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Travers-Cook TJ, Jokela J, Buser CC. The evolutionary ecology of fungal killer phenotypes. Proc Biol Sci 2023; 290:20231108. [PMID: 37583325 PMCID: PMC10427833 DOI: 10.1098/rspb.2023.1108] [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: 05/17/2023] [Accepted: 07/20/2023] [Indexed: 08/17/2023] Open
Abstract
Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.
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Affiliation(s)
- Thomas J. Travers-Cook
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Jukka Jokela
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Claudia C. Buser
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
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2
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Andreev I, Laidlaw KME, Giovanetti SM, Urtecho G, Shriner D, Bloom JS, MacDonald C, Sadhu MJ. Discovery of a rapidly evolving yeast defense factor, KTD1, against the secreted killer toxin K28. Proc Natl Acad Sci U S A 2023; 120:e2217194120. [PMID: 36800387 PMCID: PMC9974470 DOI: 10.1073/pnas.2217194120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/09/2022] [Indexed: 02/18/2023] Open
Abstract
Secreted protein toxins are widely used weapons in conflicts between organisms. Elucidating how organisms genetically adapt to defend themselves against these toxins is fundamental to understanding the coevolutionary dynamics of competing organisms. Within yeast communities, "killer" toxins are secreted to kill nearby sensitive yeast, providing a fitness advantage in competitive growth environments. Natural yeast isolates vary in their sensitivity to these toxins, but to date, no polymorphic genetic factors contributing to defense have been identified. We investigated the variation in resistance to the killer toxin K28 across diverse natural isolates of the Saccharomyces cerevisiae population. Using large-scale linkage mapping, we discovered a novel defense factor, which we named KTD1. We identified many KTD1 alleles, which provided different levels of K28 resistance. KTD1 is a member of the DUP240 gene family of unknown function, which is rapidly evolving in a region spanning its two encoded transmembrane helices. We found that this domain is critical to KTD1's protective ability. Our findings implicate KTD1 as a key polymorphic factor in the defense against K28 toxin.
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Affiliation(s)
- Ilya Andreev
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Kamilla M. E. Laidlaw
- Biology Department, University of York, YorkYO10 5DD, UK
- York Biomedical Research Institute, University of York, YorkYO10 5NG, UK
| | - Simone M. Giovanetti
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Guillaume Urtecho
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA90095
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Joshua S. Bloom
- Department of Human Genetics, University of California, Los Angeles, CA90095
- Department of Biological Chemistry, University of California, Los Angeles, CA90095
- HHMI, University of California, Los Angeles, CA90095
- Institute for Quantitative and Computational Biology, University of California, Los Angeles, CA90095
- Department of Computational Medicine, University of California, Los Angeles, CA90095
| | - Chris MacDonald
- Biology Department, University of York, YorkYO10 5DD, UK
- York Biomedical Research Institute, University of York, YorkYO10 5NG, UK
| | - Meru J. Sadhu
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD20892
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Grybchuk D, Procházková M, Füzik T, Konovalovas A, Serva S, Yurchenko V, Plevka P. Structures of L-BC virus and its open particle provide insight into Totivirus capsid assembly. Commun Biol 2022; 5:847. [PMID: 35986212 PMCID: PMC9391438 DOI: 10.1038/s42003-022-03793-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
L-BC virus persists in the budding yeast Saccharomyces cerevisiae, whereas other viruses from the family Totiviridae infect a diverse group of organisms including protists, fungi, arthropods, and vertebrates. The presence of totiviruses alters the fitness of the host organisms, for example, by maintaining the killer system in yeast or increasing the virulence of Leishmania guyanensis. Despite the importance of totiviruses for their host survival, there is limited information about Totivirus structure and assembly. Here we used cryo-electron microscopy to determine the structure of L-BC virus to a resolution of 2.9 Å. The L-BC capsid is organized with icosahedral symmetry, with each asymmetric unit composed of two copies of the capsid protein. Decamers of capsid proteins are stabilized by domain swapping of the C-termini of subunits located around icosahedral fivefold axes. We show that capsids of 9% of particles in a purified L-BC sample were open and lacked one decamer of capsid proteins. The existence of the open particles together with domain swapping within a decamer provides evidence that Totiviridae capsids assemble from the decamers of capsid proteins. Furthermore, the open particles may be assembly intermediates that are prepared for the incorporation of the virus (+) strand RNA. A 2.9 Å resolution structure of the L-BC virus provides insight into the contacts between capsid proteins and the mechanism of capsid assembly.
