1
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Sun S, Tranchina D, Gresham D. Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551843. [PMID: 37577636 PMCID: PMC10418281 DOI: 10.1101/2023.08.03.551843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Cells arrest growth and enter a quiescent state upon nutrient deprivation. However, the molecular processes by which cells respond to different starvation signals to regulate exit from the cell division cycle and initiation of quiescence remains poorly understood. To study the role of protein expression and signaling in quiescence we combined temporal profiling of the proteome and phosphoproteome using stable isotope labeling with amino acids in cell culture (SILAC) in Saccharomyces cerevisiae (budding yeast). We find that carbon and phosphorus starvation signals activate quiescence through largely distinct remodeling of the proteome and phosphoproteome. However, increased expression of mitochondrial proteins is associated with quiescence establishment in response to both starvation signals. Deletion of the putative quiescence regulator RIM15, which encodes a serine-threonine kinase, results in reduced survival of cells starved for phosphorus and nitrogen, but not carbon. However, we identified common protein phosphorylation roles for RIM15 in quiescence that are enriched for RNA metabolism and translation. We also find evidence for RIM15-mediated phosphorylation of some targets, including IGO1, prior to starvation consistent with a functional role for RIM15 in proliferative cells. Finally, our results reveal widespread catabolism of amino acids in response to nitrogen starvation, indicating widespread amino acid recycling via salvage pathways in conditions lacking environmental nitrogen. Our study defines an expanded quiescent proteome and phosphoproteome in yeast, and highlights the multiple coordinated molecular processes at the level of protein expression and phosphorylation that are required for quiescence.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Daniel Tranchina
- Department of Biology, New York University, New York, NY, 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology
- Department of Biology, New York University, New York, NY, 10003, USA
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2
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Small EM, Osley MA. A screen for histone mutations that affect quiescence in S. cerevisiae. FEBS J 2023; 290:3539-3562. [PMID: 36871139 DOI: 10.1111/febs.16759] [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: 08/07/2022] [Revised: 12/15/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Quiescence or G0 is a reversible state in which cells cease division but retain the ability to resume proliferation. Quiescence occurs in all organisms and is essential for stem cell maintenance and tissue renewal. It is also related to chronological lifespan (CLS)-the survival of postmitotic quiescent cells (Q cells) over time-and thus contributes to longevity. Important questions remain regarding the mechanisms that control entry into quiescence, maintenance of quiescence and re-entry of Q cells into the cell cycle. S. cerevisiae has emerged as an excellent organism in which to address these questions because of the ease in which Q cells can be isolated. Following entry into G0, yeast cells remain viable for an extended period and can re-enter the cell cycle when exposed to growth-promoting signals. Histone acetylation is lost during the formation of Q cells and chromatin becomes highly condensed. This unique chromatin landscape regulates quiescence-specific transcriptional repression and has been linked to the formation and maintenance of Q cells. To ask whether other chromatin features regulate quiescence, we conducted two comprehensive screens of histone H3 and H4 mutants and identified mutants that show either altered quiescence entry or CLS. Examination of several quiescence entry mutants found that none of the mutants retain histone acetylation in Q cells but show differences in chromatin condensation. A comparison of H3 and H4 mutants with altered CLS to those with altered quiescence entry found that chromatin plays both overlapping and independent roles in the continuum of the quiescence program.
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Affiliation(s)
- Eric M Small
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Mary Ann Osley
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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3
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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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4
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Abstract
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.
