1
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Xiao J, Turner JJ, Kõivomägi M, Skotheim JM. Whi5 hypo- and hyper-phosphorylation dynamics control cell-cycle entry and progression. Curr Biol 2024; 34:2434-2447.e5. [PMID: 38749424 DOI: 10.1016/j.cub.2024.04.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/18/2024] [Accepted: 04/23/2024] [Indexed: 05/28/2024]
Abstract
Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the Swi4/Swi6 (SBF) complex that promotes transcription of the cyclins CLN1 and CLN2. In late G1, Whi5 is rapidly hyper-phosphorylated by Cln1 and Cln2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on "priming" sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
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Affiliation(s)
- Jordan Xiao
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Jonathan J Turner
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892, USA.
| | - Jan M Skotheim
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Chan Zuckerberg Biohub, 499 Illinois St., San Francisco, CA 94158, USA.
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2
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Brambila A, Prichard BE, DeWitt JT, Kellogg DR. Evidence for novel mechanisms that control cell-cycle entry and cell size. Mol Biol Cell 2024; 35:ar46. [PMID: 38231863 PMCID: PMC11064657 DOI: 10.1091/mbc.e23-05-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024] Open
Abstract
Entry into the cell cycle in late G1 phase occurs only when sufficient growth has occurred. In budding yeast, a cyclin called Cln3 is thought to link cell-cycle entry to cell growth. Cln3 accumulates during growth in early G1 phase and eventually helps trigger expression of late G1 phase cyclins that drive cell-cycle entry. All current models for cell-cycle entry assume that expression of late G1 phase cyclins is initiated at the transcriptional level. Current models also assume that the sole function of Cln3 in cell-cycle entry is to promote transcription of late G1 phase cyclins, and that Cln3 works solely in G1 phase. Here, we show that cell cycle-dependent expression of the late G1 phase cyclin Cln2 does not require any functions of the CLN2 promoter. Moreover, Cln3 can influence accumulation of Cln2 protein via posttranscriptional mechanisms. Finally, we show that Cln3 has functions in mitosis that strongly influence cell size. Together, these discoveries reveal the existence of surprising new mechanisms that challenge current models for control of cell-cycle entry and cell size.
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Affiliation(s)
- Amanda Brambila
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
| | - Beth E. Prichard
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
| | - Jerry T. DeWitt
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
| | - Douglas R. Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064
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3
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Hall D. Equations describing semi-confluent cell growth (I) Analytical approximations. Biophys Chem 2024; 307:107173. [PMID: 38241828 DOI: 10.1016/j.bpc.2024.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024]
Abstract
A set of differential equations with analytical solutions are presented that can quantitatively account for variable degrees of contact inhibition on cell growth in two- and three-dimensional cultures. The developed equations can be used for comparative purposes when assessing contribution of higher-order effects, such as culture geometry and nutrient depletion, on mean cell growth rate. These equations also offer experimentalists the opportunity to characterize cell culture experiments using a single reductive parameter.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164, Japan.
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4
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Zhang L, Meng Z, Calderone R, Liu W, She X, Li D. Mitochondria complex I deficiency in Candida albicans arrests the cell cycle at S phase through suppressive TOR and PKA pathways. FEMS Yeast Res 2024; 24:foae010. [PMID: 38592962 PMCID: PMC11008738 DOI: 10.1093/femsyr/foae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/16/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024] Open
Abstract
How mutations in mitochondrial electron transport chain (ETC) proteins impact the cell cycle of Candida albicans was investigated in this study. Using genetic null mutants targeting ETC complexes I (CI), III (CIII), and IV (CIV), the cell cycle stages (G0/G1, S phase, and G2/M) were analyzed via fluorescence-activated cell sorting (FACS). Four CI null mutants exhibited distinct alterations, including extended S phase, shortened G2/M population, and a reduction in cells size exceeding 10 µM. Conversely, CIII mutants showed an increased population in G1/G0 phase. Among four CI mutants, ndh51Δ/Δ and goa1Δ/Δ displayed aberrant cell cycle patterns correlated with previously reported cAMP/PKA downregulation. Specifically, nuo1Δ/Δ and nuo2Δ/Δ mutants exhibited increased transcription of RIM15, a central hub linking cell cycle with nutrient-dependent TOR1 and cAMP/PKA pathways and Snf1 aging pathway. These findings suggest that suppression of TOR1 and cAMP/PKA pathways or enhanced Snf1 disrupts cell cycle progression, influencing cell longevity and growth among CI mutants. Overall, our study highlights the intricate interplay between mitochondrial ETC, cell cycle, and signaling pathways.
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Affiliation(s)
- Lulu Zhang
- Department of Dermatology, Jiangsu Province Hospital of Traditional Chinese Medicine, No.155 Hanzhong Road, Qinhuai District, Nanjing, 210029, China
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington DC, 20057, United States
| | - Zhou Meng
- Institute of Dermatology, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), No. 12 Jiangwangmiao Street, Xuanwu District, Naning, 210042, China
| | - Richard Calderone
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington DC, 20057, United States
| | - Weida Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), No. 12 Jiangwangmiao Street, Xuanwu District, Naning, 210042, China
| | - Xiaodong She
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington DC, 20057, United States
- Institute of Dermatology, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), No. 12 Jiangwangmiao Street, Xuanwu District, Naning, 210042, China
| | - Dongmei Li
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington DC, 20057, United States
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5
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Xiao J, Turner JJ, Kõivomägi M, Skotheim JM. Whi5 hypo- and hyper-phosphorylation dynamics control cell cycle entry and progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565392. [PMID: 37961465 PMCID: PMC10635099 DOI: 10.1101/2023.11.02.565392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates the G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the SBF complex that promotes transcription of the cyclins CLN1 and CLN2 . In late-G1, Whi5 is rapidly hyper-phosphorylated by Cln1,2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on 'priming' sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
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6
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Hall D. MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:673-704. [PMID: 37670150 PMCID: PMC10682183 DOI: 10.1007/s00249-023-01679-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023]
Abstract
The single-celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (Monitoring Induction and Loss of prions in Cells; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa, 920-1164, Japan.
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7
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Williamson D, Tasker-Brown W, Murray JAH, Jones AR, Band LR. Modelling how plant cell-cycle progression leads to cell size regulation. PLoS Comput Biol 2023; 19:e1011503. [PMID: 37862377 PMCID: PMC10653611 DOI: 10.1371/journal.pcbi.1011503] [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: 03/06/2023] [Revised: 11/16/2023] [Accepted: 09/07/2023] [Indexed: 10/22/2023] Open
Abstract
Populations of cells typically maintain a consistent size, despite cell division rarely being precisely symmetrical. Therefore, cells must possess a mechanism of "size control", whereby the cell volume at birth affects cell-cycle progression. While size control mechanisms have been elucidated in a number of other organisms, it is not yet clear how this mechanism functions in plants. Here, we present a mathematical model of the key interactions in the plant cell cycle. Model simulations reveal that the network of interactions exhibits limit-cycle solutions, with biological switches underpinning both the G1/S and G2/M cell-cycle transitions. Embedding this network model within growing cells, we test hypotheses as to how cell-cycle progression can depend on cell size. We investigate two different mechanisms at both the G1/S and G2/M transitions: (i) differential expression of cell-cycle activator and inhibitor proteins (with synthesis of inhibitor proteins being independent of cell size), and (ii) equal inheritance of inhibitor proteins after cell division. The model demonstrates that both these mechanisms can lead to larger daughter cells progressing through the cell cycle more rapidly, and can thus contribute to cell-size control. To test how these features enable size homeostasis over multiple generations, we then simulated these mechanisms in a cell-population model with multiple rounds of cell division. These simulations suggested that integration of size-control mechanisms at both G1/S and G2/M provides long-term cell-size homeostasis. We concluded that while both size independence and equal inheritance of inhibitor proteins can reduce variations in cell size across individual cell-cycle phases, combining size-control mechanisms at both G1/S and G2/M is essential to maintain size homeostasis over multiple generations. Thus, our study reveals how features of the cell-cycle network enable cell-cycle progression to depend on cell size, and provides a mechanistic understanding of how plant cell populations maintain consistent size over generations.
