1
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Farag N, Sacharen C, Avni L, Nachman I. Coordination between endoderm progression and mouse gastruloid elongation controls endodermal morphotype choice. Dev Cell 2024; 59:2364-2374.e4. [PMID: 38838673 DOI: 10.1016/j.devcel.2024.05.017] [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: 03/24/2023] [Revised: 09/11/2023] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Embryonic development is highly robust. Morphogenetic variability between embryos (under ideal conditions) is largely quantitative. This robustness stands in contrast to in vitro embryo-like models, which, like most organoids, can display a high degree of tissue morphogenetic variability. The source of this difference is not fully understood. We use the mouse gastruloid model to study the morphogenetic progression of definitive endoderm (DE) and its divergence. We first catalog the different morphologies and characterize their statistics. We then learn predictive models for DE morphotype based on earlier expression and morphology measurements. Finally, we analyze these models to identify key drivers of morphotype variability and devise gastruloid-specific and global interventions that can lower this variability and steer morphotype choice. In the process, we identify two types of coordination lacking in the in vitro model but required for robust gut-tube formation. This approach can help improve the quality and usability of 3D embryo-like models.
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Affiliation(s)
- Naama Farag
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Chen Sacharen
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Lara Avni
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Iftach Nachman
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel.
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2
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Xiao J, Turner JJ, Kõivomägi M, Skotheim JM. Whi5 hypo- and hyper-phosphorylation dynamics control cell-cycle entry and progression. Curr Biol 2024; 34:2434-2447.e5. [PMID: 38749424 PMCID: PMC11247822 DOI: 10.1016/j.cub.2024.04.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/18/2024] [Accepted: 04/23/2024] [Indexed: 05/28/2024]
Abstract
Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the Swi4/Swi6 (SBF) complex that promotes transcription of the cyclins CLN1 and CLN2. In late G1, Whi5 is rapidly hyper-phosphorylated by Cln1 and Cln2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5's multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on "priming" sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
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Affiliation(s)
- Jordan Xiao
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Jonathan J Turner
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD 20892, USA.
| | - Jan M Skotheim
- Department of Biology, Stanford University, 327 Campus Dr., Stanford, CA 94305, USA; Chan Zuckerberg Biohub, 499 Illinois St., San Francisco, CA 94158, USA.
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3
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Ramakanth S, Kennedy T, Yalcinkaya B, Neupane S, Tadic N, Buchler NE, Argüello-Miranda O. Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591211. [PMID: 38712227 PMCID: PMC11071524 DOI: 10.1101/2024.04.25.591211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The life cycle of biomedical and agriculturally relevant eukaryotic microorganisms involves complex transitions between proliferative and non-proliferative states such as dormancy, mating, meiosis, and cell division. New drugs, pesticides, and vaccines can be created by targeting specific life cycle stages of parasites and pathogens. However, defining the structure of a microbial life cycle often relies on partial observations that are theoretically assembled in an ideal life cycle path. To create a more quantitative approach to studying complete eukaryotic life cycles, we generated a deep learning-driven imaging framework to track microorganisms across sexually reproducing generations. Our approach combines microfluidic culturing, life cycle stage-specific segmentation of microscopy images using convolutional neural networks, and a novel cell tracking algorithm, FIEST, based on enhancing the overlap of single cell masks in consecutive images through deep learning video frame interpolation. As proof of principle, we used this approach to quantitatively image and compare cell growth and cell cycle regulation across the sexual life cycle of Saccharomyces cerevisiae . We developed a fluorescent reporter system based on a fluorescently labeled Whi5 protein, the yeast analog of mammalian Rb, and a new High-Cdk1 activity sensor, LiCHI, designed to report during DNA replication, mitosis, meiotic homologous recombination, meiosis I, and meiosis II. We found that cell growth preceded the exit from non-proliferative states such as mitotic G1, pre-meiotic G1, and the G0 spore state during germination. A decrease in the total cell concentration of Whi5 characterized the exit from non-proliferative states, which is consistent with a Whi5 dilution model. The nuclear accumulation of Whi5 was developmentally regulated, being at its highest during meiotic exit and spore formation. The temporal coordination of cell division and growth was not significantly different across three sexually reproducing generations. Our framework could be used to quantitatively characterize other single-cell eukaryotic life cycles that remain incompletely described. An off-the-shelf user interface Yeastvision provides free access to our image processing and single-cell tracking algorithms.
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4
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Huang R, Situ Q, Lei J. Dynamics of cell-type transition mediated by epigenetic modifications. J Theor Biol 2024; 577:111664. [PMID: 37977478 DOI: 10.1016/j.jtbi.2023.111664] [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: 04/15/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of the probability landscape to develop into distinct cell types. However, how adult stem cells achieve a delicate balance between self-renewal and differentiation remains unclear. We propose that random inheritance of epigenetic states plays a pivotal role in stem cell differentiation and present a hybrid model of stem cell differentiation induced by epigenetic modifications. Our comprehensive model integrates gene regulation networks, epigenetic state inheritance, and cell regeneration, encompassing multi-scale dynamics ranging from transcription regulation to cell population. Through model simulations, we demonstrate that random inheritance of epigenetic states during cell divisions can spontaneously induce cell differentiation, dedifferentiation, and transdifferentiation. Furthermore, we investigate the influences of interfering with epigenetic modifications and introducing additional transcription factors on the probabilities of dedifferentiation and transdifferentiation, revealing the underlying mechanism of cell reprogramming. This in silico model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming and offers a promising path to enhance the field of regenerative medicine.
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Affiliation(s)
- Rongsheng Huang
- School of Science, Jimei University, Xiamen, Fujian, 361021, China
| | - Qiaojun Situ
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, 100084, China
| | - Jinzhi Lei
- School of Mathematical Sciences, Center for Applied Mathematics, Tiangong University, Tianjin, 300387, China.
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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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Foltman M, Sanchez-Diaz A. TOR Complex 1: Orchestrating Nutrient Signaling and Cell Cycle Progression. Int J Mol Sci 2023; 24:15745. [PMID: 37958727 PMCID: PMC10647266 DOI: 10.3390/ijms242115745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The highly conserved TOR signaling pathway is crucial for coordinating cellular growth with the cell cycle machinery in eukaryotes. One of the two TOR complexes in budding yeast, TORC1, integrates environmental cues and promotes cell growth. While cells grow, they need to copy their chromosomes, segregate them in mitosis, divide all their components during cytokinesis, and finally physically separate mother and daughter cells to start a new cell cycle apart from each other. To maintain cell size homeostasis and chromosome stability, it is crucial that mechanisms that control growth are connected and coordinated with the cell cycle. Successive periods of high and low TORC1 activity would participate in the adequate cell cycle progression. Here, we review the known molecular mechanisms through which TORC1 regulates the cell cycle in the budding yeast Saccharomyces cerevisiae that have been extensively used as a model organism to understand the role of its mammalian ortholog, mTORC1.
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Affiliation(s)
- Magdalena Foltman
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
| | - Alberto Sanchez-Diaz
- Mechanisms and Regulation of Cell Division Research Unit, Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain
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7
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Li S, Liu Q, Wang E, Wang J. Global quantitative understanding of non-equilibrium cell fate decision-making in response to pheromone. iScience 2023; 26:107885. [PMID: 37766979 PMCID: PMC10520453 DOI: 10.1016/j.isci.2023.107885] [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: 05/23/2023] [Revised: 08/09/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-cycle arrest and polarized growth are commonly used to characterize the response of yeast to pheromone. However, the quantitative decision-making processes underlying time-dependent changes in cell fate remain unclear. In this study, we conducted single-cell level experiments to observe multidimensional responses, uncovering diverse fates of yeast cells. Multiple states are revealed, along with the kinetic switching rates and pathways among them, giving rise to a quantitative landscape of mating response. To quantify the experimentally observed cell fates, we developed a theoretical framework based on non-equilibrium landscape and flux theory. Additionally, we performed stochastic simulations of biochemical reactions to elucidate signal transduction and cell growth. Notably, our experimental findings have provided the first global quantitative evidence of the real-time synchronization between intracellular signaling, physiological growth, and morphological functions. These results validate the proposed underlying mechanism governing the emergence of multiple cell fate states. This study introduces an emerging mechanistic approach to understand non-equilibrium cell fate decision-making in response to pheromone.