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Affiliation(s)
- Linda L Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
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5
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On the Ecological Significance of Phenotypic Heterogeneity in Microbial Populations Undergoing Starvation. Microbiol Spectr 2022; 10:e0045021. [PMID: 35019773 PMCID: PMC8754142 DOI: 10.1128/spectrum.00450-21] [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] [Indexed: 11/20/2022] Open
Abstract
To persist in variable environments, populations of microorganisms have to survive periods of starvation and be able to restart cell division in nutrient-rich conditions. Typically, starvation signals initiate a transition to a quiescent state in a fraction of individual cells, while the rest of the cells remain nonquiescent. It is widely believed that, while quiescent (Q) cells help the population to survive long starvation, the nonquiescent (NQ) cells are a side effect of imperfect transition. We analyzed the regrowth of starved monocultures of Q and NQ cells compared to that of mixed, heterogeneous cultures from simple and complex starvation environments. Our experiments, as well as mathematical modeling, demonstrate that Q monocultures benefit from better survival during long starvation and from a shorter lag phase after resupply of rich medium. However, when the starvation period is very short, the NQ monocultures outperform Q and mixed cultures due to their short lag phase. In addition, only NQ monocultures benefit from complex starvation environments, where nutrient recycling is possible. Our study suggests that phenotypic heterogeneity in starved populations could be a form of bet hedging that is adaptive when environmental determinants, such as the length of the starvation period, the length of the regrowth phase, and the complexity of the starvation environment, vary over time. IMPORTANCE Nongenetic cell heterogeneity is present in glucose-starved yeast populations in the form of quiescent (Q) and nonquiescent (NQ) phenotypes. There is evidence that Q cells help the population survive long starvation. However, the role of the NQ cell type is not known, and it has been speculated that the NQ phenotype is just a side effect of the imperfect transition to the Q phenotype. Here, we show that, in contrast, there are ecological scenarios in which NQ cells perform better than monocultures of Q cells or naturally occurring mixed populations containing both Q and NQ cells. NQ cells benefit when the starvation period is very short and environmental conditions allow nutrient recycling during starvation. Our experimental and mathematical modeling results suggest a novel hypothesis: the presence of both Q and NQ phenotypes within starved yeast populations may reflect a form of bet hedging where different phenotypes provide fitness advantages depending on the environmental conditions.
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6
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McKnight LE, Crandall JG, Bailey TB, Banks OGB, Orlandi KN, Truong VN, Donovan DA, Waddell GL, Wiles ET, Hansen SD, Selker EU, McKnight JN. Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms. STAR Protoc 2021; 2:100486. [PMID: 34041500 PMCID: PMC8141940 DOI: 10.1016/j.xpro.2021.100486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
MNase-seq (micrococcal nuclease sequencing) is used to map nucleosome positions in eukaryotic genomes to study the relationship between chromatin structure and DNA-dependent processes. Current protocols require at least two days to isolate nucleosome-protected DNA fragments. We have developed a streamlined protocol for S. cerevisiae and other fungi which takes only three hours. Modified protocols were developed for wild fungi and mammalian cells. This method for rapidly producing sequencing-ready nucleosome footprints from several organisms makes MNase-seq faster and easier, with less chemical waste. A fast way to prepare micrococcal nuclease nucleosome footprints for MNase-seq Eliminates use of phenol and chloroform and reduces the amount of cells required Adaptable for a variety of organisms
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Affiliation(s)
- Laura E McKnight
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | | | - Thomas B Bailey
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Orion G B Banks
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Kona N Orlandi
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Vi N Truong
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Drake A Donovan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Grace L Waddell
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Elizabeth T Wiles
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Scott D Hansen
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Jeffrey N McKnight
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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7
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Gu Z. An improved staining method of cell cycle analysis with Sybr Green I for fungi: Cryptococcus neoformans and Saccharomyces cerevisiae. Cell Cycle 2021; 20:271-282. [PMID: 33463377 PMCID: PMC7889188 DOI: 10.1080/15384101.2020.1870334] [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: 11/20/2019] [Revised: 12/13/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022] Open
Abstract
Cryptococcus neoformans is a pathogenic fungus which causes millions of deaths and infections, especially threatening immunocompromised individuals. During the development of new drugs, the ubiquitination has been found to play an important role in the regulation of the virulence and cell cycle of this fungus. Based on this mechanism, ubiquitination-related mutant strains exhibiting cell cycle arrest have been established for drug development for the fungus. However, flow cytometry detection of the cell cycle in fungi is generally difficult because the thick cell wall and capsule of fungi generally contribute to a nonspecific signal of cytometry. In this study, an improved method, derived from Saccharomyces cerevisiae assays, is developed to specifically stain C. neoformans, in whose cell cycle the G1 and G2 peaks are separated enough to be allowed for cell cycle analysis. As a result, the improved method facilitates the detection of the alterations in the cell cycle of C. neoformans with a mutation that results in cell cycle arrest, which distinctly delays the cell division of C. neoformans. Thus, the improved method reported here provides detailed technical information regarding assays on C. neoformans and, more importantly, offers a solution for assessing the cell cycle in other fungi in the future. Abbreviation: PI: propidium iodide.
