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Suda K, Moriyama Y, Razali N, Chiu Y, Masukagami Y, Nishimura K, Barbee H, Takase H, Sugiyama S, Yamazaki Y, Sato Y, Higashiyama T, Johmura Y, Nakanishi M, Kono K. Plasma membrane damage limits replicative lifespan in yeast and induces premature senescence in human fibroblasts. NATURE AGING 2024; 4:319-335. [PMID: 38388781 PMCID: PMC10950784 DOI: 10.1038/s43587-024-00575-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
Plasma membrane damage (PMD) occurs in all cell types due to environmental perturbation and cell-autonomous activities. However, cellular outcomes of PMD remain largely unknown except for recovery or death. In this study, using budding yeast and normal human fibroblasts, we found that cellular senescence-stable cell cycle arrest contributing to organismal aging-is the long-term outcome of PMD. Our genetic screening using budding yeast unexpectedly identified a close genetic association between PMD response and replicative lifespan regulations. Furthermore, PMD limits replicative lifespan in budding yeast; upregulation of membrane repair factors ESCRT-III (SNF7) and AAA-ATPase (VPS4) extends it. In normal human fibroblasts, PMD induces premature senescence via the Ca2+-p53 axis but not the major senescence pathway, DNA damage response pathway. Transient upregulation of ESCRT-III (CHMP4B) suppressed PMD-dependent senescence. Together with mRNA sequencing results, our study highlights an underappreciated but ubiquitous senescent cell subtype: PMD-dependent senescent cells.
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Affiliation(s)
- Kojiro Suda
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yohsuke Moriyama
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Nurhanani Razali
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yatzu Chiu
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yumiko Masukagami
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Hyogo, Japan
| | - Hunter Barbee
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hiroshi Takase
- Core Laboratory, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Shinju Sugiyama
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yuta Yamazaki
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Department of Biological Science, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Yoshikazu Johmura
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Keiko Kono
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
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2
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Chaux F, Agier N, Garrido C, Fischer G, Eberhard S, Xu Z. Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii. Genome Res 2023; 33:1582-1598. [PMID: 37580131 PMCID: PMC10620057 DOI: 10.1101/gr.278043.123] [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: 04/27/2023] [Accepted: 08/09/2023] [Indexed: 08/16/2023]
Abstract
Telomeres and subtelomeres, the genomic regions located at chromosome extremities, are essential for genome stability in eukaryotes. In the absence of the canonical maintenance mechanism provided by telomerase, telomere shortening induces genome instability. The landscape of the ensuing genome rearrangements is not accessible by short-read sequencing. Here, we leverage Oxford Nanopore Technologies long-read sequencing to survey the extensive repertoire of genome rearrangements in telomerase mutants of the model green microalga Chlamydomonas reinhardtii In telomerase-mutant strains grown for hundreds of generations, most chromosome extremities were capped by short telomere sequences that were either recruited de novo from other loci or maintained in a telomerase-independent manner. Other extremities did not end with telomeres but only with repeated subtelomeric sequences. The subtelomeric elements, including rDNA, were massively rearranged and involved in breakage-fusion-bridge cycles, translocations, recombinations, and chromosome circularization. These events were established progressively over time and displayed heterogeneity at the subpopulation level. New telomere-capped extremities composed of sequences originating from more internal genomic regions were associated with high DNA methylation, suggesting that de novo heterochromatin formation contributes to the restoration of chromosome end stability in C. reinhardtii The diversity of alternative strategies present in the same organism to maintain chromosome integrity and the variety of rearrangements found in telomerase mutants are remarkable, and illustrate genome plasticity at short timescales.
