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Ravi J, Samart K, Zwolak J. Modeling the START transition in the budding yeast cell cycle. PLoS Comput Biol 2024; 20:e1012048. [PMID: 39093881 DOI: 10.1371/journal.pcbi.1012048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/02/2024] [Indexed: 08/04/2024] Open
Abstract
Budding yeast, Saccharomyces cerevisiae, is widely used as a model organism to study the genetics underlying eukaryotic cellular processes and growth critical to cancer development, such as cell division and cell cycle progression. The budding yeast cell cycle is also one of the best-studied dynamical systems owing to its thoroughly resolved genetics. However, the dynamics underlying the crucial cell cycle decision point called the START transition, at which the cell commits to a new round of DNA replication and cell division, are under-studied. The START machinery involves a central cyclin-dependent kinase; cyclins responsible for starting the transition, bud formation, and initiating DNA synthesis; and their transcriptional regulators. However, evidence has shown that the mechanism is more complicated than a simple irreversible transition switch. Activating a key transcription regulator SBF requires the phosphorylation of its inhibitor, Whi5, or an SBF/MBF monomeric component, Swi6, but not necessarily both. Also, the timing and mechanism of the inhibitor Whi5's nuclear export, while important, are not critical for the timing and execution of START. Therefore, there is a need for a consolidated model for the budding yeast START transition, reconciling regulatory and spatial dynamics. We built a detailed mathematical model (START-BYCC) for the START transition in the budding yeast cell cycle based on established molecular interactions and experimental phenotypes. START-BYCC recapitulates the underlying dynamics and correctly emulates key phenotypic traits of ~150 known START mutants, including regulation of size control, localization of inhibitor/transcription factor complexes, and the nutritional effects on size control. Such a detailed mechanistic understanding of the underlying dynamics gets us closer towards deconvoluting the aberrant cellular development in cancer.
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Affiliation(s)
- Janani Ravi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kewalin Samart
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Computational Bioscience program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jason Zwolak
- InSilica Labs, Asheville, North Carolina, United States of America
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2
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Huang Y, Chen J, Xia H, Gao Z, Gu Q, Liu W, Tang G. FvMbp1-Swi6 complex regulates vegetative growth, stress tolerance, and virulence in Fusarium verticillioides. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134576. [PMID: 38759405 DOI: 10.1016/j.jhazmat.2024.134576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
The mycotoxigenic fungus Fusarium verticillioides is a common pathogen of grain and medicine that contaminates the host with fumonisin B1 (FB1) mycotoxin, poses serious threats to human and animal health. Therefore, it is crucial to unravel the regulatory mechanisms of growth, and pathogenicity of F. verticillioides. Mbp1 is a component of the MluI cell cycle box binding factor complex and acts as an APSES-type transcription factor that regulates cell cycle progression. However, no information is available regarding its role in F. verticillioides. In this study, we demonstrate that FvMbp1 interacts with FvSwi6 that acts as the cell cycle transcription factor, to form the heteromeric transcription factor complexes in F. verticillioides. Our results show that ΔFvMbp1 and ΔFvSwi6 both cause a severe reduction of vegetative growth, conidiation, and increase tolerance to diverse environmental stresses. Moreover, ΔFvMbp1 and ΔFvSwi6 dramatically decrease the virulence of the pathogen on the stalk and ear of maize. Transcriptome profiling show that FvMbp1-Swi6 complex co-regulates the expression of genes associated with multiple stress responses. These results indicate the functional importance of the FvMbp1-Swi6 complex in the filamentous fungi F. verticillioides and reveal a potential target for the effective prevention and control of Fusarium diseases.
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Affiliation(s)
- Yufei Huang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jinfeng Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haoxue Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zenggui Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing 210095, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guangfei Tang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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3
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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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4
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Pérez-Ortín JE, García-Marcelo MJ, Delgado-Román I, Muñoz-Centeno MC, Chávez S. Influence of cell volume on the gene transcription rate. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195008. [PMID: 38246270 DOI: 10.1016/j.bbagrm.2024.195008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Cells vary in volume throughout their life cycle and in many other circumstances, while their genome remains identical. Hence, the RNA production factory must adapt to changing needs, while maintaining the same production lines. This paradox is resolved by different mechanisms in distinct cells and circumstances. RNA polymerases have evolved to cope with the particular circumstances of each case and the different characteristics of the several RNA molecule types, especially their stabilities. Here we review current knowledge on these issues. We focus on the yeast Saccharomyces cerevisiae, where many of the studies have been performed, although we compare and discuss the results obtained in other eukaryotes and propose several ideas and questions to be tested and solved in the future. TAKE AWAY.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain.
| | - María J García-Marcelo
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Irene Delgado-Román
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María C Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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5
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Su AJ, Yendluri SC, Ünal E. Control of meiotic entry by dual inhibition of a key mitotic transcription factor. eLife 2024; 12:RP90425. [PMID: 38411169 PMCID: PMC10939502 DOI: 10.7554/elife.90425] [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] [Indexed: 02/28/2024] Open
Abstract
The mitosis to meiosis transition requires dynamic changes in gene expression, but whether and how the mitotic transcriptional machinery is regulated during this transition is unknown. In budding yeast, SBF and MBF transcription factors initiate the mitotic gene expression program. Here, we report two mechanisms that work together to restrict SBF activity during meiotic entry: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a functional homolog of the Rb tumor suppressor. We find that untimely SBF activation causes downregulation of early meiotic genes and delays meiotic entry. These defects are largely driven by the SBF-target G1 cyclins, which block the interaction between the central meiotic regulator Ime1 and its cofactor Ume6. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.
