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Rasheed MA, Mohy-Ud-Din R, Anwar T, Faiz M. A novel cell biological tool to explain mechanics and dynamics in fission yeast. J Basic Microbiol 2024; 64:e2300605. [PMID: 38168868 DOI: 10.1002/jobm.202300605] [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: 10/16/2023] [Revised: 11/24/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
The Rho guanosine triphosphatase hydrolase enzyme (GTPase) is required for the control of the actin cytoskeleton, but its activation in vivo condition is unknown. The study's goal was to find a new synthetic nanobody VHH (P-36 tagged with mNeonGreen) that interacts strongly with the Rho GTPase. We present the first novel synthetic nanobody, VHH (P-36 tagged with mNeonGreen), tested in fission yeast cells and found to have a particular interaction with Rho1GTPase. Plasmids were constructed by using of certain enzymes to digest the pDUAL-pef1a vector plasmid to produce a protein that was encoded by cloned genes. A varied VHH library was created synthetically, then transformed into yeast cells, and positive clones were chosen using chemical agents. To investigate protein interactions and cellular reactions, several studies were carried out, such as live cell imaging, growth curve analysis, coimmunoprecipitation, structural analysis, and cell therapies. Prism and RStudio were used for the statistical analysis. The presence of VHH (P-36) has no effect on the growth pattern making it an appropriate model for studying cytokinesis in vivo. According to a computational biological study, its affinity to interact with Rho1GTPase with all the complementarity-determining region (CDR) regions found on VHH (P-36) is extremely strong. We were able to track its subcellular target by localization using a fluorescent confocal microscope, ensuring the maintenance of cell polarity and morphology. Spheroplast analysis revealed a circular-shaped cell with an even distribution of Rho1 tagged VHH (P-36), indicating that the interaction occurs near the plasma membrane. The introduction of latrunculin-A (Lat-A) disrupted Rho GTPase localization, demonstrating the control over actin production, and the cell did not show evidence of mitotic phase commencement while Lat-A was present. Finally, this important biological tool can aid in our understanding of the mechanics and dynamics of cytokinesis in relation to Rho1GTPase.
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Affiliation(s)
| | - Raza Mohy-Ud-Din
- Institute of Biochemistry and Biotechnology, Faculty of Bio-Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Tehreem Anwar
- Lahore Medical Research Center LLP, Lahore, Punjab, Pakistan
| | - Muhammad Faiz
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences BUITEMS, Quetta, Balochistan, Pakistan
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2
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Fischer SC, Schardt S, Lilao-Garzón J, Muñoz-Descalzo S. The salt-and-pepper pattern in mouse blastocysts is compatible with signaling beyond the nearest neighbors. iScience 2023; 26:108106. [PMID: 37915595 PMCID: PMC10616410 DOI: 10.1016/j.isci.2023.108106] [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: 05/08/2023] [Revised: 08/03/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
Embryos develop in a concerted sequence of spatiotemporal arrangements of cells. In the preimplantation mouse embryo, the distribution of the cells in the inner cell mass evolves from a salt-and-pepper pattern to spatial segregation of two distinct cell types. The exact properties of the salt-and-pepper pattern have not been analyzed so far. We investigate the spatiotemporal distribution of NANOG- and GATA6-expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single-cell-based neighborhood analyses. A combination of spatial statistics and agent-based modeling reveals that the cell fate distribution follows a local clustering pattern. Using ordinary differential equations modeling, we show that this pattern can be established by a distance-based signaling mechanism enabling cells to integrate information from the whole inner cell mass into their cell fate decision. Our work highlights the importance of longer-range signaling to ensure coordinated decisions in groups of cells to successfully build embryos.
