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Acs-Szabo L, Papp LA, Miklos I. Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:288-311. [PMID: 39104724 PMCID: PMC11299203 DOI: 10.15698/mic2024.08.833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024]
Abstract
The role of model organisms such as yeasts in life science research is crucial. Although the baker's yeast (Saccharomyces cerevisiae) is the most popular model among yeasts, the contribution of the fission yeasts (Schizosaccharomyces) to life science is also indisputable. Since both types of yeasts share several thousands of common orthologous genes with humans, they provide a simple research platform to investigate many fundamental molecular mechanisms and functions, thereby contributing to the understanding of the background of human diseases. In this review, we would like to highlight the many advantages of fission yeasts over budding yeasts. The usefulness of fission yeasts in virus research is shown as an example, presenting the most important research results related to the Human Immunodeficiency Virus Type 1 (HIV-1) Vpr protein. Besides, the potential role of fission yeasts in the study of prion biology is also discussed. Furthermore, we are keen to promote the uprising model yeast Schizosaccharomyces japonicus, which is a dimorphic species in the fission yeast genus. We propose the hyphal growth of S. japonicus as an unusual opportunity as a model to study the invadopodia of human cancer cells since the two seemingly different cell types can be compared along fundamental features. Here we also collect the latest laboratory protocols and bioinformatics tools for the fission yeasts to highlight the many possibilities available to the research community. In addition, we present several limiting factors that everyone should be aware of when working with yeast models.
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Affiliation(s)
- Lajos Acs-Szabo
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Laszlo Attila Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Ida Miklos
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
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2
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Fukunaga T, Ohashi T, Tanaka Y, Yoshimatsu T, Higuchi Y, Maekawa H, Takegawa K. Galactosylation of cell-surface glycoprotein required for hyphal growth and cell wall integrity in Schizosaccharomyces japonicus. J Biosci Bioeng 2022; 134:384-392. [DOI: 10.1016/j.jbiosc.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 12/01/2022]
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Abstract
Sunlight drives phototrophic metabolism, which affects redox conditions and produces substrates for nonphototrophs. These environmental parameters fluctuate daily due to Earth’s rotation, and nonphototrophic organisms can therefore benefit from the ability to respond to, or even anticipate, such changes. Circadian rhythms, such as daily changes in body temperature, in host organisms can also affect local conditions for colonizing bacteria. Here, we investigated the effects of light/dark and temperature cycling on biofilms of the opportunistic pathogen Pseudomonas aeruginosa PA14. We grew biofilms in the presence of a respiratory indicator dye and found that enhanced dye reduction occurred in biofilm zones that formed during dark intervals and at lower temperatures. This pattern formation occurred with cycling of blue, red, or far-red light, and a screen of mutants representing potential sensory proteins identified two with defects in pattern formation, specifically under red light cycling. We also found that the physiological states of biofilm subzones formed under specific light and temperature conditions were retained during subsequent condition cycling. Light/dark and temperature cycling affected expression of genes involved in primary metabolic pathways and redox homeostasis, including those encoding electron transport chain components. Consistent with this, we found that cbb3-type oxidases contribute to dye reduction under light/dark cycling conditions. Together, our results indicate that cyclic changes in light exposure and temperature have lasting effects on redox metabolism in biofilms formed by a nonphototrophic, pathogenic bacterium.
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Pócsi I, Szigeti ZM, Emri T, Boczonádi I, Vereb G, Szöllősi J. Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi. Appl Microbiol Biotechnol 2022; 106:3895-3912. [PMID: 35599256 PMCID: PMC9200671 DOI: 10.1007/s00253-022-11967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Abstract While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light. Key points • Fungal biological processes alter upon illumination, also under the microscope • Red shifted fluorescent protein toolboxes decrease interference by illumination • Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity
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Affiliation(s)
- István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Imre Boczonádi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
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5
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Rutherford KM, Harris MA, Oliferenko S, Wood V. JaponicusDB: rapid deployment of a model organism database for an emerging model species. Genetics 2021; 220:6481558. [PMID: 35380656 PMCID: PMC9209809 DOI: 10.1093/genetics/iyab223] [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: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023] Open
Abstract
The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.
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Affiliation(s)
- Kim M Rutherford
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Midori A Harris
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, London NW1 1AT, UK,Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London SE1 1UL, UK,Corresponding author: (S.O.); (V.W.)
| | - Valerie Wood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK,Corresponding author: (S.O.); (V.W.)