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Affiliation(s)
- Amanda J Su
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Siri C Yendluri
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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6
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Su AJ, Yendluri SC, Ünal E. Control of meiotic entry by dual inhibition of a key mitotic transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533246. [PMID: 36993411 PMCID: PMC10055192 DOI: 10.1101/2023.03.17.533246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The mitosis to meiosis transition requires dynamic changes in gene expression, but whether and how the mitotic transcriptional machinery is regulated during this transition is unknown. In budding yeast, SBF and MBF transcription factors initiate the mitotic gene expression program. Here, we report two mechanisms that work together to restrict SBF activity during meiotic entry: repression of the SBF-specific Swi4 subunit through LUTI-based regulation and inhibition of SBF by Whi5, a homolog of the Rb tumor suppressor. We find that untimely SBF activation causes downregulation of early meiotic genes and delays meiotic entry. These defects are largely driven by the SBF-target G1 cyclins, which block the interaction between the central meiotic regulator Ime1 and its cofactor Ume6. Our study provides insight into the role of SWI4LUTI in establishing the meiotic transcriptional program and demonstrates how the LUTI-based regulation is integrated into a larger regulatory network to ensure timely SBF activity.
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7
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Schwarz LV, Sandri FK, Scariot F, Delamare APL, Valera MJ, Carrau F, Echeverrigaray S. High nitrogen concentration causes G2/M arrest in Hanseniaspora vineae. Yeast 2023; 40:640-650. [PMID: 37997429 DOI: 10.1002/yea.3911] [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: 07/04/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Yeasts have been widely used as a model to better understand cell cycle mechanisms and how nutritional and genetic factors can impact cell cycle progression. While nitrogen scarcity is well known to modulate cell cycle progression, the relevance of nitrogen excess for microorganisms has been overlooked. In our previous work, we observed an absence of proper entry into the quiescent state in Hanseniaspora vineae and identified a potential link between this behavior and nitrogen availability. Furthermore, the Hanseniaspora genus has gained attention due to a significant loss of genes associated with DNA repair and cell cycle. Thus, the aim of our study was to investigate the effects of varying nitrogen concentrations on H. vineae's cell cycle progression. Our findings demonstrated that nitrogen excess, regardless of the source, disrupts cell cycle progression and induces G2/M arrest in H. vineae after reaching the stationary phase. Additionally, we observed a viability decline in H. vineae cells in an ammonium-dependent manner, accompanied by increased production of reactive oxygen species, mitochondrial hyperpolarization, intracellular acidification, and DNA fragmentation. Overall, our study highlights the events of the cell cycle arrest in H. vineae induced by nitrogen excess and attempts to elucidate the possible mechanism triggering this absence of proper entry into the quiescent state.
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Affiliation(s)
- Luisa Vivian Schwarz
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
| | - Fernanda Knaach Sandri
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
| | - Fernando Scariot
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
| | | | - Maria Jose Valera
- Enology and Fermentation Biotechnology Area, Departamento Ciencia y Tecnología Alimentos, Facultad de Química, Universidad de la Republica, Montevideo, Uruguay
| | - Francisco Carrau
- Enology and Fermentation Biotechnology Area, Departamento Ciencia y Tecnología Alimentos, Facultad de Química, Universidad de la Republica, Montevideo, Uruguay
| | - Sergio Echeverrigaray
- Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil
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8
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Gorospe CM, Carvalho G, Herrera Curbelo A, Marchhart L, Mendes IC, Niedźwiecka K, Wanrooij PH. Mitochondrial membrane potential acts as a retrograde signal to regulate cell cycle progression. Life Sci Alliance 2023; 6:e202302091. [PMID: 37696576 PMCID: PMC10494934 DOI: 10.26508/lsa.202302091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Mitochondria are central to numerous metabolic pathways whereby mitochondrial dysfunction has a profound impact and can manifest in disease. The consequences of mitochondrial dysfunction can be ameliorated by adaptive responses that rely on crosstalk from the mitochondria to the rest of the cell. Such mito-cellular signalling slows cell cycle progression in mitochondrial DNA-deficient (ρ0) Saccharomyces cerevisiae cells, but the initial trigger of the response has not been thoroughly studied. Here, we show that decreased mitochondrial membrane potential (ΔΨm) acts as the initial signal of mitochondrial stress that delays G1-to-S phase transition in both ρ0 and control cells containing mtDNA. Accordingly, experimentally increasing ΔΨm was sufficient to restore timely cell cycle progression in ρ0 cells. In contrast, cellular levels of oxidative stress did not correlate with the G1-to-S delay. Restored G1-to-S transition in ρ0 cells with a recovered ΔΨm is likely attributable to larger cell size, whereas the timing of G1/S transcription remained delayed. The identification of ΔΨm as a regulator of cell cycle progression may have implications for disease states involving mitochondrial dysfunction.
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Affiliation(s)
- Choco Michael Gorospe
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Gustavo Carvalho
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Alicia Herrera Curbelo
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Lisa Marchhart
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela C Mendes
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Katarzyna Niedźwiecka
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Paulina H Wanrooij
- https://ror.org/05kb8h459 Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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9
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Royer CA, Tyers M, Tollis S. Absolute quantification of protein number and dynamics in single cells. Curr Opin Struct Biol 2023; 82:102673. [PMID: 37595512 DOI: 10.1016/j.sbi.2023.102673] [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: 04/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]
Abstract
Quantitative characterization of protein abundance and interactions in live cells is necessary to understand and predict cellular behavior. The accurate determination of copy number for individual proteins and heterologous complexes in individual cells is critical because small changes in protein dosage, often less than two-fold, can have strong phenotypic consequences. Here, we review the merits and pitfalls of different quantitative fluorescence imaging methods for single-cell determination of protein abundance, localization, interactions, and dynamics. In particular, we discuss how scanning number and brightness (sN&B) and its variation, Raster scanning image correlation spectroscopy (RICS), exploit stochastic noise in small measurement volumes to quantify protein abundance, stoichiometry, and dynamics with high accuracy.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy NY 12180, USA.
