1
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Talavera RA, Prichard BE, Sommer RA, Leitao RM, Sarabia CJ, Hazir S, Paulo JA, Gygi SP, Kellogg DR. Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast. J Cell Biol 2024; 223:e202305008. [PMID: 38722822 PMCID: PMC11082370 DOI: 10.1083/jcb.202305008] [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: 05/07/2023] [Revised: 01/03/2024] [Accepted: 04/04/2024] [Indexed: 05/13/2024] Open
Abstract
Cell growth is required for cell cycle progression. The amount of growth required for cell cycle progression is reduced in poor nutrients, which leads to a reduction in cell size. In budding yeast, nutrients can influence cell size by modulating the extent of bud growth, which occurs predominantly in mitosis. However, the mechanisms are unknown. Here, we used mass spectrometry to identify proteins that modulate bud growth in response to nutrient availability. This led to the discovery that nutrients regulate numerous components of the mitotic exit network (MEN), which controls exit from mitosis. A key component of the MEN undergoes gradual multisite phosphorylation during bud growth that is dependent upon bud growth and correlated with the extent of growth. Furthermore, activation of the MEN is sufficient to override a growth requirement for mitotic exit. The data suggest a model in which the MEN ensures that mitotic exit occurs only when an appropriate amount of bud growth has occurred.
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Affiliation(s)
- Rafael A. Talavera
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Beth E. Prichard
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Robert A. Sommer
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Ricardo M. Leitao
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Christopher J. Sarabia
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Semin Hazir
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Douglas R. Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Xiao J, Turner JJ, Kõivomägi M, Skotheim JM. Whi5 hypo- and hyper-phosphorylation dynamics control cell-cycle entry and progression. Curr Biol 2024; 34:2434-2447.e5. [PMID: 38749424 PMCID: PMC11247822 DOI: 10.1016/j.cub.2024.04.052] [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: 09/13/2023] [Revised: 03/18/2024] [Accepted: 04/23/2024] [Indexed: 05/28/2024]
Abstract
Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the Swi4/Swi6 (SBF) complex that promotes transcription of the cyclins CLN1 and CLN2. In late G1, Whi5 is rapidly hyper-phosphorylated by Cln1 and Cln2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on "priming" sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
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Affiliation(s)
- Jordan Xiao
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Jonathan J Turner
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892, USA.
| | - Jan M Skotheim
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Chan Zuckerberg Biohub, 499 Illinois St., San Francisco, CA 94158, USA.
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3
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Brambila A, Prichard BE, DeWitt JT, Kellogg DR. Evidence for novel mechanisms that control cell-cycle entry and cell size. Mol Biol Cell 2024; 35:ar46. [PMID: 38231863 PMCID: PMC11064657 DOI: 10.1091/mbc.e23-05-0174] [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: 05/18/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
Entry into the cell cycle in late G1 phase occurs only when sufficient growth has occurred. In budding yeast, a cyclin called Cln3 is thought to link cell-cycle entry to cell growth. Cln3 accumulates during growth in early G1 phase and eventually helps trigger expression of late G1 phase cyclins that drive cell-cycle entry. All current models for cell-cycle entry assume that expression of late G1 phase cyclins is initiated at the transcriptional level. Current models also assume that the sole function of Cln3 in cell-cycle entry is to promote transcription of late G1 phase cyclins, and that Cln3 works solely in G1 phase. Here, we show that cell cycle-dependent expression of the late G1 phase cyclin Cln2 does not require any functions of the CLN2 promoter. Moreover, Cln3 can influence accumulation of Cln2 protein via posttranscriptional mechanisms. Finally, we show that Cln3 has functions in mitosis that strongly influence cell size. Together, these discoveries reveal the existence of surprising new mechanisms that challenge current models for control of cell-cycle entry and cell size.