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Affiliation(s)
- Sheng Li
- College of Chemistry, Jilin University, Changchun, Jilin 130012, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Qiong Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Erkang Wang
- College of Chemistry, Jilin University, Changchun, Jilin 130012, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jin Wang
- Department of Chemistry and of Physics and Astronomy, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
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8
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Irvali D, Schlottmann FP, Muralidhara P, Nadelson I, Kleemann K, Wood NE, Doncic A, Ewald JC. When yeast cells change their mind: cell cycle "Start" is reversible under starvation. EMBO J 2023; 42:e110321. [PMID: 36420556 PMCID: PMC9841329 DOI: 10.15252/embj.2021110321] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Eukaryotic cells decide in late G1 phase of the cell cycle whether to commit to another round of division. This point of cell cycle commitment is termed "Restriction Point" in mammals and "Start" in the budding yeast Saccharomyces cerevisiae. At Start, yeast cells integrate multiple signals such as pheromones and nutrients, and will not pass Start if nutrients are lacking. However, how cells respond to nutrient depletion after the Start decision remains poorly understood. Here, we analyze how post-Start cells respond to nutrient depletion, by monitoring Whi5, the cell cycle inhibitor whose export from the nucleus determines Start. Surprisingly, we find that cells that have passed Start can re-import Whi5 into the nucleus. In these cells, the positive feedback loop activating G1/S transcription is interrupted, and the Whi5 repressor re-binds DNA. Cells which re-import Whi5 become again sensitive to mating pheromone, like pre-Start cells, and CDK activation can occur a second time upon replenishment of nutrients. These results demonstrate that upon starvation, the commitment decision at Start can be reversed. We therefore propose that cell cycle commitment in yeast is a multi-step process, similar to what has been suggested for mammalian cells.
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Affiliation(s)
- Deniz Irvali
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Fabian P Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | | | - Iliya Nadelson
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Katja Kleemann
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - N Ezgi Wood
- The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Doncic
- The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer C Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen, Germany
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9
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Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
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Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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10
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Schmoller KM, Lanz MC, Kim J, Koivomagi M, Qu Y, Tang C, Kukhtevich IV, Schneider R, Rudolf F, Moreno DF, Aldea M, Lucena R, Skotheim JM. Whi5 is diluted and protein synthesis does not dramatically increase in pre- Start G1. Mol Biol Cell 2022; 33:lt1. [PMID: 35482510 PMCID: PMC9282012 DOI: 10.1091/mbc.e21-01-0029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Michael C Lanz
- Department of Biology, Stanford University, Stanford CA 94305
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford CA 94305
| | - Mardo Koivomagi
- Department of Biology, Stanford University, Stanford CA 94305
| | - Yimiao Qu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Igor V Kukhtevich
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Germany
| | - Fabian Rudolf
- D-BSSE, ETH Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - David F Moreno
- Molecular Biology Institute of Barcelona, CSIC, Catalonia, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona, CSIC, Catalonia, Spain
| | - Rafael Lucena
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford CA 94305
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11
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Belanger KD, Yewdell WT, Barber MF, Russo AN, Pettit MA, Damuth EK, Hussain N, Geier SJ, Belanger KG. Exportin Crm1 is important for Swi6 nuclear shuttling and MBF transcription activation in Saccharomyces cerevisiae. BMC Mol Cell Biol 2022; 23:10. [PMID: 35189816 PMCID: PMC8862259 DOI: 10.1186/s12860-022-00409-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/07/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Swi6 acts as a transcription factor in budding yeast, functioning in two different heterodimeric complexes, SBF and MBF, that activate the expression of distinct but overlapping sets of genes. Swi6 undergoes regulated changes in nucleocytoplasmic localization throughout the cell cycle that correlate with changes in gene expression. This study investigates how nucleocytoplasmic transport by multiple transport factors may influence specific Swi6 activities. RESULTS Here we show that the exportin Crm1 is important for Swi6 nuclear export and activity. Loss of a putative Crm1 NES or inhibition of Crm1 activity results in changes in nucleocytoplasmic Swi6 localization. Alteration of the Crm1 NES in Swi6 results in decreased MBF-mediated gene expression, but does not affect SBF reporter expression, suggesting that export of Swi6 by Crm1 regulates a subset of Swi6 transcription activation activity. Finally, alteration of the putative Crm1 NES in Swi6 results in cells that are larger than wild type, and this increase in cell size is exacerbated by deletion of Msn5. CONCLUSIONS These data provide evidence that Swi6 has at least two different exportins, Crm1 and Msn5, each of which interacts with a distinct nuclear export signal. We identify a putative nuclear export signal for Crm1 within Swi6, and observe that export by Crm1 or Msn5 independently influences Swi6-regulated expression of a different subset of Swi6-controlled genes. These findings provide new insights into the complex regulation of Swi6 transcription activation activity and the role of nucleocytoplasmic shuttling in regulated gene expression.
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Affiliation(s)
| | - William T. Yewdell
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Matthew F. Barber
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: Department of Biology, University of Oregon, Eugene, OR USA
| | - Amy N. Russo
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: The Estée Lauder Companies, Inc., Mellville, NY USA
| | - Mark A. Pettit
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: Department of Emergency Medicine, Rochester General Hospital, Rochester, NY USA
| | - Emily K. Damuth
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: Department of Emergency Medicine, Cooper University Health Care, Camden, NJ USA
| | - Naveen Hussain
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: Kerry’s Place Autism Services, Aurora, ON Canada
| | - Susan J. Geier
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: Department of Chemistry, Colgate University, Hamilton, NY USA
| | - Karyn G. Belanger
- Department of Biology, Colgate University, Hamilton, NY USA
- Present Address: Center for Learning, Teaching, and Research, Colgate University, Hamilton, NY USA
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12
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Philip J, Örd M, Silva A, Singh S, Diffley JFX, Remus D, Loog M, Ikui AE. Cdc6 is sequentially regulated by PP2A-Cdc55, Cdc14, and Sic1 for origin licensing in S. cerevisiae. eLife 2022; 11:e74437. [PMID: 35142288 PMCID: PMC8830886 DOI: 10.7554/elife.74437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/15/2021] [Indexed: 01/31/2023] Open
Abstract
Cdc6, a subunit of the pre-replicative complex (pre-RC), contains multiple regulatory cyclin-dependent kinase (Cdk1) consensus sites, SP or TP motifs. In Saccharomyces cerevisiae, Cdk1 phosphorylates Cdc6-T7 to recruit Cks1, the Cdk1 phospho-adaptor in S phase, for subsequent multisite phosphorylation and protein degradation. Cdc6 accumulates in mitosis and is tightly bound by Clb2 through N-terminal phosphorylation in order to prevent premature origin licensing and degradation. It has been extensively studied how Cdc6 phosphorylation is regulated by the cyclin-Cdk1 complex. However, a detailed mechanism on how Cdc6 phosphorylation is reversed by phosphatases has not been elucidated. Here, we show that PP2ACdc55 dephosphorylates Cdc6 N-terminal sites to release Clb2. Cdc14 dephosphorylates the C-terminal phospho-degron, leading to Cdc6 stabilization in mitosis. In addition, Cdk1 inhibitor Sic1 releases Clb2·Cdk1·Cks1 from Cdc6 to load Mcm2-7 on the chromatin upon mitotic exit. Thus, pre-RC assembly and origin licensing are promoted by phosphatases through the attenuation of distinct Cdk1-dependent Cdc6 inhibitory mechanisms.
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Affiliation(s)
- Jasmin Philip
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
| | | | - Andriele Silva
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
| | - Shaneen Singh
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
| | | | - Dirk Remus
- Memorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | | | - Amy E Ikui
- The PhD Program in Biochemistry, The Graduate Center, CUNYBrooklynUnited States
- Brooklyn CollegeBrooklynUnited States
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13
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Lv M, Xu Q, Zhang B, Yang Z, Xie J, Guo J, He F, Wang W. Imperatorin induces autophagy and G0/G1 phase arrest via PTEN-PI3K-AKT-mTOR/p21 signaling pathway in human osteosarcoma cells in vitro and in vivo. Cancer Cell Int 2021; 21:689. [PMID: 34923996 PMCID: PMC8684670 DOI: 10.1186/s12935-021-02397-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Osteosarcoma is the third most common cancer in adolescence and the first common primary malignant tumor of bone. The long-term prognosis of osteosarcoma still remains unsatisfactory in the past decades. Therefore, development of novel therapeutic agents which are effective to osteosarcoma and are safe to normal tissue simultaneously is quite essential and urgent. METHODS Firstly, MTT assay, cell colony formation assay, cell migration and invasion assays were conducted to evaluate the inhibitory effects of imperatorin towards human osteosarcoma cells. RNA-sequence assay and bioinformatic analysis were then performed to filtrate and assume the potential imperatorin-induced cell death route and signaling pathway. Moreover, quantitative real-time PCR assay, western blot assay and rescue experiments were conducted to confirm the assumptions of bioinformatic analysis. Finally, a subcutaneous tumor-transplanted nude mouse model was established and applied to evaluate the internal effect of imperatorin on osteosarcoma by HE and immunohistochemistry staining. RESULTS Imperatorin triggered time-dependent and dose-dependent inhibition of tumor growth mainly by inducing autophagy promotion and G0/G1 phase arrest in vitro and in vivo. Besides, imperatorin treatment elevated the expression level of PTEN and p21, down-regulated the phosphorylation of AKT and mTOR. In contrast, the inhibition of PTEN using Bpv (HOpic), a potential and selective inhibitor of PTEN, concurrently rescued imperatorin-induced autophagy promotion, cell cycle arrest and inactivation of PTEN-PI3K-AKT-mTOR/p21 pathway. CONCLUSIONS This work firstly revealed that imperatorin induced autophagy and cell cycle arrest through PTEN-PI3K-AKT-mTOR/p21 signaling pathway by targeting and up-regulating PTEN in human osteosarcoma cells. Hence, imperatorin is a desirable candidate for clinical treatments of osteosarcoma.