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Affiliation(s)
- Zhongkai Gu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People’s Republic of China
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8
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Sun S, Gresham D. Cellular quiescence in budding yeast. Yeast 2021; 38:12-29. [PMID: 33350503 DOI: 10.1002/yea.3545] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022] Open
Abstract
Cellular quiescence, the temporary and reversible exit from proliferative growth, is the predominant state of all cells. However, our understanding of the biological processes and molecular mechanisms that underlie cell quiescence remains incomplete. As with the mitotic cell cycle, budding and fission yeast are preeminent model systems for studying cellular quiescence owing to their rich experimental toolboxes and the evolutionary conservation across eukaryotes of pathways and processes that control quiescence. Here, we review current knowledge of cell quiescence in budding yeast and how it pertains to cellular quiescence in other organisms, including multicellular animals. Quiescence entails large-scale remodeling of virtually every cellular process, organelle, gene expression, and metabolic state that is executed dynamically as cells undergo the initiation, maintenance, and exit from quiescence. We review these major transitions, our current understanding of their molecular bases, and highlight unresolved questions. We summarize the primary methods employed for quiescence studies in yeast and discuss their relative merits. Understanding cell quiescence has important consequences for human disease as quiescent single-celled microbes are notoriously difficult to kill and quiescent human cells play important roles in diseases such as cancer. We argue that research on cellular quiescence will be accelerated through the adoption of common criteria, and methods, for defining cell quiescence. An integrated approach to studying cell quiescence, and a focus on the behavior of individual cells, will yield new insights into the pathways and processes that underlie cell quiescence leading to a more complete understanding of the life cycle of cells. TAKE AWAY: Quiescent cells are viable cells that have reversibly exited the cell cycle Quiescence is induced in response to a variety of nutrient starvation signals Quiescence is executed dynamically through three phases: initiation, maintenance, and exit Quiescence entails large-scale remodeling of gene expression, organelles, and metabolism Single-cell approaches are required to address heterogeneity among quiescent cells.
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Affiliation(s)
- Siyu Sun
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, New York University, New York, New York, 10003, USA.,Department of Biology, New York University, New York, New York, 10003, USA
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9
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Genome Profiling for Aflatoxin B 1 Resistance in Saccharomyces cerevisiae Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B 1-Associated DNA Damage. G3-GENES GENOMES GENETICS 2020; 10:3929-3947. [PMID: 32994210 PMCID: PMC7642924 DOI: 10.1534/g3.120.401723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exposure to the mycotoxin aflatoxin B1 (AFB1) strongly correlates with hepatocellular carcinoma (HCC). P450 enzymes convert AFB1 into a highly reactive epoxide that forms unstable 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 (AFB1-N 7-Gua) DNA adducts, which convert to stable mutagenic AFB1 formamidopyrimidine (FAPY) DNA adducts. In CYP1A2-expressing budding yeast, AFB1 is a weak mutagen but a potent recombinagen. However, few genes have been identified that confer AFB1 resistance. Here, we profiled the yeast genome for AFB1 resistance. We introduced the human CYP1A2 into ∼90% of the diploid deletion library, and pooled samples from CYP1A2-expressing libraries and the original library were exposed to 50 μM AFB1 for 20 hs. By using next generation sequencing (NGS) to count molecular barcodes, we initially identified 86 genes from the CYP1A2-expressing libraries, of which 79 were confirmed to confer AFB1 resistance. While functionally diverse genes, including those that function in proteolysis, actin reorganization, and tRNA modification, were identified, those that function in postreplication DNA repair and encode proteins that bind to DNA damage were over-represented, compared to the yeast genome, at large. DNA metabolism genes also included those functioning in checkpoint recovery and replication fork maintenance, emphasizing the potency of the mycotoxin to trigger replication stress. Among genes involved in postreplication repair, we observed that CSM2, a member of the CSM2 (SHU) complex, functioned in AFB1-associated sister chromatid recombination while suppressing AFB1-associated mutations. These studies thus broaden the number of AFB1 resistance genes and have elucidated a mechanism of error-free bypass of AFB1-associated DNA adducts.