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Affiliation(s)
- Amanda Brambila
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
| | - Beth E. Prichard
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
| | - Jerry T. DeWitt
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
| | - Douglas R. Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
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4
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Litsios A, Grys BT, Kraus OZ, Friesen H, Ross C, Masinas MPD, Forster DT, Couvillion MT, Timmermann S, Billmann M, Myers C, Johnsson N, Churchman LS, Boone C, Andrews BJ. Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle. Cell 2024; 187:1490-1507.e21. [PMID: 38452761 PMCID: PMC10947830 DOI: 10.1016/j.cell.2024.02.014] [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: 09/12/2023] [Revised: 12/01/2023] [Accepted: 02/12/2024] [Indexed: 03/09/2024]
Abstract
Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.
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Affiliation(s)
- Athanasios Litsios
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Benjamin T Grys
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Oren Z Kraus
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Helena Friesen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Catherine Ross
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Myra Paz David Masinas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Duncan T Forster
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mary T Couvillion
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stefanie Timmermann
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm 89081, Germany
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Chad Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm 89081, Germany
| | | | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; RIKEN Center for Sustainable Resource Science, Wako 351-0198 Saitama, Japan.
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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5
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Diehl FF, Sapp KM, Vander Heiden MG. The bidirectional relationship between metabolism and cell cycle control. Trends Cell Biol 2024; 34:136-149. [PMID: 37385879 DOI: 10.1016/j.tcb.2023.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
The relationship between metabolism and cell cycle progression is complex and bidirectional. Cells must rewire metabolism to meet changing biosynthetic demands across cell cycle phases. In turn, metabolism can influence cell cycle progression through direct regulation of cell cycle proteins, through nutrient-sensing signaling pathways, and through its impact on cell growth, which is linked to cell division. Furthermore, metabolism is a key player in mediating quiescence-proliferation transitions in physiologically important cell types, such as stem cells. How metabolism impacts cell cycle progression, exit, and re-entry, as well as how these processes impact metabolism, is not fully understood. Recent advances uncovering mechanistic links between cell cycle regulators and metabolic processes demonstrate a complex relationship between metabolism and cell cycle control, with many questions remaining.
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Affiliation(s)
- Frances F Diehl
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
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6
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Xiao J, Turner JJ, Kõivomägi M, Skotheim JM. Whi5 hypo- and hyper-phosphorylation dynamics control cell cycle entry and progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565392. [PMID: 37961465 PMCID: PMC10635099 DOI: 10.1101/2023.11.02.565392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates the G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the SBF complex that promotes transcription of the cyclins CLN1 and CLN2 . In late-G1, Whi5 is rapidly hyper-phosphorylated by Cln1,2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on 'priming' sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
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7
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Foltman M, Sanchez-Diaz A. TOR Complex 1: Orchestrating Nutrient Signaling and Cell Cycle Progression. Int J Mol Sci 2023; 24:15745. [PMID: 37958727 PMCID: PMC10647266 DOI: 10.3390/ijms242115745] [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: 09/01/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The highly conserved TOR signaling pathway is crucial for coordinating cellular growth with the cell cycle machinery in eukaryotes. One of the two TOR complexes in budding yeast, TORC1, integrates environmental cues and promotes cell growth. While cells grow, they need to copy their chromosomes, segregate them in mitosis, divide all their components during cytokinesis, and finally physically separate mother and daughter cells to start a new cell cycle apart from each other. To maintain cell size homeostasis and chromosome stability, it is crucial that mechanisms that control growth are connected and coordinated with the cell cycle. Successive periods of high and low TORC1 activity would participate in the adequate cell cycle progression. Here, we review the known molecular mechanisms through which TORC1 regulates the cell cycle in the budding yeast Saccharomyces cerevisiae that have been extensively used as a model organism to understand the role of its mammalian ortholog, mTORC1.