| | - Mike Tyers
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210 Finland
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10
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Ji X, Lin J. Implications of differential size-scaling of cell-cycle regulators on cell size homeostasis. PLoS Comput Biol 2023; 19:e1011336. [PMID: 37506170 PMCID: PMC10411824 DOI: 10.1371/journal.pcbi.1011336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/09/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Accurate timing of division and size homeostasis is crucial for cells. A potential mechanism for cells to decide the timing of division is the differential scaling of regulatory protein copy numbers with cell size. However, it remains unclear whether such a mechanism can lead to robust growth and division, and how the scaling behaviors of regulatory proteins influence the cell size distribution. Here we study a mathematical model combining gene expression and cell growth, in which the cell-cycle activators scale superlinearly with cell size while the inhibitors scale sublinearly. The cell divides once the ratio of their concentrations reaches a threshold value. We find that the cell can robustly grow and divide within a finite range of the threshold value with the cell size proportional to the ploidy. In a stochastic version of the model, the cell size at division is uncorrelated with that at birth. Also, the more differential the cell-size scaling of the cell-cycle regulators is, the narrower the cell-size distribution is. Intriguingly, our model with multiple regulators rationalizes the observation that after the deletion of a single regulator, the coefficient of variation of cell size remains roughly the same though the average cell size changes significantly. Our work reveals that the differential scaling of cell-cycle regulators provides a robust mechanism of cell size control.
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Affiliation(s)
- Xiangrui Ji
- Yuanpei College, Peking University, Beijing, China
| | - Jie Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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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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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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14
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A quantitative and spatial analysis of cell cycle regulators during the fission yeast cycle. Proc Natl Acad Sci U S A 2022; 119:e2206172119. [PMID: 36037351 PMCID: PMC9457408 DOI: 10.1073/pnas.2206172119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Across eukaryotes, the increasing level of cyclin-dependent kinase (CDK) activity drives progression through the cell cycle. As most cells divide at specific sizes, information responding to the size of the cell must feed into the regulation of CDK activity. In this study, we use fission yeast to precisely measure how proteins that have been previously identified in genome-wide screens as cell cycle regulators change in their levels with cell cycle progression. We identify the mitotic B-type cyclin Cdc13 and the mitotic inhibitory phosphatase Cdc25 as the only two proteins that change in both whole-cell and nuclear concentration through the cell cycle, making them potential candidates for universal cell size sensors at the onset of mitosis and cell division. We have carried out a systems-level analysis of the spatial and temporal dynamics of cell cycle regulators in the fission yeast Schizosaccharomyces pombe. In a comprehensive single-cell analysis, we have precisely quantified the levels of 38 proteins previously identified as regulators of the G2 to mitosis transition and of 7 proteins acting at the G1- to S-phase transition. Only 2 of the 38 mitotic regulators exhibit changes in concentration at the whole-cell level: the mitotic B-type cyclin Cdc13, which accumulates continually throughout the cell cycle, and the regulatory phosphatase Cdc25, which exhibits a complex cell cycle pattern. Both proteins show similar patterns of change within the nucleus as in the whole cell but at higher concentrations. In addition, the concentrations of the major fission yeast cyclin-dependent kinase (CDK) Cdc2, the CDK regulator Suc1, and the inhibitory kinase Wee1 also increase in the nucleus, peaking at mitotic onset, but are constant in the whole cell. The significant increase in concentration with size for Cdc13 supports the view that mitotic B-type cyclin accumulation could act as a cell size sensor. We propose a two-step process for the control of mitosis. First, Cdc13 accumulates in a size-dependent manner, which drives increasing CDK activity. Second, from mid-G2, the increasing nuclear accumulation of Cdc25 and the counteracting Wee1 introduce a bistability switch that results in a rapid rise of CDK activity at the end of G2 and thus, brings about an orderly progression into mitosis.
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15
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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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16
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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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17
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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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18
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Stephan OOH. Interactions, structural aspects, and evolutionary perspectives of the yeast 'START'-regulatory network. FEMS Yeast Res 2021; 22:6461095. [PMID: 34905017 DOI: 10.1093/femsyr/foab064] [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: 08/30/2021] [Accepted: 12/11/2021] [Indexed: 11/12/2022] Open
Abstract
Molecular signal transduction networks which conduct transcription at the G1 to S phase transition of the eukaryotic cell division cycle have been identified in diverse taxa from mammals to baker´s yeast with analogous functional organization. However, regarding some network components, such as the transcriptional regulators STB1 and WHI5, only few orthologs exist which are confined to individual Saccharomycotina species. While Whi5 has been characterized as yeast analog of human Rb protein, in the particular case of Stb1 (Sin three binding protein 1) identification of functional analogs emerges as difficult because to date its exact functionality still remains obscured. By aiming to resolve Stb1´s enigmatic role this Perspectives article especially surveys works covering relations between Cyclin/CDKs, the heteromeric transcription factor complexes SBF (Swi4/Swi6) and MBF (Mbp1/Swi6), as well as additional coregulators (Whi5, Sin3, Rpd3, Nrm1) which are collectively associated with the orderly transcription at 'Start' of the Saccharomyces cerevisiae cell cycle. In this context, interaction capacities of the Sin3-scaffold protein are widely surveyed because its four PAH domains (Paired Amphiphatic Helix) represent a 'recruitment-code' for gene-specific targeting of repressive histone deacetylase activity (Rpd3) via different transcription factors. Here Stb1 plays a role in Sin3´s action on transcription at the G1/S-boundary. Through bioinformatic analyses a potential Sin3-interaction domain (SID) was detected in Stb1, and beyond that, connections within the G1/S-regulatory network are discussed in structural and evolutionary context thereby providing conceptual perspectives.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Bavaria, Germany
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19
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Swaffer MP, Kim J, Chandler-Brown D, Langhinrichs M, Marinov GK, Greenleaf WJ, Kundaje A, Schmoller KM, Skotheim JM. Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size. Mol Cell 2021; 81:4861-4875.e7. [PMID: 34731644 PMCID: PMC8642314 DOI: 10.1016/j.molcel.2021.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/01/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
Abstract
Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 "sub-scales" with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that transcriptional control uncouples Whi5 synthesis from cell size, and we identify histones as the major class of sub-scaling transcripts besides WHI5 by screening for similar genes. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to newborn cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each newborn cell regardless of cell size. Disrupting both Whi5 synthesis and chromatin-based partitioning weakens G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.
