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Zemlianski V, Marešová A, Princová J, Holič R, Häsler R, Ramos Del Río MJ, Lhoste L, Zarechyntsava M, Převorovský M. Nitrogen availability is important for preventing catastrophic mitosis in fission yeast. J Cell Sci 2024; 137:jcs262196. [PMID: 38780300 DOI: 10.1242/jcs.262196] [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: 04/10/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Mitosis is a crucial stage in the cell cycle, controlled by a vast network of regulators responding to multiple internal and external factors. The fission yeast Schizosaccharomyces pombe demonstrates catastrophic mitotic phenotypes due to mutations or drug treatments. One of the factors provoking catastrophic mitosis is a disturbed lipid metabolism, resulting from, for example, mutations in the acetyl-CoA/biotin carboxylase (cut6), fatty acid synthase (fas2, also known as lsd1) or transcriptional regulator of lipid metabolism (cbf11) genes, as well as treatment with inhibitors of fatty acid synthesis. It has been previously shown that mitotic fidelity in lipid metabolism mutants can be partially rescued by ammonium chloride supplementation. In this study, we demonstrate that mitotic fidelity can be improved by multiple nitrogen sources. Moreover, this improvement is not limited to lipid metabolism disturbances but also applies to a number of unrelated mitotic mutants. Interestingly, the partial rescue is not achieved by restoring the lipid metabolism state, but rather indirectly. Our results highlight a novel role for nitrogen availability in mitotic fidelity.
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Affiliation(s)
- Viacheslav Zemlianski
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Anna Marešová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Jarmila Princová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Roman Holič
- Centre of Biosciences SAS, Institute of Animal Biochemistry and Genetics, Dúbravská cesta 9, 840 05 Bratislava, Slovak Republic
| | - Robert Häsler
- Center for Inflammatory Skin Diseases, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Rosalind-Franklin-Straße 9, 24105 Kiel, Germany
| | - Manuel José Ramos Del Río
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Laurane Lhoste
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Maryia Zarechyntsava
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czechia
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2
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Morozumi Y, Mahayot F, Nakase Y, Soong JX, Yamawaki S, Sofyantoro F, Imabata Y, Oda AH, Tamura M, Kofuji S, Akikusa Y, Shibatani A, Ohta K, Shiozaki K. Rapamycin-sensitive mechanisms confine the growth of fission yeast below the temperatures detrimental to cell physiology. iScience 2024; 27:108777. [PMID: 38269097 PMCID: PMC10805665 DOI: 10.1016/j.isci.2023.108777] [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: 05/25/2023] [Revised: 10/12/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024] Open
Abstract
Cells cease to proliferate above their growth-permissible temperatures, a ubiquitous phenomenon generally attributed to heat damage to cellular macromolecules. We here report that, in the presence of rapamycin, a potent inhibitor of Target of Rapamycin Complex 1 (TORC1), the fission yeast Schizosaccharomyces pombe can proliferate at high temperatures that usually arrest its growth. Consistently, mutations to the TORC1 subunit RAPTOR/Mip1 and the TORC1 substrate Sck1 significantly improve cellular heat resistance, suggesting that TORC1 restricts fission yeast growth at high temperatures. Aiming for a more comprehensive understanding of the negative regulation of high-temperature growth, we conducted genome-wide screens, which identified additional factors that suppress cell proliferation at high temperatures. Among them is Mks1, which is phosphorylated in a TORC1-dependent manner, forms a complex with the 14-3-3 protein Rad24, and suppresses the high-temperature growth independently of Sck1. Our study has uncovered unexpected mechanisms of growth restraint even below the temperatures deleterious to cell physiology.
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Affiliation(s)
- Yuichi Morozumi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Fontip Mahayot
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yukiko Nakase
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Jia Xin Soong
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Sayaka Yamawaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Fajar Sofyantoro
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Faculty of Biology, Universitas Gadjah Mada, Sleman, Yogyakarta 55281, Indonesia
| | - Yuki Imabata
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Arisa H. Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Miki Tamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Shunsuke Kofuji
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yutaka Akikusa
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ayu Shibatani
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Kazuhiro Shiozaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
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3
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Otsubo Y, Yamashita A, Goto Y, Sakai K, Iida T, Yoshimura S, Johzuka K. Cellular responses to compound stress induced by atmospheric-pressure plasma in fission yeast. J Cell Sci 2023; 136:jcs261292. [PMID: 37990810 DOI: 10.1242/jcs.261292] [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: 04/28/2023] [Accepted: 11/13/2023] [Indexed: 11/23/2023] Open
Abstract
The stress response is one of the most fundamental cellular processes. Although the molecular mechanisms underlying responses to a single stressor have been extensively studied, cellular responses to multiple stresses remain largely unknown. Here, we characterized fission yeast cellular responses to a novel stress inducer, non-thermal atmospheric-pressure plasma. Plasma irradiation generates ultraviolet radiation, electromagnetic fields and a variety of chemically reactive species simultaneously, and thus can impose multiple stresses on cells. We applied direct plasma irradiation to fission yeast and showed that strong plasma irradiation inhibited fission yeast growth. We demonstrated that mutants lacking sep1 and ace2, both of which encode transcription factors required for proper cell separation, were resistant to plasma irradiation. Sep1-target transcripts were downregulated by mild plasma irradiation. We also demonstrated that plasma irradiation inhibited the target of rapamycin kinase complex 1 (TORC1). These observations indicate that two pathways, namely the Sep1-Ace2 cell separation pathway and TORC1 pathway, operate when fission yeast cope with multiple stresses induced by plasma irradiation.
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Affiliation(s)
- Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Tetsushi Iida
- Gene Engineering Division, RIKEN BioResource Research Center (BRC), 3-1-1 Koyadai, Tsukuba-shi, Ibaraki 305-0074, Japan
| | - Shinji Yoshimura
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292, Japan
| | - Katsuki Johzuka
- Interdisciplinary Research Unit, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Astrobiology Center, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Aichi 444-8585, Japan
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4
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Ohtsuka H, Sakata H, Kitazaki Y, Tada M, Shimasaki T, Otsubo Y, Maekawa Y, Kobayashi M, Imada K, Yamashita A, Aiba H. The ecl family gene ecl3+ is induced by phosphate starvation and contributes to sexual differentiation in fission yeast. J Cell Sci 2023; 136:287015. [PMID: 36779416 PMCID: PMC10038150 DOI: 10.1242/jcs.260759] [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: 10/27/2022] [Accepted: 02/07/2023] [Indexed: 02/14/2023] Open
Abstract
In Schizosaccharomyces pombe, ecl family genes are induced by several signals, such as starvation of various nutrients, including sulfur, amino acids and Mg2+, and environmental stress, including heat or oxidative stress. These genes mediate appropriate cellular responses and contribute to the maintenance of cell viability and induction of sexual differentiation. Although this yeast has three ecl family genes with overlapping functions, any environmental conditions that induce ecl3+ remain unidentified. We demonstrate that ecl3+ is induced by phosphate starvation, similar to its chromosomally neighboring genes, pho1+ and pho84+, which respectively encode an extracellular acid phosphatase and an inorganic phosphate transporter. ecl3+ expression was induced by the transcription factor Pho7 and affected by the cyclin-dependent kinase (CDK)-activating kinase Csk1. Phosphate starvation induced G1 arrest and sexual differentiation via ecl family genes. Biochemical analyses suggested that this G1 arrest was mediated by the stabilization of the CDK inhibitor Rum1, which was dependent on ecl family genes. This study shows that ecl family genes are required for appropriate responses to phosphate starvation and provides novel insights into the diversity and similarity of starvation responses.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Hiroki Sakata
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yuto Kitazaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Masanobu Tada
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Aichi 444-858, Japan
- National Institute for Fusion Science, Toki, Gifu 509-5292, Japan
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Yasukichi Maekawa
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mikuto Kobayashi
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kazuki Imada
- Department of Chemistry and Biochemistry, National Institute of Technology (KOSEN), Suzuka College, Suzuka 510-0294, Japan
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Aichi 444-858, Japan
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Aichi 464-8603, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
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5
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Alao JP, Legon L, Dabrowska A, Tricolici AM, Kumar J, Rallis C. Interplays of AMPK and TOR in Autophagy Regulation in Yeast. Cells 2023; 12:cells12040519. [PMID: 36831186 PMCID: PMC9953913 DOI: 10.3390/cells12040519] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Cells survey their environment and need to balance growth and anabolism with stress programmes and catabolism towards maximum cellular bioenergetics economy and survival. Nutrient-responsive pathways, such as the mechanistic target of rapamycin (mTOR) interact and cross-talk, continuously, with stress-responsive hubs such as the AMP-activated protein kinase (AMPK) to regulate fundamental cellular processes such as transcription, protein translation, lipid and carbohydrate homeostasis. Especially in nutrient stresses or deprivations, cells tune their metabolism accordingly and, crucially, recycle materials through autophagy mechanisms. It has now become apparent that autophagy is pivotal in lifespan, health and cell survival as it is a gatekeeper of clearing damaged macromolecules and organelles and serving as quality assurance mechanism within cells. Autophagy is hard-wired with energy and nutrient levels as well as with damage-response, and yeasts have been instrumental in elucidating such connectivities. In this review, we briefly outline cross-talks and feedback loops that link growth and stress, mainly, in the fission yeast Schizosaccharomyces pombe, a favourite model in cell and molecular biology.