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Affiliation(s)
- Magdalena Foltman
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
| | - Alberto Sanchez-Diaz
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
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8
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DeWitt JT, Chinwuba JC, Kellogg DR. Hyperactive Ras disrupts cell size control and a key step in cell cycle entry in budding yeast. Genetics 2023; 225:iyad144. [PMID: 37531631 PMCID: PMC10758756 DOI: 10.1093/genetics/iyad144] [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: 06/08/2023] [Revised: 06/08/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023] Open
Abstract
Severe defects in cell size are a nearly universal feature of cancer cells. However, the underlying causes are unknown. A previous study suggested that a hyperactive mutant of yeast Ras (ras2G19V) that is analogous to the human Ras oncogene causes cell size defects, which could provide clues to how oncogenes influence cell size. However, the mechanisms by which ras2G19V influences cell size are unknown. Here, we found that ras2G19V inhibits a critical step in cell cycle entry, in which an early G1 phase cyclin induces transcription of late G1 phase cyclins. Thus, ras2G19V drives overexpression of the early G1 phase cyclin Cln3, yet Cln3 fails to induce normal transcription of late G1 phase cyclins, leading to delayed cell cycle entry and increased cell size. ras2G19V influences transcription of late G1 phase cyclins via a poorly understood step in which Cln3 inactivates the Whi5 transcriptional repressor. Previous studies found that yeast Ras relays signals via protein kinase A (PKA); however, ras2G19V appears to influence late G1 phase cyclin expression via novel PKA-independent signaling mechanisms. Together, the data define new mechanisms by which hyperactive Ras influences cell cycle entry and cell size in yeast. Hyperactive Ras also influences expression of G1 phase cyclins in mammalian cells, but the mechanisms remain unclear. Further analysis of Ras signaling in yeast could lead to discovery of new mechanisms by which Ras family members control expression of G1 phase cyclins.
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Affiliation(s)
- Jerry T DeWitt
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Jennifer C Chinwuba
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Douglas R Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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9
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Okreglak V, Ling R, Ingaramo M, Thayer NH, Millett-Sikking A, Gottschling DE. Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth. Nat Metab 2023; 5:1803-1819. [PMID: 37640943 PMCID: PMC10590757 DOI: 10.1038/s42255-023-00872-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Amino acid homeostasis is critical for many cellular processes. It is well established that amino acids are compartmentalized using pH gradients generated between organelles and the cytoplasm; however, the dynamics of this partitioning has not been explored. Here we develop a highly sensitive pH reporter and find that the major amino acid storage compartment in Saccharomyces cerevisiae, the lysosome-like vacuole, alkalinizes before cell division and re-acidifies as cells divide. The vacuolar pH dynamics require the uptake of extracellular amino acids and activity of TORC1, the v-ATPase and the cycling of the vacuolar specific lipid phosphatidylinositol 3,5-bisphosphate, which is regulated by the cyclin-dependent kinase Pho85 (CDK5 in mammals). Vacuolar pH regulation enables amino acid sequestration and mobilization from the organelle, which is important for mitochondrial function, ribosome homeostasis and cell size control. Collectively, our data provide a new paradigm for the use of dynamic pH-dependent amino acid compartmentalization during cell growth/division.
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Affiliation(s)
- Voytek Okreglak
- Calico Life Sciences, LLC, South San Francisco, CA, USA.
- Altos Labs, Redwood City, CA, USA.
| | - Rachel Ling
- Calico Life Sciences, LLC, South San Francisco, CA, USA
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10
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Wagner ER, Nightingale NM, Jen A, Overmyer KA, McGee M, Coon JJ, Gasch AP. PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae. PLoS Genet 2023; 19:e1010593. [PMID: 37410771 DOI: 10.1371/journal.pgen.1010593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
Organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These pathways must be properly coordinated to elicit the appropriate response to an ever-changing environment. While individual pathways have been well studied in a variety of model systems, there remains much to uncover about how pathways are integrated to produce systemic changes in a cell, especially in dynamic conditions. We previously showed that deletion of Protein Kinase A (PKA) regulatory subunit BCY1 can decouple growth and metabolism in Saccharomyces cerevisiae engineered for anaerobic xylose fermentation, allowing for robust fermentation in the absence of division. This provides an opportunity to understand how PKA signaling normally coordinates these processes. Here, we integrated transcriptomic, lipidomic, and phospho-proteomic responses upon a glucose to xylose shift across a series of strains with different genetic mutations promoting either coupled or decoupled xylose-dependent growth and metabolism. Together, results suggested that defects in lipid homeostasis limit growth in the bcy1Δ strain despite robust metabolism. To further understand this mechanism, we performed adaptive laboratory evolutions to re-evolve coupled growth and metabolism in the bcy1Δ parental strain. The evolved strain harbored mutations in PKA subunit TPK1 and lipid regulator OPI1, among other genes, and evolved changes in lipid profiles and gene expression. Deletion of the evolved opi1 gene partially reverted the strain's phenotype to the bcy1Δ parent, with reduced growth and robust xylose fermentation. We suggest several models for how cells coordinate growth, metabolism, and other responses in budding yeast and how restructuring these processes enables anaerobic xylose utilization.