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Papp LA, Ács-Szabó L, Batta G, Miklós I. Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes. Curr Genet 2021; 67:953-968. [PMID: 34427722 PMCID: PMC8594269 DOI: 10.1007/s00294-021-01206-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 08/04/2021] [Accepted: 08/08/2021] [Indexed: 11/25/2022]
Abstract
Fungal pathogens, from phytopathogenic fungus to human pathogens, are able to alternate between the yeast-like form and filamentous forms. This morphological transition (dimorphism) is in close connection with their pathogenic lifestyles and with their responses to changing environmental conditions. The mechanisms governing these morphogenetic conversions are still not fully understood. Therefore, we studied the filamentous growth of the less-known, non-pathogenic dimorphic fission yeast, S. japonicus, which belongs to an ancient and early evolved branch of the Ascomycota. Its RNA sequencing revealed that several hundred genes were up- or down-regulated in the hyphae compared to the yeast-phase cells. These genes belonged to different GO categories, confirming that mycelial growth is a rather complex process. The genes of transport- and metabolic processes appeared especially in high numbers among them. High expression of genes involved in glycolysis and ethanol production was found in the hyphae, while other results pointed to the regulatory role of the protein kinase A (PKA) pathway. The homologues of 49 S. japonicus filament-associated genes were found by sequence alignments also in seven distantly related dimorphic and filamentous species. The comparative genomic analyses between S. japonicus and the closely related but non-dimorphic S. pombe shed some light on the differences in their genomes. All these data can contribute to a better understanding of hyphal growth and those genomic rearrangements that underlie it.
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Affiliation(s)
- László Attila Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Lajos Ács-Szabó
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Gyula Batta
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Ida Miklós
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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Bouwknegt J, Wiersma SJ, Ortiz-Merino RA, Doornenbal ESR, Buitenhuis P, Giera M, Müller C, Pronk JT. A squalene-hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments. Proc Natl Acad Sci U S A 2021; 118:e2105225118. [PMID: 34353908 PMCID: PMC8364164 DOI: 10.1073/pnas.2105225118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder, Antonie Van Leeuwenhoek, 37, 353-358 (1971)] that Schizosaccharomyces japonicus is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown Sch. japonicus showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in Sch. japonicus showed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those of Acetobacter species. No orthologs of the putative Sch. japonicus SHC were found in other yeast species. Expression of the Sch. japonicus SHC gene (Sjshc1) in Saccharomyces cerevisiae enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of Sch. japonicus in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.
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Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sanne J Wiersma
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Eline S R Doornenbal
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Petrik Buitenhuis
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph Müller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximillians University Munich, 81377 Munich, Germany
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands;
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Seike T, Sakata N, Matsuda F, Furusawa C. Elevated Sporulation Efficiency in Fission Yeast Schizosaccharomyces japonicus Strains Isolated from Drosophila. J Fungi (Basel) 2021; 7:jof7050350. [PMID: 33947067 PMCID: PMC8146891 DOI: 10.3390/jof7050350] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 01/06/2023] Open
Abstract
The fission yeast Schizosaccharomyces japonicus, comprising S. japonicus var. japonicus and S. japonicus var. versatilis varieties, has unique characteristics such as striking hyphal growth not seen in other Schizosaccharomyces species; however, information on its diversity and evolution, in particular mating and sporulation, remains limited. Here we compared the growth and mating phenotypes of 17 wild strains of S. japonicus, including eight S. japonicus var. japonicus strains newly isolated from an insect (Drosophila). Unlike existing wild strains isolated from fruits/plants, the strains isolated from Drosophila sporulated at high frequency even under nitrogen-abundant conditions. In addition, one of the strains from Drosophila was stained by iodine vapor, although the type strain of S. japonicus var. japonicus is not stained. Sequence analysis further showed that the nucleotide and amino acid sequences of pheromone-related genes have diversified among the eight strains from Drosophila, suggesting crossing between S. japonicus cells of different genetic backgrounds occurs frequently in this insect. Much of yeast ecology remains unclear, but our findings suggest that insects such as Drosophila might be a good niche for mating and sporulation, and will provide a basis for the understanding of sporulation mechanisms via signal transduction, as well as the ecology and evolution of yeast.
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Affiliation(s)
- Taisuke Seike
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; (N.S.); (C.F.)
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan;
- Correspondence: ; Tel.: +81-6-6879-7433
| | - Natsue Sakata
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; (N.S.); (C.F.)
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; (N.S.); (C.F.)