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Affiliation(s)
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kurt M Schmoller
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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20
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Sommer RA, DeWitt JT, Tan R, Kellogg DR. Growth-dependent signals drive an increase in early G1 cyclin concentration to link cell cycle entry with cell growth. eLife 2021; 10:64364. [PMID: 34713806 PMCID: PMC8592568 DOI: 10.7554/elife.64364] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 10/29/2021] [Indexed: 01/13/2023] Open
Abstract
Entry into the cell cycle occurs only when sufficient growth has occurred. In budding yeast, the cyclin Cln3 is thought to initiate cell cycle entry by inactivating a transcriptional repressor called Whi5. Growth-dependent changes in the concentrations of Cln3 or Whi5 have been proposed to link cell cycle entry to cell growth. However, there are conflicting reports regarding the behavior and roles of Cln3 and Whi5. Here, we found no evidence that changes in the concentration of Whi5 play a major role in controlling cell cycle entry. Rather, the data suggest that cell growth triggers cell cycle entry by driving an increase in the concentration of Cln3. We further found that accumulation of Cln3 is dependent upon homologs of mammalian SGK kinases that control cell growth and size. Together, the data are consistent with models in which Cln3 is a crucial link between cell growth and the cell cycle.
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Affiliation(s)
- Robert A Sommer
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, United States
| | - Jerry T DeWitt
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, United States
| | - Raymond Tan
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, United States
| | - Douglas R Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, United States
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21
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Chen X, Lu Z, Chen Y, Wu R, Luo Z, Lu Q, Guan N, Chen D. Deletion of the MBP1 Gene, Involved in the Cell Cycle, Affects Respiration and Pseudohyphal Differentiation in Saccharomyces cerevisiae. Microbiol Spectr 2021; 9:e0008821. [PMID: 34346754 PMCID: PMC8552743 DOI: 10.1128/spectrum.00088-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 11/20/2022] Open
Abstract
Mbp1p is a component of MBF (MluI cell cycle box binding factor, Mbp1p-Swi6p) and is well known to regulate the G1-S transition of the cell cycle. However, few studies have provided clues regarding its role in fermentation. This work aimed to recognize the function of the MBP1 gene in ethanol fermentation in a wild-type industrial Saccharomyces cerevisiae strain. MBP1 deletion caused an obvious decrease in the final ethanol concentration under oxygen-limited (without agitation), but not under aerobic, conditions (130 rpm). Furthermore, the mbp1Δ strain showed 84% and 35% decreases in respiration intensity under aerobic and oxygen-limited conditions, respectively. These findings indicate that MBP1 plays an important role in responding to variations in oxygen content and is involved in the regulation of respiration and fermentation. Unexpectedly, mbp1Δ also showed pseudohyphal growth, in which cells elongated and remained connected in a multicellular arrangement on yeast extract-peptone-dextrose (YPD) plates. In addition, mbp1Δ showed an increase in cell volume, associated with a decrease in the fraction of budded cells. These results provide more detailed information about the function of MBP1 and suggest some clues to efficiently improve ethanol production by industrially engineered yeast strains. IMPORTANCE Saccharomyces cerevisiae is an especially favorable organism used for ethanol production. However, inhibitors and high osmolarity conferred by fermentation broth, and high concentrations of ethanol as fermentation runs to completion, affect cell growth and ethanol production. Therefore, yeast strains with high performance, such as rapid growth, high tolerance, and high ethanol productivity, are highly desirable. Great efforts have been made to improve their performance by evolutionary engineering, and industrial strains may be a better start than laboratory ones for industrial-scale ethanol production. The significance of our research is uncovering the function of MBP1 in ethanol fermentation in a wild-type industrial S. cerevisiae strain, which may provide clues to engineer better-performance yeast in producing ethanol. Furthermore, the results that lacking MBP1 caused pseudohyphal growth on YPD plates could shed light on the development of xylose-fermenting S. cerevisiae, as using xylose as the sole carbon source also caused pseudohyphal growth.
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Affiliation(s)
- Xiaoling Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Zhilong Lu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Ying Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Renzhi Wu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Zhenzhen Luo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Qi Lu
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Ni Guan
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
| | - Dong Chen
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, People’s Republic of China
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22
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You Y, Chen L, Wu Y, Wang M, Lu H, Zhou X, Liu H, Fu Z, He Q, Ou J, Fu X, Liu Y, Kwan H, Liang D, Zhao X, Dai J. Silibinin Promotes Cell Proliferation Through Facilitating G1/S Transitions by Activating Drp1-Mediated Mitochondrial Fission in Cells. Cell Transplant 2021; 29:963689720950213. [PMID: 32830544 PMCID: PMC7563805 DOI: 10.1177/0963689720950213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Heart, liver, and kidney, which are known as the essential organs for metabolism,
possess the unique ability to regulate the proliferation function of the body
against injury. Silibinin (SB), a natural polyphenolic flavonoid extracted from
traditional herb Silybum marianum L., has been used to protect
hepatocytes. Whether SB can regulate mitochondrial fission in normal cells and
the underlying mechanisms remain unclear. Here, we showed that SB markedly
promoted cell proliferation by facilitating G1/S transition via activating
dynamin-related protein 1 (Drp1), which in turn mediated mitochondrial fission
in these normal cells. SB dose-dependently increased the mitochondrial mass,
mtDNA copy number, cellular adenosine triphosphate production, mitochondrial
membrane potential, and reactive oxygen species in normal cells. Furthermore, SB
dose-dependently increased the expression of Drp1. Blocking Drp1 abolished
SB-induced mitochondrial fission. In conclusion, we demonstrate that SB promotes
cell proliferation through facilitating G1/S transition by activating
Drp1-mediated mitochondrial fission. This study suggests that SB is a
potentially useful herbal derivative for the daily prevention of various
diseases caused by impaired mitochondrial fission.