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Affiliation(s)
- Daniel Williamson
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - William Tasker-Brown
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - James A. H. Murray
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Angharad R. Jones
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
| | - Leah R. Band
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
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8
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Blank HM, Reuse C, Schmidt‐Hohagen K, Hammer SE, Hiller K, Polymenis M. Branched-chain amino acid synthesis is coupled to TOR activation early in the cell cycle in yeast. EMBO Rep 2023; 24:e57372. [PMID: 37497662 PMCID: PMC10481666 DOI: 10.15252/embr.202357372] [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: 04/21/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
How cells coordinate their metabolism with division determines the rate of cell proliferation. Dynamic patterns of metabolite synthesis during the cell cycle are unexplored. We report the first isotope tracing analysis in synchronous, growing budding yeast cells. Synthesis of leucine, a branched-chain amino acid (BCAA), increases through the G1 phase of the cell cycle, peaking later during DNA replication. Cells lacking Bat1, a mitochondrial aminotransferase that synthesizes BCAAs, grow slower, are smaller, and are delayed in the G1 phase, phenocopying cells in which the growth-promoting kinase complex TORC1 is moderately inhibited. Loss of Bat1 lowers the levels of BCAAs and reduces TORC1 activity. Exogenous provision of valine and, to a lesser extent, leucine to cells lacking Bat1 promotes cell division. Valine addition also increases TORC1 activity. In wild-type cells, TORC1 activity is dynamic in the cell cycle, starting low in early G1 but increasing later in the cell cycle. These results suggest a link between BCAA synthesis from glucose to TORC1 activation in the G1 phase of the cell cycle.
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Affiliation(s)
- Heidi M Blank
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Kerstin Schmidt‐Hohagen
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Staci E Hammer
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, BRICSTechnische Universität BraunschweigBraunschweigGermany
| | - Michael Polymenis
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
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9
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Hammer SE, Polymenis M. One-carbon metabolic enzymes are regulated during cell division and make distinct contributions to the metabolome and cell cycle progression in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:6983127. [PMID: 36627750 PMCID: PMC9997564 DOI: 10.1093/g3journal/jkad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Enzymes of one-carbon (1C) metabolism play pivotal roles in proliferating cells. They are involved in the metabolism of amino acids, nucleotides, and lipids and the supply of all cellular methylations. However, there is limited information about how these enzymes are regulated during cell division and how cell cycle kinetics are affected in several loss-of-function mutants of 1C metabolism. Here, we report that the levels of the S. cerevisiae enzymes Ade17p and Cho2p, involved in the de novo synthesis of purines and phosphatidylcholine (PC), respectively, are cell cycle-regulated. Cells lacking Ade17p, Cho2p, or Shm2p (an enzyme that supplies 1C units from serine) have distinct alterations in size homeostasis and cell cycle kinetics. Loss of Ade17p leads to a specific delay at START, when cells commit to a new round of cell division, while loss of Shm2p has broader effects, reducing growth rate. Furthermore, the inability to synthesize PC de novo in cho2Δ cells delays START and reduces the coherence of nuclear elongation late in the cell cycle. Loss of Cho2p also leads to profound metabolite changes. Besides the expected changes in the lipidome, cho2Δ cells have reduced levels of amino acids, resembling cells shifted to poorer media. These results reveal the different ways that 1C metabolism allocates resources to affect cell proliferation at multiple cell cycle transitions.
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Affiliation(s)
- Staci E Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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10
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A dynamical stochastic model of yeast translation across the cell cycle. Heliyon 2023; 9:e13101. [PMID: 36793957 PMCID: PMC9922973 DOI: 10.1016/j.heliyon.2023.e13101] [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: 03/18/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Translation is a central step in gene expression, however its quantitative and time-resolved regulation is poorly understood. We developed a discrete, stochastic model for protein translation in S. cerevisiae in a whole-transcriptome, single-cell context. A "base case" scenario representing an average cell highlights translation initiation rates as the main co-translational regulatory parameters. Codon usage bias emerges as a secondary regulatory mechanism through ribosome stalling. Demand for anticodons with low abundancy is shown to cause above-average ribosome dwelling times. Codon usage bias correlates strongly both with protein synthesis rates and elongation rates. Applying the model to a time-resolved transcriptome estimated by combining data from FISH and RNA-Seq experiments, it could be shown that increased total transcript abundance during the cell cycle decreases translation efficiency at single transcript level. Translation efficiency grouped by gene function shows highest values for ribosomal and glycolytic genes. Ribosomal proteins peak in S phase while glycolytic proteins rank highest in later cell cycle phases.
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11
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A continuous-time stochastic Boolean model provides a quantitative description of the budding yeast cell cycle. Sci Rep 2022; 12:20302. [PMID: 36434030 PMCID: PMC9700812 DOI: 10.1038/s41598-022-24302-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
The cell division cycle is regulated by a complex network of interacting genes and proteins. The control system has been modeled in many ways, from qualitative Boolean switching-networks to quantitative differential equations and highly detailed stochastic simulations. Here we develop a continuous-time stochastic model using seven Boolean variables to represent the activities of major regulators of the budding yeast cell cycle plus one continuous variable representing cell growth. The Boolean variables are updated asynchronously by logical rules based on known biochemistry of the cell-cycle control system using Gillespie's stochastic simulation algorithm. Time and cell size are updated continuously. By simulating a population of yeast cells, we calculate statistical properties of cell cycle progression that can be compared directly to experimental measurements. Perturbations of the normal sequence of events indicate that the cell cycle is 91% robust to random 'flips' of the Boolean variables, but 9% of the perturbations induce lethal mistakes in cell cycle progression. This simple, hybrid Boolean model gives a good account of the growth and division of budding yeast cells, suggesting that this modeling approach may be as accurate as detailed reaction-kinetic modeling with considerably less demands on estimating rate constants.
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12
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Kellogg DR, Levin PA. Nutrient availability as an arbiter of cell size. Trends Cell Biol 2022; 32:908-919. [PMID: 35851491 PMCID: PMC9588502 DOI: 10.1016/j.tcb.2022.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023]
Abstract
Pioneering work carried out over 60 years ago discovered that bacterial cell size is proportional to the growth rate set by nutrient availability. This relationship is traditionally referred to as the 'growth law'. Subsequent studies revealed the growth law to hold across all orders of life, a remarkable degree of conservation. However, recent work suggests the relationship between growth rate, nutrients, and cell size is far more complicated and less deterministic than originally thought. Focusing on bacteria and yeast, here we review efforts to understand the molecular mechanisms underlying the relationship between growth rate and cell size.
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Affiliation(s)
- Douglas R Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St Louis, MO 63130, USA; Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St Louis, St Louis, MO 63130, USA.
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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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Saidykhan L, Correia J, Romanyuk A, Peacock AFA, Desanti GE, Taylor-Smith L, Makarova M, Ballou ER, May RC. An in vitro method for inducing titan cells reveals novel features of yeast-to-titan switching in the human fungal pathogen Cryptococcus gattii. PLoS Pathog 2022; 18:e1010321. [PMID: 35969643 PMCID: PMC9426920 DOI: 10.1371/journal.ppat.1010321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/30/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
Cryptococcosis is a potentially lethal fungal infection of humans caused by organisms within the Cryptococcus neoformans/gattii species complex. Whilst C. neoformans is a relatively common pathogen of immunocompromised individuals, C. gattii is capable of acting as a primary pathogen of immunocompetent individuals. Within the host, both species undergo morphogenesis to form titan cells: exceptionally large cells that are critical for disease establishment. To date, the induction, defining attributes, and underlying mechanism of titanisation have been mainly characterized in C. neoformans. Here, we report the serendipitous discovery of a simple and robust protocol for in vitro induction of titan cells in C. gattii. Using this in vitro approach, we reveal a remarkably high capacity for titanisation within C. gattii, especially in strains associated with the Pacific Northwest Outbreak, and characterise strain-specific differences within the clade. In particular, this approach demonstrates for the first time that cell size changes, DNA amplification, and budding are not always synchronous during titanisation. Interestingly, however, exhibition of these cell cycle phenotypes was correlated with genes associated with cell cycle progression including CDC11, CLN1, BUB2, and MCM6. Finally, our findings reveal exogenous p-Aminobenzoic acid to be a key inducer of titanisation in this organism. Consequently, this approach offers significant opportunities for future exploration of the underlying mechanism of titanisation in this genus.
