yea.3522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/07/2020] [Accepted: 09/14/2020] [Indexed: 11/06/2022] Open
Abstract
The environmental yeast Nakaseomyces delphensis is, phylogenetically, the closest known species to Candida glabrata, a major fungal pathogen of humans. C. glabrata is haploid and described as asexual, while N. delphensis is also haploid, but has been described as competent for mating and meiosis. Both genomes contain homologues of all the genes necessary for sexual reproduction and also the genes for Ho-dependent mating-type switching, like Saccharomyces cerevisiae. We first report the construction of genetically engineered strains of N. delphensis, including by CRISPR-Cas 9 gene editing. We also report the description of the sexual cycle of N. delphensis. We show that it undergoes Ho-dependent mating-type switching in culture and that deletion of the HO gene prevents such switching and allows maintenance of stable, separate, MATa and MATalpha haploid strains. Rare, genetically selected diploids can be obtained through mating of haploid strains, mutated or not for the HO gene. In contrast to HO/HO diploids, which behave as expected, Δho/Δho diploids exhibit unusual profiles in flow cytometry. Both types of diploids can produce recombined haploid cells, which grow like the original haploid-type strain. Our experiments thus allow the genetic manipulation of N. delphensis and the reconstruction, in the laboratory, of its entire life cycle.
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Affiliation(s)
- Youfang Zhou Li
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
| | - Stéphanie Boisnard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Cécile Fairhead
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
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27
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Libkind D, Čadež N, Opulente DA, Langdon QK, Rosa CA, Sampaio JP, Gonçalves P, Hittinger CT, Lachance MA. Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences. FEMS Yeast Res 2020; 20:5876348. [DOI: 10.1093/femsyr/foaa042] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/23/2020] [Indexed: 01/23/2023] Open
Abstract
ABSTRACT
In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.
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Affiliation(s)
- D Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Bariloche, Argentina
| | - N Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - D A Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Q K Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
| | - C A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270–901, Brazil
| | - J P Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - P Gonçalves
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - C T Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - M A Lachance
- Department of Biology, University of Western Ontario, London N6A 5B7, Ontario, Canada
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28
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Abstract
The gene that allows budding yeast cells to switch their mating type evolved from a newly discovered family of genes named weird HO.
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Affiliation(s)
- Laura N Rusche
- Department of Biological Science, University of Buffalo, The State University of New York, New York, United States
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29
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Coughlan AY, Lombardi L, Braun-Galleani S, Martos AA, Galeote V, Bigey F, Dequin S, Byrne KP, Wolfe KH. The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family. eLife 2020; 9:55336. [PMID: 32338594 PMCID: PMC7282813 DOI: 10.7554/elife.55336] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/24/2020] [Indexed: 01/07/2023] Open
Abstract
The mating-type switching endonuclease HO plays a central role in the natural life cycle of Saccharomyces cerevisiae, but its evolutionary origin is unknown. HO is a recent addition to yeast genomes, present in only a few genera close to Saccharomyces. Here we show that HO is structurally and phylogenetically related to a family of unorthodox homing genetic elements found in Torulaspora and Lachancea yeasts. These WHO elements home into the aldolase gene FBA1, replacing its 3' end each time they integrate. They resemble inteins but they operate by a different mechanism that does not require protein splicing. We show that a WHO protein cleaves Torulaspora delbrueckii FBA1 efficiently and in an allele-specific manner, leading to DNA repair by gene conversion or NHEJ. The DNA rearrangement steps during WHO element homing are very similar to those during mating-type switching, and indicate that HO is a domesticated WHO-like element. In the same way as a sperm from a male and an egg from a female join together to form an embryo in most animals, yeast cells have two sexes that coordinate how they reproduce. These are called “mating types” and, rather than male or female, an individual yeast cell can either be mating type “a” or “alpha”. Every yeast cell contains the genes for both mating types, and each cell’s