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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9
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Gu Y, Oliferenko S. The principles of cellular geometry scaling. Curr Opin Cell Biol 2020; 68:20-27. [PMID: 32950004 DOI: 10.1016/j.ceb.2020.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/11/2023]
Abstract
Cellular dimensions profoundly influence cellular physiology. For unicellular organisms, this has direct bearing on their ecology and evolution. The morphology of a cell is governed by scaling rules. As it grows, the ratio of its surface area to volume is expected to decrease. Similarly, if environmental conditions force proliferating cells to settle on different size optima, cells of the same type may exhibit size-dependent variation in cellular processes. In fungi, algae and plants where cells are surrounded by a rigid wall, division at smaller size often produces immediate changes in geometry, decreasing cell fitness. Here, we discuss how cells interpret their size, buffer against changes in shape and, if necessary, scale their polarity to maintain optimal shape at different cell volumes.
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Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
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Fukunaga T, Tanaka N, Furumoto T, Nakakita S, Ohashi T, Higuchi Y, Maekawa H, Takegawa K. Characterization of N- and O-linked galactosylated oligosaccharides from fission yeast species. J Biosci Bioeng 2020; 130:128-136. [DOI: 10.1016/j.jbiosc.2020.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2020] [Accepted: 03/14/2020] [Indexed: 10/24/2022]
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Makarova M, Peter M, Balogh G, Glatz A, MacRae JI, Lopez Mora N, Booth P, Makeyev E, Vigh L, Oliferenko S. Delineating the Rules for Structural Adaptation of Membrane-Associated Proteins to Evolutionary Changes in Membrane Lipidome. Curr Biol 2020; 30:367-380.e8. [PMID: 31956022 PMCID: PMC6997885 DOI: 10.1016/j.cub.2019.11.043] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/31/2019] [Accepted: 11/13/2019] [Indexed: 01/01/2023]
Abstract
Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that, unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual "asymmetrical" glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S.-japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments support the hypothesis that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.
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Affiliation(s)
- Maria Makarova
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Maria Peter
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Gabor Balogh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Attila Glatz
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - James I MacRae
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nestor Lopez Mora
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK
| | - Paula Booth
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, UK
| | - Eugene Makeyev
- MRC Centre for Developmental Neurobiology, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Laszlo Vigh
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, Guy's Campus, London SE1 1UL, UK.
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Kinnaer C, Dudin O, Martin SG. Yeast-to-hypha transition of Schizosaccharomyces japonicus in response to environmental stimuli. Mol Biol Cell 2019; 30:975-991. [PMID: 30726171 PMCID: PMC6589906 DOI: 10.1091/mbc.e18-12-0774] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 12/28/2022] Open
Abstract
Many fungal species are dimorphic, exhibiting both unicellular yeast-like and filamentous forms. Schizosaccharomyces japonicus, a member of the fission yeast clade, is one such dimorphic fungus. Here, we first identify fruit extracts as natural, stress-free, starvation-independent inducers of filamentation, which we use to describe the properties of the dimorphic switch. During the yeast-to-hypha transition, the cell evolves from a bipolar to a unipolar system with 10-fold accelerated polarized growth but constant width, vacuoles segregated to the nongrowing half of the cell, and hyper-lengthening of the cell. We demonstrate unusual features of S. japonicus hyphae: these cells lack a Spitzenkörper, a vesicle distribution center at the hyphal tip, but display more rapid cytoskeleton-based transport than the yeast form, with actin cables being essential for the transition. S. japonicus hyphae also remain mononuclear and undergo complete cell divisions, which are highly asymmetric: one daughter cell inherits the vacuole, the other the growing tip. We show that these elongated cells scale their nuclear size, spindle length, and elongation rates, but display altered division size controls. This establishes S. japonicus as a unique system that switches between symmetric and asymmetric modes of growth and division.
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Affiliation(s)
- Cassandre Kinnaer
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Omaya Dudin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Sophie G. Martin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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13
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Schizosaccharomyces japonicus: A Distinct Dimorphic Yeast among the Fission Yeasts. Cold Spring Harb Protoc 2017; 2017:pdb.top082651. [PMID: 28733412 DOI: 10.1101/pdb.top082651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomic sequencing data and morphological properties demonstrate evolutionary relationships among groups of the fission yeast, Schizosaccharomyces Phylogenetically, S. japonicus is the furthest removed from other species of fission yeast. The basic characteristics of cell proliferation are shared among all fission yeast, including the process of binary fission during vegetative growth, conjugation and karyogamy with horsetail movement, mating-type switching, and sporulation. However, S. japonicus also exhibits characteristics that are unique to filamentous fungi. S. japonicus is a nonpathogenic yeast that exhibits dimorphism. Depending on the environmental conditions, S. japonicus transforms from yeast cells into filamentous cells (hyphae), and blue light triggers synchronous septation of hyphal cells. A rough version of the whole-genome sequence is now available, facilitating genetic manipulation of S. japonicus. Furthermore, the extensive genetic knowledge available for S. pombe is aiding the development of genetic tools for analyzing S. japonicus. S. japonicus will help shed light on the evolutionary relationships among the fission yeast.
