1
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Ohtsuka H, Ohara K, Shimasaki T, Hatta Y, Maekawa Y, Aiba H. A novel transcription factor Sdr1 involving sulfur depletion response in fission yeast. Genes Cells 2024; 29:667-680. [PMID: 39105351 DOI: 10.1111/gtc.13136] [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: 02/20/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 08/07/2024]
Abstract
In the fission yeast Schizosaccharomyces pombe, the response to sulfur depletion has been less studied compared to the response to nitrogen depletion. Our study reveals that the fission yeast gene, SPCC417.09c, plays a significant role in the sulfur depletion response. This gene encodes a protein with a Zn2Cys6 fungal-type DNA-binding domain and a transcription factor domain, and we have named it sdr1+ (sulfur depletion response 1). Interestingly, while sulfur depletion typically induces autophagy akin to nitrogen depletion, we found that autophagy was not induced under sulfur depletion in the absence of sdr1+. This suggests that sdr1+ is necessary for the induction of autophagy under conditions of sulfur depletion. Although sdr1+ is not essential for the growth of fission yeast, its overexpression, driven by the nmt1 promoter, inhibits growth. This implies that Sdr1 may possess cell growth-inhibitory capabilities. In addition, our analysis of Δsdr1 cells revealed that sdr1+ also plays a role in regulating the expression of genes associated with the phosphate depletion response. In conclusion, our study introduces Sdr1 as a novel transcription factor that contributes to an appropriate cellular nutrient starvation response. It does so by inhibiting inappropriate cell growth and inducing autophagy in response to sulfur depletion.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Kotaro Ohara
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yoshiko Hatta
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yasukichi Maekawa
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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2
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Ohtsuka H, Kawai S, Otsubo Y, Shimasaki T, Yamashita A, Aiba H. Metarhizium robertsii COH1 functionally complements Schizosaccharomyces pombe Ecl family proteins. J GEN APPL MICROBIOL 2024; 69:335-338. [PMID: 37813640 DOI: 10.2323/jgam.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The fission yeast Schizosaccharomyces pombe ecl family genes respond to various starvation signals and induce appropriate intracellular responses, including the extension of chronological lifespan and induction of sexual differentiation. Herein, we propose that the colonization of hemocoel 1 (COH1) protein of Metarhizium robertsii, an insect-pathogenic fungus, is a functional homolog of S. pombe Ecl1 family proteins.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Sawa Kawai
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
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3
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Ohtsuka H, Shimasaki T, Aiba H. Low-Molecular Weight Compounds that Extend the Chronological Lifespan of Yeasts, Saccharomyces cerevisiae, and Schizosaccharomyces pombe. Adv Biol (Weinh) 2024; 8:e2400138. [PMID: 38616173 DOI: 10.1002/adbi.202400138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Yeast is an excellent model organism for research for regulating aging and lifespan, and the studies have made many contributions to date, including identifying various factors and signaling pathways related to aging and lifespan. More than 20 years have passed since molecular biological perspectives are adopted in this research field, and intracellular factors and signal pathways that control aging and lifespan have evolutionarily conserved from yeast to mammals. Furthermore, these findings have been applied to control the aging and lifespan of various model organisms by adjustment of the nutritional environment, genetic manipulation, and drug treatment using low-molecular weight compounds. Among these, drug treatment is easier than the other methods, and research into drugs that regulate aging and lifespan is consequently expected to become more active. Chronological lifespan, a definition of yeast lifespan, refers to the survival period of a cell population under nondividing conditions. Herein, low-molecular weight compounds are summarized that extend the chronological lifespan of Saccharomyces cerevisiae and Schizosaccharomyces pombe, along with their intracellular functions. The low-molecular weight compounds are also discussed that extend the lifespan of other model organisms. Compounds that have so far only been studied in yeast may soon extend lifespan in other organisms.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