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6
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Ohtsuka H, Shimasaki T, Aiba H. Response to leucine in Schizosaccharomyces pombe (fission yeast). FEMS Yeast Res 2022; 22:6553821. [PMID: 35325114 PMCID: PMC9041340 DOI: 10.1093/femsyr/foac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Leucine (Leu) is a branched-chain, essential amino acid in animals, including humans. Fungi, including the fission yeast Schizosaccharomyces pombe, can biosynthesize Leu, but deletion of any of the genes in this biosynthesis leads to Leu auxotrophy. In this yeast, although a mutation in the Leu biosynthetic pathway, leu1-32, is clearly inconvenient for this species, it has increased its usefulness as a model organism in laboratories worldwide. Leu auxotrophy produces intracellular responses and phenotypes different from those of the prototrophic strains, depending on the growing environment, which necessitates a certain degree of caution in the analysis and interpretation of the experimental results. Under amino acid starvation, the amino acid-auxotrophic yeast induces cellular responses, which are conserved in higher organisms without the ability of synthesizing amino acids. This mini-review focuses on the roles of Leu in S. pombe and discusses biosynthetic pathways, contribution to experimental convenience using a plasmid specific for Leu auxotrophic yeast, signaling pathways, and phenotypes caused by Leu starvation. An accurate understanding of the intracellular responses brought about by Leu auxotrophy can contribute to research in various fields using this model organism and to the understanding of intracellular responses in higher organisms that cannot synthesize Leu.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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7
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Fission Yeast Autophagy Machinery. Cells 2022; 11:cells11071086. [PMID: 35406650 PMCID: PMC8997447 DOI: 10.3390/cells11071086] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 01/27/2023] Open
Abstract
Autophagy is a conserved process that delivers cytoplasmic components to the vacuole/lysosome. It plays important roles in maintaining cellular homeostasis and conferring stress resistance. In the fission yeast Schizosaccharomyces pombe, autophagy is important for cell survival under nutrient depletion and ER stress conditions. Experimental analyses of fission yeast autophagy machinery in the last 10 years have unveiled both similarities and differences in autophagosome biogenesis mechanisms between fission yeast and other model eukaryotes for autophagy research, in particular, the budding yeast Saccharomyces cerevisiae. More recently, selective autophagy pathways that deliver hydrolytic enzymes, the ER, and mitochondria to the vacuole have been discovered in fission yeast, yielding novel insights into how cargo selectivity can be achieved in autophagy. Here, we review the progress made in understanding the autophagy machinery in fission yeast.
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8
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Segreto R, Bazafkan H, Millinger J, Schenk M, Atanasova L, Doppler M, Büschl C, Boeckstaens M, Soto Diaz S, Schreiner U, Sillo F, Balestrini R, Schuhmacher R, Zeilinger S. The TOR kinase pathway is relevant for nitrogen signaling and antagonism of the mycoparasite Trichoderma atroviride. PLoS One 2022; 16:e0262180. [PMID: 34972198 PMCID: PMC8719763 DOI: 10.1371/journal.pone.0262180] [Citation(s) in RCA: 3] [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: 09/10/2021] [Accepted: 12/18/2021] [Indexed: 01/14/2023] Open
Abstract
Trichoderma atroviride (Ascomycota, Sordariomycetes) is a well-known mycoparasite applied for protecting plants against fungal pathogens. Its mycoparasitic activity involves processes shared with plant and human pathogenic fungi such as the production of cell wall degrading enzymes and secondary metabolites and is tightly regulated by environmental cues. In eukaryotes, the conserved Target of Rapamycin (TOR) kinase serves as a central regulator of cellular growth in response to nutrient availability. Here we describe how alteration of the activity of TOR1, the single and essential TOR kinase of T. atroviride, by treatment with chemical TOR inhibitors or by genetic manipulation of selected TOR pathway components affected various cellular functions. Loss of TSC1 and TSC2, that are negative regulators of TOR complex 1 (TORC1) in mammalian cells, resulted in altered nitrogen source-dependent growth of T. atroviride, reduced mycoparasitic overgrowth and, in the case of Δtsc1, a diminished production of numerous secondary metabolites. Deletion of the gene encoding the GTPase RHE2, whose mammalian orthologue activates mTORC1, led to rapamycin hypersensitivity and altered secondary metabolism, but had an only minor effect on vegetative growth and mycoparasitic overgrowth. The latter also applied to mutants missing the npr1-1 gene that encodes a fungus-specific kinase known as TOR target in yeast. Genome-wide transcriptome analysis confirmed TOR1 as a regulatory hub that governs T. atroviride metabolism and processes associated to ribosome biogenesis, gene expression and translation. In addition, mycoparasitism-relevant genes encoding terpenoid and polyketide synthases, peptidases, glycoside hydrolases, small secreted cysteine-rich proteins, and G protein coupled receptors emerged as TOR1 targets. Our results provide the first in-depth insights into TOR signaling in a fungal mycoparasite and emphasize its importance in the regulation of processes that critically contribute to the antagonistic activity of T. atroviride.
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Affiliation(s)
- Rossana Segreto
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Hoda Bazafkan
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Julia Millinger
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Martina Schenk
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Lea Atanasova
- Institute of Food Technology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Maria Doppler
- Department of Agrobiotechnology IFA-Tulln, Center for Analytical Chemistry, University of Natural, Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Christoph Büschl
- Department of Agrobiotechnology IFA-Tulln, Center for Analytical Chemistry, University of Natural, Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Mélanie Boeckstaens
- Département de Biologie Moléculaire, Laboratory of Biology of Membrane Transport, Université Libre de Bruxelles, Gosselies, Belgium
| | - Silvia Soto Diaz
- Département de Biologie Moléculaire, Laboratory of Biology of Membrane Transport, Université Libre de Bruxelles, Gosselies, Belgium
| | - Ulrike Schreiner
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | | | - Rainer Schuhmacher
- Department of Agrobiotechnology IFA-Tulln, Center for Analytical Chemistry, University of Natural, Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Susanne Zeilinger
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
- * E-mail:
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9
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Morozumi Y, Hishinuma A, Furusawa S, Sofyantoro F, Tatebe H, Shiozaki K. Fission yeast TOR complex 1 phosphorylates Psk1 through an evolutionarily conserved interaction mediated by the TOS motif. J Cell Sci 2021; 134:272450. [PMID: 34499159 PMCID: PMC8542387 DOI: 10.1242/jcs.258865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/03/2021] [Indexed: 12/28/2022] Open
Abstract
TOR complex 1 (TORC1) is a multi-subunit protein kinase complex that controls cellular growth in response to environmental cues. The regulatory subunits of mammalian TORC1 (mTORC1) include RAPTOR (also known as RPTOR), which recruits mTORC1 substrates, such as S6K1 (also known as RPS6KB1) and 4EBP1 (EIF4EBP1), by interacting with their TOR signaling (TOS) motif. Despite the evolutionary conservation of TORC1, no TOS motif has been described in lower eukaryotes. In the present study, we show that the fission yeast S6 kinase Psk1 contains a TOS motif that interacts with Mip1, a RAPTOR ortholog. The TOS motif in Psk1 resembles those in mammals, including the conserved phenylalanine and aspartic acid residues essential for the Mip1 interaction and TORC1-dependent phosphorylation of Psk1. The binding of the TOS motif to Mip1 is dependent on Mip1 Tyr-533, whose equivalent in RAPTOR is known to interact with the TOS motif in their co-crystals. Furthermore, we utilized the mip1-Y533A mutation to screen the known TORC1 substrates in fission yeast and successfully identified Atg13 as a novel TOS-motif-containing substrate. These results strongly suggest that the TOS motif represents an evolutionarily conserved mechanism of the substrate recognition by TORC1. Summary: By analyzing S6 kinase in fission yeast, we have demonstrated that the TOR signaling (TOS) motif-mediated substrate recognition by TOR complex 1 is conserved from yeast to humans.