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Wang Q, Lyu X, Cheng J, Fu Y, Lin Y, Abdoulaye AH, Jiang D, Xie J. Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host. Int J Mol Sci 2022; 23:ijms23137441. [PMID: 35806445 PMCID: PMC9267111 DOI: 10.3390/ijms23137441] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Codon usage bias (CUB) could reflect co-evolutionary changes between viruses and hosts in contrast to plant and animal viruses, and the systematic analysis of codon usage among the mycoviruses that infect plant pathogenic fungi is limited. We performed an extensive analysis of codon usage patterns among 98 characterized RNA mycoviruses from eight phytopathogenic fungi. The GC and GC3s contents of mycoviruses have a wide variation from 29.35% to 64.62% and 24.32% to 97.13%, respectively. Mycoviral CUB is weak, and natural selection plays a major role in the formation of mycoviral codon usage pattern. In this study, we demonstrated that the codon usage of mycoviruses is similar to that of some host genes, especially those involved in RNA biosynthetic process and transcription, suggesting that CUB is a potential evolutionary mechanism that mycoviruses adapt to in their hosts.
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Affiliation(s)
- Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yanping Fu
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yang Lin
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Assane Hamidou Abdoulaye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: ; Tel.: +86-185-027-36960
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New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii. Toxins (Basel) 2021; 13:toxins13090615. [PMID: 34564619 PMCID: PMC8472843 DOI: 10.3390/toxins13090615] [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: 07/20/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/25/2022] Open
Abstract
Yeasts can have additional genetic information in the form of cytoplasmic linear dsDNA molecules called virus-like elements (VLEs). Some of them encode killer toxins. The aim of this work was to investigate the prevalence of such elements in D. hansenii killer yeast deposited in culture collections as well as in strains freshly isolated from blue cheeses. Possible benefits to the host from harboring such VLEs were analyzed. VLEs occurred frequently among fresh D. hansenii isolates (15/60 strains), as opposed to strains obtained from culture collections (0/75 strains). Eight new different systems were identified: four composed of two elements and four of three elements. Full sequences of three new VLE systems obtained by NGS revealed extremely high conservation among the largest molecules in these systems except for one ORF, probably encoding a protein resembling immunity determinant to killer toxins of VLE origin in other yeast species. ORFs that could be potentially involved in killer activity due to similarity to genes encoding proteins with domains of chitin-binding/digesting and deoxyribonuclease NucA/NucB activity, could be distinguished in smaller molecules. However, the discovered VLEs were not involved in the biocontrol of Yarrowia lipolytica and Penicillium roqueforti present in blue cheeses.