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4
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Maekawa Y, Matsui K, Okamoto K, Shimasaki T, Ohtsuka H, Tani M, Ihara K, Aiba H. Identification of plb1 mutation that extends longevity via activating Sty1 MAPK in Schizosaccharomyces pombe. Mol Genet Genomics 2024; 299:20. [PMID: 38424265 DOI: 10.1007/s00438-024-02107-8] [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: 08/02/2023] [Accepted: 12/04/2023] [Indexed: 03/02/2024]
Abstract
To understand the lifespan of higher organisms, including humans, it is important to understand lifespan at the cellular level as a prerequisite. So, fission yeast is a good model organism for the study of lifespan. To identify the novel factors involved in longevity, we are conducting a large-scale screening of long-lived mutant strains that extend chronological lifespan (cell survival in the stationary phase) using fission yeast. One of the newly acquired long-lived mutant strains (No.98 mutant) was selected for analysis and found that the long-lived phenotype was due to a missense mutation (92Phe → Ile) in the plb1+ gene. plb1+ gene in fission yeast is a nonessential gene encoding a homolog of phospholipase B, but its functions under normal growth conditions, as well as phospholipase B activity, remain unresolved. Our analysis of the No.98 mutant revealed that the plb1 mutation reduces the integrity of the cellular membrane and cell wall and activates Sty1 via phosphorylation.
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Affiliation(s)
- Yasukichi Maekawa
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kotaro Matsui
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Keisuke Okamoto
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Motohiro Tani
- Department of Chemistry, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan.
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5
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Park AY, Leney-Greene M, Lynberg M, Gabrielski JQ, Xu X, Schwarz B, Zheng L, Balasubramaniyam A, Ham H, Chao B, Zhang Y, Matthews HF, Cui J, Yao Y, Kubo S, Chanchu JM, Morawski AR, Cook SA, Jiang P, Ravell JC, Cheng YH, George A, Faruqi A, Pagalilauan AM, Bergerson JRE, Ganesan S, Chauvin SD, Aluri J, Edwards-Hicks J, Bohrnsen E, Tippett C, Omar H, Xu L, Butcher GW, Pascall J, Karakoc-Aydiner E, Kiykim A, Maecker H, Tezcan İ, Esenboga S, Heredia RJ, Akata D, Tekin S, Kara A, Kuloglu Z, Unal E, Kendirli T, Dogu F, Karabiber E, Atkinson TP, Cochet C, Filhol O, Bosio CM, Davis MM, Lifton RP, Pearce EL, Daumke O, Aytekin C, Şahin GE, Aksu AÜ, Uzel G, Koneti Rao V, Sari S, Dalgıç B, Boztug K, Cagdas D, Haskologlu S, Ikinciogullari A, Schwefel D, Vilarinho S, Baris S, Ozen A, Su HC, Lenardo MJ. GIMAP5 deficiency reveals a mammalian ceramide-driven longevity assurance pathway. Nat Immunol 2024; 25:282-293. [PMID: 38172257 PMCID: PMC11151279 DOI: 10.1038/s41590-023-01691-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/26/2023] [Indexed: 01/05/2024]
Abstract
Preserving cells in a functional, non-senescent state is a major goal for extending human healthspans. Model organisms reveal that longevity and senescence are genetically controlled, but how genes control longevity in different mammalian tissues is unknown. Here, we report a new human genetic disease that causes cell senescence, liver and immune dysfunction, and early mortality that results from deficiency of GIMAP5, an evolutionarily conserved GTPase selectively expressed in lymphocytes and endothelial cells. We show that GIMAP5 restricts the pathological accumulation of long-chain ceramides (CERs), thereby regulating longevity. GIMAP5 controls CER abundance by interacting with protein kinase CK2 (CK2), attenuating its ability to activate CER synthases. Inhibition of CK2 and CER synthase rescues GIMAP5-deficient T cells by preventing CER overaccumulation and cell deterioration. Thus, GIMAP5 controls longevity assurance pathways crucial for immune function and healthspan in mammals.