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10
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Miles S, Li LH, Melville Z, Breeden LL. Ssd1 and the cell wall integrity pathway promote entry, maintenance, and recovery from quiescence in budding yeast. Mol Biol Cell 2019; 30:2205-2217. [PMID: 31141453 PMCID: PMC6743469 DOI: 10.1091/mbc.e19-04-0190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Wild Saccharomyces cerevisiae strains are typically diploid. When faced with glucose and nitrogen limitation they can undergo meiosis and sporulate. Diploids can also enter a protective, nondividing cellular state or quiescence. The ability to enter quiescence is highly reproducible but shows broad natural variation. Some wild diploids can only enter cellular quiescence, which indicates that there are conditions in which sporulation is lost or selected against. Others only sporulate, but if sporulation is disabled by heterozygosity at the IME1 locus, those diploids can enter quiescence. W303 haploids can enter quiescence, but their diploid counterparts cannot. This is the result of diploidy, not mating type regulation. Introduction of SSD1 to W303 diploids switches fate, in that it rescues cellular quiescence and disrupts the ability to sporulate. Ssd1 and another RNA-binding protein, Mpt5 (Puf5), have parallel roles in quiescence in haploids. The ability of these mutants to enter quiescence, and their long-term survival in the quiescent state, can be rescued by exogenously added trehalose. The cell wall integrity pathway also promotes entry, maintenance, and recovery from quiescence through the Rlm1 transcription factor.
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Affiliation(s)
- Shawna Miles
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Li Hong Li
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Zephan Melville
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
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11
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Unraveling quiescence-specific repressive chromatin domains. Curr Genet 2019; 65:1145-1151. [PMID: 31055637 DOI: 10.1007/s00294-019-00985-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 01/30/2023]
Abstract
Quiescence is a highly conserved inactive life stage in which the cell reversibly exits the cell cycle in response to external cues. Quiescence is essential for diverse processes such as the maintenance of adult stem cell stores, stress resistance, and longevity, and its misregulation has been implicated in cancer. Although the non-cycling nature of quiescent cells has made obtaining sufficient quantities of quiescent cells for study difficult, the development of a Saccharomyces cerevisiae model of quiescence has recently enabled detailed investigation into mechanisms underlying the quiescent state. Like their metazoan counterparts, quiescent budding yeast exhibit widespread transcriptional silencing and dramatic chromatin condensation. We have recently found that the structural maintenance of chromosomes (SMC) complex condensin binds throughout the quiescent budding yeast genome and induces the formation of large chromatin loop domains. In the absence of condensin, quiescent cell chromatin is decondensed and transcription is de-repressed. Here, we briefly discuss our findings in the larger context of the genome organization field.
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12
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Swygert SG, Kim S, Wu X, Fu T, Hsieh TH, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T. Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence. Mol Cell 2019; 73:533-546.e4. [PMID: 30595435 PMCID: PMC6368455 DOI: 10.1016/j.molcel.2018.11.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/25/2018] [Accepted: 11/15/2018] [Indexed: 02/03/2023]
Abstract
Quiescence is a stress-resistant state in which cells reversibly exit the cell cycle and suspend most processes. Quiescence is essential for stem cell maintenance, and its misregulation is implicated in tumor formation. One of the hallmarks of quiescent cells is highly condensed chromatin. Because condensed chromatin often correlates with transcriptional silencing, it has been hypothesized that chromatin compaction represses transcription during quiescence. However, the technology to test this model by determining chromatin structure within cells at gene resolution has not previously been available. Here, we use Micro-C XL to map chromatin contacts at single-nucleosome resolution genome-wide in quiescent Saccharomyces cerevisiae cells. We describe chromatin domains on the order of 10-60 kilobases that, only in quiescent cells, are formed by condensin-mediated loops. Condensin depletion prevents the compaction of chromatin within domains and leads to widespread transcriptional de-repression. Finally, we demonstrate that condensin-dependent chromatin compaction is conserved in quiescent human fibroblasts.