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Affiliation(s)
- Ellen R Wagner
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicole M Nightingale
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Annie Jen
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua J Coon
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, United States of America
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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11
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Chaillot J, Cook MA, Sellam A. Novel determinants of cell size homeostasis in the opportunistic yeast Candida albicans. Curr Genet 2023; 69:67-75. [PMID: 36449086 DOI: 10.1007/s00294-022-01260-0] [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: 11/18/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
The basis for commitment to cell division in late G1 phase, called Start in yeast, is a critical but still poorly understood aspect of eukaryotic cell proliferation. Most dividing cells accumulate mass and grow to a critical cell size before traversing the cell cycle. This size threshold couples cell growth to division and thereby establishes long-term size homeostasis. At present, mechanisms involved in cell size homeostasis in fungal pathogens are not well described. Our previous survey of the size phenome in Candida albicans focused on 279 unique mutants enriched mainly in kinases and transcription factors (Sellam et al. PLoS Genet 15:e1008052, 2019). To uncover novel size regulators in C. albicans and highlight potential innovation within cell size control in pathogenic fungi, we expanded our genetic survey of cell size to include 1301 strains from the GRACE (Gene Replacement and Conditional Expression) collection. The current investigation uncovered both known and novel biological processes required for cell size homeostasis in C. albicans. We also confirmed the plasticity of the size control network as few C. albicans size genes overlapped with those of the budding yeast Saccharomyces cerevisiae. Many new size genes of C. albicans were associated with biological processes that were not previously linked to cell size control and offer an opportunity for future investigation. Additional work is needed to understand if mitochondrial activity is a critical element of the metric that dictates cell size in C. albicans and whether modulation of the onset of actomyosin ring constriction is an additional size checkpoint.
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Affiliation(s)
- Julien Chaillot
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600, Pessac, France
| | - Michael A Cook
- Department of Biochemistry and Biomedical Sciences, David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Adnane Sellam
- Montreal Heart Institute, Université de Montréal, Montréal, QC, Canada.
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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12
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Liu S, Tan C, Tyers M, Zetterberg A, Kafri R. What programs the size of animal cells? Front Cell Dev Biol 2022; 10:949382. [PMID: 36393871 PMCID: PMC9665425 DOI: 10.3389/fcell.2022.949382] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/07/2022] [Indexed: 01/19/2023] Open
Abstract
The human body is programmed with definite quantities, magnitudes, and proportions. At the microscopic level, such definite sizes manifest in individual cells - different cell types are characterized by distinct cell sizes whereas cells of the same type are highly uniform in size. How do cells in a population maintain uniformity in cell size, and how are changes in target size programmed? A convergence of recent and historical studies suggest - just as a thermostat maintains room temperature - the size of proliferating animal cells is similarly maintained by homeostatic mechanisms. In this review, we first summarize old and new literature on the existence of cell size checkpoints, then discuss additional advances in the study of size homeostasis that involve feedback regulation of cellular growth rate. We further discuss recent progress on the molecules that underlie cell size checkpoints and mechanisms that specify target size setpoints. Lastly, we discuss a less-well explored teleological question: why does cell size matter and what is the functional importance of cell size control?