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Affiliation(s)
- Yanting You
- Department of Traditional Chinese Medicine, 70570Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China.,Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Liqian Chen
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Yifen Wu
- Department of Oncology, Affiliated Dongguan People's Hospital, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Ming Wang
- Department of Traditional Chinese Medicine, 70570Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Hanqi Lu
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Xinghong Zhou
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Huaxi Liu
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Zixuan Fu
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Qiuxing He
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Jinying Ou
- Traditional Chinese Pharmacological Laboratory, School of Traditional Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Xiuqiong Fu
- School of Chinese Medicine, 26679Hong Kong Baptist University, Hong Kong, China
| | - Yanyan Liu
- Department of Traditional Chinese Medicine, 70570Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Hiuyee Kwan
- School of Chinese Medicine, 26679Hong Kong Baptist University, Hong Kong, China
| | - Donghui Liang
- Department of Traditional Chinese Medicine, 70570Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoshan Zhao
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
| | - Jiaojiao Dai
- Syndrome Laboratory of Integrated Chinese and Western Medicine, School of Chinese Medicine, 70570Southern Medical University, Guangzhou, Guangdong, China
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23
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Bogdan P, Caetano-Anollés G, Jolles A, Kim H, Morris J, Murphy CA, Royer C, Snell EH, Steinbrenner A, Strausfeld N. Biological networks across scales. Integr Comp Biol 2021; 61:1991-2010. [PMID: 34021749 DOI: 10.1093/icb/icab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many biological systems across scales of size and complexity exhibit a time-varying complex network structure that emerges and self-organizes as a result of interactions with the environment. Network interactions optimize some intrinsic cost functions that are unknown and involve for example energy efficiency, robustness, resilience, and frailty. A wide range of networks exist in biology, from gene regulatory networks important for organismal development, protein interaction networks that govern physiology and metabolism, and neural networks that store and convey information to networks of microbes that form microbiomes within hosts, animal contact networks that underlie social systems, and networks of populations on the landscape connected by migration. Increasing availability of extensive (big) data is amplifying our ability to quantify biological networks. Similarly, theoretical methods that describe network structure and dynamics are being developed. Beyond static networks representing snapshots of biological systems, collections of longitudinal data series can help either at defining and characterizing network dynamics over time or analyzing the dynamics constrained to networked architectures. Moreover, due to interactions with the environment and other biological systems, a biological network may not be fully observable. Also, subnetworks may emerge and disappear as a result of the need for the biological system to cope with for example invaders or new information flows. The confluence of these developments renders tractable the question of how the structure of biological networks predicts and controls network dynamics. In particular, there may be structural features that result in homeostatic networks with specific higher-order statistics (e.g., multifractal spectrum), which maintain stability over time through robustness and/or resilience to perturbation. Alternative, plastic networks may respond to perturbation by (adaptive to catastrophic) shifts in structure. Here, we explore the opportunity for discovering universal laws connecting the structure of biological networks with their function, positioning them on the spectrum of time-evolving network structure, i.e. dynamics of networks, from highly stable to exquisitely sensitive to perturbation. If such general laws exist, they could transform our ability to predict the response of biological systems to perturbations-an increasingly urgent priority in the face of anthropogenic changes to the environment that affect life across the gamut of organizational scales.
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Affiliation(s)
- Paul Bogdan
- Ming-Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles
| | | | - Anna Jolles
- Department of Integrative Biology, Oregon State University, Corvallis
| | - Hyunju Kim
- The Beyond Center, Arizona State University, Tempe
| | - James Morris
- Baruch Institute for Marine and Coastal Sciences, University of South Carolina, Columbia
| | - Cheryl A Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing
| | | | - Edward H Snell
- Hauptman-Woodward Medical Research Institute and SUNY, Buffalo
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24
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Tan C, Ginzberg MB, Webster R, Iyengar S, Liu S, Papadopoli D, Concannon J, Wang Y, Auld DS, Jenkins JL, Rost H, Topisirovic I, Hilfinger A, Derry WB, Patel N, Kafri R. Cell size homeostasis is maintained by CDK4-dependent activation of p38 MAPK. Dev Cell 2021; 56:1756-1769.e7. [PMID: 34022133 DOI: 10.1016/j.devcel.2021.04.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 02/08/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
While molecules that promote the growth of animal cells have been identified, it remains unclear how such signals are orchestrated to determine a characteristic target size for different cell types. It is increasingly clear that cell size is determined by size checkpoints-mechanisms that restrict the cell cycle progression of cells that are smaller than their target size. Previously, we described a p38 MAPK-dependent cell size checkpoint mechanism whereby p38 is selectively activated and prevents cell cycle progression in cells that are smaller than a given target size. In this study, we show that the specific target size required for inactivation of p38 and transition through the cell cycle is determined by CDK4 activity. Our data suggest a model whereby p38 and CDK4 cooperate analogously to the function of a thermostat: while p38 senses irregularities in size, CDK4 corresponds to the thermostat dial that sets the target size.