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Affiliation(s)
- Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Justin Q Gabrielski
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xijin Xu
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Arasu Balasubramaniyam
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Hyoungjun Ham
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brittany Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yu Zhang
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helen F Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jing Cui
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jean Michel Chanchu
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aaron R Morawski
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah A Cook
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ping Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juan C Ravell
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Internal Medicine, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Yan H Cheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alex George
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aiman Faruqi
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alison M Pagalilauan
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sundar Ganesan
- Biological Imaging Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jahnavi Aluri
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joy Edwards-Hicks
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Caroline Tippett
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Habib Omar
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leilei Xu
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - John Pascall
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, United Kingdom
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Pendik, Istanbul, Turkey
| | - Ayca Kiykim
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - İlhan Tezcan
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Saliha Esenboga
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Raul Jimenez Heredia
- St Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Deniz Akata
- Department of Radiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Saban Tekin
- Department of Basic Medical Sciences, Hamidiye Faculty of Medicine, Division of Medical Biology, University of Health Sciences, İstanbul, Turkey
| | - Altan Kara
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Gebze, Turkey
| | - Zarife Kuloglu
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Ankara University School of Medicine, Ankara, Türkiye
| | - Emel Unal
- Department of Pediatric Oncology, Ankara University Medical School, Ankara, Turkey
| | - Tanıl Kendirli
- Department of Pediatric Intensive Care Unit, Ankara University Medical School, Ankara, Turkey
| | - Figen Dogu
- Department of Pediatric Immunology and Allergy, Ankara University Medical School, Ankara, Turkey
| | - Esra Karabiber
- Department of Chest Diseases, Faculty of Medicine, Division of Adult Allergy-Immunology, Marmara University, Istanbul, Turkey
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Claude Cochet
- University Grenoble Alpes, INSERM, CEA, UMR Biosanté, Grenoble, France
| | - Odile Filhol
- University Grenoble Alpes, INSERM, CEA, UMR Biosanté, Grenoble, France
| | - Catherine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Palo Alto, CA, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erika L Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Johns Hopkins University, Baltimore, MD, USA
| | - Oliver Daumke
- Department of Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Caner Aytekin
- Department of Pediatric Immunology, Dr Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Gülseren Evirgen Şahin
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, University of Health Sciences, Dr Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Aysel Ünlüsoy Aksu
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, University of Health Sciences, Dr Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sinan Sari
- Department of Pediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Buket Dalgıç
- Department of Pediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Kaan Boztug
- St Anna Children's Cancer Research Institute, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- St Anna Children's Hospital, Vienna, Austria
| | - Deniz Cagdas
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Sule Haskologlu
- Department of Pediatric Immunology and Allergy, Ankara University Medical School, Ankara, Turkey
| | - Aydan Ikinciogullari
- Department of Pediatric Immunology and Allergy, Ankara University Medical School, Ankara, Turkey
| | - David Schwefel
- Department of Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Silvia Vilarinho
- Section of Digestive Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Pendik, Istanbul, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, Marmara University, School of Medicine Pendik, Istanbul, Turkey
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, Pendik, Istanbul, Turkey
| | - Helen C Su
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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6
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de Magalhães JP, Abidi Z, dos Santos GA, Avelar RA, Barardo D, Chatsirisupachai K, Clark P, De-Souza EA, Johnson EJ, Lopes I, Novoa G, Senez L, Talay A, Thornton D, To P. Human Ageing Genomic Resources: updates on key databases in ageing research. Nucleic Acids Res 2024; 52:D900-D908. [PMID: 37933854 PMCID: PMC10767973 DOI: 10.1093/nar/gkad927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023] Open
Abstract
Ageing is a complex and multifactorial process. For two decades, the Human Ageing Genomic Resources (HAGR) have aided researchers in the study of various aspects of ageing and its manipulation. Here, we present the key features and recent enhancements of these resources, focusing on its six main databases. One database, GenAge, focuses on genes related to ageing, featuring 307 genes linked to human ageing and 2205 genes associated with longevity and ageing in model organisms. AnAge focuses on ageing, longevity, and life-history across animal species, containing data on 4645 species. DrugAge includes information about 1097 longevity drugs and compounds in model organisms such as mice, rats, flies, worms and yeast. GenDR provides a list of 214 genes associated with the life-extending benefits of dietary restriction in model organisms. CellAge contains a catalogue of 866 genes associated with cellular senescence. The LongevityMap serves as a repository for genetic variants associated with human longevity, encompassing 3144 variants pertaining to 884 genes. Additionally, HAGR provides various tools as well as gene expression signatures of ageing, dietary restriction, and replicative senescence based on meta-analyses. Our databases are integrated, regularly updated, and manually curated by experts. HAGR is freely available online (https://genomics.senescence.info/).