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Affiliation(s)
- Yuichi Morozumi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ai Hishinuma
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Daisen, Akita 019-2112, Japan
| | - Suguru Furusawa
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Fajar Sofyantoro
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Department of Animal Physiology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Hisashi Tatebe
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazuhiro Shiozaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
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10
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Matsuda S, Kikkawa U, Uda H, Nakashima A. The S. pombe CDK5 ortholog Pef1 regulates sexual differentiation through control of the TORC1 pathway and autophagy. J Cell Sci 2020; 133:jcs247817. [PMID: 32788233 DOI: 10.1242/jcs.247817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
In Schizosaccharomyces pombe, a general strategy for survival in response to environmental changes is sexual differentiation, which is triggered by TORC1 inactivation. However, mechanisms of TORC1 regulation in fission yeast remain poorly understood. In this study, we found that Pef1, which is an ortholog of mammalian CDK5, regulates the initiation of sexual differentiation through positive regulation of TORC1 activity. Conversely, deletion of pef1 leads to activation of autophagy and subsequent excessive TORC1 reactivation during the early phases of the nitrogen starvation response. This excessive TORC1 reactivation results in the silencing of the Ste11-Mei2 pathway and mating defects. Additionally, we found that pef1 genetically interacts with tsc1 and tsc2 for TORC1 regulation, and physically interacts with three cyclins, Clg1, Pas1 and Psl1. The double deletion of clg1 and pas1 promotes activation of autophagy and TORC1 during nitrogen starvation, similar to what is seen in pef1Δ cells. Overall, our work suggests that Pef1-Clg1 and Pef1-Pas1 complexes regulate initiation of sexual differentiation through control of the TSC-TORC1 pathway and autophagy.
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Affiliation(s)
- Shinya Matsuda
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Ushio Kikkawa
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Haruka Uda
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Akio Nakashima
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
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11
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Otsubo Y, Kamada Y, Yamashita A. Novel Links between TORC1 and Traditional Non-Coding RNA, tRNA. Genes (Basel) 2020; 11:E956. [PMID: 32825021 PMCID: PMC7563549 DOI: 10.3390/genes11090956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
Target of rapamycin (TOR) is a serine/threonine kinase that modulates cell growth and metabolism in response to environmental changes. Transfer RNA (tRNA) is an abundant and ubiquitous small non-coding RNA that is essential in the translation of mRNAs. Beyond its canonical role, it has been revealed that tRNAs have more diverse functions. TOR complex 1 (TORC1), which is one of the two TOR complexes, regulates tRNA synthesis by controlling RNA polymerase III. In addition to tRNA synthesis regulation, recent studies have revealed hidden connections between TORC1 and tRNA, which are both essential players in eukaryotic cellular activities. Here, we review the accumulating findings on the regulatory links between TORC1 and tRNA-particularly those links in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe.
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Affiliation(s)
- Yoko Otsubo
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292, Japan
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yoshiaki Kamada
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Akira Yamashita
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; (Y.O.); (Y.K.)
- Center for Novel Science Initiatives, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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12
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Laribee RN, Weisman R. Nuclear Functions of TOR: Impact on Transcription and the Epigenome. Genes (Basel) 2020; 11:E641. [PMID: 32532005 PMCID: PMC7349558 DOI: 10.3390/genes11060641] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
The target of rapamycin (TOR) protein kinase is at the core of growth factor- and nutrient-dependent signaling pathways that are well-known for their regulation of metabolism, growth, and proliferation. However, TOR is also involved in the regulation of gene expression, genomic and epigenomic stability. TOR affects nuclear functions indirectly through its activity in the cytoplasm, but also directly through active nuclear TOR pools. The mechanisms by which TOR regulates its nuclear functions are less well-understood compared with its cytoplasmic activities. TOR is an important pharmacological target for several diseases, including cancer, metabolic and neurological disorders. Thus, studies of the nuclear functions of TOR are important for our understanding of basic biological processes, as well as for clinical implications.
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Affiliation(s)
- R. Nicholas Laribee
- Department of Pathology and Laboratory Medicine, College of Medicine and Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Cancer Research Building Rm 318, Memphis, TN 38163, USA
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, University Road 1, Ra’anana 4353701, Israel
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13
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Rapamycin induces morphological and physiological changes without increase in lipid content in Ustilago maydis. Arch Microbiol 2020; 202:1211-1221. [PMID: 32088730 DOI: 10.1007/s00203-020-01833-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/19/2022]
Abstract
The evolutionarily conserved serine/threonine kinase TOR recruits different subunits to assemble the Target of Rapamycin Complex 1 (TORC1), which is inhibited by rapamycin and regulates ribosome biogenesis, autophagy, and lipid metabolism by regulating the expression of lipogenic genes. In addition, TORC1 participates in the cell cycle, increasing the length of the G2 phase. In the present work, we investigated the effect of rapamycin on cell growth, cell morphology and neutral lipid metabolism in the phytopathogenic fungus Ustilago maydis. Inhibition of TORC1 by rapamycin induced the formation of septa that separate the nuclei that were formed after mitosis. Regarding neutral lipid metabolism, a higher accumulation of triacylglycerols was not detected, but the cells did contain large lipid bodies, which suggests that small lipid bodies became fused into big lipid droplets. Vacuoles showed a similar behavior as the lipid bodies, and double labeling with Blue-CMAC and BODIPY indicates that vacuoles and lipid bodies were independent organelles. The results suggest that TORC1 has a role in cell morphology, lipid metabolism, and vacuolar physiology in U. maydis.
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14
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Reidman S, Cohen A, Kupiec M, Weisman R. The cytosolic form of aspartate aminotransferase is required for full activation of TOR complex 1 in fission yeast. J Biol Chem 2019; 294:18244-18255. [PMID: 31641022 DOI: 10.1074/jbc.ra119.010101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/18/2019] [Indexed: 12/17/2022] Open
Abstract
The evolutionarily conserved TOR complex 1 (TORC1) activates cell growth and proliferation in response to nutritional signals. In the fission yeast Schizosaccharomyces pombe, TORC1 is essential for vegetative growth, and its activity is regulated in response to nitrogen quantity and quality. Yet, how TORC1 senses nitrogen is poorly understood. Rapamycin, a specific TOR inhibitor, inhibits growth in S. pombe only under conditions in which the activity of TORC1 is compromised. In a genetic screen for rapamycin-sensitive mutations, we isolated caa1-1, a loss-of-function mutation of the cytosolic form of aspartate aminotransferase (Caa1). We demonstrate that loss of caa1 + partially mimics loss of TORC1 activity and that Caa1 is required for full TORC1 activity. Disruption of caa1 + resulted in aspartate auxotrophy, a finding that prompted us to assess the role of aspartate in TORC1 activation. We found that the amino acids glutamine, asparagine, arginine, aspartate, and serine activate TORC1 most efficiently following nitrogen starvation. The glutamine synthetase inhibitor l-methionine sulfoximine abolished the ability of asparagine, arginine, aspartate, or serine, but not that of glutamine, to induce TORC1 activity, consistent with a central role for glutamine in activating TORC1. Neither addition of aspartate nor addition of glutamine restored TORC1 activity in caa1-deleted cells or in cells carrying a Caa1 variant with a catalytic site substitution, suggesting that the catalytic activity of Caa1 is required for TORC1 activation. Taken together, our results reveal the contribution of the key metabolic enzyme Caa1 to TORC1 activity in S. pombe.
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Affiliation(s)
- Sophie Reidman
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Adiel Cohen
- Department of Natural and Life Sciences, the Open University of Israel, University Road 1, 4353701 Ra'anana, Israel
| | - Martin Kupiec
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv 69977801, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, the Open University of Israel, University Road 1, 4353701 Ra'anana, Israel.