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Affiliation(s)
- Minchao Lv
- Department of Orthopedics, Quzhou People's Hospital, The Quzhou Affiliated Hospital of Wenzhou Medical University, No.100, Minjiang Avenue, Quzhou, Zhejiang, China
| | - Qingxin Xu
- Department of Clinical Medicine, Second Clinical Medical College, Wenzhou Medical University, Chashan Educational District, Wenzhou, Zhejiang, China
| | - Bei Zhang
- First Clinical Medicine College, Zhejiang Chinese Medical University, No. 548, Bingwen Road, Hangzhou, Zhejiang, China
| | - Zhiqiang Yang
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuhan, Hubei, China
| | - Jun Xie
- Department of Orthopedics, Quzhou People's Hospital, The Quzhou Affiliated Hospital of Wenzhou Medical University, No.100, Minjiang Avenue, Quzhou, Zhejiang, China
| | - Jinku Guo
- Department of Orthopedics, Quzhou People's Hospital, The Quzhou Affiliated Hospital of Wenzhou Medical University, No.100, Minjiang Avenue, Quzhou, Zhejiang, China
| | - Feixiong He
- Department of Orthopedics, Quzhou People's Hospital, The Quzhou Affiliated Hospital of Wenzhou Medical University, No.100, Minjiang Avenue, Quzhou, Zhejiang, China.
| | - Wei Wang
- Department of Orthopedics, Quzhou People's Hospital, The Quzhou Affiliated Hospital of Wenzhou Medical University, No.100, Minjiang Avenue, Quzhou, Zhejiang, China.
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14
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Swaffer MP, Kim J, Chandler-Brown D, Langhinrichs M, Marinov GK, Greenleaf WJ, Kundaje A, Schmoller KM, Skotheim JM. Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size. Mol Cell 2021; 81:4861-4875.e7. [PMID: 34731644 PMCID: PMC8642314 DOI: 10.1016/j.molcel.2021.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/01/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
Abstract
Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 "sub-scales" with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that transcriptional control uncouples Whi5 synthesis from cell size, and we identify histones as the major class of sub-scaling transcripts besides WHI5 by screening for similar genes. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to newborn cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each newborn cell regardless of cell size. Disrupting both Whi5 synthesis and chromatin-based partitioning weakens G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.
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Affiliation(s)
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kurt M Schmoller
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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15
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Docking to a Basic Helix Promotes Specific Phosphorylation by G1-Cdk1. Int J Mol Sci 2021; 22:ijms22179514. [PMID: 34502421 PMCID: PMC8431026 DOI: 10.3390/ijms22179514] [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: 07/13/2021] [Revised: 08/02/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022] Open
Abstract
Cyclins are the activators of cyclin-dependent kinase (CDK) complex, but they also act as docking scaffolds for different short linear motifs (SLiMs) in CDK substrates and inhibitors. According to the unified model of CDK function, the cell cycle is coordinated by CDK both via general CDK activity thresholds and cyclin-specific substrate docking. Recently, it was found that the G1-cyclins of S. cerevisiae have a specific function in promoting polarization and growth of the buds, making the G1 cyclins essential for cell survival. Thus, while a uniform CDK specificity of a single cyclin can be sufficient to drive the cell cycle in some cells, such as in fission yeast, cyclin specificity can be essential in other organisms. However, the known G1-CDK specific LP docking motif, was not responsible for this essential function, indicating that G1-CDKs use yet other unknown docking mechanisms. Here we report a discovery of a G1 cyclin-specific (Cln1,2) lysine-arginine-rich helical docking motif (the K/R motif) in G1-CDK targets involved in the mating pathway (Ste7), transcription (Xbp1), bud morphogenesis (Bud2) and spindle pole body (Spc29, Spc42, Spc110, Sli15) function of S. cerevisiae. We also show that the docking efficiency of K/R motif can be regulated by basophilic kinases such as protein kinase A. Our results further widen the list of cyclin specificity mechanisms and may explain the recently demonstrated unique essential function of G1 cyclins in budding yeast.
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16
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Matos GS, Madeira JB, Fernandes CM, Dasilva D, Masuda CA, Del Poeta M, Montero-Lomelí M. Regulation of sphingolipid synthesis by the G1/S transcription factor Swi4. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158983. [PMID: 34062255 PMCID: PMC8512607 DOI: 10.1016/j.bbalip.2021.158983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/23/2022]
Abstract
SBF (Swi4/Swi6 Binding Factor) complex is a crucial regulator of G1/S transition in Saccharomyces cerevisiae. Here, we show that SBF complex is required for myriocin resistance, an inhibitor of sphingolipid synthesis. This phenotype was not shared with MBF complex mutants nor with deletion of the Swi4p downstream targets, CLN1/CLN2. Based on data mining results, we selected putative Swi4p targets related to sphingolipid metabolism and studied their gene transcription as well as metabolite levels during progression of the cell cycle. Genes which encode key enzymes for the synthesis of long chain bases (LCBs) and ceramides were periodically transcribed during the mitotic cell cycle, having a peak at G1/S, and required SWI4 for full transcription at this stage. In addition, HPLC-MS/MS data indicated that swi4Δ cells have decreased levels of sphingolipids during progression of the cell cycle, particularly, dihydrosphingosine (DHS), C24-phytoceramides and C24-inositolphosphoryl ceramide (IPC) while it had increased levels of mannosylinositol phosphorylceramide (MIPC). Furthermore, we demonstrated that both inhibition of de novo sphingolipid synthesis by myriocin or SWI4 deletion caused partial arrest at the G2/M phase. Importantly, our lipidomic data demonstrated that the sphingolipid profile of WT cells treated with myriocin resembled that of swi4Δ cells, with lower levels of DHS, IPC and higher levels of MIPC. Taken together, these results show that SBF complex plays an essential role in the regulation of sphingolipid homeostasis, which reflects in the correct progression through the G2/M phase of the cell cycle.
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Affiliation(s)
- Gabriel S Matos
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana B Madeira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Deveney Dasilva
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Claudio A Masuda
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA; Veteran Administration Medical Center, Northport, NY, USA; MicroRid Technologies Inc., Dix Hills, NY, USA; Division of Infectious Diseases, School of Medicine, Stony Brook University, NY, USA
| | - Monica Montero-Lomelí
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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17
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Chiou JG, Moran KD, Lew DJ. How cells determine the number of polarity sites. eLife 2021; 10:e58768. [PMID: 33899733 PMCID: PMC8116050 DOI: 10.7554/elife.58768] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 04/23/2021] [Indexed: 12/15/2022] Open
Abstract
The diversity of cell morphologies arises, in part, through regulation of cell polarity by Rho-family GTPases. A poorly understood but fundamental question concerns the regulatory mechanisms by which different cells generate different numbers of polarity sites. Mass-conserved activator-substrate (MCAS) models that describe polarity circuits develop multiple initial polarity sites, but then those sites engage in competition, leaving a single winner. Theoretical analyses predicted that competition would slow dramatically as GTPase concentrations at different polarity sites increase toward a 'saturation point', allowing polarity sites to coexist. Here, we test this prediction using budding yeast cells, and confirm that increasing the amount of key polarity proteins results in multiple polarity sites and simultaneous budding. Further, we elucidate a novel design principle whereby cells can switch from competition to equalization among polarity sites. These findings provide insight into how cells with diverse morphologies may determine the number of polarity sites.
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Affiliation(s)
- Jian-geng Chiou
- Department of Pharmacology and Cancer Biology, Duke University Medical CenterDurhamUnited States
| | - Kyle D Moran
- Department of Pharmacology and Cancer Biology, Duke University Medical CenterDurhamUnited States
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University Medical CenterDurhamUnited States
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18
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Clark-Cotton MR, Henderson NT, Pablo M, Ghose D, Elston TC, Lew DJ. Exploratory polarization facilitates mating partner selection in Saccharomyces cerevisiae. Mol Biol Cell 2021; 32:1048-1063. [PMID: 33689470 PMCID: PMC8101489 DOI: 10.1091/mbc.e21-02-0068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Yeast decode pheromone gradients to locate mating partners, providing a model for chemotropism. How yeast polarize toward a single partner in crowded environments is unclear. Initially, cells often polarize in unproductive directions, but then they relocate the polarity site until two partners’ polarity sites align, whereupon the cells “commit” to each other by stabilizing polarity to promote fusion. Here we address the role of the early mobile polarity sites. We found that commitment by either partner failed if just one partner was defective in generating, orienting, or stabilizing its mobile polarity sites. Mobile polarity sites were enriched for pheromone receptors and G proteins, and we suggest that such sites engage in an exploratory search of the local pheromone landscape, stabilizing only when they detect elevated pheromone levels. Mobile polarity sites were also enriched for pheromone secretion factors, and simulations suggest that only focal secretion at polarity sites would produce high pheromone concentrations at the partner’s polarity site, triggering commitment.