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Affiliation(s)
- João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Zoya Abidi
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Gabriel Arantes dos Santos
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Diogo Barardo
- NOVOS Labs, 100 Park Avenue, 16th Fl, New York, NY 10017, USA
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Peter Clark
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Evandro A De-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas 13083-970, SP, Brazil
| | - Emily J Johnson
- Computational Biology Facility, Liverpool Shared Research Facilities, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Guy Novoa
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Ludovic Senez
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Angelo Talay
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Paul Ka Po To
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, UK
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7
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Ohtsuka H, Otsubo Y, Shimasaki T, Yamashita A, Aiba H. ecl family genes: Factors linking starvation and lifespan extension in Schizosaccharomyces pombe. Mol Microbiol 2023; 120:645-657. [PMID: 37525511 DOI: 10.1111/mmi.15134] [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: 04/18/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
In the fission yeast Schizosaccharomyces pombe, the duration of survival in the stationary phase, termed the chronological lifespan (CLS), is affected by various environmental factors and the corresponding gene activities. The ecl family genes were identified in the genomic region encoding non-coding RNA as positive regulators of CLS in S. pombe, and subsequently shown to encode relatively short proteins. Several studies revealed that ecl family genes respond to various nutritional starvation conditions via different mechanisms, and they are additionally involved in stress resistance, autophagy, sexual differentiation, and cell cycle control. Recent studies reported that Ecl family proteins strongly suppress target of rapamycin complex 1, which is a conserved eukaryotic nutrient-sensing kinase complex that also regulates longevity in a variety of organisms. In this review, we introduce the regulatory mechanisms of Ecl family proteins and discuss their emerging findings.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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8
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Garg A, Sanchez AM, Miele M, Schwer B, Shuman S. Cellular responses to long-term phosphate starvation of fission yeast: Maf1 determines fate choice between quiescence and death associated with aberrant tRNA biogenesis. Nucleic Acids Res 2023; 51:3094-3115. [PMID: 36794724 PMCID: PMC10123115 DOI: 10.1093/nar/gkad063] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
Inorganic phosphate is an essential nutrient acquired by cells from their environment. Here, we characterize the adaptative responses of fission yeast to chronic phosphate starvation, during which cells enter a state of quiescence, initially fully reversible upon replenishing phosphate after 2 days but resulting in gradual loss of viability during 4 weeks of starvation. Time-resolved analyses of changes in mRNA levels revealed a coherent transcriptional program in which phosphate dynamics and autophagy were upregulated, while the machineries for rRNA synthesis and ribosome assembly, and for tRNA synthesis and maturation, were downregulated in tandem with global repression of genes encoding ribosomal proteins and translation factors. Consistent with the transcriptome changes, proteome analysis highlighted global depletion of 102 ribosomal proteins. Concomitant with this ribosomal protein deficit, 28S and 18S rRNAs became vulnerable to site-specific cleavages that generated temporally stable rRNA fragments. The finding that Maf1, a repressor of RNA polymerase III transcription, was upregulated during phosphate starvation prompted a hypothesis that its activity might prolong lifespan of the quiescent cells by limiting production of tRNAs. Indeed, we found that deletion of maf1 results in precocious death of phosphate-starved cells via a distinctive starvation-induced pathway associated with tRNA overproduction and dysfunctional tRNA biogenesis.