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Affiliation(s)
- Sabine C. Fischer
- Julius-Maximilians-Universität Würzburg, Faculty of Biology, Center for Computational and Theoretical Biology, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | - Simon Schardt
- Julius-Maximilians-Universität Würzburg, Faculty of Biology, Center for Computational and Theoretical Biology, Klara-Oppenheimer-Weg 32, Campus Hubland Nord, 97074 Würzburg, Germany
| | - Joaquín Lilao-Garzón
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad Las Palmas de Gran Canaria (ULPGC), Paseo Blas Cabrera Felipe "Físico" 17, Las Palmas de Gran Canaria 35016, Spain
| | - Silvia Muñoz-Descalzo
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Universidad Las Palmas de Gran Canaria (ULPGC), Paseo Blas Cabrera Felipe "Físico" 17, Las Palmas de Gran Canaria 35016, Spain
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3
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Le NT. Metabolic regulation of endothelial senescence. Front Cardiovasc Med 2023; 10:1232681. [PMID: 37649668 PMCID: PMC10464912 DOI: 10.3389/fcvm.2023.1232681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/18/2023] [Indexed: 09/01/2023] Open
Abstract
Endothelial cell (EC) senescence is increasingly recognized as a significant contributor to the development of vascular dysfunction and age-related disorders and diseases, including cancer and cardiovascular diseases (CVD). The regulation of cellular senescence is known to be influenced by cellular metabolism. While extensive research has been conducted on the metabolic regulation of senescence in other cells such as cancer cells and fibroblasts, our understanding of the metabolic regulation of EC senescence remains limited. The specific metabolic changes that drive EC senescence are yet to be fully elucidated. The objective of this review is to provide an overview of the intricate interplay between cellular metabolism and senescence, with a particular emphasis on recent advancements in understanding the metabolic changes preceding cellular senescence. I will summarize the current knowledge on the metabolic regulation of EC senescence, aiming to offer insights into the underlying mechanisms and future research directions.
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Affiliation(s)
- Nhat-Tu Le
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
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4
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Malik MZ, Dashti M, Fatima Y, Channanath A, John SE, Singh RKB, Al-Mulla F, Thanaraj TA. Disruption in the regulation of casein kinase 2 in circadian rhythm leads to pathological states: cancer, diabetes and neurodegenerative disorders. Front Mol Neurosci 2023; 16:1217992. [PMID: 37475884 PMCID: PMC10354274 DOI: 10.3389/fnmol.2023.1217992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/12/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction Circadian rhythm maintains the sleep-wake cycle in biological systems. Various biological activities are regulated and modulated by the circadian rhythm, disruption of which can result in onset of diseases. Robust rhythms of phosphorylation profiles and abundances of PERIOD (PER) proteins are thought to be the master keys that drive circadian clock functions. The role of casein kinase 2 (CK2) in circadian rhythm via its direct interactions with the PER protein has been extensively studied; however, the exact mechanism by which it affects circadian rhythms at the molecular level is not known. Methods Here, we propose an extended circadian rhythm model in Drosophila that incorporates the crosstalk between the PER protein and CK2. We studied the regulatory role of CK2 in the dynamics of PER proteins involved in circadian rhythm using the stochastic simulation algorithm. Results We observed that variations in the concentration of CK2 in the circadian rhythm model modulates the PER protein dynamics at different cellular states, namely, active, weakly active, and rhythmic death. These oscillatory states may correspond to distinct pathological cellular states of the living system. We find molecular noise at the expression level of CK2 to switch normal circadian rhythm to any of the three above-mentioned circadian oscillatory states. Our results suggest that the concentration levels of CK2 in the system has a strong impact on its dynamics, which is reflected in the time evolution of PER protein. Discussion We believe that our findings can contribute towards understanding the molecular mechanisms of circadian dysregulation in pathways driven by the PER mutant genes and their pathological states, including cancer, obesity, diabetes, neurodegenerative disorders, and socio-psychological disease.
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Affiliation(s)
- Md. Zubbair Malik
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Mohammed Dashti
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Yasmin Fatima
- Department of Computational Biology and Bioinformatics, Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly Allahabad Agricultural Institute-Deemed University), Allahabad, India
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - R. K. Brojen Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
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5
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Liu S, Tan C, Tyers M, Zetterberg A, Kafri R. What programs the size of animal cells? Front Cell Dev Biol 2022; 10:949382. [PMID: 36393871 PMCID: PMC9665425 DOI: 10.3389/fcell.2022.949382] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/07/2022] [Indexed: 01/19/2023] Open
Abstract
The human body is programmed with definite quantities, magnitudes, and proportions. At the microscopic level, such definite sizes manifest in individual cells - different cell types are characterized by distinct cell sizes whereas cells of the same type are highly uniform in size. How do cells in a population maintain uniformity in cell size, and how are changes in target size programmed? A convergence of recent and historical studies suggest - just as a thermostat maintains room temperature - the size of proliferating animal cells is similarly maintained by homeostatic mechanisms. In this review, we first summarize old and new literature on the existence of cell size checkpoints, then discuss additional advances in the study of size homeostasis that involve feedback regulation of cellular growth rate. We further discuss recent progress on the molecules that underlie cell size checkpoints and mechanisms that specify target size setpoints. Lastly, we discuss a less-well explored teleological question: why does cell size matter and what is the functional importance of cell size control?