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Affiliation(s)
- Shixuan Liu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States,*Correspondence: Shixuan Liu, ; Ran Kafri,
| | - Ceryl Tan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC, Canada
| | - Anders Zetterberg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ran Kafri
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada,*Correspondence: Shixuan Liu, ; Ran Kafri,
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13
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Kellogg DR, Levin PA. Nutrient availability as an arbiter of cell size. Trends Cell Biol 2022; 32:908-919. [PMID: 35851491 PMCID: PMC9588502 DOI: 10.1016/j.tcb.2022.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023]
Abstract
Pioneering work carried out over 60 years ago discovered that bacterial cell size is proportional to the growth rate set by nutrient availability. This relationship is traditionally referred to as the 'growth law'. Subsequent studies revealed the growth law to hold across all orders of life, a remarkable degree of conservation. However, recent work suggests the relationship between growth rate, nutrients, and cell size is far more complicated and less deterministic than originally thought. Focusing on bacteria and yeast, here we review efforts to understand the molecular mechanisms underlying the relationship between growth rate and cell size.
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Affiliation(s)
- Douglas R Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St Louis, MO 63130, USA; Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St Louis, St Louis, MO 63130, USA.
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14
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Abstract
The most fundamental feature of cellular form is size, which sets the scale of all cell biological processes. Growth, form, and function are all necessarily linked in cell biology, but we often do not understand the underlying molecular mechanisms nor their specific functions. Here, we review progress toward determining the molecular mechanisms that regulate cell size in yeast, animals, and plants, as well as progress toward understanding the function of cell size regulation. It has become increasingly clear that the mechanism of cell size regulation is deeply intertwined with basic mechanisms of biosynthesis, and how biosynthesis can be scaled (or not) in proportion to cell size. Finally, we highlight recent findings causally linking aberrant cell size regulation to cellular senescence and their implications for cancer therapies.
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Affiliation(s)
- Shicong Xie
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Matthew Swaffer
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, California, USA;
- Chan Zuckerberg Biohub, San Francisco, California, USA
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15
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TOR complex 2 is a master regulator of plasma membrane homeostasis. Biochem J 2022; 479:1917-1940. [PMID: 36149412 PMCID: PMC9555796 DOI: 10.1042/bcj20220388] [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: 07/22/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
As first demonstrated in budding yeast (Saccharomyces cerevisiae), all eukaryotic cells contain two, distinct multi-component protein kinase complexes that each harbor the TOR (Target Of Rapamycin) polypeptide as the catalytic subunit. These ensembles, dubbed TORC1 and TORC2, function as universal, centrally important sensors, integrators, and controllers of eukaryotic cell growth and homeostasis. TORC1, activated on the cytosolic surface of the lysosome (or, in yeast, on the cytosolic surface of the vacuole), has emerged as a primary nutrient sensor that promotes cellular biosynthesis and suppresses autophagy. TORC2, located primarily at the plasma membrane, plays a major role in maintaining the proper levels and bilayer distribution of all plasma membrane components (sphingolipids, glycerophospholipids, sterols, and integral membrane proteins). This article surveys what we have learned about signaling via the TORC2 complex, largely through studies conducted in S. cerevisiae. In this yeast, conditions that challenge plasma membrane integrity can, depending on the nature of the stress, stimulate or inhibit TORC2, resulting in, respectively, up-regulation or down-regulation of the phosphorylation and thus the activity of its essential downstream effector the AGC family protein kinase Ypk1. Through the ensuing effect on the efficiency with which Ypk1 phosphorylates multiple substrates that control diverse processes, membrane homeostasis is maintained. Thus, the major focus here is on TORC2, Ypk1, and the multifarious targets of Ypk1 and how the functions of these substrates are regulated by their Ypk1-mediated phosphorylation, with emphasis on recent advances in our understanding of these processes.