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Affiliation(s)
- Angad Garg
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ana M Sanchez
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Matthew Miele
- Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Beate Schwer
- Correspondence may also be addressed to Beate Schwer. Tel: +1 212 746 6518;
| | - Stewart Shuman
- To whom correspondence should be addressed. Tel: +1 212 639 7145;
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9
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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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10
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Ebrahim A, Alfwuaires MA, Abukhalil MH, Alasmari F, Ahmad F, Yao R, Luo Y, Huang Y. Schizosaccharomyces pombe Grx4, Fep1, and Php4: In silico analysis and expression response to different iron concentrations. Front Genet 2022; 13:1069068. [PMID: 36568394 PMCID: PMC9768344 DOI: 10.3389/fgene.2022.1069068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Due to iron's essential role in cellular metabolism, most organisms must maintain their homeostasis. In this regard, the fission yeast Schizosaccharomyces pombe (sp) uses two transcription factors to regulate intracellular iron levels: spFep1 under iron-rich conditions and spPhp4 under iron-deficient conditions, which are controlled by spGrx4. However, bioinformatics analysis to understand the role of the spGrx4/spFep1/spPhp4 axis in maintaining iron homeostasis in S. pombe is still lacking. Our study aimed to perform bioinformatics analysis on S. pombe proteins and their sequence homologs in Aspergillus flavus (af), Saccharomyces cerevisiae (sc), and Homo sapiens (hs) to understand the role of spGrx4, spFep1, and spPhp4 in maintaining iron homeostasis. The three genes' expression patterns were also examined at various iron concentrations. A multiple sequence alignment analysis of spGrx4 and its sequence homologs revealed a conserved cysteine residue in each PF00085 domain. Blast results showed that hsGLRX3 is most similar to spGrx4. In addition, spFep1 is most closely related in sequence to scDal80, whereas scHap4 is most similar to spFep1. We also found two highly conserved motifs in spFep1 and its sequence homologs that are significant for iron transport systems because they contain residues involved in iron homeostasis. The scHap4 is most similar to spPhp4. Using STRING to analyze protein-protein interactions, we found that spGrx4 interacts strongly with spPhp4 and spFep1. Furthermore, spGrx4, spPhp4, and spFep1 interact with spPhp2, spPhp3, and spPhp5, indicating that the three proteins play cooperative roles in iron homeostasis. At the highest level of Fe, spgrx4 had the highest expression, followed by spfep1, while spphp4 had the lowest expression; a contrast occurred at the lowest level of Fe, where spgrx4 expression remained constant. Our findings support the notion that organisms develop diverse strategies to maintain iron homeostasis.
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Affiliation(s)
- Alia Ebrahim
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Manal A. Alfwuaires
- Department of Biological Sciences, Faculty of Science, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mohammad H. Abukhalil
- Department of Medical Analysis, Princess Aisha Bint Al-Hussein College of Nursing and Health Sciences, Al-Hussein Bin Talal University, Ma’an, Jordan,Department of Biology, College of Science, Al-Hussein Bin Talal University, Ma’an, Jordan
| | - Fawaz Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fawad Ahmad
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Rui Yao
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Luo
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China,*Correspondence: Ying Huang,
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11
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Ohtsuka H, Imada K, Shimasaki T, Aiba H. Sporulation: A response to starvation in the fission yeast Schizosaccharomyces pombe. Microbiologyopen 2022; 11:e1303. [PMID: 35765188 PMCID: PMC9214231 DOI: 10.1002/mbo3.1303] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/02/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe employs two main strategies to adapt to the environment and survive when starved for nutrients. The strategies employ sporulation via sexual differentiation and extension of the chronological lifespan. When a cell is exposed to nutrient starvation in the presence of a cell of the opposite sex, the cells undergo fusion through conjugation and sporulation through meiosis. S. pombe spores are highly resistant to diverse stresses and may survive for a very long time. In this minireview, among the various sexual differentiation processes induced by starvation, we focused on and summarized the findings of the molecular mechanisms of spore formation in fission yeast. Furthermore, comparative measurements of the chronological lifespan of stationary phase cells and G0 cells and the survival period of spore cells revealed that the spore cells survived for a long period, indicating the presence of an effective mechanism for survival. Currently, many molecules involved in sporulation and their functions are being discovered; however, our understanding of these is not complete. Further understanding of spores may not only deepen our comprehension of sexual differentiation but may also provide hints for sustaining life.