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15
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Andreadis C, Hulme L, Wensley K, Liu JL. The TOR pathway modulates cytoophidium formation in Schizosaccharomyces pombe. J Biol Chem 2019; 294:14686-14703. [PMID: 31431504 PMCID: PMC6779450 DOI: 10.1074/jbc.ra119.009913] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/09/2019] [Indexed: 12/30/2022] Open
Abstract
CTP synthase (CTPS) has been demonstrated to form evolutionarily-conserved filamentous structures termed cytoophidia whose exact cellular functions remain unclear, but they may play a role in intracellular compartmentalization. We have previously shown that the mammalian target of rapamycin complex 1 (mTORC1)-S6K1 pathway mediates cytoophidium assembly in mammalian cells. Here, using the fission yeast Schizosaccharomyces pombe as a model of a unicellular eukaryote, we demonstrate that the target of rapamycin (TOR)-signaling pathway regulates cytoophidium formation (from the S. pombe CTPS ortholog Cts1) also in S. pombe Conducting a systematic analysis of all viable single TOR subunit-knockout mutants and of several major downstream effector proteins, we found that Cts1 cytoophidia are significantly shortened and often dissociate when TOR is defective. We also found that the activities of the downstream effector kinases of the TORC1 pathway, Sck1, Sck2, and Psk1 S6, as well as of the S6K/AGC kinase Gad8, the major downstream effector kinase of the TORC2 pathway, are necessary for proper cytoophidium filament formation. Interestingly, we observed that the Crf1 transcriptional corepressor for ribosomal genes is a strong effector of Cts1 filamentation. Our findings connect TOR signaling, a major pathway required for cell growth, with the compartmentalization of the essential nucleotide synthesis enzyme CTPS, and we uncover differences in the regulation of its filamentation among higher multicellular and unicellular eukaryotic systems.
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Affiliation(s)
- Christos Andreadis
- School of Life Sciences and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Lydia Hulme
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Katherine Wensley
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Ji-Long Liu
- School of Life Sciences and Technology, ShanghaiTech University, 201210 Shanghai, China .,MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
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16
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Suda K, Kaneko A, Shimobayashi M, Nakashima A, Maeda T, Hall MN, Ushimaru T. TORC1 regulates autophagy induction in response to proteotoxic stress in yeast and human cells. Biochem Biophys Res Commun 2019; 511:434-439. [PMID: 30797551 DOI: 10.1016/j.bbrc.2019.02.077] [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: 02/05/2019] [Accepted: 02/15/2019] [Indexed: 11/18/2022]
Abstract
Misfolded and aggregated proteins are eliminated to maintain protein homeostasis. Autophagy contributes to the removal of protein aggregates. However, if and how proteotoxic stress induces autophagy is poorly understood. Here we show that proteotoxic stress after treatment with azetidine-2-carboxylic acid (AZC), a toxic proline analog, induces autophagy in budding yeast. AZC treatment attenuated target of rapamycin complex 1 (TORC1) activity, resulting in the dephosphorylation of Atg13, a key factor of autophagy. By contrast, AZC treatment did not affect target of rapamycin complex 2 (TORC2). Proteotoxic stress also induced TORC1 inactivation and autophagy in fission yeast and human cells. This study suggested that TORC1 is a conserved key factor to cope with proteotoxic stress in eukaryotic cells.
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Affiliation(s)
- Kazuki Suda
- Department of Biological Science, Shizuoka University, Shizuoka, 422-8021, Japan
| | - Atsuki Kaneko
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8021, Japan
| | | | - Akio Nakashima
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Michael N Hall
- Biozentrum, University of Basel, 4056, Basel, Switzerland, Switzerland
| | - Takashi Ushimaru
- Department of Biological Science, Shizuoka University, Shizuoka, 422-8021, Japan; Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8021, Japan.
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17
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Tay YD, Leda M, Goryachev AB, Sawin KE. Local and global Cdc42 guanine nucleotide exchange factors for fission yeast cell polarity are coordinated by microtubules and the Tea1-Tea4-Pom1 axis. J Cell Sci 2018; 131:jcs.216580. [PMID: 29930085 PMCID: PMC6080602 DOI: 10.1242/jcs.216580] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/14/2018] [Indexed: 12/30/2022] Open
Abstract
The conserved Rho-family GTPase Cdc42 plays a central role in eukaryotic cell polarity. The rod-shaped fission yeast Schizosaccharomyces pombe has two Cdc42 guanine nucleotide exchange factors (GEFs), Scd1 and Gef1, but little is known about how they are coordinated in polarized growth. Although the microtubule cytoskeleton is normally not required for polarity maintenance in fission yeast, we show here that when scd1 function is compromised, disruption of microtubules or the polarity landmark proteins Tea1, Tea4 or Pom1 leads to disruption of polarized growth. Instead, cells adopt an isotropic-like pattern of growth, which we term PORTLI growth. Surprisingly, PORTLI growth is caused by spatially inappropriate activity of Gef1. Although most Cdc42 GEFs are membrane associated, we find that Gef1 is a broadly distributed cytosolic protein rather than a membrane-associated protein at cell tips like Scd1. Microtubules and the Tea1–Tea4–Pom1 axis counteract inappropriate Gef1 activity by regulating the localization of the Cdc42 GTPase-activating protein Rga4. Our results suggest a new model of fission yeast cell polarity regulation, involving coordination of ‘local’ (Scd1) and ‘global’ (Gef1) Cdc42 GEFs via microtubules and microtubule-dependent polarity landmarks. Highlighted Article: Cell polarity in fission yeast is regulated by two different Cdc42 guanine nucleotide exchange factors, coordinated by the microtubule-dependent landmark system.
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Affiliation(s)
- Ye Dee Tay
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Marcin Leda
- SynthSys - Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Andrew B Goryachev
- SynthSys - Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Kenneth E Sawin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
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18
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Koh CS, Sarin LP. Transfer RNA modification and infection – Implications for pathogenicity and host responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:419-432. [DOI: 10.1016/j.bbagrm.2018.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/04/2018] [Accepted: 01/19/2018] [Indexed: 12/19/2022]
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19
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Chia KH, Fukuda T, Sofyantoro F, Matsuda T, Amai T, Shiozaki K. Ragulator and GATOR1 complexes promote fission yeast growth by attenuating TOR complex 1 through Rag GTPases. eLife 2017; 6:30880. [PMID: 29199950 PMCID: PMC5752196 DOI: 10.7554/elife.30880] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 12/02/2017] [Indexed: 12/18/2022] Open
Abstract
TOR complex 1 (TORC1) is an evolutionarily conserved protein kinase complex that promotes cellular macromolecular synthesis and suppresses autophagy. Amino-acid-induced activation of mammalian TORC1 is initiated by its recruitment to the RagA/B-RagC/D GTPase heterodimer, which is anchored to lysosomal membranes through the Ragulator complex. We have identified in the model organism Schizosaccharomyces pombe a Ragulator-like complex that tethers the Gtr1-Gtr2 Rag heterodimer to the membranes of vacuoles, the lysosome equivalent in yeasts. Unexpectedly, the Ragulator-Rag complex is not required for the vacuolar targeting of TORC1, but the complex plays a crucial role in attenuating TORC1 activity independently of the Tsc1-Tsc2 complex, a known negative regulator of TORC1 signaling. The GATOR1 complex, which functions as Gtr1 GAP, is essential for the TORC1 attenuation by the Ragulator-Rag complex, suggesting that Gtr1GDP-Gtr2 on vacuolar membranes moderates TORC1 signaling for optimal cellular response to nutrients.
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Affiliation(s)
- Kim Hou Chia
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Tomoyuki Fukuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.,Department of Cellular Physiology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Fajar Sofyantoro
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.,Department of Animal Physiology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Takato Matsuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Takamitsu Amai
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Kazuhiro Shiozaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan.,Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
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20
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TORC1-Dependent Phosphorylation Targets in Fission Yeast. Biomolecules 2017; 7:biom7030050. [PMID: 28671615 PMCID: PMC5618231 DOI: 10.3390/biom7030050] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 12/11/2022] Open
Abstract
Target of rapamycin (TOR) kinase controls cell metabolism and growth in response to environmental cues such as nutrients, growth factors, and stress. TOR kinase is widely conserved across eukaryotes. As in other organisms, the fission yeast Schizosaccharomyces pombe has two types of TOR complex, namely TOR complex 1 (TORC1) and TORC2. It is interesting that the two TOR complexes in S. pombe have opposite roles in sexual differentiation, which is induced by nutrient starvation. TORC1, which contains Tor2 as a catalytic subunit, promotes vegetative growth and represses sexual differentiation in nutrient-rich conditions, while TORC2 is required for the initiation of sexual differentiation. Multiple targets of TORC1 have been identified. Some of these, such as S6 kinase and an autophagy regulator Atg13, are known targets in other organisms. In addition, there is a novel group of TORC1 targets involved in the regulation of sexual differentiation. Here, we review recent findings on phosphorylation targets of TORC1 in S. pombe. Furthermore, we briefly report a novel S. pombe target of TORC1.