mating type is determined by which of those genes it has active. Only one mating type gene can be ‘on’ at a time, but some yeast species can swap mating type on demand by switching the corresponding genes ‘on’ or ‘off’. This switch is unusual. Rather than simply activate one of the genes it already has, the yeast cell keeps an inactive version of each mating type gene tucked away, makes a copy of the gene it wants to be active and pastes that copy into a different location in its genome. To do all of this yeast need another gene called HO. This gene codes for an enzyme that cuts the DNA at the location of the active mating type gene. This makes an opening that allows the cell to replace the ‘a’ gene with the ‘alpha’ gene, or vice versa. This system allows yeast cells to continue mating even if all the cells in a colony start off as the same mating type. But, cutting into the DNA is risky, and can damage the health of the cell. So, why did yeast cells evolve a system that could cause them harm? To find out where the HO gene came from, Coughlan et al. searched through all the available genomes from yeast species for other genes with similar sequences and identified a cluster which they nicknamed “weird HO” genes, or WHO genes for short. Testing these genes revealed that they also code for enzymes that make cuts in the yeast genome, but the way the cell repairs the cuts is different. The WHO genes are jumping genes. When the enzyme encoded by a WHO gene makes a cut in the genome, the yeast cell copies the gene into the gap, allowing the gene to ‘jump’ from one part of the genome to another. It is possible that this was the starting point for the evolution of the HO gene. Changes to a WHO gene could have allowed it to cut into the mating type region of the yeast genome, giving the yeast an opportunity to ‘domesticate’ it. Over time, the yeast cell stopped the WHO gene from jumping into the gap and started using the cut to change its mating type. Understanding how cells adapt genes for different purposes is a key question in evolutionary biology. There are many other examples of domesticated jumping genes in other organisms, including in the human immune system. Understanding the evolution of HO not only sheds light on how yeast mating type switching evolved, but on how other species might harness and adapt their genes.
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Affiliation(s)
- Aisling Y Coughlan
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Lisa Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | | | - Alexandre Ar Martos
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Virginie Galeote
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bigey
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Kevin P Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
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31
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Mating-type switching and mating-type gene array expression in the methylotrophic yeast Ogataea thermomethanolica TBRC656. Microbiol Res 2019; 232:126372. [PMID: 31759230 DOI: 10.1016/j.micres.2019.126372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/16/2019] [Accepted: 11/07/2019] [Indexed: 11/22/2022]
Abstract
The methylotrophic yeast, Ogataea thermomethanolica TBRC656, is an attractive host organism for heterologous protein production owing to the availability of protein expression vectors and a genome-editing tool. In this study, we focused on mating-type switching and gene expression in order to elucidate its sexual life cycle and establish genetic approaches applicable for the strain. A putative mating-type gene cluster was identified in TBRC656 that is syntenic to the cluster in Ogataea parapolymorpha DL-1 (previously named Hansenula polymorpha). Like DL-1, TBRC656 possesses two mating loci, namely MATa and MATα, and also shows flip-flop mating-type switching. Interestingly, unlike any other methylotrophic yeast, TBRC656 robustly switched mating type during late growth in rich medium (YPD). Under nutrient depletion, mating-type switching was observed within one hour. Transcription from both MATa and MATα mating loci was detected during growth in YPD, and possibly induced upon nitrogen depletion. Gene expression from MATα was detected as a single co-transcript from a three-gene array (α2-α1-a1S). Deletion of a putative a1S ORF at the MATα locus had no observed effect on mating-type switching but demonstrated significant effect on mating-type gene expression at both MATa and MATα loci.
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32
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Abstract
Fungi reproduce via both heterothallic outcrossing and homothallic selfing modes, and transitions between the two are common throughout the tree of life. A new study reports that the transition from heterothallism to homothallism is common and has repeatedly punctuated the evolutionary trajectory across a major lineage of the fungal kingdom.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA 30605, USA
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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