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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, Japan
| | - Kazuki Imada
- Department of Chemistry and Biochemistry, National Institute of Technology (KOSEN), Suzuka College, Suzuka, Japan.,Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, Japan
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12
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Yaakoub H, Mina S, Calenda A, Bouchara JP, Papon N. Oxidative stress response pathways in fungi. Cell Mol Life Sci 2022; 79:333. [PMID: 35648225 PMCID: PMC11071803 DOI: 10.1007/s00018-022-04353-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Fungal response to any stress is intricate, specific, and multilayered, though it employs only a few evolutionarily conserved regulators. This comes with the assumption that one regulator operates more than one stress-specific response. Although the assumption holds true, the current understanding of molecular mechanisms that drive response specificity and adequacy remains rudimentary. Deciphering the response of fungi to oxidative stress may help fill those knowledge gaps since it is one of the most encountered stress types in any kind of fungal niche. Data have been accumulating on the roles of the HOG pathway and Yap1- and Skn7-related pathways in mounting distinct and robust responses in fungi upon exposure to oxidative stress. Herein, we review recent and most relevant studies reporting the contribution of each of these pathways in response to oxidative stress in pathogenic and opportunistic fungi after giving a paralleled overview in two divergent models, the budding and fission yeasts. With the concept of stress-specific response and the importance of reactive oxygen species in fungal development, we first present a preface on the expanding domain of redox biology and oxidative stress.
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Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France
| | - Sara Mina
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | | | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France.
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13
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Ohtsuka H, Matsumoto T, Mochida T, Shimasaki T, Shibuya M, Yamamoto Y, Aiba H. Tschimganine has different targets for chronological lifespan extension and growth inhibition in fission yeast. Biosci Biotechnol Biochem 2022; 86:775-779. [PMID: 35416247 DOI: 10.1093/bbb/zbac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/25/2022] [Indexed: 11/14/2022]
Abstract
Tschimganine inhibits growth and extends the chronological lifespan in Schizosaccharomyces pombe. We synthesized a Tschimganine analog, Mochimganine, which extends the lifespan similar to Tschimganine but exhibits a significantly weaker growth inhibition effect. Based on the comparative analysis of these compounds, we propose that Tschimganine has at least 2 targets: one extends the lifespan and the other inhibits growth.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takuma Matsumoto
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takahiro Mochida
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Masatoshi Shibuya
- Laboratory of Molecular Design, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yoshihiko Yamamoto
- Laboratory of Molecular Design, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
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14
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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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15
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Matsui K, Okamoto K, Hasegawa T, Ohtsuka H, Shimasaki T, Ihara K, Goto Y, Aoki K, Aiba H. Identification of ksg1 mutation showing long-lived phenotype in fission yeast. Genes Cells 2021; 26:967-978. [PMID: 34534388 DOI: 10.1111/gtc.12897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/19/2022]
Abstract
Fission yeast is a good model organism for the study of lifespan. To elucidate the mechanism, we screened for long-lived mutants. We found a nonsense mutation in the ksg1+ gene, which encodes an ortholog of mammalian PDK1 (phosphoinositide-dependent protein kinase). The mutation was in the PH domain of Ksg1 and caused defect in membrane localization and protein stability. Analysis of the ksg1 mutant revealed that the reduced amounts and/or activity of the Ksg1 protein are responsible for the increased lifespan. Ksg1 is essential for growth and known to phosphorylate multiple substrates, but the substrate responsible for the long-lived phenotype of ksg1 mutation is not yet known. Genetic analysis showed that deletion of pck2 suppressed the long-lived phenotype of ksg1 mutant, suggesting that Pck2 might be involved in the lifespan extension caused by ksg1 mutation.