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Boynton PJ, Wloch‐Salamon D, Landermann D, Stukenbrock EH. Forest Saccharomyces paradoxus are robust to seasonal biotic and abiotic changes. Ecol Evol 2021; 11:6604-6619. [PMID: 34141244 PMCID: PMC8207440 DOI: 10.1002/ece3.7515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/25/2021] [Accepted: 03/16/2021] [Indexed: 01/02/2023] Open
Abstract
Microorganisms are famous for adapting quickly to new environments. However, most evidence for rapid microbial adaptation comes from laboratory experiments or domesticated environments, and it is unclear how rates of adaptation scale from human-influenced environments to the great diversity of wild microorganisms. We examined potential monthly-scale selective pressures in the model forest yeast Saccharomyces paradoxus. Contrary to expectations of seasonal adaptation, the S. paradoxus population was stable over four seasons in the face of abiotic and biotic environmental changes. While the S. paradoxus population was diverse, including 41 unique genotypes among 192 sampled isolates, there was no correlation between S. paradoxus genotypes and seasonal environments. Consistent with observations from other S. paradoxus populations, the forest population was highly clonal and inbred. This lack of recombination, paired with population stability, implies that selection is not acting on the forest S. paradoxus population on a seasonal timescale. Saccharomyces paradoxus may instead have evolved generalism or phenotypic plasticity with regard to seasonal environmental changes long ago. Similarly, while the forest population included diversity among phenotypes related to intraspecific interference competition, there was no evidence for active coevolution among these phenotypes. At least ten percent of the forest S. paradoxus individuals produced "killer toxins," which kill sensitive Saccharomyces cells, but the presence of a toxin-producing isolate did not predict resistance to the toxin among nearby isolates. How forest yeasts acclimate to changing environments remains an open question, and future studies should investigate the physiological responses that allow microbial cells to cope with environmental fluctuations in their native habitats.
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Affiliation(s)
- Primrose J. Boynton
- Biology DepartmentWheaton CollegeNortonMAUSA
- Environmental Genomics Research GroupMax‐Planck Institute for Evolutionary BiologyPlönGermany
| | - Dominika Wloch‐Salamon
- Faculty of BiologyInstitute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - Doreen Landermann
- Environmental Genomics Research GroupMax‐Planck Institute for Evolutionary BiologyPlönGermany
| | - Eva H. Stukenbrock
- Environmental Genomics Research GroupMax‐Planck Institute for Evolutionary BiologyPlönGermany
- Botanical InstituteChristian‐Albrechts UniversitätKielGermany
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Díaz MA, Pereyra MM, Picón-Montenegro E, Meinhardt F, Dib JR. Killer Yeasts for the Biological Control of Postharvest Fungal Crop Diseases. Microorganisms 2020; 8:microorganisms8111680. [PMID: 33138117 PMCID: PMC7693540 DOI: 10.3390/microorganisms8111680] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 01/14/2023] Open
Abstract
Every year and all over the world the fungal decay of fresh fruit and vegetables frequently generates substantial economic losses. Synthetic fungicides, traditionally used to efficiently combat the putrefactive agents, emerged, however, as the cause of environmental and human health issues. Given the need to seek for alternatives, several biological approaches were followed, among which those with killer yeasts stand out. Here, after the elaboration of the complex of problems, we explain the hitherto known yeast killer mechanisms and present the implementation of yeasts displaying such phenotype in biocontrol strategies for pre- or postharvest treatments to be aimed at combating postharvest fungal decay in numerous agricultural products.
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Affiliation(s)
- Mariana Andrea Díaz
- Planta Piloto de Procesos Industriales Microbiológicos–CONICET, Av. Belgrano y Pje. Caseros, Tucumán 4000, Argentina; (M.A.D.); (M.M.P.); (E.P.-M.)
| | - Martina María Pereyra
- Planta Piloto de Procesos Industriales Microbiológicos–CONICET, Av. Belgrano y Pje. Caseros, Tucumán 4000, Argentina; (M.A.D.); (M.M.P.); (E.P.-M.)
| | - Ernesto Picón-Montenegro
- Planta Piloto de Procesos Industriales Microbiológicos–CONICET, Av. Belgrano y Pje. Caseros, Tucumán 4000, Argentina; (M.A.D.); (M.M.P.); (E.P.-M.)
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms Universität Münster, Corrensstr. 3, 48149 Münster, Germany
- Correspondence: (F.M.); (J.R.D.); Tel.: +49-251-83-39819 (F.M.); +54-381-4344888 (J.R.D.)
| | - Julián Rafael Dib
- Planta Piloto de Procesos Industriales Microbiológicos–CONICET, Av. Belgrano y Pje. Caseros, Tucumán 4000, Argentina; (M.A.D.); (M.M.P.); (E.P.-M.)
- Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, Tucumán 4000, Argentina
- Correspondence: (F.M.); (J.R.D.); Tel.: +49-251-83-39819 (F.M.); +54-381-4344888 (J.R.D.)