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Affiliation(s)
- Sarah G Swygert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Seungsoo Kim
- Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Xiaoying Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Tianhong Fu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Tsung-Han Hsieh
- Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, MA 01605, USA
| | - Oliver J Rando
- Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, MA 01605, USA
| | - Robert N Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jay Shendure
- Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Jeffrey N McKnight
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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13
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Abstract
Saccharomyces cerevisiae enter quiescence during extended growth in culture (greater than 7 days). Here, we describe a method to separate quiescent from non-quiescent cells by density gradient. We also describe approaches for DAPI staining the chromatin of quiescent cells, measuring quiescent cell viability, and extracting RNA from quiescent cells for use in genomics experiments.
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14
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Gu ZC, Wu E, Sailer C, Jando J, Styles E, Eisenkolb I, Kuschel M, Bitschar K, Wang X, Huang L, Vissa A, Yip CM, Yedidi RS, Friesen H, Enenkel C. Ubiquitin orchestrates proteasome dynamics between proliferation and quiescence in yeast. Mol Biol Cell 2017; 28:2479-2491. [PMID: 28768827 PMCID: PMC5597321 DOI: 10.1091/mbc.e17-03-0162] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022] Open
Abstract
Proteasomes are key protease complexes responsible for protein degradation, and their localization changes with the growth conditions. This work in yeast shows that proteasomes exit the nucleus with the transition from proliferation to quiescence. Ubiquitin is a key player in proteasome dynamics and cytoplasmic proteasome granule formation. Proteasomes are essential for protein degradation in proliferating cells. Little is known about proteasome functions in quiescent cells. In nondividing yeast, a eukaryotic model of quiescence, proteasomes are depleted from the nucleus and accumulate in motile cytosolic granules termed proteasome storage granules (PSGs). PSGs enhance resistance to genotoxic stress and confer fitness during aging. Upon exit from quiescence PSGs dissolve, and proteasomes are rapidly delivered into the nucleus. To identify key players in PSG organization, we performed high-throughput imaging of green fluorescent protein (GFP)-labeled proteasomes in the yeast null-mutant collection. Mutants with reduced levels of ubiquitin are impaired in PSG formation. Colocalization studies of PSGs with proteins of the yeast GFP collection, mass spectrometry, and direct stochastic optical reconstitution microscopy of cross-linked PSGs revealed that PSGs are densely packed with proteasomes and contain ubiquitin but no polyubiquitin chains. Our results provide insight into proteasome dynamics between proliferating and quiescent yeast in response to cellular requirements for ubiquitin-dependent degradation.