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Affiliation(s)
- Lamin Saidykhan
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
- Division of Physical and Natural Science, University of The Gambia, Brikama, The Gambia
| | - Joao Correia
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Andrey Romanyuk
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
- School of Chemistry, University of Birmingham, Edgbaston, United Kingdom
| | - Anna F. A. Peacock
- School of Chemistry, University of Birmingham, Edgbaston, United Kingdom
| | - Guillaume E. Desanti
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Leanne Taylor-Smith
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Maria Makarova
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Elizabeth R. Ballou
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
- MRC Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
- * E-mail: (ERB); (RCM)
| | - Robin C. May
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
- * E-mail: (ERB); (RCM)
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15
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Ali A, Manzoor MF, Ahmad N, Aadil RM, Qin H, Siddique R, Riaz S, Ahmad A, Korma SA, Khalid W, Aizhong L. The Burden of Cancer, Government Strategic Policies, and Challenges in Pakistan: A Comprehensive Review. Front Nutr 2022; 9:940514. [PMID: 35938114 PMCID: PMC9355152 DOI: 10.3389/fnut.2022.940514] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
Cancer is a severe condition characterized by uncontrolled cell division and increasing reported mortality and diagnostic cases. In 2040, an estimated 28.4 million cancer cases are expected to happen globally. In 2020, an estimated 19.3 million new cancer cases (18.1 million excluding non-melanoma skin cancer) had been diagnosed worldwide, with around 10.0 million cancer deaths. Breast cancer cases have increased by 2.26 million, lung cancer by 2.21 million, stomach by 1.089 million, liver by 0.96 million, and colon cancer by 1.93 million. Cancer is becoming more prevalent in Pakistan, with 19 million new cancer cases recorded in 2020. Food adulteration, gutkha, paan, and nutritional deficiencies are major cancer risk factors that interplay with cancer pathogenesis in this country. Government policies and legislation, cancer treatment challenges, and prevention must be revised seriously. This review presents the current cancer epidemiology in Pakistan to better understand cancer basis. It summarizes current cancer risk factors, causes, and the strategies and policies of the country against cancer.
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Affiliation(s)
- Anwar Ali
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
- Food and Nutrition Society, Gilgit Baltistan, Pakistan
| | | | - Nazir Ahmad
- Department of Nutritional Science, Government College University Faisalabad, Faisalabad, Pakistan
| | - Rana Muhammad Aadil
- National Institute of Food Science and Technology, University of Agriculture, Faisalabad, Pakistan
| | - Hong Qin
- School of Nutrition and Food Hygiene, Xiangya School of Public Health, Central South University, Changsha, China
| | - Rabia Siddique
- Department of Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sakhawat Riaz
- Department of Home Economics, Government College University Faisalabad, Faisalabad, Pakistan
| | - Arslan Ahmad
- Department of Home Economics, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sameh A. Korma
- Department of Food Science, Faculty of Agriculture, Zagazig, Egypt
| | - Waseem Khalid
- Department of Food Sciences, Government College University, Faisalabad, Pakistan
| | - Liu Aizhong
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
- *Correspondence: Liu Aizhong
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16
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High-resolution mass measurements of single budding yeast reveal linear growth segments. Nat Commun 2022; 13:3483. [PMID: 35732645 PMCID: PMC9217925 DOI: 10.1038/s41467-022-30781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
The regulation of cell growth has fundamental physiological, biotechnological and medical implications. However, methods that can continuously monitor individual cells at sufficient mass and time resolution hardly exist. Particularly, detecting the mass of individual microbial cells, which are much smaller than mammalian cells, remains challenging. Here, we modify a previously described cell balance ('picobalance') to monitor the proliferation of single cells of the budding yeast, Saccharomyces cerevisiae, under culture conditions in real time. Combined with optical microscopy to monitor the yeast morphology and cell cycle phase, the picobalance approaches a total mass resolution of 0.45 pg. Our results show that single budding yeast cells (S/G2/M phase) increase total mass in multiple linear segments sequentially, switching their growth rates. The growth rates weakly correlate with the cell mass of the growth segments, and the duration of each growth segment correlates negatively with cell mass. We envision that our technology will be useful for direct, accurate monitoring of the growth of single cells throughout their cycle.
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17
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Zhao X, Oh SH, Coleman DA, Hoyer LL. ALS1 Deletion Increases the Proportion of Small Cells in a Candida albicans Culture Population: Hypothesizing a Novel Role for Als1. Front Cell Infect Microbiol 2022; 12:895068. [PMID: 35646731 PMCID: PMC9130707 DOI: 10.3389/fcimb.2022.895068] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Candida albicans Als1 is a large cell-surface glycoprotein most often discussed for its role in mediating ligand-binding and aggregative interactions. Relative to a wild-type control, deletion of ALS1 produced a strain that showed delayed germ-tube formation and delayed disease progression in a murine model of disseminated candidiasis. Populations of Δals1/Δals1 cultured cells had a higher proportion of smaller cells compared to wild-type or ALS1 reintegrant control cultures. The goal of this work was to investigate whether this difference in cell-size distributions was responsible for delayed germ-tube formation and delayed disease progression. Flow cytometry was used to select populations of wild-type and Δals1/Δals1 cells with varied cell-size distributions. Delayed germ-tube formation was demonstrated for small cells sorted from a wild-type (ALS1/ALS1) culture population. Large cells sorted from a Δals1/Δals1 culture formed germ tubes as quickly as the wild-type control demonstrating clearly that the Δals1/Δals1 germ-tube formation delays were attributable to cell size. In vivo, smaller-sized cells of the wild-type control showed fewer colony-forming units (cfu) per gram of kidney tissue and less-severe histopathology lesions compared to larger cells of the same strain. The Δals1/Δals1 strain showed reduced cfu/g of kidney tissue and less-severe lesions compared to the wild-type control. However, isolation and testing of the larger cells from the Δals1/Δals1 population increased cfu/g of tissue and showed increased lesion severity compared to the overall mutant cell population. In vivo hypha lengths from the large, sorted Δals1/Δals1 cells were comparable to those for the wild-type control strain. These results demonstrated that a large share of the Δals1/Δals1 in-vivo phenotype was attributable to cell size. Collectively, the data suggest a role for Als1 in C. albicans cell size homeostasis, a novel hypothesis for further exploration.
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18
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Pérez AP, Artés MH, Moreno DF, Clotet J, Aldea M. Mad3 modulates the G 1 Cdk and acts as a timer in the Start network. SCIENCE ADVANCES 2022; 8:eabm4086. [PMID: 35522754 PMCID: PMC9075807 DOI: 10.1126/sciadv.abm4086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Cells maintain their size within limits over successive generations to maximize fitness and survival. Sizer, timer, and adder behaviors have been proposed as possible alternatives to coordinate growth and cell cycle progression. Regarding budding yeast cells, a sizer mechanism is thought to rule cell cycle entry at Start. However, while many proteins controlling the size of these cells have been identified, the mechanistic framework in which they participate to achieve cell size homeostasis is not understood. We show here that intertwined APC and SCF degradation machineries with specific adaptor proteins drive cyclic accumulation of the G1 Cdk in the nucleus, reaching maximal levels at Start. The mechanism incorporates Mad3, a centromeric-signaling protein that subordinates G1 progression to the previous mitosis as a memory factor. This alternating-degradation device displays the properties of a timer and, together with the sizer device, would constitute a key determinant of cell cycle entry.