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Affiliation(s)
| | - Nicholas T Henderson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Michael Pablo
- Department of Chemistry, Chapel Hill, NC 27599.,Program in Molecular and Cellular Biophysics, Chapel Hill, NC 27599
| | - Debraj Ghose
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
| | - Timothy C Elston
- Department of Pharmacology and Computational Medicine Program, UNC Chapel Hill, Chapel Hill, NC 27599
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708
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19
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Nutrient Signaling, Stress Response, and Inter-organelle Communication Are Non-canonical Determinants of Cell Fate. Cell Rep 2020; 33:108446. [PMID: 33264609 PMCID: PMC9744185 DOI: 10.1016/j.celrep.2020.108446] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/06/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022] Open
Abstract
Isogenic cells manifest distinct cellular fates for a single stress; however, the nongenetic mechanisms driving such fates remain poorly understood. Here, we implement a robust multi-channel live-cell imaging approach to uncover noncanonical factors governing cell fate. We show that in response to acute glucose removal (AGR), budding yeast undergoes distinct fates, becoming either quiescent or senescent. Senescent cells fail to resume mitotic cycles following glucose replenishment but remain responsive to nutrient stimuli. Whereas quiescent cells manifest starvation-induced adaptation, senescent cells display perturbed endomembrane trafficking and defective nucleus-vacuole junction (NVJ) expansion. Surprisingly, senescence occurs even in the absence of lipid droplets. Importantly, we identify the nutrient-sensing kinase Rim15 as a key biomarker predicting cell fates before AGR stress. We propose that isogenic yeast challenged with acute nutrient shortage contains determinants influencing post-stress fate and demonstrate that specific nutrient signaling, stress response, trafficking, and inter-organelle biomarkers are early indicators for long-term fate outcomes.
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20
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The Path towards Predicting Evolution as Illustrated in Yeast Cell Polarity. Cells 2020; 9:cells9122534. [PMID: 33255231 PMCID: PMC7760196 DOI: 10.3390/cells9122534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 01/14/2023] Open
Abstract
A bottom-up route towards predicting evolution relies on a deep understanding of the complex network that proteins form inside cells. In a rapidly expanding panorama of experimental possibilities, the most difficult question is how to conceptually approach the disentangling of such complex networks. These can exhibit varying degrees of hierarchy and modularity, which obfuscate certain protein functions that may prove pivotal for adaptation. Using the well-established polarity network in budding yeast as a case study, we first organize current literature to highlight protein entrenchments inside polarity. Following three examples, we see how alternating between experimental novelties and subsequent emerging design strategies can construct a layered understanding, potent enough to reveal evolutionary targets. We show that if you want to understand a cell’s evolutionary capacity, such as possible future evolutionary paths, seemingly unimportant proteins need to be mapped and studied. Finally, we generalize this research structure to be applicable to other systems of interest.
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21
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Faustova I, Bulatovic L, Matiyevskaya F, Valk E, Örd M, Loog M. A new linear cyclin docking motif that mediates exclusively S-phase CDK-specific signaling. EMBO J 2020; 40:e105839. [PMID: 33210757 PMCID: PMC7809796 DOI: 10.15252/embj.2020105839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/23/2020] [Accepted: 10/13/2020] [Indexed: 01/20/2023] Open
Abstract
Cyclin‐dependent kinases (CDKs), the master regulators of cell division, are activated by different cyclins at different cell cycle stages. In addition to being activators of CDKs, cyclins recognize various linear motifs to target CDK activity to specific proteins. We uncovered a cyclin docking motif, NLxxxL, that contributes to phosphorylation‐dependent degradation of the CDK inhibitor Far1 at the G1/S stage in the yeast Saccharomyces cerevisiae. This motif is recognized exclusively by S‐phase CDK (S‐CDK) Clb5/6‐Cdc28 and is considerably more potent than the conventional RxL docking motif. The NLxxxL and RxL motifs were found to overlap in some target proteins, suggesting that cyclin docking motifs can evolve to switch from one to another for fine‐tuning of cell cycle events. Using time‐lapse fluorescence microscopy, we show how different docking connections temporally control phosphorylation‐driven target degradation. This also revealed a differential function of the phosphoadaptor protein Cks1, as Cks1 docking potentiated degron phosphorylation of RxL‐containing but not of NLxxxL‐containing substrates. The NLxxxL motif was found to govern S‐cyclin‐specificity in multiple yeast CDK targets including Fin1, Lif1, and Slx4, suggesting its wider importance.
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Affiliation(s)
- Ilona Faustova
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Luka Bulatovic
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Ervin Valk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
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22
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Young TZ, Liu P, Urbonaite G, Acar M. Quantitative Insights into Age-Associated DNA-Repair Inefficiency in Single Cells. Cell Rep 2020; 28:2220-2230.e7. [PMID: 31433994 PMCID: PMC6744837 DOI: 10.1016/j.celrep.2019.07.082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/02/2019] [Accepted: 07/23/2019] [Indexed: 01/03/2023] Open
Abstract
Although double-strand break (DSB) repair is essential for a cell's survival, little is known about how DSB repair mechanisms are affected by age. Here we characterize the impact of cellular aging on the efficiency of single-strand annealing (SSA), a DSB repair mechanism. We measure SSA repair efficiency in young and old yeast cells and report a 23.4% decline in repair efficiency. This decline is not due to increased use of non-homologous end joining. Instead, we identify increased G1 phase duration in old cells as a factor responsible for the decreased SSA repair efficiency. Expression of 3xCLN2 leads to higher SSA repair efficiency in old cells compared with expression of 1xCLN2, confirming the involvement of cell-cycle regulation in age-associated repair inefficiency. Examining how SSA repair efficiency is affected by sequence heterology, we find that heteroduplex rejection remains high in old cells. Our work provides insights into the links between single-cell aging and DSB repair efficiency.
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Affiliation(s)
- Thomas Z Young
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Ping Liu
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Guste Urbonaite
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA.
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23
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Abstract
The Rho GTPase Cdc42 is a central regulator of cell polarity in diverse cell types. The activity of Cdc42 is dynamically controlled in time and space to enable distinct polarization events, which generally occur along a single axis in response to spatial cues. Our understanding of the mechanisms underlying Cdc42 polarization has benefited largely from studies of the budding yeast Saccharomyces cerevisiae, a genetically tractable model organism. In budding yeast, Cdc42 activation occurs in two temporal steps in the G1 phase of the cell cycle to establish a proper growth site. Here, we review findings in budding yeast that reveal an intricate crosstalk among polarity proteins for biphasic Cdc42 regulation. The first step of Cdc42 activation may determine the axis of cell polarity, while the second step ensures robust Cdc42 polarization for growth. Biphasic Cdc42 polarization is likely to ensure the proper timing of events including the assembly and recognition of spatial landmarks and stepwise assembly of a new ring of septins, cytoskeletal GTP-binding proteins, at the incipient bud site. Biphasic activation of GTPases has also been observed in mammalian cells, suggesting that biphasic activation could be a general mechanism for signal-responsive cell polarization. Cdc42 activity is necessary for polarity establishment during normal cell division and development, but its activity has also been implicated in the promotion of aging. We also discuss negative polarity signaling and emerging concepts of Cdc42 signaling in cellular aging.
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Affiliation(s)
- Kristi E Miller
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210.,Present address: Department of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Pil Jung Kang
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Hay-Oak Park
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
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24
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Effects of 5'-3' Exonuclease Xrn1 on Cell Size, Proliferation and Division, and mRNA Levels of Periodic Genes in Cryptococcus neoformans. Genes (Basel) 2020; 11:genes11040430. [PMID: 32316250 PMCID: PMC7230856 DOI: 10.3390/genes11040430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 11/17/2022] Open
Abstract
Cell size affects almost all biosynthetic processes by controlling the size of organelles and disrupting the nutrient uptake process. Yeast cells must reach a critical size to be able to enter a new cell cycle stage. Abnormal changes in cell size are often observed under pathological conditions such as cancer disease. Thus, cell size must be strictly controlled during cell cycle progression. Here, we reported that the highly conserved 5′-3′ exonuclease Xrn1 could regulate the gene expression involved in the cell cycle pathway of Cryptococcus neoformans. Chromosomal deletion of XRN1 caused an increase in cell size, defects in cell growth and altered DNA content at 37 °C. RNA-sequencing results showed that the difference was significantly enriched in genes involved in membrane components, DNA metabolism, integration and recombination, DNA polymerase activity, meiotic cell cycle, nuclear division, organelle fission, microtubule-based process and reproduction. In addition, the proportion of the differentially expressed periodic genes was up to 19.8% when XRN1 was deleted, including cell cycle-related genes, chitin synthase genes and transcription factors, indicating the important role of Xrn1 in the control of cell cycle. This work provides insights into the roles of RNA decay factor Xrn1 in maintaining appropriate cell size, DNA content and cell cycle progression.