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Affiliation(s)
- Shixuan Liu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, United States,*Correspondence: Shixuan Liu, ; Ran Kafri,
| | - Ceryl Tan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC, Canada
| | - Anders Zetterberg
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ran Kafri
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada,*Correspondence: Shixuan Liu, ; Ran Kafri,
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6
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Abstract
The most fundamental feature of cellular form is size, which sets the scale of all cell biological processes. Growth, form, and function are all necessarily linked in cell biology, but we often do not understand the underlying molecular mechanisms nor their specific functions. Here, we review progress toward determining the molecular mechanisms that regulate cell size in yeast, animals, and plants, as well as progress toward understanding the function of cell size regulation. It has become increasingly clear that the mechanism of cell size regulation is deeply intertwined with basic mechanisms of biosynthesis, and how biosynthesis can be scaled (or not) in proportion to cell size. Finally, we highlight recent findings causally linking aberrant cell size regulation to cellular senescence and their implications for cancer therapies.
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Affiliation(s)
- Shicong Xie
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Matthew Swaffer
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, California, USA;
- Chan Zuckerberg Biohub, San Francisco, California, USA
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7
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A mechanistic mathematical model of initiation and malignant transformation in sporadic vestibular schwannoma. Br J Cancer 2022; 127:1843-1857. [PMID: 36097176 DOI: 10.1038/s41416-022-01955-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND A vestibular schwannoma (VS) is a relatively rare, benign tumour of the eighth cranial nerve, often involving alterations to the gene NF2. Previous mathematical models of schwannoma incidence have not attempted to account for alterations in specific genes, and could not distinguish between nonsense mutations and loss of heterozygosity (LOH). METHODS Here, we present a mechanistic approach to modelling initiation and malignant transformation in schwannoma. Each parameter is associated with a specific gene or mechanism operative in Schwann cells, and can be determined by combining incidence data with empirical frequencies of pathogenic variants and LOH. RESULTS This results in new estimates for the base-pair mutation rate u = 4.48 × 10-10 and the rate of LOH = 2.03 × 10-6/yr in Schwann cells. In addition to new parameter estimates, we extend the approach to estimate the risk of both spontaneous and radiation-induced malignant transformation. DISCUSSION We conclude that radiotherapy is likely to have a negligible excess risk of malignancy for sporadic VS, with a possible exception of rapidly growing tumours.
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8
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Chien CC, Jiang J, Gong B, Li T, Gaitas A. AFM Microfluidic Cantilevers as Weight Sensors for Live Single Cell Mass Measurements. MEASUREMENT SCIENCE & TECHNOLOGY 2022; 33:095009. [PMID: 35832465 PMCID: PMC9273105 DOI: 10.1088/1361-6501/ac7280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reliably measuring small mass changes at the single-cell level is challenging. In this manuscript, we report the use of microfluidic cantilevers in liquid with sub-nanogram scale weight sensing capability for the measurement of cellular mass changes of living single cells. With this instrumentation, we were able to perform fast mass measurements within 3 minutes. We show results of mass measurements of polystyrene and metal beads of various sizes (smallest weight measured at 280 ± 95 pg) and live single-cell mass measurements in a physiologically relevant environment. We also performed finite element analysis to simulate and optimize the structural design and materials of cantilevers. Our simulation results indicate that using polymer materials, such as SU8 and polyimide, could improve the minimal detectable mass by 3-fold compared to conventional silicon cantilevers. The simulations also suggest that smaller dimensions of length, width, and thickness would improve the mass detection capability of microfluidic cantilevers.