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16
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Tollis S. The G1/S repressor WHI5 is expressed at similar levels throughout the cell cycle. BMC Res Notes 2022; 15:248. [PMID: 35841111 PMCID: PMC9284753 DOI: 10.1186/s13104-022-06142-9] [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: 04/07/2022] [Accepted: 06/30/2022] [Indexed: 11/19/2022] Open
Abstract
Objectives While it is clear that cells need to grow before committing to division at the G1/S transition of the cell cycle, how cells sense their growth rate or size at the molecular level is unknown. It has been proposed that, in budding yeast, the dilution of the Whi5 G1/S transcriptional repressor as cells grow in G1 is the main driver of G1/S commitment. This model implies that Whi5 synthesis is substantially reduced in G1 phase. Recent work has reported that the concentration of Whi5 is size- and time-independent in G1 cells, challenging the dilution model. These results in turn imply that Whi5 must be synthesized in G1 phase, but the cell cycle dependence of WHI5 mRNA expression has not been examined in live cells. Results description To address this question, we monitored single WHI5 mRNA molecules in single live cells using confocal microscopy, and quantified WHI5 mRNA copy number in G1, G1/S, and S/G2/M phase cells. We observed that WHI5 mRNA is found in very similar amount irrespective of cell cycle stage. The constant WHI5 mRNA copy number throughout G1 phase rules out alterations in mRNA abundance as a contributing factor for any putative dilution of Whi5. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06142-9.
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Affiliation(s)
- Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.
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17
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Pérez AP, Artés MH, Moreno DF, Clotet J, Aldea M. Mad3 modulates the G 1 Cdk and acts as a timer in the Start network. SCIENCE ADVANCES 2022; 8:eabm4086. [PMID: 35522754 PMCID: PMC9075807 DOI: 10.1126/sciadv.abm4086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Cells maintain their size within limits over successive generations to maximize fitness and survival. Sizer, timer, and adder behaviors have been proposed as possible alternatives to coordinate growth and cell cycle progression. Regarding budding yeast cells, a sizer mechanism is thought to rule cell cycle entry at Start. However, while many proteins controlling the size of these cells have been identified, the mechanistic framework in which they participate to achieve cell size homeostasis is not understood. We show here that intertwined APC and SCF degradation machineries with specific adaptor proteins drive cyclic accumulation of the G1 Cdk in the nucleus, reaching maximal levels at Start. The mechanism incorporates Mad3, a centromeric-signaling protein that subordinates G1 progression to the previous mitosis as a memory factor. This alternating-degradation device displays the properties of a timer and, together with the sizer device, would constitute a key determinant of cell cycle entry.
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Affiliation(s)
- Alexis P. Pérez
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
| | - Marta H. Artés
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
| | - David F. Moreno
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
| | - Josep Clotet
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
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18
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Litsios A, Goswami P, Terpstra HM, Coffin C, Vuillemenot LA, Rovetta M, Ghazal G, Guerra P, Buczak K, Schmidt A, Tollis S, Tyers M, Royer CA, Milias-Argeitis A, Heinemann M. The timing of Start is determined primarily by increased synthesis of the Cln3 activator rather than dilution of the Whi5 inhibitor. Mol Biol Cell 2022; 33:rp2. [PMID: 35482514 PMCID: PMC9282015 DOI: 10.1091/mbc.e21-07-0349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Athanasios Litsios
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Pooja Goswami
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Hanna M Terpstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Carleton Coffin
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Mattia Rovetta
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Ghada Ghazal
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, H3T 1J4 QC, Canada
| | - Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Sylvain Tollis
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, H3T 1J4 QC, Canada.,Institute of Biomedicine, University of Eastern Finland, FI-70210 Kuopio, Finland
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, H3T 1J4 QC, Canada
| | - Catherine A Royer
- Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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19
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Schmoller KM, Lanz MC, Kim J, Koivomagi M, Qu Y, Tang C, Kukhtevich IV, Schneider R, Rudolf F, Moreno DF, Aldea M, Lucena R, Skotheim JM. Whi5 is diluted and protein synthesis does not dramatically increase in pre- Start G1. Mol Biol Cell 2022; 33:lt1. [PMID: 35482510 PMCID: PMC9282012 DOI: 10.1091/mbc.e21-01-0029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Michael C Lanz
- Department of Biology, Stanford University, Stanford CA 94305
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford CA 94305
| | - Mardo Koivomagi
- Department of Biology, Stanford University, Stanford CA 94305
| | - Yimiao Qu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Igor V Kukhtevich
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Fabian Rudolf
- D-BSSE, ETH Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - David F Moreno
- Molecular Biology Institute of Barcelona, CSIC, Catalonia, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona, CSIC, Catalonia, Spain
| | - Rafael Lucena
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford CA 94305
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