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Affiliation(s)
- Frédéric Chaux
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Nicolas Agier
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Clotilde Garrido
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Gilles Fischer
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France
| | - Stephan Eberhard
- Sorbonne Université, CNRS, UMR7141, Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light-Sensing in Microalgae, 75005 Paris, France
| | - Zhou Xu
- Sorbonne Université, CNRS, UMR7238, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, 75005 Paris, France;
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3
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Pai CC, Durley SC, Cheng WC, Chiang NY, Peters J, Kasparek T, Blaikley E, Wee BY, Walker C, Kearsey SE, Buffa F, Murray JM, Humphrey TC. Homologous recombination suppresses transgenerational DNA end resection and chromosomal instability in fission yeast. Nucleic Acids Res 2023; 51:3205-3222. [PMID: 36951111 PMCID: PMC10123110 DOI: 10.1093/nar/gkad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023] Open
Abstract
Chromosomal instability (CIN) drives cell-to-cell heterogeneity, and the development of genetic diseases, including cancer. Impaired homologous recombination (HR) has been implicated as a major driver of CIN, however, the underlying mechanism remains unclear. Using a fission yeast model system, we establish a common role for HR genes in suppressing DNA double-strand break (DSB)-induced CIN. Further, we show that an unrepaired single-ended DSB arising from failed HR repair or telomere loss is a potent driver of widespread CIN. Inherited chromosomes carrying a single-ended DSB are subject to cycles of DNA replication and extensive end-processing across successive cell divisions. These cycles are enabled by Cullin 3-mediated Chk1 loss and checkpoint adaptation. Subsequent propagation of unstable chromosomes carrying a single-ended DSB continues until transgenerational end-resection leads to fold-back inversion of single-stranded centromeric repeats and to stable chromosomal rearrangements, typically isochromosomes, or to chromosomal loss. These findings reveal a mechanism by which HR genes suppress CIN and how DNA breaks that persist through mitotic divisions propagate cell-to-cell heterogeneity in the resultant progeny.
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Affiliation(s)
- Chen-Chun Pai
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Samuel C Durley
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Wei-Chen Cheng
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Nien-Yi Chiang
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jennifer Peters
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Torben Kasparek
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Elizabeth Blaikley
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Boon-Yu Wee
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Carol Walker
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stephen E Kearsey
- Department of Biology, University of Oxford, Zoology Research and Administration Building, Mansfield Road, Oxford OX1 3SZ, UK
| | - Francesca Buffa
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Johanne M Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, SussexBN1 9RQ, UK
| | - Timothy C Humphrey
- MRC Oxford Institute for Radiation Oncology & Biology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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4
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Bernardi B, Michling F, Muno-Bender J, Matti K, Wendland J. The genome sequence of the Champagne Epernay Geisenheim wine yeast reveals its hybrid nature. FEMS Yeast Res 2023; 23:foad033. [PMID: 37500257 DOI: 10.1093/femsyr/foad033] [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: 04/11/2023] [Revised: 06/02/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Lager yeasts are hybrids between Saccharomyces cerevisiae and S. eubayanus. Wine yeast biodiversity, however, has only recently been discovered to include besides pure S. cerevisiae strains also hybrids between different Saccharomyces yeasts as well as introgressions from non-Saccharomyces species. Here, we analysed the genome of the Champagne Epernay Geisenheim (CEG) wine yeast. This yeast is an allotetraploid (4n - 1) hybrid of S. cerevisiae harbouring a substantially reduced S. kudriavzevii genome contributing only 1/3 of a full genome equivalent. We identified a novel oligopeptide transporter gene, FOT4, in CEG located on chromosome XVI. FOT genes were originally derived from Torulaspora microellipsoides and FOT4 arose by non-allelic recombination between adjacent FOT1 and FOT2 genes. Fermentations of CEG in Riesling and Müller-Thurgau musts were compared with the S. cerevisiae Geisenheim wine yeast GHM, which does not carry FOT genes. At low temperature (10°C), CEG completed fermentations faster and produced increased levels of higher alcohols (e.g. isoamyl alcohol). At higher temperature (18°C), CEG produced higher amounts of the pineapple-like alkyl esters i-butyric and propionic acid ethyl esters compared to GHM. The hybrid nature of CEG thus provides advantages in grape must fermentations over S. cerevisiae wine yeasts, especially with regard to aroma production.