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Affiliation(s)
- Chen-Chi Chien
- The Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jiaxin Jiang
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Bin Gong
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA. Sealy Center for Vector Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas 77555, USA
- Center of Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas 77555, USA
- Institute for Human Infectious and Immunity, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Tao Li
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Angelo Gaitas
- The Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- BioMedical Engineering & Imaging Institute, Leon and Norma Hess Center for Science and Medicine, New York, New York 10029, USA
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9
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High-resolution mass measurements of single budding yeast reveal linear growth segments. Nat Commun 2022; 13:3483. [PMID: 35732645 PMCID: PMC9217925 DOI: 10.1038/s41467-022-30781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
The regulation of cell growth has fundamental physiological, biotechnological and medical implications. However, methods that can continuously monitor individual cells at sufficient mass and time resolution hardly exist. Particularly, detecting the mass of individual microbial cells, which are much smaller than mammalian cells, remains challenging. Here, we modify a previously described cell balance ('picobalance') to monitor the proliferation of single cells of the budding yeast, Saccharomyces cerevisiae, under culture conditions in real time. Combined with optical microscopy to monitor the yeast morphology and cell cycle phase, the picobalance approaches a total mass resolution of 0.45 pg. Our results show that single budding yeast cells (S/G2/M phase) increase total mass in multiple linear segments sequentially, switching their growth rates. The growth rates weakly correlate with the cell mass of the growth segments, and the duration of each growth segment correlates negatively with cell mass. We envision that our technology will be useful for direct, accurate monitoring of the growth of single cells throughout their cycle.
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10
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Jia C, Singh A, Grima R. Cell size distribution of lineage data: analytic results and parameter inference. iScience 2021; 24:102220. [PMID: 33748708 PMCID: PMC7961097 DOI: 10.1016/j.isci.2021.102220] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/29/2021] [Accepted: 02/17/2021] [Indexed: 01/06/2023] Open
Abstract
Recent advances in single-cell technologies have enabled time-resolved measurements of the cell size over several cell cycles. These data encode information on how cells correct size aberrations so that they do not grow abnormally large or small. Here, we formulate a piecewise deterministic Markov model describing the evolution of the cell size over many generations, for all three cell size homeostasis strategies (timer, sizer, and adder). The model is solved to obtain an analytical expression for the non-Gaussian cell size distribution in a cell lineage; the theory is used to understand how the shape of the distribution is influenced by the parameters controlling the dynamics of the cell cycle and by the choice of cell tracking protocol. The theoretical cell size distribution is found to provide an excellent match to the experimental cell size distribution of E. coli lineage data collected under various growth conditions.
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Affiliation(s)
- Chen Jia
- Applied and Computational Mathematics Division, Beijing Computational Science Research Center, Beijing 100193, China
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, EH9 3JH, UK
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11
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Liu X, Oh S, Peshkin L, Kirschner MW. Computationally enhanced quantitative phase microscopy reveals autonomous oscillations in mammalian cell growth. Proc Natl Acad Sci U S A 2020; 117:27388-27399. [PMID: 33087574 PMCID: PMC7959529 DOI: 10.1073/pnas.2002152117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The fine balance of growth and division is a fundamental property of the physiology of cells, and one of the least understood. Its study has been thwarted by difficulties in the accurate measurement of cell size and the even greater challenges of measuring growth of a single cell over time. We address these limitations by demonstrating a computationally enhanced methodology for quantitative phase microscopy for adherent cells, using improved image processing algorithms and automated cell-tracking software. Accuracy has been improved more than twofold and this improvement is sufficient to establish the dynamics of cell growth and adherence to simple growth laws. It is also sufficient to reveal unknown features of cell growth, previously unmeasurable. With these methodological and analytical improvements, in several cell lines we document a remarkable oscillation in growth rate, occurring throughout the cell cycle, coupled to cell division or birth yet independent of cell cycle progression. We expect that further exploration with this advanced tool will provide a better understanding of growth rate regulation in mammalian cells.
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Affiliation(s)
- Xili Liu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Seungeun Oh
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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12
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Teimouri H, Mukherjee R, Kolomeisky AB. Stochastic Mechanisms of Cell-Size Regulation in Bacteria. J Phys Chem Lett 2020; 11:8777-8782. [PMID: 33001652 DOI: 10.1021/acs.jpclett.0c02627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
How bacteria are able to maintain their sizes remains an open question. It is believed that cells have narrow distributions of sizes as a consequence of a homeostasis that allows bacteria to function at the optimal conditions. Several phenomenological approaches to explain these observations have been presented, but the microscopic origins of the cell-size regulation are still not understood. Here, we propose a new stochastic approach to investigate the molecular mechanisms of maintaining the cell sizes in bacteria. It is argued that the cell-size regulation is a result of coupling of two stochastic processes, cell growth and division, which eliminates the need for introducing the thresholds. Dynamic properties of the system are explicitly evaluated, and it is shown that the model is consistent with the experimentally supported adder principle of the cell-size regulation. In addition, theoretical predictions agree with experimental observations on E. coli bacteria. Theoretical analysis clarifies some important features of bacterial cell growth.