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Affiliation(s)
- Ceryl Tan
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam B Ginzberg
- Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Rachel Webster
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Seshu Iyengar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, ON L5L 1C6, Canada
| | - Shixuan Liu
- Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - David Papadopoli
- Gerald Bronfman Department of Oncology and Lady Davis Institute, McGill University Montreal, QC H4A 3T2, Canada
| | - John Concannon
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Douglas S Auld
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Hannes Rost
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada
| | - Ivan Topisirovic
- Gerald Bronfman Department of Oncology and Lady Davis Institute, McGill University Montreal, QC H4A 3T2, Canada
| | - Andreas Hilfinger
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, ON L5L 1C6, Canada
| | - W Brent Derry
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nish Patel
- Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ran Kafri
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
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25
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Méndez E, Gomar-Alba M, Bañó MC, Mendoza M, Quilis I, Igual JC. The budding yeast Start repressor Whi7 differs in regulation from Whi5, emerging as a major cell cycle brake in response to stress. J Cell Sci 2020; 133:133/24/jcs251413. [PMID: 33443080 PMCID: PMC7774886 DOI: 10.1242/jcs.251413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/09/2020] [Indexed: 11/20/2022] Open
Abstract
Start is the main decision point in the eukaryotic cell cycle at which cells commit to a new round of cell division. It involves the irreversible activation of a transcriptional programme through the inactivation of Start transcriptional repressors: the retinoblastoma family in mammals, or Whi5 and its recently identified paralogue Whi7 (also known as Srl3) in budding yeast. Here, we provide a comprehensive comparison of Whi5 and Whi7 that reveals significant qualitative differences. Indeed, the expression, subcellular localization and functionality of Whi7 and Whi5 are differentially regulated. Importantly, Whi7 shows specific properties in its association with promoters not shared by Whi5, and for the first time, we demonstrate that Whi7, and not Whi5, can be the main contributor to Start inhibition such as it occurs in the response to cell wall stress. Our results help to improve understanding of the interplay between multiple differentially regulated Start repressors in order to face specific cellular conditions. Highlighted Article: Cells can use the interplay between functionally redundant but differentially regulated cell-cycle repressors in order to confer new repression capabilities and to respond to specific cellular conditions.
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Affiliation(s)
- Ester Méndez
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot (Valencia), Spain
| | - Mercè Gomar-Alba
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot (Valencia), Spain.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67000 Strasbourg, France
| | - M Carmen Bañó
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot (Valencia), Spain
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France.,Université de Strasbourg, 67000 Strasbourg, France
| | - Inma Quilis
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot (Valencia), Spain
| | - J Carlos Igual
- Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot (Valencia), Spain
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26
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Gu Y, Oliferenko S. The principles of cellular geometry scaling. Curr Opin Cell Biol 2020; 68:20-27. [PMID: 32950004 DOI: 10.1016/j.ceb.2020.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/11/2023]
Abstract
Cellular dimensions profoundly influence cellular physiology. For unicellular organisms, this has direct bearing on their ecology and evolution. The morphology of a cell is governed by scaling rules. As it grows, the ratio of its surface area to volume is expected to decrease. Similarly, if environmental conditions force proliferating cells to settle on different size optima, cells of the same type may exhibit size-dependent variation in cellular processes. In fungi, algae and plants where cells are surrounded by a rigid wall, division at smaller size often produces immediate changes in geometry, decreasing cell fitness. Here, we discuss how cells interpret their size, buffer against changes in shape and, if necessary, scale their polarity to maintain optimal shape at different cell volumes.
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Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
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27
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Black L, Tollis S, Fu G, Fiche JB, Dorsey S, Cheng J, Ghazal G, Notley S, Crevier B, Bigness J, Nollmann M, Tyers M, Royer CA. G1/S transcription factors assemble in increasing numbers of discrete clusters through G1 phase. J Cell Biol 2020; 219:151997. [PMID: 32744610 PMCID: PMC7480102 DOI: 10.1083/jcb.202003041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 02/03/2023] Open
Abstract
In budding yeast, the transcription factors SBF and MBF activate a large program of gene expression in late G1 phase that underlies commitment to cell division, termed Start. SBF/MBF are limiting with respect to target promoters in small G1 phase cells and accumulate as cells grow, raising the questions of how SBF/MBF are dynamically distributed across the G1/S regulon and how this impacts the Start transition. Super-resolution Photo-Activatable Localization Microscopy (PALM) mapping of the static positions of SBF/MBF subunits in fixed cells revealed each transcription factor was organized into discrete clusters containing approximately eight copies regardless of cell size and that the total number of clusters increased as cells grew through G1 phase. Stochastic modeling using reasonable biophysical parameters recapitulated growth-dependent SBF/MBF clustering and predicted TF dynamics that were confirmed in live cell PALM experiments. This spatio-temporal organization of SBF/MBF may help coordinate activation of G1/S regulon and the Start transition.
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Affiliation(s)
- Labe Black
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Sylvain Tollis
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Guo Fu
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique UMR5048, Institut National de la Santé et de la Recherche Médicale U1054, Université de Montpellier, Montpellier, France
| | - Savanna Dorsey
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Jing Cheng
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Ghada Ghazal
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Stephen Notley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Benjamin Crevier
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Jeremy Bigness
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique UMR5048, Institut National de la Santé et de la Recherche Médicale U1054, Université de Montpellier, Montpellier, France
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Catherine Ann Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
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28
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Barber F, Amir A, Murray AW. Cell-size regulation in budding yeast does not depend on linear accumulation of Whi5. Proc Natl Acad Sci U S A 2020; 117:14243-14250. [PMID: 32518113 PMCID: PMC7321981 DOI: 10.1073/pnas.2001255117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cells must couple cell-cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at a smaller size. We tested this model using the inducible GAL1 promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous and GAL1 promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings indicate that size control in budding yeast does not fundamentally originate from the linear accumulation of Whi5, contradicting a previous claim and demonstrating the need for further models of cell-cycle regulation to explain how cell size controls passage through Start.