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Affiliation(s)
- Alexis P. Pérez
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
| | - Marta H. Artés
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
| | - David F. Moreno
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
| | - Josep Clotet
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028 Barcelona, Catalonia, Spain
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
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19
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20
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Wu Y, Pegoraro AF, Weitz DA, Janmey P, Sun SX. The correlation between cell and nucleus size is explained by an eukaryotic cell growth model. PLoS Comput Biol 2022; 18:e1009400. [PMID: 35180215 PMCID: PMC8893647 DOI: 10.1371/journal.pcbi.1009400] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 03/03/2022] [Accepted: 01/12/2022] [Indexed: 12/19/2022] Open
Abstract
In eukaryotes, the cell volume is observed to be strongly correlated with the nuclear volume. The slope of this correlation depends on the cell type, growth condition, and the physical environment of the cell. We develop a computational model of cell growth and proteome increase, incorporating the kinetics of amino acid import, protein/ribosome synthesis and degradation, and active transport of proteins between the cytoplasm and the nucleoplasm. We also include a simple model of ribosome biogenesis and assembly. Results show that the cell volume is tightly correlated with the nuclear volume, and the cytoplasm-nucleoplasm transport rates strongly influence the cell growth rate as well as the cell/nucleus volume ratio (C/N ratio). Ribosome assembly and the ratio of ribosomal proteins to mature ribosomes also influence the cell volume and the cell growth rate. We find that in order to regulate the cell growth rate and the cell/nucleus volume ratio, the cell must optimally control groups of kinetic and transport parameters together, which could explain the quantitative roles of canonical growth pathways. Finally, although not explicitly demonstrated in this work, we point out that it is possible to construct a detailed proteome distribution using our model and RNAseq data, provided that a quantitative cell division mechanism is known.
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Affiliation(s)
- Yufei Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - David A. Weitz
- Department of Physics, Harvard University, Boston, Massachusetts, United States of America
| | - Paul Janmey
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sean X. Sun
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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21
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Greenwood BL, Stuart DT. Synchronization of Saccharomyces cerevisiae Cells for Analysis of Progression Through the Cell Cycle. Methods Mol Biol 2022; 2579:145-168. [PMID: 36045205 DOI: 10.1007/978-1-0716-2736-5_12] [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] [Indexed: 06/15/2023]
Abstract
The cell division cycle is a fundamental process required for proliferation of all living organisms. The eukaryotic cell cycle follows a basic template with an ordered series of events beginning with G1 (Gap1) phase, followed successively by S (Synthesis) phase, G2 (Gap 2) phase, and M-phase (Mitosis). The process is tightly regulated in response to signals from both the internal and external milieu. The budding yeast S. cerevisiae is an outstanding model for the study of the cell cycle and its regulatory process. The basic events and regulatory processes of the S. cerevisiae cell cycle are highly conserved with other eukaryotes. The organism grows rapidly in simple medium, has a sequenced annotated genome, well-established genetics, and is amenable to analysis by proteomics and microscopy. Additionally, a range of tools and techniques are available to generate cultures of S. cerevisiae that are homogenously arrested or captured at specific phases of the cell cycle and upon release from that arrest these can be used to monitor cell cycle events as the cells synchronously proceed through a division cycle. In this chapter, we describe a series of commonly used techniques that are used to generate synchronized populations of S. cerevisiae and provide an overview of methods that can be used to monitor the progression of the cells through the cell division cycle.
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Affiliation(s)
| | - David T Stuart
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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22
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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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23
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Srivastava R, Sahoo L. Cowpea NAC Transcription Factors Positively Regulate Cellular Stress Response and Balance Energy Metabolism in Yeast via Reprogramming of Biosynthetic Pathways. ACS Synth Biol 2021; 10:2286-2307. [PMID: 34470212 DOI: 10.1021/acssynbio.1c00208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Yeast is a dominant host for recombinant production of heterologous proteins, high-value biochemical compounds, and microbial fermentation. During bioprocess operations, pH fluctuations, organic solvents, drying, starvation, osmotic pressure, and often a combination of these stresses cause growth inhibition or death, markedly limiting its industrial use. Thus, stress-tolerant yeast strains with balanced energy-bioenergetics are highly desirous for sustainable improvement of quality biotechnological production. We isolated two NAC transcription factors (TFs), VuNAC1 and VuNAC2, from a wild cowpea genotype, improving both stress tolerance and growth when expressed in yeast. The GFP-fused proteins were localized to the nucleus. Y2H and reporter assay demonstrated the dimerization and transactivation abilities of the VuNAC proteins having structural folds similar to rice SNAC1. The gel-shift assay indicated that the TFs recognize an "ATGCGTG" motif for DNA-binding shared by several native TFs in yeast. The heterologous expression of VuNAC1/2 in yeast improved growth, biomass, lifespan, fermentation efficiency, and altered cellular composition of biomolecules. The transgenic strains conferred tolerance to multiple stresses such as high salinity, osmotic stress, freezing, and aluminum toxicity. Analysis of the metabolome revealed reprogramming of major pathways synthesizing nucleotides, vitamin B complex, amino acids, antioxidants, flavonoids, and other energy currencies and cofactors. Consequently, the transcriptional tuning of stress signaling and biomolecule metabolism improved the survival of the transgenic strains during starvation and stress recovery. VuNAC1/2-based synthetic gene expression control may contribute to designing robust industrial yeast strains with value-added productivity.
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Affiliation(s)
- Richa Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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24
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Barber F, Min J, Murray AW, Amir A. Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells. PLoS Comput Biol 2021; 17:e1009080. [PMID: 34153030 PMCID: PMC8248971 DOI: 10.1371/journal.pcbi.1009080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/01/2021] [Accepted: 05/14/2021] [Indexed: 11/18/2022] Open
Abstract
Microbial populations show striking diversity in cell growth morphology and lifecycle; however, our understanding of how these factors influence the growth rate of cell populations remains limited. We use theory and simulations to predict the impact of asymmetric cell division, cell size regulation and single-cell stochasticity on the population growth rate. Our model predicts that coarse-grained noise in the single-cell growth rate λ decreases the population growth rate, as previously seen for symmetrically dividing cells. However, for a given noise in λ we find that dividing asymmetrically can enhance the population growth rate for cells with strong size control (between a “sizer” and an “adder”). To reconcile this finding with the abundance of symmetrically dividing organisms in nature, we propose that additional constraints on cell growth and division must be present which are not included in our model, and we explore the effects of selected extensions thereof. Further, we find that within our model, epigenetically inherited generation times may arise due to size control in asymmetrically dividing cells, providing a possible explanation for recent experimental observations in budding yeast. Taken together, our findings provide insight into the complex effects generated by non-canonical growth morphologies. How rapidly a population of single-celled organisms can grow will strongly impact their long-term success. Prior work has shown that many factors impact this population growth rate, including the rate at which single cells grow, random variability between cells, and whether cells regulate their own size. Here we show that cell division asymmetry can also have a strong impact on the population growth rate. We use theory and computer simulations to study the growth rate of cells that divide asymmetrically, producing one smaller cell and one larger cell with each cell division event. We show that variability in how fast single cells grow will still decrease the population growth rate, when asymmetry is moderate or size control is weak, but that cells with strong size control can diminish this decrease by dividing more asymmetrically. We also demonstrate that cell cycle lengths can be positively correlated for closely related cells when they both divide asymmetrically and regulate their size. This counter-intuitive result contrasts with previous findings based on cell size regulation in symmetrically dividing cells that if cells grow for “too long” in one cell cycle, this will be corrected for by reduced growth during a shorter, subsequent cell cycle.