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Affiliation(s)
- Hamid Teimouri
- Department of Chemistry, Rice University, Houston, Texas 77251, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77251, United States
| | - Rupsha Mukherjee
- MTech, Biological Engineering, Indian Institute of Technology, Gandhinagar, Gujarat 382355, India
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas 77251, United States
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77251, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
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13
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Siponen M, Klaavuniemi T. Demystifying beliefs about the natural sciences in information system. JOURNAL OF INFORMATION TECHNOLOGY 2020. [DOI: 10.1177/0268396220901535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Zatulovskiy E, Zhang S, Berenson DF, Topacio BR, Skotheim JM. Cell growth dilutes the cell cycle inhibitor Rb to trigger cell division. Science 2020; 369:466-471. [PMID: 32703881 PMCID: PMC7489475 DOI: 10.1126/science.aaz6213] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
Cell size is fundamental to cell physiology. For example, cell size determines the spatial scale of organelles and intracellular transport and thereby affects biosynthesis. Although some genes that affect mammalian cell size have been identified, the molecular mechanisms through which cell growth drives cell division have remained elusive. We show that cell growth during the G1 phase of the cell division cycle dilutes the cell cycle inhibitor Retinoblastoma protein (Rb) to trigger division in human cells. RB overexpression increased cell size and G1 duration, whereas RB deletion decreased cell size and removed the inverse correlation between cell size at birth and the duration of the G1 phase. Thus, Rb dilution through cell growth in G1 provides one of the long-sought molecular mechanisms that promotes cell size homeostasis.
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Affiliation(s)
| | - Shuyuan Zhang
- 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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15
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Zatulovskiy E, Skotheim JM. On the Molecular Mechanisms Regulating Animal Cell Size Homeostasis. Trends Genet 2020; 36:360-372. [PMID: 32294416 PMCID: PMC7162994 DOI: 10.1016/j.tig.2020.01.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/19/2022]
Abstract
Cell size is fundamental to cell physiology because it sets the scale of intracellular geometry, organelles, and biosynthetic processes. In animal cells, size homeostasis is controlled through two phenomenologically distinct mechanisms. First, size-dependent cell cycle progression ensures that smaller cells delay cell cycle progression to accumulate more biomass than larger cells prior to cell division. Second, size-dependent cell growth ensures that larger and smaller cells grow slower per unit mass than more optimally sized cells. This decade has seen dramatic progress in single-cell technologies establishing the diverse phenomena of cell size control in animal cells. Here, we review this recent progress and suggest pathways forward to determine the underlying molecular mechanisms.
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Affiliation(s)
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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16
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Xie S, Skotheim JM. A G1 Sizer Coordinates Growth and Division in the Mouse Epidermis. Curr Biol 2020; 30:916-924.e2. [PMID: 32109398 PMCID: PMC7158888 DOI: 10.1016/j.cub.2019.12.062] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/16/2019] [Accepted: 12/19/2019] [Indexed: 01/09/2023]
Abstract
Cell size homeostasis is often achieved by coupling cell-cycle progression to cell growth. Growth has been shown to drive cell-cycle progression in bacteria and yeast through "sizers," wherein cells of varying birth size divide at similar final sizes [1-3], and "adders," wherein cells increase in size a fixed amount per cell cycle [4-6]. Intermediate control phenomena are also observed, and even the same organism can exhibit different control phenomena depending on growth conditions [2, 7, 8]. Although studying unicellular organisms in laboratory conditions may give insight into their growth control in the wild, this is less apparent for studies of mammalian cells growing outside the organism. Sizers, adders, and intermediate phenomena have been observed in vitro [9-12], but it is unclear how this relates to mammalian cell proliferation in vivo. To address this question, we analyzed time-lapse images of the mouse epidermis taken over 1 week during normal tissue turnover [13]. We quantified the 3D volume growth and cell-cycle progression of single cells within the mouse skin. In dividing epidermal stem cells, we found that cell growth is coupled to division through a sizer operating largely in the G1 phase of the cell cycle. Thus, although the majority of tissue culture studies have identified adders, our analysis demonstrates that sizers are important in vivo and highlights the need to determine their underlying molecular origin.