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25
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A processive phosphorylation circuit with multiple kinase inputs and mutually diversional routes controls G1/S decision. Nat Commun 2020; 11:1836. [PMID: 32296067 PMCID: PMC7160111 DOI: 10.1038/s41467-020-15685-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/23/2020] [Indexed: 12/14/2022] Open
Abstract
Studies on multisite phosphorylation networks of cyclin-dependent kinase (CDK) targets have opened a new level of signaling complexity by revealing signal processing routes encoded into disordered proteins. A model target, the CDK inhibitor Sic1, contains linear phosphorylation motifs, docking sites, and phosphodegrons to empower an N-to-C terminally directed phosphorylation process. Here, we uncover a signal processing mechanism involving multi-step competition between mutually diversional phosphorylation routes within the S-CDK-Sic1 inhibitory complex. Intracomplex phosphorylation plays a direct role in controlling Sic1 degradation, and provides a mechanism to sequentially integrate both the G1- and S-CDK activities while keeping S-CDK inhibited towards other targets. The competing phosphorylation routes prevent premature Sic1 degradation and demonstrate how integration of MAPK from the pheromone pathway allows one to tune the competition of alternative phosphorylation paths. The mutually diversional phosphorylation circuits may be a general way for processing multiple kinase signals to coordinate cellular decisions in eukaryotes. The decision of whether and when a cell divides is tightly controlled. Here, the authors show in yeast that there is a multi-step competition between different phosphorylation states and sites in the S phase CDK-Sic1 complex, which controls Sic1 degradation and coordinates the precise timing of the G1/S transition.
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26
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Berenson DF, Zatulovskiy E, Xie S, Skotheim JM. Constitutive expression of a fluorescent protein reports the size of live human cells. Mol Biol Cell 2019; 30:2985-2995. [PMID: 31599704 PMCID: PMC6857566 DOI: 10.1091/mbc.e19-03-0171] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/11/2022] Open
Abstract
Cell size is important for cell physiology because it sets the geometric scale of organelles and biosynthesis. A number of methods exist to measure different aspects of cell size, but each has significant drawbacks. Here, we present an alternative method to measure the size of single human cells using a nuclear localized fluorescent protein expressed from a constitutive promoter. We validate this method by comparing it to several established cell size measurement strategies, including flow cytometry optical scatter, total protein dyes, and quantitative phase microscopy. We directly compare our fluorescent protein measurement with the commonly used measurement of nuclear volume and show that our measurements are more robust and less dependent on image segmentation. We apply our method to examine how cell size impacts the cell division cycle and reaffirm that there is a negative correlation between size at cell birth and G1 duration. Importantly, combining our size reporter with fluorescent labeling of a different protein in a different color channel allows measurement of concentration dynamics using simple wide-field fluorescence imaging. Thus, we expect our method will be of use to researchers interested in how dynamically changing protein concentrations control cell fates.
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Affiliation(s)
| | | | - Shicong Xie
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305
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27
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Sloin H, Stark E. Response and sample bridging in a primate short-term memory task. Neurobiol Learn Mem 2019; 166:107106. [PMID: 31705981 DOI: 10.1016/j.nlm.2019.107106] [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: 01/28/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 11/26/2022]
Abstract
Freely-moving rodents can solve short-term memory (STM) tasks using "response bridging" strategies, relying on motor patterns instead of mnemonic functions. This limits the interpretational power of results yielded by some STM tasks in rodents. To determine whether head-fixed monkeys can employ parallel non-mnemonic strategies, we measured eye position and velocity of two head-fixed monkeys performing a delayed response reaching and grasping task. We found that eye position during the delay period was correlated with reach direction. Moreover, reach direction as well as grasp object could be predicted from eye kinematics during the delay. Both eye velocity and eye position contributed to the prediction of reach direction. These results show that motor signals carry sufficient information to allow monkeys to solve STM tasks without using any mnemonic functions. Thus, the potential of animals to solve STM tasks using motor patterns is more diverse than previously recognized.
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Affiliation(s)
- Hadas Sloin
- Sagol School of Neuroscience and Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eran Stark
- Sagol School of Neuroscience and Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
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28
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Litsios A, Huberts DHEW, Terpstra HM, Guerra P, Schmidt A, Buczak K, Papagiannakis A, Rovetta M, Hekelaar J, Hubmann G, Exterkate M, Milias-Argeitis A, Heinemann M. Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast. Nat Cell Biol 2019; 21:1382-1392. [PMID: 31685990 DOI: 10.1038/s41556-019-0413-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 09/25/2019] [Indexed: 12/28/2022]
Abstract
In the unicellular eukaryote Saccharomyces cerevisiae, Cln3-cyclin-dependent kinase activity enables Start, the irreversible commitment to the cell division cycle. However, the concentration of Cln3 has been paradoxically considered to remain constant during G1, due to the presumed scaling of its production rate with cell size dynamics. Measuring metabolic and biosynthetic activity during cell cycle progression in single cells, we found that cells exhibit pulses in their protein production rate. Rather than scaling with cell size dynamics, these pulses follow the intrinsic metabolic dynamics, peaking around Start. Using a viral-based bicistronic construct and targeted proteomics to measure Cln3 at the single-cell and population levels, we show that the differential scaling between protein production and cell size leads to a temporal increase in Cln3 concentration, and passage through Start. This differential scaling causes Start in both daughter and mother cells across growth conditions. Thus, uncoupling between two fundamental physiological parameters drives cell cycle commitment.
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Affiliation(s)
- Athanasios Litsios
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Daphne H E W Huberts
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hanna M Terpstra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Mattia Rovetta
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Johan Hekelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Georg Hubmann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Department of Biology, Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Heverlee, Belgium
| | - Marten Exterkate
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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29
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Miller KE, Lo WC, Chou CS, Park HO. Temporal regulation of cell polarity via the interaction of the Ras GTPase Rsr1 and the scaffold protein Bem1. Mol Biol Cell 2019; 30:2543-2557. [PMID: 31411940 PMCID: PMC6740199 DOI: 10.1091/mbc.e19-02-0106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The Cdc42 guanosine triphosphatase (GTPase) plays a central role in polarity development in species ranging from yeast to humans. In budding yeast, a specific growth site is selected in the G1 phase. Rsr1, a Ras GTPase, interacts with Cdc42 and its associated proteins to promote polarized growth at the proper bud site. Yet how Rsr1 regulates cell polarization is not fully understood. Here, we show that Rsr1-GDP interacts with the scaffold protein Bem1 in early G1, likely hindering the role of Bem1 in Cdc42 polarization and polarized secretion. Consistent with these in vivo observations, mathematical modeling predicts that Bem1 is unable to promote Cdc42 polarization in early G1 in the presence of Rsr1-GDP. We find that a part of the Bem1 Phox homology domain, which overlaps with a region interacting with the exocyst component Exo70, is necessary for the association of Bem1 with Rsr1-GDP. Overexpression of the GDP-locked Rsr1 interferes with Bem1-dependent Exo70 polarization. We thus propose that Rsr1 functions in spatial and temporal regulation of polarity establishment by associating with distinct polarity factors in its GTP- and GDP-bound states.
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Affiliation(s)
- Kristi E Miller
- Molecular Cellular Developmental Biology Program, The Ohio State University, Columbus, OH 43210
| | - Wing-Cheong Lo
- Department of Mathematics, City University of Hong Kong, Kowloon, Hong Kong
| | - Ching-Shan Chou
- Department of Mathematics, The Ohio State University, Columbus, OH 43210
| | - Hay-Oak Park
- Molecular Cellular Developmental Biology Program, The Ohio State University, Columbus, OH 43210.,Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
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30
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Abstract
The quantitative model of cyclin-dependent kinase (CDK) function states that cyclins temporally order cell cycle events at different CDK activity levels, or thresholds. The model lacks a mechanistic explanation, as it is not understood how different thresholds are encoded into substrates. We show that a multisite phosphorylation code governs the phosphorylation of CDK targets and that phosphorylation clusters act as timing tags that trigger specific events at different CDK thresholds. Using phospho-degradable CDK threshold sensors with rationally encoded phosphorylation patterns, we were able to predictably program thresholds over the entire range of the Saccharomyces cerevisiae cell cycle. We defined three levels of CDK multisite phosphorylation encoding: (i) Ser-Thr swapping in phosphorylation sites, (ii) patterning of phosphorylation sites, and (iii) cyclin-specific docking combined with modulation of CDK activity. Thus, CDK can signal via hundreds of differentially encoded targets at precise times to provide a temporally ordered phosphorylation pattern required for cell division.