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Affiliation(s)
- Zhu Chao Gu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Edwin Wu
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Carolin Sailer
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Julia Jando
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Erin Styles
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ina Eisenkolb
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Maike Kuschel
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Katharina Bitschar
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Xiaorong Wang
- Department of Physics and Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physics and Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Adriano Vissa
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ravikiran S Yedidi
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Helena Friesen
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
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15
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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16
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Miles S, Croxford MW, Abeysinghe AP, Breeden LL. Msa1 and Msa2 Modulate G1-Specific Transcription to Promote G1 Arrest and the Transition to Quiescence in Budding Yeast. PLoS Genet 2016; 12:e1006088. [PMID: 27272642 PMCID: PMC4894574 DOI: 10.1371/journal.pgen.1006088] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/09/2016] [Indexed: 12/23/2022] Open
Abstract
Yeast that naturally exhaust their glucose source can enter a quiescent state that is characterized by reduced cell size, and high cell density, stress tolerance and longevity. The transition to quiescence involves highly asymmetric cell divisions, dramatic reprogramming of transcription and global changes in chromatin structure and chromosome topology. Cells enter quiescence from G1 and we find that there is a positive correlation between the length of G1 and the yield of quiescent cells. The Swi4 and Swi6 transcription factors, which form the SBF transcription complex and promote the G1 to S transition in cycling cells, are also critical for the transition to quiescence. Swi6 forms a second complex with Mbp1 (MBF), which is not required for quiescence. These are the functional analogues of the E2F complexes of higher eukaryotes. Loss of the RB analogue, Whi5, and the related protein Srl3/Whi7, delays G1 arrest, but it also delays recovery from quiescence. Two MBF- and SBF-Associated proteins have been identified that have little effect on SBF or MBF activity in cycling cells. We show that these two related proteins, Msa1 and Msa2, are specifically required for the transition to quiescence. Like the E2F complexes that are quiescence-specific, Msa1 and Msa2 are required to repress the transcription of many SBF target genes, including SWI4, the CLN2 cyclin and histones, specifically after glucose is exhausted from the media. They also activate transcription of many MBF target genes. msa1msa2 cells fail to G1 arrest and rapidly lose viability upon glucose exhaustion. msa1msa2 mutants that survive this transition are very large, but they attain the same thermo-tolerance and longevity of wild type quiescent cells. This indicates that Msa1 and Msa2 are required for successful transition to quiescence, but not for the maintenance of that state. In spite of the many differences between yeast and humans, the basic strategies that regulate the cell division cycle are fundamentally conserved. In this study, we extend these parallels to include a common strategy by which cells transition from proliferation to quiescence. The decision to divide is made in the G1 phase of the cell cycle. During G1, the genes that drive DNA replication are repressed by the E2F/RB complex. When a signal to divide is received, RB is removed and the complex is activated. When cells commit to a long term, but reversible G1 arrest, or quiescence, they express a novel E2F/RB-like complex, which promotes and maintains a stable repressive state. Yeast cells contain a functional analog of E2F/RB, called SBF/Whi5, which is activated by a similar mechanism in proliferating yeast cells. In this study, we identify two novel components of the SBF/Whi5 complex whose activity is specific to the transition to quiescence. These factors, Msa1 and Msa2, repress SBF targets and are required for the long term, but reversible G1 arrest that is critical for achieving a quiescent state.
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Affiliation(s)
- Shawna Miles
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Matthew W Croxford
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Amali P Abeysinghe
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Linda L Breeden
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Lee HY, Cheng KY, Chao JC, Leu JY. Differentiated cytoplasmic granule formation in quiescent and non-quiescent cells upon chronological aging. MICROBIAL CELL 2016; 3:109-119. [PMID: 28357341 PMCID: PMC5349021 DOI: 10.15698/mic2016.03.484] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Stationary phase cultures represent a complicated cell population comprising at
least two different cell types, quiescent (Q) and non-quiescent (NQ) cells. Q
and NQ cells have different lifespans and cell physiologies. However, less is
known about the organization of cytosolic protein structures in these two cell
types. In this study, we examined Q and NQ cells for the formation of several
stationary phase-prevalent granule structures including actin bodies, proteasome
storage granules, stress granules, P-bodies, the compartment for unconventional
protein secretion (CUPS), and Hsp42-associated stationary phase granules
(Hsp42-SPGs). Most of these structures preferentially form in NQ cells, except
for Hsp42-SPGs, which are enriched in Q cells. When nutrients are provided, NQ
cells enter mitosis less efficiently than Q cells, likely due to the time
requirement for reorganizing some granule structures. We observed that heat
shock-induced misfolded proteins often colocalize to Hsp42-SPGs, and Q cells
clear these protein aggregates more efficiently, suggesting that Hsp42-SPGs may
play an important role in the stress resistance of Q cells. Finally, we show
that the cell fate of NQ cells is largely irreversible even if they are allowed
to reenter mitosis. Our results reveal that the formation of different granule
structures may represent the early stage of cell type differentiation in yeast
stationary phase cultures.
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Affiliation(s)
- Hsin-Yi Lee
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan. ; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kuo-Yu Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan. ; Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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