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Affiliation(s)
- Kotaro Matsui
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Keisuke Okamoto
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Tomoka Hasegawa
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Yuhei Goto
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Aichi, Japan
| | - Kazuhiro Aoki
- Division of Quantitative Biology, Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi, Japan.,Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Aichi, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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16
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Ohtsuka H, Shimasaki T, Aiba H. Response to sulfur in Schizosaccharomyces pombe. FEMS Yeast Res 2021; 21:6324000. [PMID: 34279603 PMCID: PMC8310684 DOI: 10.1093/femsyr/foab041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Sulfur is an essential component of various biologically important molecules, including methionine, cysteine and glutathione, and it is also involved in coping with oxidative and heavy metal stress. Studies using model organisms, including budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe), have contributed not only to understanding various cellular processes but also to understanding the utilization and response mechanisms of each nutrient, including sulfur. Although fission yeast can use sulfate as a sulfur source, its sulfur metabolism pathway is slightly different from that of budding yeast because it does not have a trans-sulfuration pathway. In recent years, it has been found that sulfur starvation causes various cellular responses in S. pombe, including sporulation, cell cycle arrest at G2, chronological lifespan extension, autophagy induction and reduced translation. This MiniReview identifies two sulfate transporters in S. pombe, Sul1 (encoded by SPBC3H7.02) and Sul2 (encoded by SPAC869.05c), and summarizes the metabolic pathways of sulfur assimilation and cellular response to sulfur starvation. Understanding these responses, including metabolism and adaptation, will contribute to a better understanding of the various stress and nutrient starvation responses and chronological lifespan regulation caused by sulfur starvation.
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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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17
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Romila CA, Townsend S, Malecki M, Kamrad S, Rodríguez-López M, Hillson O, Cotobal C, Ralser M, Bähler J. Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast. MICROBIAL CELL (GRAZ, AUSTRIA) 2021; 8:146-160. [PMID: 34250083 PMCID: PMC8246024 DOI: 10.15698/mic2021.07.754] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022]
Abstract
Ageing-related processes are largely conserved, with simple organisms remaining the main platform to discover and dissect new ageing-associated genes. Yeasts provide potent model systems to study cellular ageing owing their amenability to systematic functional assays under controlled conditions. Even with yeast cells, however, ageing assays can be laborious and resource-intensive. Here we present improved experimental and computational methods to study chronological lifespan in Schizosaccharomyces pombe. We decoded the barcodes for 3206 mutants of the latest gene-deletion library, enabling the parallel profiling of ~700 additional mutants compared to previous screens. We then applied a refined method of barcode sequencing (Bar-seq), addressing technical and statistical issues raised by persisting DNA in dead cells and sampling bottlenecks in aged cultures, to screen for mutants showing altered lifespan during stationary phase. This screen identified 341 long-lived mutants and 1246 short-lived mutants which point to many previously unknown ageing-associated genes, including 46 conserved but entirely uncharacterized genes. The ageing-associated genes showed coherent enrichments in processes also associated with human ageing, particularly with respect to ageing in non-proliferative brain cells. We also developed an automated colony-forming unit assay to facilitate medium- to high-throughput chronological-lifespan studies by saving time and resources compared to the traditional assay. Results from the Bar-seq screen showed good agreement with this new assay. This study provides an effective methodological platform and identifies many new ageing-associated genes as a framework for analysing cellular ageing in yeast and beyond.