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31
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Bállega E, Carballar R, Samper B, Ricco N, Ribeiro MP, Bru S, Jiménez J, Clotet J. Comprehensive and quantitative analysis of G1 cyclins. A tool for studying the cell cycle. PLoS One 2019; 14:e0218531. [PMID: 31237904 PMCID: PMC6592645 DOI: 10.1371/journal.pone.0218531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
In eukaryotes, the cell cycle is driven by the actions of several cyclin dependent kinases (CDKs) and an array of regulatory proteins called cyclins, due to the cyclical expression patterns of the latter. In yeast, the accepted pattern of cyclin waves is based on qualitative studies performed by different laboratories using different strain backgrounds, different growing conditions and media, and different kinds of genetic manipulation. Additionally, only the subset of cyclins regulating Cdc28 was included, while the Pho85 cyclins were excluded. We describe a comprehensive, quantitative and accurate blueprint of G1 cyclins in the yeast Saccharomyces cerevisiae that, in addition to validating previous conclusions, yields new findings and establishes an accurate G1 cyclin blueprint. For the purposes of this research, we produced a collection of strains with all G1 cyclins identically tagged using the same and most respectful procedure possible. We report the contribution of each G1 cyclin for a broad array of growing and stress conditions, describe an unknown role for Pcl2 in heat-stress conditions and demonstrate the importance of maintaining the 3’UTR sequence of cyclins untouched during the tagging process.
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Affiliation(s)
- Elisabet Bállega
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Reyes Carballar
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Bàrbara Samper
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Natalia Ricco
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariana P. Ribeiro
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Samuel Bru
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Javier Jiménez
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
- * E-mail: (JJ); (JC)
| | - Josep Clotet
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
- * E-mail: (JJ); (JC)
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32
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A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle. Sci Rep 2019; 9:3343. [PMID: 30833602 PMCID: PMC6399449 DOI: 10.1038/s41598-019-39850-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022] Open
Abstract
Oscillating gene expression is crucial for correct timing and progression through cell cycle. In Saccharomyces cerevisiae, G1 cyclins Cln1-3 are essential drivers of the cell cycle and have an important role for temporal fine-tuning. We measured time-resolved transcriptome-wide gene expression for wild type and cyclin single and double knockouts over cell cycle with and without osmotic stress. Clustering of expression profiles, peak time detection of oscillating genes, integration with transcription factor network dynamics, and assignment to cell cycle phases allowed us to quantify the effect of genetic or stress perturbations on the duration of cell cycle phases. Cln1 and Cln2 showed functional differences, especially affecting later phases. Deletion of Cln3 led to a delay of START followed by normal progression through later phases. Our data and network analysis suggest mutual effects of cyclins with the transcriptional regulators SBF and MBF.
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33
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Repetto MV, Winters MJ, Bush A, Reiter W, Hollenstein DM, Ammerer G, Pryciak PM, Colman-Lerner A. CDK and MAPK Synergistically Regulate Signaling Dynamics via a Shared Multi-site Phosphorylation Region on the Scaffold Protein Ste5. Mol Cell 2019; 69:938-952.e6. [PMID: 29547722 DOI: 10.1016/j.molcel.2018.02.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/13/2017] [Accepted: 02/12/2018] [Indexed: 01/19/2023]
Abstract
We report an unanticipated system of joint regulation by cyclin-dependent kinase (CDK) and mitogen-activated protein kinase (MAPK), involving collaborative multi-site phosphorylation of a single substrate. In budding yeast, the protein Ste5 controls signaling through a G1 arrest pathway. Upon cell-cycle entry, CDK inhibits Ste5 via multiple phosphorylation sites, disrupting its membrane association. Using quantitative time-lapse microscopy, we examined Ste5 membrane recruitment dynamics at different cell-cycle stages. Surprisingly, in S phase, where Ste5 recruitment should be blocked, we observed an initial recruitment followed by a steep drop-off. This delayed inhibition revealed a requirement for both CDK activity and negative feedback from the pathway MAPK Fus3. Mutagenesis, mass spectrometry, and electrophoretic analyses suggest that the CDK and MAPK modify shared sites, which are most extensively phosphorylated when both kinases are active and able to bind their docking sites on Ste5. Such collaborative phosphorylation can broaden regulatory inputs and diversify output dynamics of signaling pathways.
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Affiliation(s)
- María Victoria Repetto
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA Buenos Aires, Argentina; CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires C1428EHA, Argentina
| | - Matthew J Winters
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alan Bush
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA Buenos Aires, Argentina; CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires C1428EHA, Argentina
| | - Wolfgang Reiter
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - David Maria Hollenstein
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Gustav Ammerer
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Peter M Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Alejandro Colman-Lerner
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA Buenos Aires, Argentina; CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires C1428EHA, Argentina.
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34
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Daniels CN, Zyla TR, Lew DJ. A role for Gic1 and Gic2 in Cdc42 polarization at elevated temperature. PLoS One 2018; 13:e0200863. [PMID: 30566437 PMCID: PMC6300207 DOI: 10.1371/journal.pone.0200863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/09/2018] [Indexed: 12/27/2022] Open
Abstract
The conserved Rho-family GTPase Cdc42 is a master regulator of polarity establishment in many cell types. Cdc42 becomes activated and concentrated in a region of the cell cortex, and recruits a variety of effector proteins to that site. In turn, many effectors participate in regulation of cytoskeletal elements in order to remodel the cytoskeleton in a polarized manner. The budding yeast Saccharomyces cerevisiae has served as a tractable model system for studies of cell polarity. In yeast cells, Cdc42 polarization involves a positive feedback loop in which effectors called p21-activated kinases (PAKs) act to recruit a Cdc42-directed guanine nucleotide exchange factor (GEF), generating more GTP-Cdc42 in areas that already have GTP-Cdc42. The GTPase-interacting components (GICs) Gic1 and Gic2 are also Cdc42 effectors, and have been implicated in regulation of the actin and septin cytoskeleton. However, we report that cells lacking GICs are primarily defective in polarizing Cdc42 itself, suggesting that they act upstream as well as downstream of Cdc42 in yeast. Our findings suggest that feedback pathways involving GTPase effectors may be more prevalent than had been appreciated.
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Affiliation(s)
- Christine N. Daniels
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
| | - Trevin R. Zyla
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
| | - Daniel J. Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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35
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Moran KD, Kang H, Araujo AV, Zyla TR, Saito K, Tsygankov D, Lew DJ. Cell-cycle control of cell polarity in yeast. J Cell Biol 2018; 218:171-189. [PMID: 30459262 PMCID: PMC6314536 DOI: 10.1083/jcb.201806196] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/21/2018] [Accepted: 10/18/2018] [Indexed: 11/30/2022] Open
Abstract
In Saccharomyces cerevisiae, polarization of Cdc42 is regulated by the cell cycle, but the regulatory mechanisms are not well understood. Moran et al. show that G1 cyclin–dependent kinase activity enables localization of a subset of Cdc42 effectors to sites enriched for Cdc42. In many cells, morphogenetic events are coordinated with the cell cycle by cyclin-dependent kinases (CDKs). For example, many mammalian cells display extended morphologies during interphase but round up into more spherical shapes during mitosis (high CDK activity) and constrict a furrow during cytokinesis (low CDK activity). In the budding yeast Saccharomyces cerevisiae, bud formation reproducibly initiates near the G1/S transition and requires activation of CDKs at a point called “start” in G1. Previous work suggested that CDKs acted by controlling the ability of cells to polarize Cdc42, a conserved Rho-family GTPase that regulates cell polarity and the actin cytoskeleton in many systems. However, we report that yeast daughter cells can polarize Cdc42 before CDK activation at start. This polarization operates via a positive feedback loop mediated by the Cdc42 effector Ste20. We further identify a major and novel locus of CDK action downstream of Cdc42 polarization, affecting the ability of several other Cdc42 effectors to localize to the polarity site.
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Affiliation(s)
- Kyle D Moran
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
| | - Hui Kang
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
| | - Ana V Araujo
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
| | - Trevin R Zyla
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
| | - Koji Saito
- Department of Biosciences, School of Science, Kitasato University, Kitasato, Sagamihara, Kanagawa, Japan
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC
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36
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Argüello-Miranda O, Liu Y, Wood NE, Kositangool P, Doncic A. Integration of Multiple Metabolic Signals Determines Cell Fate Prior to Commitment. Mol Cell 2018; 71:733-744.e11. [PMID: 30174289 DOI: 10.1016/j.molcel.2018.07.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/13/2018] [Accepted: 07/27/2018] [Indexed: 11/18/2022]
Abstract
Cell-fate decisions are central to the survival and development of both uni- and multicellular organisms. It remains unclear when and to what degree cells can decide on future fates prior to commitment. This uncertainty stems from experimental and theoretical limitations in measuring and integrating multiple signals at the single-cell level during a decision process. Here, we combine six-color live-cell imaging with the Bayesian method of statistical evidence to study the meiosis/quiescence decision in budding yeast. Integration of multiple upstream metabolic signals predicts individual cell fates with high probability well before commitment. Cells "decide" their fates before birth, well before the activation of pathways characteristic of downstream cell fates. This decision, which remains stable through several cell cycles, occurs when multiple metabolic parameters simultaneously cross cell-fate-specific thresholds. Taken together, our results show that cells can decide their future fates long before commitment mechanisms are activated.