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Affiliation(s)
- Felix Barber
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Jiseon Min
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Andrew W. Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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25
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Fuhrmann-Lieker T, Kubetschek N, Ziebarth J, Klassen R, Seiler W. Is the diatom sex clock a clock? J R Soc Interface 2021; 18:20210146. [PMID: 34129790 PMCID: PMC8205531 DOI: 10.1098/rsif.2021.0146] [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] [Indexed: 12/02/2022] Open
Abstract
The unique life cycle of diatoms with continuous decreasing and restoration of the cell size leads to periodic fluctuations in cell size distribution and has been regarded as a multi-annual clock. To understand the long-term behaviour of a population analytically, generic mathematical models are investigated algebraically and numerically for their capability to describe periodic oscillations. Whereas the generally accepted simple concepts for the proliferation dynamics do not sustain oscillating behaviour owing to broadening of the size distribution, simulations show that a proposed limited lifetime of a newly synthesized cell wall slows down the relaxation towards a time-invariant equilibrium state to the order of a hundred thousand generations. In combination with seasonal perturbation events, the proliferation scheme with limited lifetime is able to explain long-lasting rhythms that are characteristic for diatom population dynamics. The life cycle thus resembles a pendulum clock that has to be wound up from time to time by seasonal perturbations rather than an oscillator represented by a limit cycle.
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Affiliation(s)
- Thomas Fuhrmann-Lieker
- Physical Chemistry of Nanomaterials, Institute of Chemistry and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, 34109 Kassel, Germany
| | - Nico Kubetschek
- Physical Chemistry of Nanomaterials, Institute of Chemistry and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, 34109 Kassel, Germany
| | - Jonas Ziebarth
- Physical Chemistry of Nanomaterials, Institute of Chemistry and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, 34109 Kassel, Germany
| | - Roland Klassen
- Microbiology, Institute of Biology and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, 34109 Kassel, Germany
| | - Werner Seiler
- Algorithmic Algebra and Discrete Mathematics, Institute of Mathematics, Faculty of Mathematics and Natural Sciences, University of Kassel, 34109 Kassel, Germany
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26
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Gihana GM, Cross-Najafi AA, Lacefield S. The mitotic exit network regulates the spatiotemporal activity of Cdc42 to maintain cell size. J Cell Biol 2021; 220:211575. [PMID: 33284320 PMCID: PMC7721911 DOI: 10.1083/jcb.202001016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 09/29/2020] [Accepted: 10/29/2020] [Indexed: 12/29/2022] Open
Abstract
During G1 in budding yeast, the Cdc42 GTPase establishes a polar front, along which actin is recruited to direct secretion for bud formation. Cdc42 localizes at the bud cortex and then redistributes between mother and daughter in anaphase. The molecular mechanisms that terminate Cdc42 bud-localized activity during mitosis are poorly understood. We demonstrate that the activity of the Cdc14 phosphatase, released through the mitotic exit network, is required for Cdc42 redistribution between mother and bud. Induced Cdc14 nucleolar release results in premature Cdc42 redistribution between mother and bud. Inhibition of Cdc14 causes persistence of Cdc42 bud localization, which perturbs normal cell size and spindle positioning. Bem3, a Cdc42 GAP, binds Cdc14 and is dephosphorylated at late anaphase in a Cdc14-dependent manner. We propose that Cdc14 dephosphorylates and activates Bem3 to allow Cdc42 inactivation and redistribution. Our results uncover a mechanism through which Cdc14 regulates the spatiotemporal activity of Cdc42 to maintain normal cell size at cytokinesis.
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Affiliation(s)
| | | | - Soni Lacefield
- Department of Biology, Indiana University, Bloomington, IN
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27
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Perrino G, Napolitano S, Galdi F, La Regina A, Fiore D, Giuliano T, di Bernardo M, di Bernardo D. Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control. Nat Commun 2021; 12:2452. [PMID: 33907191 PMCID: PMC8079375 DOI: 10.1038/s41467-021-22689-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/24/2021] [Indexed: 12/18/2022] Open
Abstract
The cell cycle is the process by which eukaryotic cells replicate. Yeast cells cycle asynchronously with each cell in the population budding at a different time. Although there are several experimental approaches to synchronise cells, these usually work only in the short-term. Here, we build a cyber-genetic system to achieve long-term synchronisation of the cell population, by interfacing genetically modified yeast cells with a computer by means of microfluidics to dynamically change medium, and a microscope to estimate cell cycle phases of individual cells. The computer implements a controller algorithm to decide when, and for how long, to change the growth medium to synchronise the cell-cycle across the population. Our work builds upon solid theoretical foundations provided by Control Engineering. In addition to providing an avenue for yeast cell cycle synchronisation, our work shows that control engineering can be used to automatically steer complex biological processes towards desired behaviours similarly to what is currently done with robots and autonomous vehicles.
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Affiliation(s)
| | - Sara Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
| | - Francesca Galdi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Davide Fiore
- Department of Mathematics and Applications "R. Caccioppoli", University of Naples Federico II, Naples, Italy
| | - Teresa Giuliano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
- SSM - School for Advanced Studies, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy.
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28
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Chen Y, Futcher B. Scaling gene expression for cell size control and senescence in Saccharomyces cerevisiae. Curr Genet 2020; 67:41-47. [PMID: 33151380 PMCID: PMC7886820 DOI: 10.1007/s00294-020-01098-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/08/2020] [Accepted: 07/15/2020] [Indexed: 11/29/2022]
Abstract
Cells divide with appropriate frequency by coupling division to growth—that is, cells divide only when they have grown sufficiently large. This process is poorly understood, but has been studied using cell size mutants. In principle, mutations affecting cell size could affect the mean size (“set-point” mutants), or they could affect the variability of sizes (“homeostasis” mutants). In practice, almost all known size mutants affect set-point, with little effect on size homeostasis. One model for size-dependent division depends on a size-dependent gene expression program: Activators of cell division are over-expressed at larger and larger sizes, while inhibitors are under-expressed. At sufficiently large size, activators overcome inhibitors, and the cell divides. Amounts of activators and inhibitors determine the set-point, but the gene expression program (the rate at which expression changes with cell size) determines the breadth of the size distribution (homeostasis). In this model, set-point mutants identify cell cycle activators and inhibitors, while homeostasis mutants identify regulators that couple expression of activators and inhibitors to size. We consider recent results suggesting that increased cell size causes senescence, and suggest that at very large sizes, an excess of DNA binding proteins leads to size induced senescence.
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Affiliation(s)
- Yuping Chen
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, CA, 94305-5174, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, 11794-5222, USA.
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29
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Excessive rDNA Transcription Drives the Disruption in Nuclear Homeostasis during Entry into Senescence in Budding Yeast. Cell Rep 2020; 28:408-422.e4. [PMID: 31291577 DOI: 10.1016/j.celrep.2019.06.032] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/09/2019] [Accepted: 06/07/2019] [Indexed: 01/11/2023] Open
Abstract
Budding yeast cells undergo a limited number of divisions before they enter senescence and die. Despite recent mechanistic advances, whether and how molecular events are temporally and causally linked during the transition to senescence remain elusive. Here, using real-time observation of the accumulation of extrachromosomal rDNA circles (ERCs) in single cells, we provide evidence that ERCs build up rapidly with exponential kinetics well before any physiological decline. We then show that ERCs fuel a massive increase in ribosomal RNA (rRNA) levels in the nucleolus, which do not mature into functional ribosomes. This breakdown in nucleolar coordination is followed by a loss of nuclear homeostasis, thus defining a chronology of causally related events leading to cell death. A computational analysis supports a model in which a series of age-independent processes lead to an age-dependent increase in cell mortality, hence explaining the emergence of aging in budding yeast.