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Affiliation(s)
- Catalina A. Romila
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- These authors contributed equally
| | - StJohn Townsend
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- These authors contributed equally
| | - Michal Malecki
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- Current address: Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
| | - Stephan Kamrad
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- Current address: Charité Universitätsmedizin Berlin, Department of Biochemistry, Germany
| | - María Rodríguez-López
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Olivia Hillson
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Cristina Cotobal
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, NW1 1AT, UK
- Charité Universitätsmedizin Berlin, Department of Biochemistry, Germany
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
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Ohtsuka H, Shimasaki T, Aiba H. Extension of chronological lifespan in Schizosaccharomyces pombe. Genes Cells 2021; 26:459-473. [PMID: 33977597 PMCID: PMC9290682 DOI: 10.1111/gtc.12854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023]
Abstract
There are several examples in the nature wherein the mechanism of longevity control of unicellular organisms is evolutionarily conserved with that of higher multicellular organisms. The present microreview focuses on aging and longevity studies, particularly on chronological lifespan (CLS) concerning the unicellular eukaryotic fission yeast Schizosaccharomyces pombe. In S. pombe, >30 compounds, 8 types of nutrient restriction, and >80 genes that extend CLS have been reported. Several CLS control mechanisms are known to be involved in nutritional response, energy utilization, stress responses, translation, autophagy, and sexual differentiation. In unicellular organisms, the control of CLS is directly linked to the mechanism by which cells are maintained in limited‐resource environments, and their genetic information is left to posterity. We believe that this important mechanism may have been preserved as a lifespan control mechanism for higher organisms.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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19
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Legon L, Rallis C. Genome-wide screens in yeast models towards understanding chronological lifespan regulation. Brief Funct Genomics 2021; 21:4-12. [PMID: 33728458 PMCID: PMC8834652 DOI: 10.1093/bfgp/elab011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022] Open
Abstract
Cellular models such as yeasts are a driving force in biogerontology studies. Their simpler genome, short lifespans and vast genetic and genomics resources make them ideal to characterise pro-ageing and anti-ageing genes and signalling pathways. Over the last three decades, yeasts have contributed to the understanding of fundamental aspects of lifespan regulation including the roles of nutrient response, global protein translation rates and quality, DNA damage, oxidative stress, mitochondrial function and dysfunction as well as autophagy. In this short review, we focus on approaches used for competitive and non-competitive cell-based screens using the budding yeast Saccharomyces cerevisiae, and the fission yeast Schizosaccharomyces pombe, for deciphering the molecular mechanisms underlying chronological ageing. Automation accompanied with appropriate computational tools allowed manipulation of hundreds of thousands of colonies, generation, processing and analysis of genome-wide lifespan data. Together with barcoding and modern mutagenesis technologies, these approaches have allowed to take decisive steps towards a global, comprehensive view of cellular ageing.
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Affiliation(s)
- Luc Legon
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Charalampos Rallis
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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20
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Ohtsuka H, Shimasaki T, Aiba H. Genes affecting the extension of chronological lifespan in Schizosaccharomyces pombe (fission yeast). Mol Microbiol 2020; 115:623-642. [PMID: 33064911 PMCID: PMC8246873 DOI: 10.1111/mmi.14627] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/17/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023]
Abstract
So far, more than 70 genes involved in the chronological lifespan (CLS) of Schizosaccharomyces pombe (fission yeast) have been reported. In this mini‐review, we arrange and summarize these genes based on the reported genetic interactions between them and the physical interactions between their products. We describe the signal transduction pathways that affect CLS in S. pombe: target of rapamycin complex 1, cAMP‐dependent protein kinase, Sty1, and Pmk1 pathways have important functions in the regulation of CLS extension. Furthermore, the Php transcription complex, Ecl1 family proteins, cyclin Clg1, and the cyclin‐dependent kinase Pef1 are important for the regulation of CLS extension in S. pombe. Most of the known genes involved in CLS extension are related to these pathways and genes. In this review, we focus on the individual genes regulating CLS extension in S. pombe and discuss the interactions among them.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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