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Walker RM, Sanabria VC, Youk H. Microbial life in slow and stopped lanes. Trends Microbiol 2024; 32:650-662. [PMID: 38123400 PMCID: PMC11187706 DOI: 10.1016/j.tim.2023.11.014] [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: 10/16/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Microbes in nature often lack nutrients and face extreme or widely fluctuating temperatures, unlike microbes in growth-optimized settings in laboratories that much of the literature examines. Slowed or suspended lives are the norm for microbes. Studying them is important for understanding the consequences of climate change and for addressing fundamental questions about life: are there limits to how slowly a cell's life can progress, and how long cells can remain viable without self-replicating? Recent studies began addressing these questions with single-cell-level measurements and mathematical models. Emerging principles that govern slowed or suspended lives of cells - including lives of dormant spores and microbes at extreme temperatures - are re-defining discrete cellular states as continuums and revealing intracellular dynamics at new timescales. Nearly inactive, lifeless-appearing microbes are transforming our understanding of life.
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Affiliation(s)
- Rachel M Walker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Valeria C Sanabria
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hyun Youk
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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2
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Escalante LE, Hose J, Howe H, Paulsen N, Place M, Gasch AP. Premature aging in aneuploid yeast is caused in part by aneuploidy-induced defects in Ribosome Quality Control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.22.600216. [PMID: 38948718 PMCID: PMC11213126 DOI: 10.1101/2024.06.22.600216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Premature aging is a hallmark of Down syndrome, caused by trisomy of human chromosome 21, but the reason is unclear and difficult to study in humans. We used an aneuploid model in wild yeast to show that chromosome amplification disrupts nutrient-induced cell-cycle arrest, quiescence entry, and healthy aging, across genetic backgrounds and amplified chromosomes. We discovered that these defects are due in part to aneuploidy-induced dysfunction in Ribosome Quality Control (RQC). Compared to euploids, aneuploids entering quiescence display aberrant ribosome profiles, accumulate RQC intermediates, and harbor an increased load of protein aggregates. Although they have normal proteasome capacity, aneuploids show signs of ubiquitin dysregulation, which impacts cyclin abundance to disrupt arrest. Remarkably, inducing ribosome stalling in euploids produces similar aberrations, while up-regulating limiting RQC subunits or proteins in ubiquitin metabolism alleviates many of the aneuploid defects. Our results provide implications for other aneuploidy disorders including Down syndrome.
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Affiliation(s)
- Leah E. Escalante
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Hollis Howe
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Norah Paulsen
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706
| | - Audrey P. Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706
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3
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Greenlaw A, Dell R, Tsukiyama T. Initial acidic media promotes quiescence entry in Saccharomyces cerevisiae. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001071. [PMID: 38463631 PMCID: PMC10924235 DOI: 10.17912/micropub.biology.001071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/12/2024]
Abstract
Quiescence is a conserved cellular state wherein cells cease proliferation and remain poised to re-enter the cell cycle when conditions are appropriate. Budding yeast is a powerful model for studying cellular quiescence. In this work, we demonstrate that the pH of the YPD media strongly affects quiescence entry efficiency in Saccharomyces cerevisiae. Adjusting the initial media pH to 5.5 significantly improves quiescence entry efficiency compared to unadjusted YPD media. Thermotolerance of the produced quiescence yeast are similar, suggesting the media pH influences the quantity of quiescent cells more than quality of quiescence reached.
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Affiliation(s)
- Alison Greenlaw
- Basic Sciences Division, Fred Hutch Cancer Center, Seattle, Washington, United States
| | - Rachel Dell
- Basic Sciences Division, Fred Hutch Cancer Center, Seattle, Washington, United States
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutch Cancer Center, Seattle, Washington, United States
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Greenlaw AC, Alavattam KG, Tsukiyama T. Post-transcriptional regulation shapes the transcriptome of quiescent budding yeast. Nucleic Acids Res 2024; 52:1043-1063. [PMID: 38048329 PMCID: PMC10853787 DOI: 10.1093/nar/gkad1147] [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: 08/09/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023] Open
Abstract
To facilitate long-term survival, cells must exit the cell cycle and enter quiescence, a reversible non-replicative state. Budding yeast cells reprogram their gene expression during quiescence entry to silence transcription, but how the nascent transcriptome changes in quiescence is unknown. By investigating the nascent transcriptome, we identified over a thousand noncoding RNAs in quiescent and G1 yeast cells, and found noncoding transcription represented a larger portion of the quiescent transcriptome than in G1. Additionally, both mRNA and ncRNA are subject to increased post-transcriptional regulation in quiescence compared to G1. We found that, in quiescence, the nuclear exosome-NNS pathway suppresses over one thousand mRNAs, in addition to canonical noncoding RNAs. RNA sequencing through quiescent entry revealed two distinct time points at which the nuclear exosome controls the abundance of mRNAs involved in protein production, cellular organization, and metabolism, thereby facilitating efficient quiescence entry. Our work identified a previously unknown key biological role for the nuclear exosome-NNS pathway in mRNA regulation and uncovered a novel layer of gene-expression control in quiescence.