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Mohammad K, Baratang Junio JA, Tafakori T, Orfanos E, Titorenko VI. Mechanisms that Link Chronological Aging to Cellular Quiescence in Budding Yeast. Int J Mol Sci 2020; 21:ijms21134717. [PMID: 32630624 PMCID: PMC7369985 DOI: 10.3390/ijms21134717] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022] Open
Abstract
After Saccharomyces cerevisiae cells cultured in a medium with glucose consume glucose, the sub-populations of quiescent and non-quiescent cells develop in the budding yeast culture. An age-related chronology of quiescent and non-quiescent yeast cells within this culture is discussed here. We also describe various hallmarks of quiescent and non-quiescent yeast cells. A complex aging-associated program underlies cellular quiescence in budding yeast. This quiescence program includes a cascade of consecutive cellular events orchestrated by an intricate signaling network. We examine here how caloric restriction, a low-calorie diet that extends lifespan and healthspan in yeast and other eukaryotes, influences the cellular quiescence program in S. cerevisiae. One of the main objectives of this review is to stimulate an exploration of the mechanisms that link cellular quiescence to chronological aging of budding yeast. Yeast chronological aging is defined by the length of time during which a yeast cell remains viable after its growth and division are arrested, and it becomes quiescent. We propose a hypothesis on how caloric restriction can slow chronological aging of S. cerevisiae by altering the chronology and properties of quiescent cells. Our hypothesis posits that caloric restriction delays yeast chronological aging by targeting four different processes within quiescent cells.
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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 DOI: 10.1073/pnas.2001255117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [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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Growth-Dependent Activation of Protein Kinases Suggests a Mechanism for Measuring Cell Growth. Genetics 2020; 215:729-746. [PMID: 32461268 DOI: 10.1534/genetics.120.303200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/17/2020] [Indexed: 11/18/2022] Open
Abstract
In all cells, progression through the cell cycle occurs only when sufficient growth has occurred. Thus, cells must translate growth into a proportional signal that can be used to measure and transmit information about growth. Previous genetic studies in budding yeast suggested that related kinases called Gin4 and Hsl1 could function in mechanisms that measure bud growth; however, interpretation of the data was complicated by the use of gene deletions that cause complex terminal phenotypes. Here, we used the first conditional alleles of Gin4 and Hsl1 to more precisely define their functions. We show that excessive bud growth during a prolonged mitotic delay is an immediate consequence of inactivating Gin4 and Hsl1 Thus, acute loss of Gin4 and Hsl1 causes cells to behave as though they cannot detect that bud growth has occurred. We further show that Gin4 and Hsl1 undergo gradual hyperphosphorylation during bud growth that is dependent upon growth and correlated with the extent of growth. Moreover, gradual hyperphosphorylation of Gin4 during bud growth requires binding to anionic phospholipids that are delivered to the growing bud. While alternative models are possible, the data suggest that signaling lipids delivered to the growing bud generate a growth-dependent signal that could be used to measure bud growth.
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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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34
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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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35
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Gomar-Alba M, Mendoza M. Modulation of Cell Identity by Modification of Nuclear Pore Complexes. Front Genet 2020; 10:1301. [PMID: 31969901 PMCID: PMC6960265 DOI: 10.3389/fgene.2019.01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/26/2019] [Indexed: 11/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) are protein assemblies that form channels across the nuclear envelope to mediate communication between the nucleus and the cytoplasm. Additionally, NPCs interact with chromatin and influence the position and expression of multiple genes. Interestingly, the composition of NPCs can vary in different cell-types, tissues, and developmental states. Here, we review recent findings suggesting that modifications of NPC composition, including post-translational modifications, play an instructive role in cell fate establishment. In particular, we focus on the role of cell-specific NPC deacetylation in asymmetrically dividing budding yeast, which modulates transport-dependent and transport-independent NPC functions to determine the time of commitment to a new division cycle in daughter cells. By modulating protein localization and gene expression, NPCs are therefore emerging as central regulators of cell identity.
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Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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36
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Valiakhmetov AY, Kuchin AV, Suzina NE, Zvonarev AN, Shepelyakovskaya AO. Glucose causes primary necrosis in exponentially grown yeast Saccharomyces cerevisiae. FEMS Yeast Res 2019; 19:5347945. [PMID: 30785621 DOI: 10.1093/femsyr/foz019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/19/2019] [Indexed: 02/07/2023] Open
Abstract
In this paper, we present data on sugar-induced cell death (SICD) in the yeast Saccharomyces cerevisiae in the exponential phase of growth. We suggest that the nature of SICD in exponentially grown yeast is primary necrosis, in contrast to cells in the stationary growth phase, which exhibit apoptotic SICD. The following findings confirm this conclusion: (i) the process rate; (ii) the impairments of plasma membrane integrity; (iii) the drastic morphological changes in the intracellular content; (iv) the absence of chromatin condensation; (v) the absence of externalization of phosphotidylserine (PS) on the outer leaflet of plasma membrane and (vi) the insensitivity of the SICD process to cycloheximide (CHX). Research shows that SICD occurs in a subpopulation of cells in the S-phase.
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Affiliation(s)
- A Ya Valiakhmetov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PCBR RAS.,Moscow Region State University
| | - A V Kuchin
- Institute of Cell Biophysics, FRC PCBR RAS
| | - N E Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PCBR RAS
| | - A N Zvonarev
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PCBR RAS
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37
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Leitao RM, Jasani A, Talavara RA, Pham A, Okobi QJ, Kellogg DR. A Conserved PP2A Regulatory Subunit Enforces Proportional Relationships Between Cell Size and Growth Rate. Genetics 2019; 213:517-528. [PMID: 31488515 PMCID: PMC6781898 DOI: 10.1534/genetics.119.301012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/10/2019] [Indexed: 11/18/2022] Open
Abstract
Cell size is proportional to growth rate. Thus, cells growing rapidly in rich nutrients can be nearly twice the size of cells growing slowly in poor nutrients. This proportional relationship appears to hold across all orders of life, yet the underlying mechanisms are unknown. In budding yeast, most growth occurs during mitosis, and the proportional relationship between cell size and growth rate is therefore enforced primarily by modulating growth in mitosis. When growth is slow, the duration of mitosis is increased to allow more time for growth, yet the amount of growth required to complete mitosis is reduced, which leads to the birth of small daughter cells. Previous studies have found that Rts1, a member of the conserved B56 family of protein phosphatase 2A regulatory subunits, works in a TORC2 signaling network that influences cell size and growth rate. However, it was unclear whether Rts1 influences cell growth and size in mitosis. Here, we show that Rts1 is required for the proportional relationship between cell size and growth rate during mitosis. Moreover, nutrients and Rts1 influence the duration and extent of growth in mitosis via Wee1 and Pds1/securin, two conserved regulators of mitotic progression. Together, the data are consistent with a model in which global signals that set growth rate also set the critical amount of growth required for cell cycle progression, which would provide a simple mechanistic explanation for the proportional relationship between cell size and growth rate.
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Affiliation(s)
- Ricardo M Leitao
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Akshi Jasani
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Rafael A Talavara
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Annie Pham
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Quincy J Okobi
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Douglas R Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
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38
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O'Laughlin R, Jin M, Li Y, Pillus L, Tsimring LS, Hasty J, Hao N. Advances in quantitative biology methods for studying replicative aging in Saccharomyces cerevisiae. TRANSLATIONAL MEDICINE OF AGING 2019; 4:151-160. [PMID: 33880425 PMCID: PMC8054985 DOI: 10.1016/j.tma.2019.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Aging is a complex, yet pervasive phenomenon in biology. As human cells steadily succumb to the deteriorating effects of aging, so too comes a host of age-related ailments such as neurodegenerative disorders, cardiovascular disease and cancer. Therefore, elucidation of the molecular networks that drive aging is of paramount importance to human health. Progress toward this goal has been aided by studies from simple model organisms such as Saccharomyces cerevisiae. While work in budding yeast has already revealed much about the basic biology of aging as well as a number of evolutionarily conserved pathways involved in this process, recent technological advances are poised to greatly expand our knowledge of aging in this simple eukaryote. Here, we review the latest developments in microfluidics, single-cell analysis and high-throughput technologies for studying single-cell replicative aging in S. cerevisiae. We detail the challenges each of these methods addresses as well as the unique insights into aging that each has provided. We conclude with a discussion of potential future applications of these techniques as well as the importance of single-cell dynamics and quantitative biology approaches for understanding cell aging.