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8
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Boynton PJ. The ecology of killer yeasts: Interference competition in natural habitats. Yeast 2019; 36:473-485. [PMID: 31050852 DOI: 10.1002/yea.3398] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022] Open
Abstract
Killer yeasts are ubiquitous in the environment: They have been found in diverse habitats ranging from ocean sediment to decaying cacti to insect bodies and on all continents including Antarctica. However, environmental killer yeasts are poorly studied compared with laboratory and domesticated killer yeasts. Killer yeasts secrete so-called killer toxins that inhibit nearby sensitive yeasts, and the toxins are frequently assumed to be tools for interference competition in diverse yeast communities. The diversity and ubiquity of killer yeasts imply that interference competition is crucial for shaping yeast communities. Additionally, these toxins may have ecological functions beyond use in interference competition. This review introduces readers to killer yeasts in environmental systems, with a focus on what is and is not known about their ecology and evolution. It also explores how results from experimental killer systems in laboratories can be extended to understand how competitive strategies shape yeast communities in nature. Overall, killer yeasts are likely to occur everywhere yeasts are found, and the killer phenotype has the potential to radically shape yeast diversity in nature.
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Affiliation(s)
- Primrose J Boynton
- Max-Planck Institute for Evolutionary Biology, Environmental Genomics Group, Plön, Germany
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Sýkora M, Pospíšek M, Novák J, Mrvová S, Krásný L, Vopálenský V. Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin. PLoS Pathog 2018; 14:e1007377. [PMID: 30346988 PMCID: PMC6211774 DOI: 10.1371/journal.ppat.1007377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/01/2018] [Accepted: 10/03/2018] [Indexed: 11/19/2022] Open
Abstract
Extrachromosomal hereditary elements such as organelles, viruses, and plasmids are important for the cell fitness and survival. Their transcription is dependent on host cellular RNA polymerase (RNAP) or intrinsic RNAP encoded by these elements. The yeast Kluyveromyces lactis contains linear cytoplasmic DNA virus-like elements (VLEs, also known as linear plasmids) that bear genes encoding putative non-canonical two-subunit RNAP. Here, we describe the architecture and identify the evolutionary origin of this transcription machinery. We show that the two RNAP subunits interact in vivo, and this complex interacts with another two VLE-encoded proteins, namely the mRNA capping enzyme and a putative helicase. RNAP, mRNA capping enzyme and the helicase also interact with VLE-specific DNA in vivo. Further, we identify a promoter sequence element that causes 5' mRNA polyadenylation of VLE-specific transcripts via RNAP slippage at the transcription initiation site, and structural elements that precede the termination sites. As a result, we present a first model of the yeast virus-like element transcription initiation and intrinsic termination. Finally, we demonstrate that VLE RNAP and its promoters display high similarity to poxviral RNAP and promoters of early poxviral genes, respectively, thereby pointing to their evolutionary origin.
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Affiliation(s)
- Michal Sýkora
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Pospíšek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail: (MP); (VV)
| | - Josef Novák
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Silvia Mrvová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Václav Vopálenský
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail: (MP); (VV)
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Saccharomyces paradoxus K66 Killer System Evidences Expanded Assortment of Helper and Satellite Viruses. Viruses 2018; 10:v10100564. [PMID: 30332789 PMCID: PMC6213463 DOI: 10.3390/v10100564] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 12/29/2022] Open
Abstract
The Saccharomycetaceae yeast family recently became recognized for expanding of the repertoire of different dsRNA-based viruses, highlighting the need for understanding of their cross-dependence. We isolated the Saccharomyces paradoxus AML-15-66 killer strain from spontaneous fermentation of serviceberries and identified helper and satellite viruses of the family Totiviridae, which are responsible for the killing phenotype. The corresponding full dsRNA genomes of viruses have been cloned and sequenced. Sequence analysis of SpV-LA-66 identified it to be most similar to S. paradoxus LA-28 type viruses, while SpV-M66 was mostly similar to the SpV-M21 virus. Sequence and functional analysis revealed significant differences between the K66 and the K28 toxins. The structural organization of the K66 protein resembled those of the K1/K2 type toxins. The AML-15-66 strain possesses the most expressed killing property towards the K28 toxin-producing strain. A genetic screen performed on S. cerevisiae YKO library strains revealed 125 gene products important for the functioning of the S. paradoxus K66 toxin, with 85% of the discovered modulators shared with S. cerevisiae K2 or K1 toxins. Investigation of the K66 protein binding to cells and different polysaccharides implies the β-1,6 glucans to be the primary receptors of S. paradoxus K66 toxin. For the first time, we demonstrated the coherent habitation of different types of helper and satellite viruses in a wild-type S. paradoxus strain.