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14
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Franco DL, Canessa P, Bellora N, Risau-Gusman S, Olivares-Yañez C, Pérez-Lara R, Libkind D, Larrondo LF, Marpegan L. Spontaneous circadian rhythms in a cold-adapted natural isolate of Aureobasidium pullulans. Sci Rep 2017; 7:13837. [PMID: 29062053 PMCID: PMC5653790 DOI: 10.1038/s41598-017-14085-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 09/15/2017] [Indexed: 01/01/2023] Open
Abstract
Circadian systems enable organisms to synchronize their physiology to daily and seasonal environmental changes relying on endogenous pacemakers that oscillate with a period close to 24 h even in the absence of external timing cues. The oscillations are achieved by intracellular transcriptional/translational feedback loops thoroughly characterized for many organisms, but still little is known about the presence and characteristics of circadian clocks in fungi other than Neurospora crassa. We sought to characterize the circadian system of a natural isolate of Aureobasidium pullulans, a cold-adapted yeast bearing great biotechnological potential. A. pullulans formed daily concentric rings that were synchronized by light/dark cycles and were also formed in constant darkness with a period of 24.5 h. Moreover, these rhythms were temperature compensated, as evidenced by experiments conducted at temperatures as low as 10 °C. Finally, the expression of clock-essential genes, frequency, white collar-1, white collar-2 and vivid was confirmed. In summary, our results indicate the existence of a functional circadian clock in A. pullulans, capable of sustaining rhythms at very low temperatures and, based on the presence of conserved clock-gene homologues, suggest a molecular and functional relationship to well-described circadian systems.
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Affiliation(s)
- Diana L Franco
- Instituto de Investigaciones en Biodiversidad y Medio Ambiente (INIBIOMA), Universidad Nacional del Comahue, CONICET, CRUB, San Carlos de Bariloche, Río Negro, Argentina.,Departamento de Física Médica Centro Atómico Bariloche and Instituto Balseiro, CONICET, San Carlos de Bariloche, Río Negro, Argentina
| | - Paulo Canessa
- Centro de Biotecnologia Vegetal, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.,Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile
| | - Nicolás Bellora
- Instituto de Investigaciones en Biodiversidad y Medio Ambiente (INIBIOMA), Universidad Nacional del Comahue, CONICET, CRUB, San Carlos de Bariloche, Río Negro, Argentina
| | | | - Consuelo Olivares-Yañez
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo Pérez-Lara
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Diego Libkind
- Instituto de Investigaciones en Biodiversidad y Medio Ambiente (INIBIOMA), Universidad Nacional del Comahue, CONICET, CRUB, San Carlos de Bariloche, Río Negro, Argentina
| | - Luis F Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luciano Marpegan
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.
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15
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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol 2017; 15:55. [PMID: 28662661 PMCID: PMC5492503 DOI: 10.1186/s12915-017-0391-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
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Affiliation(s)
- James J Russell
- Department of Biology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Departments of Biochemistry and of Microbiology & Immunology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA.
| | - Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA
| | | | - Jessica K Polka
- Visiting Scholar, Whitehead Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Therese Gerbich
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Amy Gladfelter
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - James Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | | | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH, Cambridge, UK
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, CA, 94305, USA
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16
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Seike T, Niki H. Mating response and construction of heterothallic strains of the fission yeast Schizosaccharomyces octosporus. FEMS Yeast Res 2017; 17:3888668. [DOI: 10.1093/femsyr/fox045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/20/2017] [Indexed: 12/25/2022] Open
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17
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Abstract
ABSTRACT
Life, as we know it, would not be possible without light. Light is not only a primary source of energy, but also an important source of information for many organisms. To sense light, only a few photoreceptor systems have developed during evolution. They are all based on an organic molecule with conjugated double bonds that allows energy transfer from visible (or UV) light to its cognate protein to translate the primary physical photoresponse to cell-biological actions. The three main classes of receptors are flavin-based blue-light, retinal-based green-light (such as rhodopsin), and linear tetrapyrrole-based red-light sensors. Light not only controls the behavior of motile organisms, but is also important for many sessile microorganisms including fungi. In fungi, light controls developmental decisions and physiological adaptations as well as the circadian clock. Although all major classes of photoreceptors are found in fungi, a good level of understanding of the signaling processes at the molecular level is limited to some model fungi. However, current knowledge suggests a complex interplay between light perception systems, which goes far beyond the simple sensing of light and dark. In this article we focus on recent results in several fungi, which suggest a strong link between light-sensing and stress-activated mitogen-activated protein kinases.