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Affiliation(s)
- Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Meng Jin
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nan Hao
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Abeywickrema M, Vachova H, Farr H, Mohr T, Wheeler RJ, Lai DH, Vaughan S, Gull K, Sunter JD, Varga V. Non-equivalence in old- and new-flagellum daughter cells of a proliferative division in Trypanosoma brucei. Mol Microbiol 2019; 112:1024-1040. [PMID: 31286583 PMCID: PMC6771564 DOI: 10.1111/mmi.14345] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2019] [Indexed: 12/15/2022]
Abstract
Differentiation of Trypanosoma brucei, a flagellated protozoan parasite, between life cycle stages typically occurs through an asymmetric cell division process, producing two morphologically distinct daughter cells. Conversely, proliferative cell divisions produce two daughter cells, which look similar but are not identical. To examine in detail differences between the daughter cells of a proliferative division of procyclic T. brucei we used the recently identified constituents of the flagella connector. These segregate asymmetrically during cytokinesis allowing the new‐flagellum and the old‐flagellum daughters to be distinguished. We discovered that there are distinct morphological differences between the two daughters, with the new‐flagellum daughter in particular re‐modelling rapidly and extensively in early G1. This re‐modelling process involves an increase in cell body, flagellum and flagellum attachment zone length and is accompanied by architectural changes to the anterior cell end. The old‐flagellum daughter undergoes a different G1 re‐modelling, however, despite this there was no difference in G1 duration of their respective cell cycles. This work demonstrates that the two daughters of a proliferative division of T. brucei are non‐equivalent and enables more refined morphological analysis of mutant phenotypes. We suggest all proliferative divisions in T. brucei and related organisms will involve non‐equivalence.
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Affiliation(s)
- Movin Abeywickrema
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Hana Vachova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
| | - Helen Farr
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Timm Mohr
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Richard J Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 3SY, UK
| | - De-Hua Lai
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P.R. China
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Keith Gull
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Jack D Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Vladimir Varga
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 14220, Czech Republic
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40
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Abstract
BACKGROUND Cell size is a key characteristic that significantly affects many aspects of cellular physiology. There are specific control mechanisms during cell cycle that maintain the cell size within a range from generation to generation. Such control mechanisms introduce substantial variabilities to important properties of the cell cycle such as growth and division. To quantitatively study the effect of such variability in progression through cell cycle, detailed stochastic models are required. RESULTS In this paper, a new hybrid stochastic model is proposed to study the effect of molecular noise and size control mechanism on the variabilities in cell cycle of the budding yeast Saccharomyces cerevisiae. The proposed model provides an accurate, yet computationally efficient approach for simulation of an intricate system by integrating the deterministic and stochastic simulation schemes. The developed hybrid stochastic model can successfully capture several key features of the cell cycle observed in experimental data. In particular, the proposed model: 1) confirms that the majority of noise in size control stems from low copy numbers of transcripts in the G1 phase, 2) identifies the size and time regulation modules in the size control mechanism, and 3) conforms with phenotypes of early G1 mutants in exquisite detail. CONCLUSIONS Hybrid stochastic modeling approach can be used to provide quantitative descriptions for stochastic properties of the cell cycle within a computationally efficient framework.
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Affiliation(s)
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Yang Cao
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.
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41
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Laflamme G, Sim S, Leary A, Pascariu M, Vogel J, D’Amours D. Interphase Microtubules Safeguard Mitotic Progression by Suppressing an Aurora B-Dependent Arrest Induced by DNA Replication Stress. Cell Rep 2019; 26:2875-2889.e3. [DOI: 10.1016/j.celrep.2019.02.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/21/2018] [Accepted: 02/13/2019] [Indexed: 10/27/2022] Open
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42
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Suresh S, Osmani SA. Poring over chromosomes: mitotic nuclear pore complex segregation. Curr Opin Cell Biol 2019; 58:42-49. [PMID: 30798206 DOI: 10.1016/j.ceb.2019.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/09/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023]
Abstract
Eukaryotic cells rely on flux of macromolecules between the nucleus and the cytoplasm for growth and survival. Bidirectional transport is achieved through Nuclear Pore Complexes (NPCs) embedded in the Nuclear Envelope (NE). NPC proteins perform other cellular functions during mitosis, chromatin organization, DNA repair and gene regulation. Dysregulation of NPC number, or defects in their structure and function, are linked to numerous diseases but how NPCs are faithfully inherited during mitosis is poorly understood. In this review, we discuss recent insights to mechanisms of mammalian mitotic NPC segregation and NPC assembly as well as mitotic NPC inheritance via the mitotic chromatin located NPC protein Nup2 in Aspergillus nidulans. We suggest mitotic Nup2 chromatin-based mechanisms could also operate in vertebrate cells.
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Affiliation(s)
- Subbulakshmi Suresh
- Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
| | - Stephen A Osmani
- Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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43
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Allard CAH, Decker F, Weiner OD, Toettcher JE, Graziano BR. A size-invariant bud-duration timer enables robustness in yeast cell size control. PLoS One 2018; 13:e0209301. [PMID: 30576342 PMCID: PMC6303054 DOI: 10.1371/journal.pone.0209301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022] Open
Abstract
Cell populations across nearly all forms of life generally maintain a characteristic cell type-dependent size, but how size control is achieved has been a long-standing question. The G1/S boundary of the cell cycle serves as a major point of size control, and mechanisms operating here restrict passage of cells to Start if they are too small. In contrast, it is less clear how size is regulated post-Start, during S/G2/M. To gain further insight into post-Start size control, we prepared budding yeast that can be reversibly blocked from bud initiation. While blocked, cells continue to grow isotropically, increasing their volume by more than an order of magnitude over unperturbed cells. Upon release from their block, giant mothers reenter the cell cycle and their progeny rapidly return to the original unperturbed size. We found this behavior to be consistent with a size-invariant 'timer' specifying the duration of S/G2/M. These results indicate that yeast use at least two distinct mechanisms at different cell cycle phases to ensure size homeostasis.
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Affiliation(s)
- Corey A. H. Allard
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Dept. of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Franziska Decker
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Max Planck Institute for the Physics of Complex Systems, Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden, Dresden, Germany
| | - Orion D. Weiner
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Cardiovascular Research Institute and Dept. of Biochemistry and Biophysics, UC San Francisco, San Francisco, United States of America
| | - Jared E. Toettcher
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Brian R. Graziano
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Cardiovascular Research Institute and Dept. of Biochemistry and Biophysics, UC San Francisco, San Francisco, United States of America
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44
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Aon JC, Tecson RC, Loladze V. Saccharomyces cerevisiae morphological changes and cytokinesis arrest elicited by hypoxia during scale-up for production of therapeutic recombinant proteins. Microb Cell Fact 2018; 17:195. [PMID: 30572885 PMCID: PMC6300885 DOI: 10.1186/s12934-018-1044-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/11/2018] [Indexed: 11/26/2022] Open
Abstract
Background Scaling up of bioprocesses represents a crucial step in the industrial production of biologicals. However, our knowledge about the impact of scale-up on the organism’s physiology and function is still incomplete. Our previous studies have suggested the existence of morphological changes during the scale-up of a yeast (Saccharomyces cerevisiae) fermentation process as inferred from the volume fraction occupied by yeast cells and exometabolomics analyses. In the current study, we noticed cell morphology changes during scale-up of a yeast fermentation process from bench (10 L) to industrial scale (10,000 L). We hypothesized that hypoxia observed during scale-up partially impaired the availability of N-acetyl-glucosamine, a precursor of chitin synthesis, a key polysaccharide component of yeast mother-daughter neck formation. Results Using a combination of flow cytometry with two high throughput cell imaging technologies, Vi-CELL and Flow Imaging, we found changes in the distribution of cell size and morphology as a function of process duration at the industrial scale of the production process. At the end of run, concomitantly with lowest levels of dissolved oxygen (DO), we detected an increase in cell subpopulations exhibiting low aspect ratio corresponding to morphologies exhibited by large-single-budded and multi-budded cells, reflecting incomplete cytokinesis at the M phase of the yeast mitotic cycle. Metabolomics from the intracellular milieu pointed to an impaired supply of precursors for chitin biosynthesis likely affecting the septum formation between mother and daughter and cytokinesis. Inducing hypoxia at the 10 L bench scale by varying DO levels, confirmed the existence and impact of hypoxic conditions on yeast cell size and morphology observed at the industrial scale. Conclusions We conclude that the observed increments in wet cell weight at the industrial scale correspond to morphological changes characterized by the large diameter and low aspect ratio exhibited by cell subpopulations comprising large single-budded and multi-budded cells. These changes are consistent with impairment of cytokinesis triggered by hypoxia as indicated by experiments mimicking this condition at DO 5% and 10 L scale. Mechanistically, hypoxia impairs N-acetyl-glucosamine availability, a key precursor of chitin synthesis.