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Affiliation(s)
- Alison C Greenlaw
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, Fred Hutchinson Cancer Center and University of Washington, Seattle, WA 98195, USA
| | - Kris G Alavattam
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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5
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Solari CA, Ortolá Martínez MC, Fernandez JM, Bates C, Cueto G, Valacco MP, Morales-Polanco F, Moreno S, Rossi S, Ashe MP, Portela P. Riboproteome remodeling during quiescence exit in Saccharomyces cerevisiae. iScience 2024; 27:108727. [PMID: 38235324 PMCID: PMC10792236 DOI: 10.1016/j.isci.2023.108727] [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: 02/02/2023] [Revised: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
The quiescent state is the prevalent mode of cellular life in most cells. Saccharomyces cerevisiae is a useful model for studying the molecular basis of the cell cycle, quiescence, and aging. Previous studies indicate that heterogeneous ribosomes show a specialized translation function to adjust the cellular proteome upon a specific stimulus. Using nano LC-MS/MS, we identified 69 of the 79 ribosomal proteins (RPs) that constitute the eukaryotic 80S ribosome during quiescence. Our study shows that the riboproteome is composed of 444 accessory proteins comprising cellular functions such as translation, protein folding, amino acid and glucose metabolism, cellular responses to oxidative stress, and protein degradation. Furthermore, the stoichiometry of both RPs and accessory proteins on ribosome particles is different depending on growth conditions and among monosome and polysome fractions. Deficiency of different RPs resulted in defects of translational capacity, suggesting that ribosome composition can result in changes in translational activity during quiescence.
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Affiliation(s)
- Clara A. Solari
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - María Clara Ortolá Martínez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Juan M. Fernandez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Christian Bates
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Gerardo Cueto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - María Pía Valacco
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Fabián Morales-Polanco
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Silvia Moreno
- CEQUIBIEM- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
| | - Mark P. Ashe
- The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas (IQUIBICEN-CONICET), Buenos Aires, Argentina
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Greenlaw AC, Tsukiyama T. Acidic media promotes quiescence entry in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567958. [PMID: 38045406 PMCID: PMC10690216 DOI: 10.1101/2023.11.20.567958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Quiescence is a conserved cellular state wherein cells cease proliferation and remain poised to re-enter the cell cycle when conditions are appropriate. Budding yeast is a powerful model for studying cellular quiescence. In this work, we demonstrate that the pH of the YPD media strongly affects quiescence entry efficiency in Saccharomyces cerevisiae. Adjusting media pH to 5.5 significantly improves quiescence entry efficiency compared to unadjusted YPD media. Thermotolerance of the produced quiescence yeast are similar, suggesting the media pH influences the quantity of quiescent cells more than quality of quiescence reached.
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Affiliation(s)
- Alison C. Greenlaw
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, Fred Hutchinson Cancer Center and University of Washington
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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Opalek M, Tutaj H, Pirog A, Smug BJ, Rutkowska J, Wloch-Salamon D. A Systematic Review on Quiescent State Research Approaches in S. cerevisiae. Cells 2023; 12:1608. [PMID: 37371078 DOI: 10.3390/cells12121608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast Saccharomyces cerevisiae. We group research articles into those that consider all cells comprising the stationary-phase (SP) population as quiescent and those that recognize heterogeneity within the SP by distinguishing phenotypically distinct subpopulations. Furthermore, we investigate the chronological age of the quiescent populations under study and the methods used to induce the quiescent state, such as gradual starvation or abrupt environmental change. We also assess whether the strains used in research are prototrophic or auxotrophic. By combining the above features, we identify 48 possible experimental setups that can be used to study quiescence, which can be misleading when drawing general conclusions. We therefore summarize our review by proposing guidelines and recommendations pertaining to the information included in research articles. We believe that more rigorous reporting on the features of quiescent populations will facilitate knowledge transfer within and between disciplines, thereby stimulating valuable scientific discussion.
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Affiliation(s)
- Monika Opalek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Hanna Tutaj
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Rutkowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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Miles S, Lee C, Breeden L. BY4741 cannot enter quiescence from rich medium. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000742. [PMID: 37012989 PMCID: PMC10066452 DOI: 10.17912/micropub.biology.000742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 04/05/2023]
Abstract
In rich medium, W303 Saccharomyces cerevisiae begins to accumulate in G1 an hour before it exhausts the available glucose. It undergoes one more asymmetrical cell division, then stops dividing in G1. In contrast, BY4741, stops dividing four hours before glucose exhaustion, at one-fourth the cell density achieved by W303. There is no asymmetrical cell division and only 50% of the cells arrest in G1. We conclude that BY4741 growth is not limited by glucose and they do not go through the stereotypical events carried out by other strains as they enter quiescence from rich medium. In W303, the timing of glucose limitation and the transition to quiescence is correlated with the rate of biomass accumulation and cell doubling time.
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Affiliation(s)
- Shawna Miles
- Basic Science, Fred Hutchinson Cancer Center, Seattle, Washington, United States
| | - Cameron Lee
- Tune Therapeutics, 1930 Boren Ave., Seattle, Washington, United States
| | - Linda Breeden
- Basic Science, Fred Hutchinson Cancer Center, Seattle, Washington, United States
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Breeden L, Miles S. A common SSD1 truncation is toxic to cells entering quiescence and promotes sporulation. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000671. [PMID: 36575737 PMCID: PMC9790081 DOI: 10.17912/micropub.biology.000671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022]
Abstract
Ssd1p is an RNA binding protein in Saccharomyces cerevisiae that plays an important role in cell division, cell fate decisions, stress response and virulence. Lab strain W303 encodes the terminal truncation ssd1-2, which is typically interpreted to be a loss of function allele. We have shown that ssd1-2 is toxic to mpt5-Δ mutants and to diploids entering stationary phase and quiescence. The ssd1-Δ null shows no toxicity, indicating that ssd1-2 is disrupting an essential function that does not solely require Ssd1p. ssd1-2 cells are also more sensitive to stress than ssd1-Δ . These phenotypes are recessive to SSD1-1 . In contrast, ssd1-2 plays a dominant role in promoting sporulation.
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Affiliation(s)
- Linda Breeden
- Fred Hutchinson Cancer Center, Basic Science Division, Seattle, WA, USA
| | - Shawna Miles
- Fred Hutchinson Cancer Center, Basic Science Division, Seattle, WA, USA
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