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Affiliation(s)
- Orlando Argüello-Miranda
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Yanjie Liu
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - N Ezgi Wood
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Piya Kositangool
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Andreas Doncic
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA; Green Center for Systems Biology, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
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37
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Lai H, Chiou JG, Zhurikhina A, Zyla TR, Tsygankov D, Lew DJ. Temporal regulation of morphogenetic events in Saccharomyces cerevisiae. Mol Biol Cell 2018; 29:2069-2083. [PMID: 29927361 PMCID: PMC6232962 DOI: 10.1091/mbc.e18-03-0188] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Tip growth in fungi involves highly polarized secretion and modification of the cell wall at the growing tip. The genetic requirements for initiating polarized growth are perhaps best understood for the model budding yeast Saccharomyces cerevisiae. Once the cell is committed to enter the cell cycle by activation of G1 cyclin/cyclin-dependent kinase (CDK) complexes, the polarity regulator Cdc42 becomes concentrated at the presumptive bud site, actin cables are oriented toward that site, and septin filaments assemble into a ring around the polarity site. Several minutes later, the bud emerges. Here, we investigated the mechanisms that regulate the timing of these events at the single-cell level. Septin recruitment was delayed relative to polarity establishment, and our findings suggest that a CDK-dependent septin “priming” facilitates septin recruitment by Cdc42. Bud emergence was delayed relative to the initiation of polarized secretion, and our findings suggest that the delay reflects the time needed to weaken the cell wall sufficiently for the cell to bud. Rho1 activation by Rom2 occurred at around the time of bud emergence, perhaps in response to local cell-wall weakening. This report reveals regulatory mechanisms underlying the morphogenetic events in the budding yeast.
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Affiliation(s)
- Helen Lai
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710.,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Jian-Geng Chiou
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710
| | - Anastasia Zhurikhina
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332
| | - Trevin R Zyla
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332
| | - Daniel J Lew
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710.,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
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38
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Aymoz D, Solé C, Pierre JJ, Schmitt M, de Nadal E, Posas F, Pelet S. Timing of gene expression in a cell-fate decision system. Mol Syst Biol 2018; 14:e8024. [PMID: 29695607 PMCID: PMC5916086 DOI: 10.15252/msb.20178024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During development, morphogens provide extracellular cues allowing cells to select a specific fate by inducing complex transcriptional programs. The mating pathway in budding yeast offers simplified settings to understand this process. Pheromone secreted by the mating partner triggers the activity of a MAPK pathway, which results in the expression of hundreds of genes. Using a dynamic expression reporter, we quantified the kinetics of gene expression in single cells upon exogenous pheromone stimulation and in the physiological context of mating. In both conditions, we observed striking differences in the timing of induction of mating‐responsive promoters. Biochemical analyses and generation of synthetic promoter variants demonstrated how the interplay between transcription factor binding and nucleosomes contributes to determine the kinetics of transcription in a simplified cell‐fate decision system.
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Affiliation(s)
- Delphine Aymoz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Carme Solé
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jean-Jerrold Pierre
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marta Schmitt
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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39
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Schwarz C, Johnson A, Kõivomägi M, Zatulovskiy E, Kravitz CJ, Doncic A, Skotheim JM. A Precise Cdk Activity Threshold Determines Passage through the Restriction Point. Mol Cell 2018; 69:253-264.e5. [PMID: 29351845 PMCID: PMC5790185 DOI: 10.1016/j.molcel.2017.12.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/28/2017] [Accepted: 12/19/2017] [Indexed: 11/24/2022]
Abstract
At the restriction point (R), mammalian cells irreversibly commit to divide. R has been viewed as a point in G1 that is passed when growth factor signaling initiates a positive feedback loop of Cdk activity. However, recent studies have cast doubt on this model by claiming R occurs prior to positive feedback activation in G1 or even before completion of the previous cell cycle. Here we reconcile these results and show that whereas many commonly used cell lines do not exhibit a G1 R, primary fibroblasts have a G1 R that is defined by a precise Cdk activity threshold and the activation of cell-cycle-dependent transcription. A simple threshold model, based solely on Cdk activity, predicted with more than 95% accuracy whether individual cells had passed R. That a single measurement accurately predicted cell fate shows that the state of complex regulatory networks can be assessed using a few critical protein activities.
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Affiliation(s)
- Clayton Schwarz
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Amy Johnson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Mardo Kõivomägi
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Andreas Doncic
- Department of Cell Biology & Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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40
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The phenomenology of cell size control. Curr Opin Cell Biol 2017; 49:53-58. [DOI: 10.1016/j.ceb.2017.11.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/05/2017] [Accepted: 11/26/2017] [Indexed: 01/27/2023]
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41
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Chandler-Brown D, Schmoller KM, Winetraub Y, Skotheim JM. The Adder Phenomenon Emerges from Independent Control of Pre- and Post-Start Phases of the Budding Yeast Cell Cycle. Curr Biol 2017; 27:2774-2783.e3. [PMID: 28889980 DOI: 10.1016/j.cub.2017.08.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/16/2017] [Accepted: 08/04/2017] [Indexed: 12/26/2022]
Abstract
Although it has long been clear that cells actively regulate their size, the molecular mechanisms underlying this regulation have remained poorly understood. In budding yeast, cell size primarily modulates the duration of the cell-division cycle by controlling the G1/S transition known as Start. We have recently shown that the rate of progression through Start increases with cell size, because cell growth dilutes the cell-cycle inhibitor Whi5 in G1. Recent phenomenological studies in yeast and bacteria have shown that these cells add an approximately constant volume during each complete cell cycle, independent of their size at birth. These results seem to be in conflict, as the phenomenological studies suggest that cells measure the amount they grow, rather than their size, and that size control acts over the whole cell cycle, rather than specifically in G1. Here, we propose an integrated model that unifies the adder phenomenology with the molecular mechanism of G1/S cell-size control. We use single-cell microscopy to parameterize a full cell-cycle model based on independent control of pre- and post-Start cell-cycle periods. We find that our model predicts the size-independent amount of cell growth during the full cell cycle. This suggests that the adder phenomenon is an emergent property of the independent regulation of pre- and post-Start cell-cycle periods rather than the consequence of an underlying molecular mechanism measuring a fixed amount of growth.
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Affiliation(s)
| | - Kurt M Schmoller
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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42
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Ewald JC, Kuehne A, Zamboni N, Skotheim JM. The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression. Mol Cell 2017; 62:532-45. [PMID: 27203178 DOI: 10.1016/j.molcel.2016.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/26/2015] [Accepted: 02/11/2016] [Indexed: 01/12/2023]
Abstract
Cell division entails a sequence of processes whose specific demands for biosynthetic precursors and energy place dynamic requirements on metabolism. However, little is known about how metabolic fluxes are coordinated with the cell division cycle. Here, we examine budding yeast to show that more than half of all measured metabolites change significantly through the cell division cycle. Cell cycle-dependent changes in central carbon metabolism are controlled by the cyclin-dependent kinase (Cdk1), a major cell cycle regulator, and the metabolic regulator protein kinase A. At the G1/S transition, Cdk1 phosphorylates and activates the enzyme Nth1, which funnels the storage carbohydrate trehalose into central carbon metabolism. Trehalose utilization fuels anabolic processes required to reliably complete cell division. Thus, the cell cycle entrains carbon metabolism to fuel biosynthesis. Because the oscillation of Cdk activity is a conserved feature of the eukaryotic cell cycle, we anticipate its frequent use in dynamically regulating metabolism for efficient proliferation.
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Affiliation(s)
- Jennifer C Ewald
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; PhD Program Systems Biology, Life Science Zurich Graduate School, 8057 Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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43
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Dmowski M, Fijałkowska IJ. Diverse roles of Dpb2, the non-catalytic subunit of DNA polymerase ε. Curr Genet 2017; 63:983-987. [PMID: 28516230 PMCID: PMC5668336 DOI: 10.1007/s00294-017-0706-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022]
Abstract
Timely progression of living cells through the cell cycle is precisely regulated. This involves a series of phosphorylation events which are regulated by various cyclins, activated in coordination with the cell cycle progression. Phosphorylated proteins govern cell growth, division as well as duplication of the genetic material and transcriptional activation of genes involved in these processes. A subset of these tightly regulated genes, which depend on the MBF transcription factor and are mainly involved in DNA replication and cell division, is transiently activated at the transition from G1 to S phase. A Saccharomyces cerevisiae mutant in the Dpb2 non-catalytic subunit of DNA polymerase ε (Polε) demonstrates abnormalities in transcription of MBF-dependent genes even in normal growth conditions. It is, therefore, tempting to speculate that Dpb2 which, as described previously, participates in the early stages of DNA replication initiation, has an impact on the regulation of replication-related genes expression with possible implications for genomic stability.