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11
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Rowley PA. The frenemies within: viruses, retrotransposons and plasmids that naturally infect Saccharomyces yeasts. Yeast 2017; 34:279-292. [PMID: 28387035 DOI: 10.1002/yea.3234] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/07/2022] Open
Abstract
Viruses are a major focus of current research efforts because of their detrimental impact on humanity and their ubiquity within the environment. Bacteriophages have long been used to study host-virus interactions within microbes, but it is often forgotten that the single-celled eukaryote Saccharomyces cerevisiae and related species are infected with double-stranded RNA viruses, single-stranded RNA viruses, LTR-retrotransposons and double-stranded DNA plasmids. These intracellular nucleic acid elements have some similarities to higher eukaryotic viruses, i.e. yeast retrotransposons have an analogous lifecycle to retroviruses, the particle structure of yeast totiviruses resembles the capsid of reoviruses and segregation of yeast plasmids is analogous to segregation strategies used by viral episomes. The powerful experimental tools available to study the genetics, cell biology and evolution of S. cerevisiae are well suited to further our understanding of how cellular processes are hijacked by eukaryotic viruses, retrotransposons and plasmids. This article has been written to briefly introduce viruses, retrotransposons and plasmids that infect Saccharomyces yeasts, emphasize some important cellular proteins and machineries with which they interact, and suggest the evolutionary consequences of these interactions. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Paul A Rowley
- Department of Biological Sciences, The University of Idaho, Moscow, Idaho, USA
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12
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Belda I, Ruiz J, Alonso A, Marquina D, Santos A. The Biology of Pichia membranifaciens Killer Toxins. Toxins (Basel) 2017; 9:toxins9040112. [PMID: 28333108 PMCID: PMC5408186 DOI: 10.3390/toxins9040112] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/07/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
The killer phenomenon is defined as the ability of some yeast to secrete toxins that are lethal to other sensitive yeasts and filamentous fungi. Since the discovery of strains of Saccharomyces cerevisiae capable of secreting killer toxins, much information has been gained regarding killer toxins and this fact has substantially contributed knowledge on fundamental aspects of cell biology and yeast genetics. The killer phenomenon has been studied in Pichia membranifaciens for several years, during which two toxins have been described. PMKT and PMKT2 are proteins of low molecular mass that bind to primary receptors located in the cell wall structure of sensitive yeast cells, linear (1→6)-β-d-glucans and mannoproteins for PMKT and PMKT2, respectively. Cwp2p also acts as a secondary receptor for PMKT. Killing of sensitive cells by PMKT is characterized by ionic movements across plasma membrane and an acidification of the intracellular pH triggering an activation of the High Osmolarity Glycerol (HOG) pathway. On the contrary, our investigations showed a mechanism of killing in which cells are arrested at an early S-phase by high concentrations of PMKT2. However, we concluded that induced mortality at low PMKT2 doses and also PMKT is indeed of an apoptotic nature. Killer yeasts and their toxins have found potential applications in several fields: in food and beverage production, as biocontrol agents, in yeast bio-typing, and as novel antimycotic agents. Accordingly, several applications have been found for P. membranifaciens killer toxins, ranging from pre- and post-harvest biocontrol of plant pathogens to applications during wine fermentation and ageing (inhibition of Botrytis cinerea, Brettanomyces bruxellensis, etc.).