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18
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Comparative biology of cell division in the fission yeast clade. Curr Opin Microbiol 2015; 28:18-25. [PMID: 26263485 DOI: 10.1016/j.mib.2015.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/07/2015] [Accepted: 07/17/2015] [Indexed: 11/21/2022]
Abstract
Cytokinesis must be regulated in time and space in order to preserve genome integrity during cell proliferation and to allow daughter cells to adopt distinct fates and geometries during differentiation. The fission yeast Schizosaccharomyces pombe has been a popular model organism for understanding spatiotemporal regulation of cytokinesis in a symmetrically dividing cell. Recent work on another member of the same genus, Schisozaccharomyces japonicus, suggests that S. pombe may have evolved an unusual division site placement mechanism based on a recently duplicated anillin paralog. Here we discuss an extraordinary evolutionary plasticity of cytokinesis within the fission yeast clade and argue that the comparative cell biology approach may provide functional insights beyond those afforded by scrutinizing individual model species.
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19
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Fuller KK, Loros JJ, Dunlap JC. Fungal photobiology: visible light as a signal for stress, space and time. Curr Genet 2014; 61:275-88. [PMID: 25323429 DOI: 10.1007/s00294-014-0451-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/25/2014] [Accepted: 08/29/2014] [Indexed: 12/25/2022]
Abstract
Visible light is an important source of energy and information for much of life on this planet. Though fungi are neither photosynthetic nor capable of observing adjacent objects, it is estimated that the majority of fungal species display some form of light response, ranging from developmental decision-making to metabolic reprogramming to pathogenesis. As such, advances in our understanding of fungal photobiology will likely reach the broad fields impacted by these organisms, including agriculture, industry and medicine. In this review, we will first describe the mechanisms by which fungi sense light and then discuss the selective advantages likely imparted by their ability to do so.
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Affiliation(s)
- Kevin K Fuller
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA,
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20
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He Y, Yam C, Pomraning K, Chin JSR, Yew JY, Freitag M, Oliferenko S. Increase in cellular triacylglycerol content and emergence of large ER-associated lipid droplets in the absence of CDP-DG synthase function. Mol Biol Cell 2014; 25:4083-95. [PMID: 25318672 PMCID: PMC4263451 DOI: 10.1091/mbc.e14-03-0832] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cds1 is an evolutionarily conserved CDP-DG synthase. Fission yeast are used to demonstrate that cells deficient in its function exhibit markedly increased triacylglycerol content and assemble unusual ER-associated lipid droplets that recruit the triacylglycerol synthesis machinery and grow by expansion. Excess fatty acids and sterols are stored as triacylglycerols and sterol esters in specialized cellular organelles, called lipid droplets. Understanding what determines the cellular amount of neutral lipids and their packaging into lipid droplets is of fundamental and applied interest. Using two species of fission yeast, we show that cycling cells deficient in the function of the ER-resident CDP-DG synthase Cds1 exhibit markedly increased triacylglycerol content and assemble large lipid droplets closely associated with the ER membranes. We demonstrate that these unusual structures recruit the triacylglycerol synthesis machinery and grow by expansion rather than by fusion. Our results suggest that interfering with the CDP-DG route of phosphatidic acid utilization rewires cellular metabolism to adopt a triacylglycerol-rich lifestyle reliant on the Kennedy pathway.
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Affiliation(s)
- Yue He
- Temasek Life Sciences Laboratory, 117604 Singapore Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Candice Yam
- Temasek Life Sciences Laboratory, 117604 Singapore Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Kyle Pomraning
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Jacqueline S R Chin
- Temasek Life Sciences Laboratory, 117604 Singapore Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Joanne Y Yew
- Temasek Life Sciences Laboratory, 117604 Singapore Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Snezhana Oliferenko
- Department of Biological Sciences, National University of Singapore, 117543 Singapore Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
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21
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Niki H. Schizosaccharomyces japonicus
: the fission yeast is a fusion of yeast and hyphae. Yeast 2014; 31:83-90. [DOI: 10.1002/yea.2996] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/09/2013] [Accepted: 12/10/2013] [Indexed: 11/05/2022] Open
Affiliation(s)
- Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Centre National Institute of Genetics 1111 Yata Mishima Shizuoka 411‐8540 Japan
- Department of Genetics Graduate University for Advanced Studies Sokendai, 1111 Yata Mishima Shizuoka 411‐8540 Japan
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