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Affiliation(s)
- Michał Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
| | - Iwona J Fijałkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
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44
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Fundamental trade-offs between information flow in single cells and cellular populations. Proc Natl Acad Sci U S A 2017; 114:5755-5760. [PMID: 28500273 DOI: 10.1073/pnas.1615660114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Signal transduction networks allow eukaryotic cells to make decisions based on information about intracellular state and the environment. Biochemical noise significantly diminishes the fidelity of signaling: networks examined to date seem to transmit less than 1 bit of information. It is unclear how networks that control critical cell-fate decisions (e.g., cell division and apoptosis) can function with such low levels of information transfer. Here, we use theory, experiments, and numerical analysis to demonstrate an inherent trade-off between the information transferred in individual cells and the information available to control population-level responses. Noise in receptor-mediated apoptosis reduces information transfer to approximately 1 bit at the single-cell level but allows 3-4 bits of information to be transmitted at the population level. For processes such as eukaryotic chemotaxis, in which single cells are the functional unit, we find high levels of information transmission at a single-cell level. Thus, low levels of information transfer are unlikely to represent a physical limit. Instead, we propose that signaling networks exploit noise at the single-cell level to increase population-level information transfer, allowing extracellular ligands, whose levels are also subject to noise, to incrementally regulate phenotypic changes. This is particularly critical for discrete changes in fate (e.g., life vs. death) for which the key variable is the fraction of cells engaged. Our findings provide a framework for rationalizing the high levels of noise in metazoan signaling networks and have implications for the development of drugs that target these networks in the treatment of cancer and other diseases.
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45
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Form and function of topologically associating genomic domains in budding yeast. Proc Natl Acad Sci U S A 2017; 114:E3061-E3070. [PMID: 28348222 DOI: 10.1073/pnas.1612256114] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The genome of metazoan cells is organized into topologically associating domains (TADs) that have similar histone modifications, transcription level, and DNA replication timing. Although similar structures appear to be conserved in fission yeast, computational modeling and analysis of high-throughput chromosome conformation capture (Hi-C) data have been used to argue that the small, highly constrained budding yeast chromosomes could not have these structures. In contrast, herein we analyze Hi-C data for budding yeast and identify 200-kb scale TADs, whose boundaries are enriched for transcriptional activity. Furthermore, these boundaries separate regions of similarly timed replication origins connecting the long-known effect of genomic context on replication timing to genome architecture. To investigate the molecular basis of TAD formation, we performed Hi-C experiments on cells depleted for the Forkhead transcription factors, Fkh1 and Fkh2, previously associated with replication timing. Forkhead factors do not regulate TAD formation, but do promote longer-range genomic interactions and control interactions between origins near the centromere. Thus, our work defines spatial organization within the budding yeast nucleus, demonstrates the conserved role of genome architecture in regulating DNA replication, and identifies a molecular mechanism specifically regulating interactions between pericentric origins.
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46
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Kono K, Ikui AE. A new cell cycle checkpoint that senses plasma membrane/cell wall damage in budding yeast. Bioessays 2017; 39. [PMID: 28211950 DOI: 10.1002/bies.201600210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In nature, cells face a variety of stresses that cause physical damage to the plasma membrane and cell wall. It is well established that evolutionarily conserved cell cycle checkpoints monitor various cellular perturbations, including DNA damage and spindle misalignment. However, the ability of these cell cycle checkpoints to sense a damaged plasma membrane/cell wall is poorly understood. To the best of our knowledge, our recent paper described the first example of such a checkpoint, using budding yeast as a model. In this review, we will discuss this important question as well as provide hypothetical explanations to be tested in the future.
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Affiliation(s)
- Keiko Kono
- Department of Cell Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Amy E Ikui
- Department of Biology, Brooklyn College, The City University of New York, Brooklyn, NY, USA
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47
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Relocation sensors to quantify signaling dynamics in live single cells. Curr Opin Biotechnol 2017; 45:51-58. [PMID: 28131009 DOI: 10.1016/j.copbio.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 11/22/2022]
Abstract
All cells are different. Even isogenic cells can possess diverse shapes, reside in different cell-cycle stages or express various sets of proteins. These variations can modulate the cell response to environmental stimuli and thereby provide key insights into the regulation of signal transduction cascades. Fluorescence microscopy allows to visualize these differences and monitor in real-time the responses of live single cells. In order to observe key cellular events, fluorescent biosensors have been developed. Among many assays, relocation reporters play an important role since they enable the quantification of the signal transduction dynamics. Fluorescently tagged endogenous proteins, as well as synthetic constructs, have allowed the measurement of kinase activity, transcription factor activation, transcription and protein expression in live single cells.
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48
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Atay O, Skotheim JM. Spatial and temporal signal processing and decision making by MAPK pathways. J Cell Biol 2017; 216:317-330. [PMID: 28043970 PMCID: PMC5294789 DOI: 10.1083/jcb.201609124] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/25/2016] [Accepted: 12/12/2016] [Indexed: 01/14/2023] Open
Abstract
Recent studies show that MAPK pathways perform exquisite spatial and temporal signal processing. This review discusses the mechanisms that process dynamic inputs into graded output responses, the role of positive and negative feedbacks, and feedforward regulation. Mitogen-activated protein kinase (MAPK) pathways are conserved from yeast to man and regulate a variety of cellular processes, including proliferation and differentiation. Recent developments show how MAPK pathways perform exquisite spatial and temporal signal processing and underscores the importance of studying the dynamics of signaling pathways to understand their physiological response. The importance of dynamic mechanisms that process input signals into graded downstream responses has been demonstrated in the pheromone-induced and osmotic stress–induced MAPK pathways in yeast and in the mammalian extracellular signal-regulated kinase MAPK pathway. Particularly, recent studies in the yeast pheromone response have shown how positive feedback generates switches, negative feedback enables gradient detection, and coherent feedforward regulation underlies cellular memory. More generally, a new wave of quantitative single-cell studies has begun to elucidate how signaling dynamics determine cell physiology and represents a paradigm shift from descriptive to predictive biology.
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Affiliation(s)
- Oguzhan Atay
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305
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49
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Degradation of the Mitotic Cyclin Clb3 Is not Required for Mitotic Exit but Is Necessary for G1 Cyclin Control of the Succeeding Cell Cycle. Genetics 2016; 204:1479-1494. [PMID: 27794027 DOI: 10.1534/genetics.116.194837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/25/2016] [Indexed: 02/07/2023] Open
Abstract
B-type cyclins promote mitotic entry and inhibit mitotic exit. In Saccharomyces cerevisiae, four B-type cyclins, Clb1-4, carry out essential mitotic roles, with substantial but incomplete overlap of function among them. Previous work in many organisms has indicated that B-type cyclin-dependent inhibition of mitotic exit imposes a requirement for mitotic destruction of B-type cyclins. For instance, precise genomic removal of the Clb2 destruction box (D box) prevents mitotic proteolysis of Clb2, and blocks mitotic exit. Here, we show that, despite significant functional overlap between Clb2 and Clb3, D-box-dependent Clb3 proteolysis is completely dispensable for mitotic exit. Removal of the Clb3 D box results in abundant Clb3 protein and associated kinase throughout the cell cycle, but mitotic exit occurs with close to normal timing. Clb3 degradation is required for pre-Start G1 control in the succeeding cell cycle. Deleting the CLB3 D box essentially eliminates all time delay before cell cycle Start following division, even in very small newborn cells. CLB3∆db cells show no cell cycle arrest response to mating pheromone, and CLB3∆db completely bypasses the requirement for CLN G1 cyclins, even in the absence of the early expressed B-type cyclins CLB5,6 Thus, regulated mitotic proteolysis of Clb3 is specifically required to make passage of Start in the succeeding cell cycle "memoryless"-dependent on conditions within that cycle, and independent of events such as B-type cyclin accumulation that occurred in the preceding cycle.
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50
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Abstract
How and when eukaryotic cells make the irrevocable commitment to divide remain central questions in the cell-cycle field. Parallel studies in yeast and mammalian cells seemed to suggest analogous control mechanisms operating during the G1 phase—at Start or the restriction (R) point, respectively—to integrate nutritional and developmental signals and decide between distinct cell fates: cell-cycle arrest or exit versus irreversible commitment to a round of division. Recent work has revealed molecular mechanisms underlying this decision-making process in both yeast and mammalian cells but also cast doubt on the nature and timing of cell-cycle commitment in multicellular organisms. These studies suggest an expanded temporal window of mitogen sensing under certain growth conditions, illuminate unexpected obstacles and exit ramps on the path to full cell-cycle commitment, and raise new questions regarding the functions of cyclin-dependent kinases (CDKs) that drive G1 progression and S-phase entry.
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Affiliation(s)
- Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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