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Affiliation(s)
- Ignacio Belda
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Javier Ruiz
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Alejandro Alonso
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Domingo Marquina
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Antonio Santos
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
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Wemhoff S, Klassen R, Beetz A, Meinhardt F. DNA Damage Responses Are Induced by tRNA Anticodon Nucleases and Hygromycin B. PLoS One 2016; 11:e0157611. [PMID: 27472060 PMCID: PMC4966947 DOI: 10.1371/journal.pone.0157611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/01/2016] [Indexed: 12/26/2022] Open
Abstract
Previous studies revealed DNA damage to occur during the toxic action of PaT, a fungal anticodon ribonuclease (ACNase) targeting the translation machinery via tRNA cleavage. Here, we demonstrate that other translational stressors induce DNA damage-like responses in yeast as well: not only zymocin, another ACNase from the dairy yeast Kluyveromyces lactis, but also translational antibiotics, most pronouncedly hygromycin B (HygB). Specifically, DNA repair mechanisms BER (base excision repair), HR (homologous recombination) and PRR (post replication repair) provided protection, whereas NHEJ (non-homologous end-joining) aggravated toxicity of all translational inhibitors. Analysis of specific BER mutants disclosed a strong HygB, zymocin and PaT protective effect of the endonucleases acting on apurinic sites. In cells defective in AP endonucleases, inactivation of the DNA glycosylase Ung1 increased tolerance to ACNases and HygB. In addition, Mag1 specifically contributes to the repair of DNA lesions caused by HygB. Consistent with DNA damage provoked by translation inhibitors, mutation frequencies were elevated upon exposure to both fungal ACNases and HygB. Since polymerase ζ contributed to toxicity in all instances, error-prone lesion-bypass probably accounts for the mutagenic effects. The finding that differently acting inhibitors of protein biosynthesis induce alike cellular responses in DNA repair mutants is novel and suggests the dependency of genome stability on translational fidelity.
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Affiliation(s)
- Sabrina Wemhoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Anja Beetz
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- * E-mail:
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Affiliation(s)
- Moonil Son
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jisuk Yu
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
- * E-mail:
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Wemhoff S, Klassen R, Meinhardt F. DNA damage induced by the anticodon nuclease from a Pichia acaciae killer strain is linked to ribonucleotide reductase depletion. Cell Microbiol 2015; 18:211-22. [PMID: 26247322 DOI: 10.1111/cmi.12496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/24/2015] [Accepted: 07/26/2015] [Indexed: 11/30/2022]
Abstract
Virus like element (VLE) encoded killer toxins of Pichia acaciae and Kluyveromyces lactis kill target cells through anticodon nuclease (ACNase) activity directed against tRNA(Gln) and tRNA(Glu) respectively. Not only does tRNA cleavage disable translation, it also affects DNA integrity as well. Consistent with DNA damage, which is involved in toxicity, target cells' mutation frequencies are elevated upon ACNase exposure, suggesting a link between translational integrity and genome surveillance. Here, we analysed whether ACNase action impedes the periodically and highly expressed S-phase specific ribonucleotide reductase (RNR) and proved that RNR expression is severely affected by PaT. Because RNR catalyses the rate-limiting step in dNTP synthesis, mutants affected in dNTP synthesis were scrutinized with respect to ACNase action. Mutations elevating cellular dNTPs antagonized the action of both the above ACNases, whereas mutations lowering dNTPs aggravated toxicity. Consistently, prevention of tRNA cleavage in elp3 or trm9 mutants, which both affect the wobble uridine modification of the target tRNA, suppressed the toxin hypersensitivity of a dNTP synthesis mutant. Moreover, dNTP synthesis defects exacerbated the PaT ACNase sensitivity of cells defective in homologous recombination, proving that dNTP depletion is responsible for subsequent DNA damage.
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Affiliation(s)
- Sabrina Wemhoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Roland Klassen
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
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Affiliation(s)
- Reed B. Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Herman K. Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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