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21
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An In Vitro TORC1 Kinase Assay That Recapitulates the Gtr-Independent Glutamine-Responsive TORC1 Activation Mechanism on Yeast Vacuoles. Mol Cell Biol 2017; 37:MCB.00075-17. [PMID: 28483912 DOI: 10.1128/mcb.00075-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/01/2017] [Indexed: 01/03/2023] Open
Abstract
Evolutionarily conserved target of rapamycin (TOR) complex 1 (TORC1) responds to nutrients, especially amino acids, to promote cell growth. In the yeast Saccharomyces cerevisiae, various nitrogen sources activate TORC1 with different efficiencies, although the mechanism remains elusive. Leucine, and perhaps other amino acids, was reported to activate TORC1 via the heterodimeric small GTPases Gtr1-Gtr2, the orthologues of the mammalian Rag GTPases. More recently, an alternative Gtr-independent TORC1 activation mechanism that may respond to glutamine was reported, although its molecular mechanism is not clear. In studying the nutrient-responsive TORC1 activation mechanism, the lack of an in vitro assay hinders associating particular nutrient compounds with the TORC1 activation status, whereas no in vitro assay that shows nutrient responsiveness has been reported. In this study, we have developed a new in vitro TORC1 kinase assay that reproduces, for the first time, the nutrient-responsive TORC1 activation. This in vitro TORC1 assay recapitulates the previously predicted Gtr-independent glutamine-responsive TORC1 activation mechanism. Using this system, we found that this mechanism specifically responds to l-glutamine, resides on the vacuolar membranes, and involves a previously uncharacterized Vps34-Vps15 phosphatidylinositol (PI) 3-kinase complex and the PI-3-phosphate [PI(3)P]-binding FYVE domain-containing vacuolar protein Pib2. Thus, this system was proved to be useful for dissecting the glutamine-responsive TORC1 activation mechanism.
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22
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Schweizer U, Bohleber S, Fradejas-Villar N. The modified base isopentenyladenosine and its derivatives in tRNA. RNA Biol 2017; 14:1197-1208. [PMID: 28277934 PMCID: PMC5699536 DOI: 10.1080/15476286.2017.1294309] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Base 37 in tRNA, 3′-adjacent to the anticodon, is occupied by a purine base that is thought to stabilize codon recognition by stacking interactions on the first Watson-Crick base pair. If the first codon position forms an A.U or U.A base pair, the purine is likely further modified in all domains of life. One of the first base modifications found in tRNA is N6-isopentenyl adenosine (i6A) present in a fraction of tRNAs in bacteria and eukaryotes, which can be further modified to 2-methyl-thio-N6-isopentenyladenosine (ms2i6A) in a subset of tRNAs. Homologous tRNA isopentenyl transferase enzymes have been identified in bacteria (MiaA), yeast (Mod5, Tit1), roundworm (GRO-1), and mammals (TRIT1). In eukaryotes, isopentenylation of cytoplasmic and mitochondrial tRNAs is mediated by products of the same gene. Accordingly, a patient with homozygous mutations in TRIT1 has mitochondrial disease. The role of i6A in a subset of tRNAs in gene expression has been linked with translational fidelity, speed of translation, skewed gene expression, and non-sense suppression. This review will not cover the action of i6A as a cytokinin in plants or the potential function of Mod5 as a prion in yeast.
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Affiliation(s)
- Ulrich Schweizer
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Simon Bohleber
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Noelia Fradejas-Villar
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
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23
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Kurauchi T, Hashizume A, Imai Y, Hayashi K, Tsubouchi S, Ihara K, Ohtsuka H, Aiba H. Identification of a novel protein kinase that affects the chronological lifespan in fission yeast. FEMS Microbiol Lett 2016; 364:fnw257. [PMID: 28108582 DOI: 10.1093/femsle/fnw257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/24/2016] [Accepted: 11/08/2016] [Indexed: 01/03/2023] Open
Abstract
Chronological lifespan is defined by how long a cell can survive in a non-dividing state. In yeast, it is measured by viability after entry into the stationary phase. To understand the regulatory mechanisms of chronological lifespan in Schizosaccharomyces pombe, it is necessary to identify and characterize novel factors involved in the regulation of chronological lifespan. To this end, we have screened for a long-lived mutant and identified that novel gene nnk1+ that encodes an essential protein kinase is the determinant of chronological lifespan. We showed that the expression of major glucose transporter gene, ght5+, is decreased in the isolated nnk1-35 mutant, suggesting that Nnk1 protein is involved in the regulation of ght5+ The consumption of glucose in the growth medium after saturated growth was lower in the nnk1-35 mutant than that in wild-type cell. The isolated ght5 deletion mutant showed long-lived phenotype. Based on these results, we propose that Nnk1 regulates chronological lifespan through the regulation of ght5+ Nnk1 might coordinate glucose availability and lifespan in fission yeast.
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Affiliation(s)
- Tatsuhiro Kurauchi
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Aya Hashizume
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yuki Imai
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kanako Hayashi
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Satoshi Tsubouchi
- Laboratory of Molecular Microbiology, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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24
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Hatano T, Morigasaki S, Tatebe H, Ikeda K, Shiozaki K. Fission yeast Ryh1 GTPase activates TOR Complex 2 in response to glucose. Cell Cycle 2015; 14:848-56. [PMID: 25590601 PMCID: PMC4612450 DOI: 10.1080/15384101.2014.1000215] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Target Of Rapamycin (TOR) is an evolutionarily conserved protein kinase that forms 2 distinct protein complexes referred to as TOR complex 1 (TORC1) and 2 (TORC2). Recent extensive studies have demonstrated that TORC1 is under the control of the small GTPases Rheb and Rag that funnel multiple input signals including those derived from nutritional sources; however, information is scarce as to the regulation of TORC2. A previous study using the model system provided by the fission yeast Schizosaccharomyces pombe identified Ryh1, a Rab-family GTPase, as an activator of TORC2. Here, we show that the nucleotide-binding state of Ryh1 is regulated in response to glucose, mediating this major nutrient signal to TORC2. In glucose-rich growth media, the GTP-bound form of Ryh1 induces TORC2-dependent phosphorylation of Gad8, a downstream target of TORC2 in fission yeast. Upon glucose deprivation, Ryh1 becomes inactive, which turns off the TORC2-Gad8 pathway. During glucose starvation, however, Gad8 phosphorylation by TORC2 gradually recovers independently of Ryh1, implying an additional TORC2 activator that is regulated negatively by glucose. The paired positive and negative regulatory mechanisms may allow fine-tuning of the TORC2-Gad8 pathway, which is essential for growth under glucose-limited environment.
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Affiliation(s)
- Tomoyuki Hatano
- a Graduate School of Biological Sciences , Nara Institute of Science and Technology , Ikoma , Nara , Japan
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Cytoplasmic mRNA turnover and ageing. Mech Ageing Dev 2015; 152:32-42. [PMID: 26432921 PMCID: PMC4710634 DOI: 10.1016/j.mad.2015.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/17/2015] [Accepted: 09/27/2015] [Indexed: 12/12/2022]
Abstract
We address the cytoplasmic mRNA decay processes that determine the mRNAs half-life. We briefly describe the major, evolutionary conserved, ageing pathways and mechanisms. We summarize critical findings that link mRNA turnover and ageing modulators.
Messenger RNA (mRNA) turnover that determines the lifetime of cytoplasmic mRNAs is a means to control gene expression under both normal and stress conditions, whereas its impact on ageing and age-related disorders has just become evident. Gene expression control is achieved at the level of the mRNA clearance as well as mRNA stability and accessibility to other molecules. All these processes are regulated by cis-acting motifs and trans-acting factors that determine the rates of translation and degradation of transcripts. Specific messenger RNA granules that harbor the mRNA decay machinery or various factors, involved in translational repression and transient storage of mRNAs, are also part of the mRNA fate regulation. Their assembly and function can be modulated to promote stress resistance to adverse conditions and over time affect the ageing process and the lifespan of the organism. Here, we provide insights into the complex relationships of ageing modulators and mRNA turnover mechanisms.