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Affiliation(s)
- Felix Barber
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Ariel Amir
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138
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29
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Zhao Y, Wang D, Zhang Z, Lu Y, Yang X, Ouyang Q, Tang C, Li F. Critical slowing down and attractive manifold: A mechanism for dynamic robustness in the yeast cell-cycle process. Phys Rev E 2020; 101:042405. [PMID: 32422801 DOI: 10.1103/physreve.101.042405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 01/13/2020] [Indexed: 11/07/2022]
Abstract
Biological processes that execute complex multiple functions, such as the cell cycle, must ensure the order of sequential events and maintain dynamic robustness against various fluctuations. Here, we examine the mechanisms and fundamental structure that achieve these properties in the cell cycle of the budding yeast Saccharomyces cerevisiae. We show that this process behaves like an excitable system containing three well-decoupled saddle-node bifurcations to execute DNA replication and mitosis events. The yeast cell-cycle regulatory network can be divided into three modules-the G1/S phase, early M phase, and late M phase-wherein both positive feedback loops in each module and interactions among modules play important roles. Specifically, when the cell-cycle process operates near the critical points of the saddle-node bifurcations, a critical slowing down effect takes place. Such interregnum then allows for an attractive manifold and sufficient duration for cell-cycle events, within which to assess the completion of DNA replication and mitosis, e.g., spindle assembly. Moreover, such arrangement ensures that any fluctuation in an early module or event will not transmit to a later module or event. Thus, our results suggest a possible dynamical mechanism of the cell-cycle process to ensure event order and dynamic robustness and give insight into the evolution of eukaryotic cell-cycle processes.
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Affiliation(s)
- Yao Zhao
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Dedi Wang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Zhiwen Zhang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaojing Yang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Qi Ouyang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Chao Tang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Fangting Li
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
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30
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Chen Y, Zhao G, Zahumensky J, Honey S, Futcher B. Differential Scaling of Gene Expression with Cell Size May Explain Size Control in Budding Yeast. Mol Cell 2020; 78:359-370.e6. [PMID: 32246903 DOI: 10.1016/j.molcel.2020.03.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 12/14/2019] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
Abstract
Yeast cells must grow to a critical size before committing to division. It is unknown how size is measured. We find that as cells grow, mRNAs for some cell-cycle activators scale faster than size, increasing in concentration, while mRNAs for some inhibitors scale slower than size, decreasing in concentration. Size-scaled gene expression could cause an increasing ratio of activators to inhibitors with size, triggering cell-cycle entry. Consistent with this, expression of the CLN2 activator from the promoter of the WHI5 inhibitor, or vice versa, interfered with cell size homeostasis, yielding a broader distribution of cell sizes. We suggest that size homeostasis comes from differential scaling of gene expression with size. Differential regulation of gene expression as a function of cell size could affect many cellular processes.
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Affiliation(s)
- Yuping Chen
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Gang Zhao
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Jakub Zahumensky
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague 142 20, Czech Republic
| | - Sangeet Honey
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA.
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31
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Heldt FS, Tyson JJ, Cross FR, Novák B. A Single Light-Responsive Sizer Can Control Multiple-Fission Cycles in Chlamydomonas. Curr Biol 2020; 30:634-644.e7. [DOI: 10.1016/j.cub.2019.12.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/25/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022]
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32
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Jonas F, Soifer I, Barkai N. A Visual Framework for Classifying Determinants of Cell Size. Cell Rep 2019; 25:3519-3529.e2. [PMID: 30566874 PMCID: PMC6315284 DOI: 10.1016/j.celrep.2018.11.087] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/19/2018] [Accepted: 11/20/2018] [Indexed: 12/04/2022] Open
Abstract
Cells control their size by coordinating cell cycle progression with volume growth. Size control is typically studied at specific cell cycle transitions that are delayed or accelerated depending on size. This focus is well suited for revealing mechanisms acting at these transitions, but neglects the dynamics in other cell cycle phases, and is therefore inherently limited for studying how the characteristic cell size is determined. We address this limitation through a formalism that intuitively visualizes the characteristic size emerging from integrated cell cycle dynamics of individual cells. Applying this formalism to budding yeast, we describe the contributions of the un-budded (G1) and budded (S-G2-M) phase to size adjustments following environmental or genetic perturbations. We show that although the budded phase can be perturbed with little consequences for G1 dynamics, perturbations in G1 propagate to the budded phase. Our study provides an integrated view on cell size determinants in budding yeast. An intuitive visualization framework for cell size control is described Cell size control in different environments or mutant backgrounds can be compared Mutual dependencies between size control at different cell cycle phases are described
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilya Soifer
- Calico Labs, South San Francisco, CA 94080, USA
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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33
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Ding J, Lin H, Feng M, Ying S. Mbp1, a component of the MluI cell cycle box‐binding complex, contributes to morphological transition and virulence in the filamentous entomopathogenic fungus
Beauveria bassiana. Environ Microbiol 2019; 22:584-597. [DOI: 10.1111/1462-2920.14868] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Jin‐Li Ding
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou 310058 China
| | - Hai‐Yan Lin
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou 310058 China
| | - Ming‐Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou 310058 China
| | - Sheng‐Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou 310058 China
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34
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Litsios A, Huberts DHEW, Terpstra HM, Guerra P, Schmidt A, Buczak K, Papagiannakis A, Rovetta M, Hekelaar J, Hubmann G, Exterkate M, Milias-Argeitis A, Heinemann M. Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast. Nat Cell Biol 2019; 21:1382-1392. [PMID: 31685990 DOI: 10.1038/s41556-019-0413-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 09/25/2019] [Indexed: 12/28/2022]
Abstract
In the unicellular eukaryote Saccharomyces cerevisiae, Cln3-cyclin-dependent kinase activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in their protein production rate. Rather than scaling with cell size dynamics, these pulses follow the intrinsic metabolic dynamics, peaking around Start. Using a viral-based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population levels, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells across growth conditions. Thus, uncoupling between two fundamental physiological parameters drives cell cycle commitment.