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Affiliation(s)
- Beatrice Bernardi
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
- Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Florian Michling
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
- Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Judith Muno-Bender
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
- Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Katrin Matti
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
- Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Jürgen Wendland
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
- Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
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5
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Martin H, Doumic M, Teixeira MT, Xu Z. Telomere shortening causes distinct cell division regimes during replicative senescence in Saccharomyces cerevisiae. Cell Biosci 2021; 11:180. [PMID: 34627377 PMCID: PMC8502270 DOI: 10.1186/s13578-021-00693-3] [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: 06/25/2021] [Accepted: 09/24/2021] [Indexed: 11/21/2022] Open
Abstract
Background Telomerase-negative cells have limited proliferation potential. In these cells, telomeres shorten until they reach a critical length and induce a permanently arrested state. This process called replicative senescence is associated with genomic instability and participates in tissue and organismal ageing. Experimental data using single-cell approaches in the budding yeast model organism show that telomerase-negative cells often experience abnormally long cell cycles, which can be followed by cell cycles of normal duration, before reaching the terminal senescent state. These series of non-terminal cell cycle arrests contribute to the heterogeneity of senescence and likely magnify its genomic instability. Due to their apparent stochastic nature, investigating the dynamics and the molecular origins of these arrests has been difficult. In particular, whether the non-terminal arrests series stem from a mechanism similar to the one that triggers terminal senescence is not known. Results Here, we provide a mathematical description of sequences of non-terminal arrests to understand how they appear. We take advantage of an experimental data set of cell cycle duration measurements performed in individual telomerase-negative yeast cells that keep track of the number of generations since telomerase inactivation. Using numerical simulations, we show that the occurrence of non-terminal arrests is a generation-dependent process that can be explained by the shortest telomere reaching a probabilistic threshold length. While the onset of senescence is also triggered by telomere shortening, we highlight differences in the laws that describe the number of consecutive arrests in non-terminal arrests compared to senescence arrests, suggesting distinct underlying mechanisms and cellular states. Conclusions Replicative senescence is a complex process that affects cell divisions earlier than anticipated, as exemplified by the frequent occurrence of non-terminal arrests early after telomerase inactivation. The present work unravels two kinetically and mechanistically distinct generation-dependent processes underlying non-terminal and terminal senescence arrests. We suggest that these two processes are responsible for two consequences of senescence at the population level, the increase of genome instability on the one hand, and the limitation of proliferation capacity on the other hand. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00693-3.
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Affiliation(s)
- Hugo Martin
- JL Lions Laboratory, Sorbonne Université, 75005, Paris, France
| | - Marie Doumic
- JL Lions Laboratory, Sorbonne Université, 75005, Paris, France.
| | - Maria Teresa Teixeira
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, PSL, CNRS, UMR8226, Sorbonne Université, 75005, Paris, France
| | - Zhou Xu
- Laboratory of Computational and Quantitative Biology, Institut de Biologie Paris-Seine, CNRS, UMR7238, Sorbonne Université, 75005, Paris, France.
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6
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Galli M, Frigerio C, Longhese MP, Clerici M. The regulation of the DNA damage response at telomeres: focus on kinases. Biochem Soc Trans 2021; 49:933-943. [PMID: 33769480 DOI: 10.1042/bst20200856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022]
Abstract
The natural ends of linear chromosomes resemble those of accidental double-strand breaks (DSBs). DSBs induce a multifaceted cellular response that promotes the repair of lesions and slows down cell cycle progression. This response is not elicited at chromosome ends, which are organized in nucleoprotein structures called telomeres. Besides counteracting DSB response through specialized telomere-binding proteins, telomeres also prevent chromosome shortening. Despite of the different fate of telomeres and DSBs, many proteins involved in the DSB response also localize at telomeres and participate in telomere homeostasis. In particular, the DSB master regulators Tel1/ATM and Mec1/ATR contribute to telomere length maintenance and arrest cell cycle progression when chromosome ends shorten, thus promoting a tumor-suppressive process known as replicative senescence. During senescence, the actions of both these apical kinases and telomere-binding proteins allow checkpoint activation while bulk DNA repair activities at telomeres are still inhibited. Checkpoint-mediated cell cycle arrest also prevents further telomere erosion and deprotection that would favor chromosome rearrangements, which are known to increase cancer-associated genome instability. This review summarizes recent insights into functions and regulation of Tel1/ATM and Mec1/ATR at telomeres both in the presence and in the absence of telomerase, focusing mainly on discoveries in budding yeast.
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Affiliation(s)
- Michela Galli
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Chiara Frigerio
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
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