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Hindupur SK, González A, Hall MN. The opposing actions of target of rapamycin and AMP-activated protein kinase in cell growth control. Cold Spring Harb Perspect Biol 2015; 7:a019141. [PMID: 26238356 DOI: 10.1101/cshperspect.a019141] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cell growth is a highly regulated, plastic process. Its control involves balancing positive regulation of anabolic processes with negative regulation of catabolic processes. Although target of rapamycin (TOR) is a major promoter of growth in response to nutrients and growth factors, AMP-activated protein kinase (AMPK) suppresses anabolic processes in response to energy stress. Both TOR and AMPK are conserved throughout eukaryotic evolution. Here, we review the fundamentally important roles of these two kinases in the regulation of cell growth with particular emphasis on their mutually antagonistic signaling.
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Affiliation(s)
| | - Asier González
- Biozentrum, University of Basel, CH4056 Basel, Switzerland
| | - Michael N Hall
- Biozentrum, University of Basel, CH4056 Basel, Switzerland
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Huang X, Leggas M, Dickson RC. Drug synergy drives conserved pathways to increase fission yeast lifespan. PLoS One 2015; 10:e0121877. [PMID: 25786258 PMCID: PMC4364780 DOI: 10.1371/journal.pone.0121877] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/11/2015] [Indexed: 01/02/2023] Open
Abstract
Aging occurs over time with gradual and progressive loss of physiological function. Strategies to reduce the rate of functional loss and mitigate the subsequent onset of deadly age-related diseases are being sought. We demonstrated previously that a combination of rapamycin and myriocin reduces age-related functional loss in the Baker’s yeast Saccharomyces cerevisiae and produces a synergistic increase in lifespan. Here we show that the same drug combination also produces a synergistic increase in the lifespan of the fission yeast Schizosaccharomyces pombe and does so by controlling signal transduction pathways conserved across a wide evolutionary time span ranging from yeasts to mammals. Pathways include the target of rapamycin complex 1 (TORC1) protein kinase, the protein kinase A (PKA) and a stress response pathway, which in fission yeasts contains the Sty1 protein kinase, an ortholog of the mammalian p38 MAP kinase, a type of Stress Activated Protein Kinase (SAPK). These results along with previous studies in S. cerevisiae support the premise that the combination of rapamycin and myriocin enhances lifespan by regulating signaling pathways that couple nutrient and environmental conditions to cellular processes that fine-tune growth and stress protection in ways that foster long term survival. The molecular mechanisms for fine-tuning are probably species-specific, but since they are driven by conserved nutrient and stress sensing pathways, the drug combination may enhance survival in other organisms.
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Affiliation(s)
- Xinhe Huang
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky, United States of America
- * E-mail: (RCD); (XH)
| | - Markos Leggas
- Department of Pharmaceutical Sciences and the Lucille Markey Cancer Center, College of Pharmacy, University of Kentucky, Lexington, Kentucky, United States of America
| | - Robert C. Dickson
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, Kentucky, United States of America
- * E-mail: (RCD); (XH)
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Davie E, Forte GMA, Petersen J. Nitrogen regulates AMPK to control TORC1 signaling. Curr Biol 2015; 25:445-54. [PMID: 25639242 PMCID: PMC4331286 DOI: 10.1016/j.cub.2014.12.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/06/2014] [Accepted: 12/10/2014] [Indexed: 10/29/2022]
Abstract
BACKGROUND Cell growth and cell-cycle progression are tightly coordinated to enable cells to adjust their size (timing of division) to the demands of proliferation in varying nutritional environments. In fission yeast, nitrogen stress results in sustained proliferation at a reduced size. RESULTS Here, we show that cells can sense nitrogen stress to reduce target of rapamycin complex-1 (TORC1) activity. Nitrogen-stress-induced TORC1 inhibition differs from amino-acid-dependent control of TORC1 and requires the Ssp2 (AMPKα) kinase, the Tsc1/2 complex, and Rhb1 GTPase. Importantly, the β and γ regulatory subunits of AMPK are not required to control cell division in response to nitrogen stress, providing evidence for a nitrogen-sensing mechanism that is independent of changes in intracellular ATP/AMP levels. The CaMKK homolog Ssp1 is constitutively required for phosphorylation of the AMPKα(Ssp2) T loop. However, we find that a second homolog CaMKK(Ppk34) is specifically required to stimulate AMPKα(Ssp2) activation in response to nitrogen stress. Finally, ammonia also controls mTORC1 activity in human cells; mTORC1 is activated upon the addition of ammonium to glutamine-starved Hep3B cancer cells. CONCLUSIONS The alternative nitrogen source ammonia can simulate TORC1 activity to support growth and division under challenging nutrient settings, a situation often seen in cancer.
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Affiliation(s)
- Elizabeth Davie
- Faculty of Life Sciences, University of Manchester, C.4255 Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Gabriella M A Forte
- Faculty of Life Sciences, University of Manchester, C.4255 Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Janni Petersen
- Faculty of Life Sciences, University of Manchester, C.4255 Michael Smith Building, Oxford Road, Manchester M13 9PT, UK; Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, Adelaide, SA 5001, Australia.
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Evans SK, Burgess KEV, Gray JV. Recovery from rapamycin: drug-insensitive activity of yeast target of rapamycin complex 1 (TORC1) supports residual proliferation that dilutes rapamycin among progeny cells. J Biol Chem 2014; 289:26554-26565. [PMID: 25104356 DOI: 10.1074/jbc.m114.589754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The target of rapamycin complex 1 (TORC1) is a key conserved regulator of eukaryotic cell growth. The xenobiotic rapamycin is a potent inhibitor of the yeast complex. Surprisingly, the EGO complex, a nonessential in vivo activator of TORC1, is somehow required for yeast cells to recover efficiently from a period of treatment with rapamycin. Why? Here, we found that rapamycin is only a partial inhibitor of TORC1. We confirmed that saturating amounts of rapamycin do not fully inhibit proliferation of wild-type cells, and we found that the residual proliferation in the presence of the drug is dependent on the EGO complex and on the activity of TORC1. We found that this residual TORC1-dependent proliferation is key to recovery from rapamycin treatment. First, the residual proliferation rate correlates with the ability of cells to recover from treatment. Second, the residual proliferation rate persists long after washout of the drug and until cells recover. Third, the total observable pool of cell-associated rapamycin is extremely stable and decreases only with increasing cell number after washout of the drug. Finally, consideration of the residual proliferation rate alone accurately and quantitatively accounts for the kinetics of recovery of wild-type cells and for the nature and severity of the ego- mutant defect. Overall, our results revealed that rapamycin is a partial inhibitor of yeast TORC1, that persistence of the drug limits recovery, and that rapamycin is not detoxified by yeast but is passively diluted among progeny cells because of residual proliferation.
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Affiliation(s)
- Stephanie K Evans
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ and
| | - Karl E V Burgess
- Glasgow Polyomics, Translational Cancer Research Centre, University of Glasgow, Glasgow G61 1QH, Scotland, United Kingdom
| | - Joseph V Gray
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ and.
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Cohen A, Kupiec M, Weisman R. Glucose activates TORC2-Gad8 protein via positive regulation of the cAMP/cAMP-dependent protein kinase A (PKA) pathway and negative regulation of the Pmk1 protein-mitogen-activated protein kinase pathway. J Biol Chem 2014; 289:21727-37. [PMID: 24928510 DOI: 10.1074/jbc.m114.573824] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The target of rapamycin (TOR) kinase belongs to the highly conserved eukaryotic family of phosphatidylinositol 3-kinase-related kinases. TOR proteins are found at the core of two evolutionary conserved complexes, known as TORC1 and TORC2. In fission yeast, TORC2 is dispensable for proliferation under optimal growth conditions but is required for starvation and stress responses. TORC2 has been implicated in a wide variety of functions; however, the signals that regulate TORC2 activity have so far remained obscure. TORC2 has one known direct substrate, the AGC kinase Gad8, which is related to AKT in human cells. Gad8 is phosphorylated by TORC2 at Ser-546 (equivalent to AKT Ser-473), leading to its activation. Here, we show that glucose is necessary and sufficient to induce Gad8 Ser-546 phosphorylation in vivo and Gad8 kinase activity in vitro. The glucose signal that activates TORC2-Gad8 is mediated via the cAMP/PKA pathway, a major glucose-sensing pathway. By contrast, Pmk1, similar to human extracellular signal-regulated kinases and a major stress-induced mitogen activated protein kinase (MAPK) in fission yeast, inhibits TORC2-dependent Gad8 phosphorylation and activation. Inhibition of TORC2-Gad8 also occurs in response to ionic or osmotic stress, in a manner dependent on the cAMP/PKA and Pmk1-MAPK signaling pathways. Our findings highlight the significance of glucose availability in regulation of TORC2-Gad8 and indicate a novel link between the cAMP/PKA, Pmk1/MAPK, and TORC2-Gad8 signaling.