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Affiliation(s)
- Athanasios Litsios
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Daphne H E W Huberts
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hanna M Terpstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Mattia Rovetta
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Johan Hekelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Georg Hubmann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Department of Biology, Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Heverlee, Belgium
| | - Marten Exterkate
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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35
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Qu Y, Jiang J, Liu X, Wei P, Yang X, Tang C. Cell Cycle Inhibitor Whi5 Records Environmental Information to Coordinate Growth and Division in Yeast. Cell Rep 2019; 29:987-994.e5. [DOI: 10.1016/j.celrep.2019.09.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/28/2019] [Accepted: 09/11/2019] [Indexed: 01/16/2023] Open
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36
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Özsezen S, Papagiannakis A, Chen H, Niebel B, Milias-Argeitis A, Heinemann M. Inference of the High-Level Interaction Topology between the Metabolic and Cell-Cycle Oscillators from Single-Cell Dynamics. Cell Syst 2019; 9:354-365.e6. [DOI: 10.1016/j.cels.2019.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023]
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37
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Royer CA. Characterizing proteins in their cellular environment: Examples of recent advances in quantitative fluorescence microscopy. Protein Sci 2019; 28:1210-1221. [PMID: 31012169 DOI: 10.1002/pro.3630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 11/12/2022]
Abstract
Quantitative characterization of protein interactions, both intramolecular and intermolecular, is crucial in understanding the mechanisms and regulation of their function. In recent years, it has become possible to obtain such information on protein systems in live cells, from bacteria to mammalian cell lines. This review discusses recent advances in measuring protein folding, absolute concentration, oligomerization, diffusion, transport, and organization at super-resolution.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, 12180
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38
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Blank HM, Callahan M, Pistikopoulos IPE, Polymenis AO, Polymenis M. Scaling of G1 Duration with Population Doubling Time by a Cyclin in Saccharomyces cerevisiae. Genetics 2018; 210:895-906. [PMID: 30150288 PMCID: PMC6218239 DOI: 10.1534/genetics.118.301507] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/24/2018] [Indexed: 01/09/2023] Open
Abstract
The longer cells stay in particular phases of the cell cycle, the longer it will take these cell populations to increase. However, the above qualitative description has very little predictive value, unless it can be codified mathematically. A quantitative relation that defines the population doubling time (Td) as a function of the time eukaryotic cells spend in specific cell cycle phases would be instrumental for estimating rates of cell proliferation and for evaluating introduced perturbations. Here, we show that in human cells, the length of the G1 phase (TG1) regressed on Td with a slope of ≈0.75, while in the yeast Saccharomyces cerevisiae, the slope was slightly smaller, at ≈0.60. On the other hand, cell size was not strongly associated with Td or TG1 in cell cultures that were proliferating at different rates. Furthermore, we show that levels of the yeast G1 cyclin Cln3p were positively associated with rates of cell proliferation over a broad range, at least in part through translational control mediated by a short upstream ORF (uORF) in the CLN3 transcript. Cln3p was also necessary for the proper scaling between TG1 and Td In contrast, yeast lacking the Whi5p transcriptional repressor maintained the scaling between TG1 and Td These data reveal fundamental scaling relationships between the duration of eukaryotic cell cycle phases and rates of cell proliferation, point to the necessary role of Cln3p in these relationships in yeast, and provide a mechanistic basis linking Cln3p levels to proliferation rates and the scaling of G1 with doubling time.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Michelle Callahan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | | | - Aggeliki O Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
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Heldt FS, Lunstone R, Tyson JJ, Novák B. Dilution and titration of cell-cycle regulators may control cell size in budding yeast. PLoS Comput Biol 2018; 14:e1006548. [PMID: 30356259 PMCID: PMC6218100 DOI: 10.1371/journal.pcbi.1006548] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 11/05/2018] [Accepted: 10/05/2018] [Indexed: 01/17/2023] Open
Abstract
The size of a cell sets the scale for all biochemical processes within it, thereby affecting cellular fitness and survival. Hence, cell size needs to be kept within certain limits and relatively constant over multiple generations. However, how cells measure their size and use this information to regulate growth and division remains controversial. Here, we present two mechanistic mathematical models of the budding yeast (S. cerevisiae) cell cycle to investigate competing hypotheses on size control: inhibitor dilution and titration of nuclear sites. Our results suggest that an inhibitor-dilution mechanism, in which cell growth dilutes the transcriptional inhibitor Whi5 against the constant activator Cln3, can facilitate size homeostasis. This is achieved by utilising a positive feedback loop to establish a fixed size threshold for the Start transition, which efficiently couples cell growth to cell cycle progression. Yet, we show that inhibitor dilution cannot reproduce the size of mutants that alter the cell’s overall ploidy and WHI5 gene copy number. By contrast, size control through titration of Cln3 against a constant number of genomic binding sites for the transcription factor SBF recapitulates both size homeostasis and the size of these mutant strains. Moreover, this model produces an imperfect ‘sizer’ behaviour in G1 and a ‘timer’ in S/G2/M, which combine to yield an ‘adder’ over the whole cell cycle; an observation recently made in experiments. Hence, our model connects these phenomenological data with the molecular details of the cell cycle, providing a systems-level perspective of budding yeast size control. Proliferating cells need to coordinate the initiation of genome replication and cell division with cell growth. In particular, the average time between two division events must precisely allow for a doubling in cell volume. Any systematic deviation from this balance would lead to progressive changes in cell size over consecutive generations and to a breakdown of biochemical processes. Here, we study two molecular mechanisms by which budding yeast cells might achieve this coordination. Through mathematical modelling, we show that the dilution of an inhibitor of cell cycle progression by cell growth can facilitate size homeostasis. But this mechanism fails to reproduce the size of mutant cells in which parts of the control machinery have been altered. By contrast, the titration of an activator against a constant number of genomic sites recapitulates these data and achieves size homeostasis. Since the control network of cell cycle progression in budding yeast is structurally similar to mammalian cells, our model could indicate a common mechanism for size control.
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Affiliation(s)
- Frank S. Heldt
- Department of Biochemistry, University of Oxford, Oxford,United Kingdom
- * E-mail: (FSH); (BN)
| | - Reece Lunstone
- Department of Biochemistry, University of Oxford, Oxford,United Kingdom
| | - John J. Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
- Division of Systems Biology, Academy of Integrated Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Béla Novák
- Department of Biochemistry, University of Oxford, Oxford,United Kingdom
- * E-mail: (FSH); (BN)
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