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Affiliation(s)
- Juan C Aon
- Department of Microbial and Cell Culture Development, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA, 19406, USA.
| | - Ricardo C Tecson
- Department of Microbial and Cell Culture Development, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA, 19406, USA
| | - Vakhtang Loladze
- Department of Bioanalytical Sciences, Research and Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA, 19406, USA
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45
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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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46
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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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47
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Cadart C, Monnier S, Grilli J, Sáez PJ, Srivastava N, Attia R, Terriac E, Baum B, Cosentino-Lagomarsino M, Piel M. Size control in mammalian cells involves modulation of both growth rate and cell cycle duration. Nat Commun 2018; 9:3275. [PMID: 30115907 PMCID: PMC6095894 DOI: 10.1038/s41467-018-05393-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/30/2018] [Indexed: 02/04/2023] Open
Abstract
Despite decades of research, how mammalian cell size is controlled remains unclear because of the difficulty of directly measuring growth at the single-cell level. Here we report direct measurements of single-cell volumes over entire cell cycles on various mammalian cell lines and primary human cells. We find that, in a majority of cell types, the volume added across the cell cycle shows little or no correlation to cell birth size, a homeostatic behavior called "adder". This behavior involves modulation of G1 or S-G2 duration and modulation of growth rate. The precise combination of these mechanisms depends on the cell type and the growth condition. We have developed a mathematical framework to compare size homeostasis in datasets ranging from bacteria to mammalian cells. This reveals that a near-adder behavior is the most common type of size control and highlights the importance of growth rate modulation to size control in mammalian cells.
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Affiliation(s)
- Clotilde Cadart
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Sylvain Monnier
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - Jacopo Grilli
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
| | - Pablo J Sáez
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Nishit Srivastava
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Rafaele Attia
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Emmanuel Terriac
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- INM-Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, UCL, London, WC1E 6BT, UK
- Institute of Physics of Living Systems, UCL, London, WC1E 6BT, UK
| | - Marco Cosentino-Lagomarsino
- Sorbonne Universités, Université Pierre et Marie Curie, Paris, F-75005, France.
- CNRS, UMR 7238 Computational and Quantitative Biology, Paris, F-75005, France.
- FIRC Institute of Molecular Oncology (IFOM), Milan, 20139, Italy.
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France.
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France.
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48
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Martínez-Láinez JM, Moreno DF, Parisi E, Clotet J, Aldea M. Centromeric signaling proteins boost G1 cyclin degradation and modulate cell size in budding yeast. PLoS Biol 2018; 16:e2005388. [PMID: 30080861 PMCID: PMC6095599 DOI: 10.1371/journal.pbio.2005388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 08/16/2018] [Accepted: 07/20/2018] [Indexed: 11/18/2022] Open
Abstract
Cell size scales with ploidy in a great range of eukaryotes, but the underlying mechanisms remain unknown. Using various orthogonal single-cell approaches, we show that cell size increases linearly with centromere (CEN) copy number in budding yeast. This effect is due to a G1 delay mediated by increased degradation of Cln3, the most upstream G1 cyclin acting at Start, and specific centromeric signaling proteins, namely Mad3 and Bub3. Mad3 binds both Cln3 and Cdc4, the adaptor component of the Skp1/Cul1/F-box (SCF) complex that targets Cln3 for degradation, these interactions being essential for the CEN-dosage dependent effects on cell size. Our results reveal a pathway that modulates cell size as a function of CEN number, and we speculate that, in cooperation with other CEN-independent mechanisms, it could assist the cell to attain efficient mass/ploidy ratios.
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Affiliation(s)
- Joan M. Martínez-Láinez
- Institut de Biologia Molecular de Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Spain
| | - David F. Moreno
- Institut de Biologia Molecular de Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain
| | - Eva Parisi
- Institut de Biologia Molecular de Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain
| | - Josep Clotet
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Martí Aldea
- Institut de Biologia Molecular de Barcelona IBMB-CSIC, Barcelona, Catalonia, Spain
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Spain
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49
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Garmendia-Torres C, Tassy O, Matifas A, Molina N, Charvin G. Multiple inputs ensure yeast cell size homeostasis during cell cycle progression. eLife 2018; 7:34025. [PMID: 29972352 PMCID: PMC6085122 DOI: 10.7554/elife.34025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 07/01/2018] [Indexed: 12/27/2022] Open
Abstract
Coordination of cell growth with division is essential for proper cell function. In budding yeast, although some molecular mechanisms responsible for cell size control during G1 have been elucidated, the mechanism by which cell size homeostasis is established remains to be discovered. Here, we developed a new technique based on quantification of histone levels to monitor cell cycle progression in individual cells with unprecedented accuracy. Our analysis establishes the existence of a mechanism controlling bud size in G2/M that prevents premature onset of anaphase, and controls the overall size variability. While most G1 mutants do not display impaired size homeostasis, mutants in which cyclin B-Cdk regulation is altered display large size variability. Our study thus demonstrates that size homeostasis is not controlled by a G1-specific mechanism alone but is likely to be an emergent property resulting from the integration of several mechanisms that coordinate cell and bud growth with division.
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Affiliation(s)
- Cecilia Garmendia-Torres
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Olivier Tassy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Audrey Matifas
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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50
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Kumar A, Sharma P, Gomar-Alba M, Shcheprova Z, Daulny A, Sanmartín T, Matucci I, Funaya C, Beato M, Mendoza M. Daughter-cell-specific modulation of nuclear pore complexes controls cell cycle entry during asymmetric division. Nat Cell Biol 2018. [PMID: 29531309 PMCID: PMC6029668 DOI: 10.1038/s41556-018-0056-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The acquisition of cellular identity is coupled to changes in the nuclear periphery and nuclear pore complexes (NPCs). Whether and how these changes determine cell fate remains unclear. We have uncovered a mechanism regulating NPC acetylation to direct cell fate after asymmetric division in budding yeast. The lysine deacetylase Hos3 associates specifically with daughter cell NPCs during mitosis to delay cell cycle entry (Start). Hos3-dependent deacetylation of nuclear basket and central channel nucleoporins establishes daughter cell-specific nuclear accumulation of the transcriptional repressor Whi5 during anaphase and perinuclear silencing of the CLN2 gene in the following G1 phase. Hos3-dependent coordination of both events restrains Start in daughter but not in mother cells. We propose that deacetylation modulates transport-dependent and -independent functions of NPCs, leading to differential cell cycle progression in mother and daughter cells. Similar mechanisms might regulate NPC functions in specific cell types and/or cell cycle stages in multicellular organisms.
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Affiliation(s)
- Arun Kumar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Priyanka Sharma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Zhanna Shcheprova
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anne Daulny
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Trinidad Sanmartín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Matucci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Charlotta Funaya
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manuel Mendoza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France. .,Université de Strasbourg, Strasbourg, France.
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