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Affiliation(s)
- Adiel Cohen
- From the Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana and
| | - Martin Kupiec
- the Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ronit Weisman
- From the Department of Natural and Life Sciences, Open University of Israel, University Road 1, 4353701 Ranana and
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Iida N, Yamao F, Nakamura Y, Iida T. Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence. Genes Cells 2014; 19:517-27. [PMID: 24766403 DOI: 10.1111/gtc.12151] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 03/09/2014] [Indexed: 11/30/2022]
Abstract
In forward genetics, identification of mutations is a time-consuming and laborious process. Modern whole-genome sequencing, coupled with bioinformatics analysis, has enabled fast and cost-effective mutation identification. However, for many experimental researchers, bioinformatics analysis is still a difficult aspect of whole-genome sequencing. To address this issue, we developed a browser-accessible and easy-to-use bioinformatics tool called Mutation discovery (Mudi; http://naoii.nig.ac.jp/mudi_top.html), which enables 'one-click' identification of causative mutations from whole-genome sequence data. In this study, we optimized Mudi for pooled-linkage analysis aimed at identifying mutants in yeast model systems. After raw sequencing data are uploaded, Mudi performs sequential analysis, including mapping, detection of variant alleles, filtering and removal of background polymorphisms, prioritization, and annotation. In an example study of suppressor mutants of ptr1-1 in the fission yeast Schizosaccharomyces pombe, pooled-linkage analysis with Mudi identified mip1(+) , a component of Target of Rapamycin Complex 1 (TORC1), as a novel component involved in RNA interference (RNAi)-related cell-cycle control. The accessibility of Mudi will accelerate systematic mutation analysis in forward genetics.
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Affiliation(s)
- Naoko Iida
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
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Rallis C, López-Maury L, Georgescu T, Pancaldi V, Bähler J. Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth. Biol Open 2014; 3:161-71. [PMID: 24463365 PMCID: PMC3925319 DOI: 10.1242/bio.20147245] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Target of rapamycin complex 1 (TORC1), which controls growth in response to nutrients, promotes ageing in multiple organisms. The fission yeast Schizosaccharomyces pombe emerges as a valuable genetic model system to study TORC1 function and cellular ageing. Here we exploited the combinatorial action of rapamycin and caffeine, which inhibit fission yeast growth in a TORC1-dependent manner. We screened a deletion library, comprising ∼84% of all non-essential fission yeast genes, for drug-resistant mutants. This screen identified 33 genes encoding functions such as transcription, kinases, mitochondrial respiration, biosynthesis, intra-cellular trafficking, and stress response. Among the corresponding mutants, 5 showed shortened and 21 showed increased maximal chronological lifespans; 15 of the latter mutants showed no further lifespan increase with rapamycin and might thus represent key targets downstream of TORC1. We pursued the long-lived sck2 mutant with additional functional analyses, revealing that the Sck2p kinase functions within the TORC1 network and is required for normal cell growth, global protein translation, and ribosomal S6 protein phosphorylation in a nutrient-dependent manner. Notably, slow cell growth was associated with all long-lived mutants while oxidative-stress resistance was not.
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Affiliation(s)
- Charalampos Rallis
- Department of Genetics, Evolution and Environment, and Institute of Healthy Ageing, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK
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Isp7 is a novel regulator of amino acid uptake in the TOR signaling pathway. Mol Cell Biol 2013; 34:794-806. [PMID: 24344203 DOI: 10.1128/mcb.01473-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TOR proteins reside in two distinct complexes, TOR complexes 1 and 2 (TORC1 and TORC2), that are central for the regulation of cellular growth, proliferation, and survival. TOR is also the target for the immunosuppressive and anticancer drug rapamycin. In Schizosaccharomyces pombe, disruption of the TSC complex, mutations in which can lead to the tuberous sclerosis syndrome in humans, results in a rapamycin-sensitive phenotype under poor nitrogen conditions. We show here that the sensitivity to rapamycin is mediated via inhibition of TORC1 and suppressed by overexpression of isp7(+), a member of the family of 2-oxoglutarate-Fe(II)-dependent oxygenase genes. The transcript level of isp7(+) is negatively regulated by TORC1 but positively regulated by TORC2. Yet we find extensive similarity between the transcriptome of cells disrupted for isp7(+) and cells mutated in the catalytic subunit of TORC1. Moreover, Isp7 regulates amino acid permease expression in a fashion similar to that of TORC1 and opposite that of TORC2. Overexpression of isp7(+) induces TORC1-dependent phosphorylation of ribosomal protein Rps6 while inhibiting TORC2-dependent phosphorylation and activation of the AGC-like kinase Gad8. Taken together, our findings suggest a central role for Isp7 in amino acid homeostasis and the presence of isp7(+)-dependent regulatory loops that affect both TORC1 and TORC2.
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Imamura S, Ishiwata A, Watanabe S, Yoshikawa H, Tanaka K. Expression of budding yeast FKBP12 confers rapamycin susceptibility to the unicellular red alga Cyanidioschyzon merolae. Biochem Biophys Res Commun 2013; 439:264-9. [PMID: 23973485 DOI: 10.1016/j.bbrc.2013.08.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 08/14/2013] [Indexed: 12/31/2022]
Abstract
The target of rapamycin (TOR) is serine/threonine protein kinase that is highly conserved among eukaryotes and can be inactivated by the antibiotic rapamycin through the formation of a ternary complex composed of rapamycin and two proteins, TOR and FKBP12. Differing from fungi and animals, plant FKBP12 proteins are unable to form the ternary complex, and thus plant TORs are insensitive to rapamycin. This has led to a poor understanding of TOR functions in plants. As a first step toward the understanding of TOR function in a rapamycin-insensitive unicellular red alga, Cyanidioschyzon merolae, we constructed a rapamycin-susceptible strain in which the Saccharomyces cerevisiae FKBP12 protein (ScFKBP12) was expressed. Treatment with rapamycin resulted in growth inhibition and decreased polysome formation in this strain. Binding of ScFKBP12 with C. merolae TOR in the presence of rapamycin was demonstrated in vivo and in vitro by pull-down experiments. Moreover, in vitro kinase assay showed that inhibition of C. merolae TOR kinase activity was dependent on ScFKBP12 and rapamycin.
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Affiliation(s)
- Sousuke Imamura
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama 226-8503, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
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Rallis C, Codlin S, Bähler J. TORC1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast. Aging Cell 2013; 12:563-73. [PMID: 23551936 PMCID: PMC3798131 DOI: 10.1111/acel.12080] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2013] [Indexed: 01/06/2023] Open
Abstract
Target of rapamycin complex 1 (TORC1) is implicated in growth control and aging from yeast to humans. Fission yeast is emerging as a popular model organism to study TOR signaling, although rapamycin has been thought to not affect cell growth in this organism. Here, we analyzed the effects of rapamycin and caffeine, singly and combined, on multiple cellular processes in fission yeast. The two drugs led to diverse and specific phenotypes that depended on TORC1 inhibition, including prolonged chronological lifespan, inhibition of global translation, inhibition of cell growth and division, and reprograming of global gene expression mimicking nitrogen starvation. Rapamycin and caffeine differentially affected these various TORC1-dependent processes. Combined drug treatment augmented most phenotypes and effectively blocked cell growth. Rapamycin showed a much more subtle effect on global translation than did caffeine, while both drugs were effective in prolonging chronological lifespan. Rapamycin and caffeine did not affect the lifespan via the pH of the growth media. Rapamycin prolonged the lifespan of nongrowing cells only when applied during the growth phase but not when applied after cells had stopped proliferation. The doses of rapamycin and caffeine strongly correlated with growth inhibition and with lifespan extension. This comprehensive analysis will inform future studies into TORC1 function and cellular aging in fission yeast and beyond.
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Affiliation(s)
- Charalampos Rallis
- Department of Genetics Evolution & Environment and Institute of Healthy Ageing University College London Gower Street – Darwin Building London WC1E 6BT UK
| | - Sandra Codlin
- Department of Genetics Evolution & Environment and Institute of Healthy Ageing University College London Gower Street – Darwin Building London WC1E 6BT UK
| | - Jürg Bähler
- Department of Genetics Evolution & Environment and Institute of Healthy Ageing University College London Gower Street – Darwin Building London WC1E 6BT UK
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Beuzelin C, Evnouchidou I, Rigolet P, Cauvet-Burgevin A, Girard PM, Dardalhon D, Culina S, Gdoura A, van Endert P, Francesconi S. Deletion of the fission yeast homologue of human insulinase reveals a TORC1-dependent pathway mediating resistance to proteotoxic stress. PLoS One 2013; 8:e67705. [PMID: 23826334 PMCID: PMC3691139 DOI: 10.1371/journal.pone.0067705] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/21/2013] [Indexed: 01/06/2023] Open
Abstract
Insulin Degrading Enzyme (IDE) is a protease conserved through evolution with a role in diabetes and Alzheimer's disease. The reason underlying its ubiquitous expression including cells lacking identified IDE substrates remains unknown. Here we show that the fission yeast IDE homologue (Iph1) modulates cellular sensitivity to endoplasmic reticulum (ER) stress in a manner dependent on TORC1 (Target of Rapamycin Complex 1). Reduced sensitivity to tunicamycin was associated with a smaller number of cells undergoing apoptosis. Wild type levels of tunicamycin sensitivity were restored in iph1 null cells when the TORC1 complex was inhibited by rapamycin or by heat inactivation of the Tor2 kinase. Although Iph1 cleaved hallmark IDE substrates including insulin efficiently, its role in the ER stress response was independent of its catalytic activity since expression of inactive Iph1 restored normal sensitivity. Importantly, wild type as well as inactive human IDE complemented gene-invalidated yeast cells when expressed at the genomic locus under the control of iph1+ promoter. These results suggest that IDE has a previously unknown function unrelated to substrate cleavage, which links sensitivity to ER stress to a pro-survival role of the TORC1 pathway.
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Affiliation(s)
- Clémentine Beuzelin
- Institut Curie, Centre de Recherche, Orsay, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3348, Centre Universitaire, Orsay, France
- Université Paris-sud XI, Orsay, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
| | - Irini Evnouchidou
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
| | - Pascal Rigolet
- Institut Curie, Centre de Recherche, Orsay, France
- Université Paris-sud XI, Orsay, France
| | - Anne Cauvet-Burgevin
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
| | - Pierre-Marie Girard
- Institut Curie, Centre de Recherche, Orsay, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3348, Centre Universitaire, Orsay, France
| | - Delphine Dardalhon
- Institut Curie, Centre de Recherche, Orsay, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3348, Centre Universitaire, Orsay, France
| | - Slobodan Culina
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
| | - Abdelaziz Gdoura
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
| | - Peter van Endert
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité 1013, Paris, France
| | - Stefania Francesconi
- Institut Curie, Centre de Recherche, Orsay, France
- Centre Nationale de la Recherche Scientifique, Unité Mixte de Recherche 3348, Centre Universitaire, Orsay, France
- * E-mail:
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Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast. Mol Cell Biol 2013; 33:2918-29. [PMID: 23716598 DOI: 10.1128/mcb.00278-13] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
tRNA isopentenyltransferases (Tit1) modify tRNA position 37, adjacent to the anticodon, to N6-isopentenyladenosine (i6A37) in all cells, yet the tRNA subsets selected for modification vary among species, and their relevance to phenotypes is unknown. We examined the function of i6A37 in Schizosaccharomyces pombe tit1+ and tit1-Δ cells by using a β-galactosidase codon-swap reporter whose catalytic activity is sensitive to accurate decoding of codon 503. i6A37 increased the activity of tRNACys at a cognate codon and that of tRNATyr at a near-cognate codon, suggesting that i6A37 promotes decoding activity generally and increases fidelity at cognate codons while decreasing fidelity at noncognate codons. S. pombe cells lacking tit1+ exhibit slow growth in glycerol or rapamycin. While existing data link wobble base U34 modifications to translation of functionally related mRNAs, whether this might extend to the anticodon-adjacent position 37 was unknown. Indeed, we found a biased presence of i6A37-cognate codons in high-abundance mRNAs for ribosome subunits and energy metabolism, congruent with the observed phenotypes and the idea that i6A37 promotes translational efficiency. Polysome profiles confirmed the decreased translational efficiency of mRNAs in tit1-Δ cells. Because subsets of i6A37-tRNAs differ among species, as do their cognate codon-sensitive mRNAs, these genomic variables may underlie associated phenotypic differences.
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Schonbrun M, Kolesnikov M, Kupiec M, Weisman R. TORC2 is required to maintain genome stability during S phase in fission yeast. J Biol Chem 2013; 288:19649-60. [PMID: 23703609 DOI: 10.1074/jbc.m113.464974] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA damage can occur due to environmental insults or intrinsic metabolic processes and is a major threat to genome stability. The DNA damage response is composed of a series of well coordinated cellular processes that include activation of the DNA damage checkpoint, transient cell cycle arrest, DNA damage repair, and reentry into the cell cycle. Here we demonstrate that mutant cells defective for TOR complex 2 (TORC2) or the downstream AGC-like kinase, Gad8, are highly sensitive to chronic replication stress but are insensitive to ionizing radiation. We show that in response to replication stress, TORC2 is dispensable for Chk1-mediated cell cycle arrest but is required for the return to cell cycle progression. Rad52 is a DNA repair and recombination protein that forms foci at DNA damage sites and stalled replication forks. TORC2 mutant cells show increased spontaneous nuclear Rad52 foci, particularly during S phase, suggesting that TORC2 protects cells from DNA damage that occurs during normal DNA replication. Consistently, the viability of TORC2-Gad8 mutant cells is dependent on the presence of the homologous recombination pathway and other proteins that are required for replication restart following fork replication stalling. Our findings indicate that TORC2 is required for genome integrity. This may be relevant for the growing amount of evidence implicating TORC2 in cancer development.
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Affiliation(s)
- Miriam Schonbrun
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
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Ohtsuka H, Ogawa S, Kawamura H, Sakai E, Ichinose K, Murakami H, Aiba H. Screening for long-lived genes identifies Oga1, a guanine-quadruplex associated protein that affects the chronological lifespan of the fission yeast Schizosaccharomyces pombe. Mol Genet Genomics 2013; 288:285-95. [DOI: 10.1007/s00438-013-0748-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 04/19/2013] [Indexed: 12/31/2022]
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Jaiswal P, Singh SP, Aiyar P, Akkali R, Baskar R. Regulation of multiple tip formation by caffeine in cellular slime molds. BMC DEVELOPMENTAL BIOLOGY 2012; 12:26. [PMID: 22928977 PMCID: PMC3488011 DOI: 10.1186/1471-213x-12-26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/20/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND The multicellular slug in Dictyostelium has a single tip that acts as an organising centre patterning the rest of the slug. High adenosine levels at the tip are believed to be responsible for this tip dominance and the adenosine antagonist, caffeine overrides this dominance promoting multiple tip formation. RESULTS Caffeine induced multiple tip effect is conserved in all the Dictyostelids tested. Two key components of cAMP relay namely, cAMP phosphodiesterase (Pde4) and adenyl cyclase-A (AcaA) levels get reduced during secondary tip formation in Dictyostelium discoideum. Pharmacological inhibition of cAMP phosphodiesterase also resulted in multiple tips. Caffeine reduces cAMP levels by 16.4, 2.34, 4.71 and 6.30 folds, respectively in D. discoideum, D. aureostipes, D. minutum and Polysphondylium pallidum. We propose that altered cAMP levels, perturbed cAMP gradient and impaired signalling may be the critical factors for the origin of multiple tips in other Dictyostelids as well. In the presence of caffeine, slug cell movement gets impaired and restricted. The cell type specific markers, ecmA (prestalk) and pspA (prespore) cells are not equally contributing during additional tip formation. During additional tip emergence, prespore cells transdifferentiate to compensate the loss of prestalk cells. CONCLUSION Caffeine decreases adenyl cyclase-A (AcaA) levels and as a consequence low cAMP is synthesised altering the gradient. Further if cAMP phosphodiesterase (Pde4) levels go down in the presence of caffeine, the cAMP gradient breaks down. When there is no cAMP gradient, directional movement is inhibited and might favour re-differentiation of prespore to prestalk cells.
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Affiliation(s)
- Pundrik Jaiswal
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600036, India
| | - Shashi Prakash Singh
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600036, India
| | - Prasad Aiyar
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600036, India
| | - Rakhil Akkali
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600036, India
| | - Ramamurthy Baskar
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600036, India
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