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Affiliation(s)
- Shicong Xie
- 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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17
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Ogunmoyole T, Adewale IO, Fodeke AA, Afolayan A. Catalytic studies of glutathione transferase from Clarias gariepinus (Burchell) in dilute and crowded solutions. Comp Biochem Physiol C Toxicol Pharmacol 2020; 228:108648. [PMID: 31672530 DOI: 10.1016/j.cbpc.2019.108648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 10/25/2022]
Abstract
Kinetic properties of purified Clarias gariepinus glutathione transferase (CgGST) was studied in the presence of Ficoll 70, Polyethylene glycol (PEG) 6000, bovine serum albumin (BSA) and in dilute solution. This was done to mimic the cytosol thereby unraveling the actual mechanism of detoxication involving glutathione transferase (GST) in the crowded intracellular milieu. CgGST from the liver of Clarias gariepinus was purified to homogeneity by affinity chromatography on glutathione (GSH) - agarose. Initial-velocity study was performed by varying the concentrations of GSH at various fixed concentrations of 1-chloro-2,4-dinitrobenzene (CDNB) and vice-versa. Data obtained were fitted to the three equations representing random-ordered, compulsory-ordered and ping-pong mechanisms to obtain kinetic parameters. Product inhibition studies using sodium chloride (NaCl) was done by varying the concentrations of NaCl and CDNB at a fixed concentration of GSH and vice-versa. Data obtained were fitted to three equations representing competitive, non-competitive and uncompetitive inhibitions to obtain the inhibition constants (KiGSH and KiCDNB). Optimal temperature of CgGST activity was 20 °C both in dilute and crowded solutions. Maximum velocity (Vmax) in dilute solution was decreased, while KmGSH and KmCDNB were increased in the presence of the crowding agents. Turnover number (kcat), catalytic efficiency - kcat/KmGSH,kcat/KmCDNB and inhibition constants - (KiGSH and KiCDNB) were reduced in crowded solutions. Mechanism of catalysis was steady - state random sequential in both dilute and crowded solutions. The study concluded that although the catalytic efficiency of the enzyme was reduced in crowded solution, mechanism of catalysis remains the same in both crowded and dilute solutions.
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Affiliation(s)
- Temidayo Ogunmoyole
- Department of Medical Biochemistry, College of Medicine, Ekiti State University, Ado-Ekiti, Nigeria.
| | - Isaac Olusanjo Adewale
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife 220282, Nigeria.
| | - Adedayo A Fodeke
- Department of Chemistry, Obafemi Awolowo, University, Ile-Ife 220282, Nigeria
| | - Adeyinka Afolayan
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife 220282, Nigeria
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18
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Kuchen EE, Becker NB, Claudino N, Höfer T. Hidden long-range memories of growth and cycle speed correlate cell cycles in lineage trees. eLife 2020; 9:e51002. [PMID: 31971512 PMCID: PMC7018508 DOI: 10.7554/elife.51002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
Cell heterogeneity may be caused by stochastic or deterministic effects. The inheritance of regulators through cell division is a key deterministic force, but identifying inheritance effects in a systematic manner has been challenging. Here, we measure and analyze cell cycles in deep lineage trees of human cancer cells and mouse embryonic stem cells and develop a statistical framework to infer underlying rules of inheritance. The observed long-range intra-generational correlations in cell-cycle duration, up to second cousins, seem paradoxical because ancestral correlations decay rapidly. However, this correlation pattern is naturally explained by the inheritance of both cell size and cell-cycle speed over several generations, provided that cell growth and division are coupled through a minimum-size checkpoint. This model correctly predicts the effects of inhibiting cell growth or cycle progression. In sum, we show how fluctuations of cell cycles across lineage trees help in understanding the coordination of cell growth and division.
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Affiliation(s)
- Erika E Kuchen
- Theoretical Systems BiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Bioquant CenterUniversity of HeidelbergHeidelbergGermany
| | - Nils B Becker
- Theoretical Systems BiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Bioquant CenterUniversity of HeidelbergHeidelbergGermany
| | - Nina Claudino
- Theoretical Systems BiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Bioquant CenterUniversity of HeidelbergHeidelbergGermany
| | - Thomas Höfer
- Theoretical Systems BiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Bioquant CenterUniversity of HeidelbergHeidelbergGermany
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19
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Abstract
The genetic control of the characteristic cell sizes of different species and tissues is a long-standing enigma. Plants are convenient for studying this question in a multicellular context, as their cells do not move and are easily tracked and measured from organ initiation in the meristems to subsequent morphogenesis and differentiation. In this article, we discuss cell size control in plants compared with other organisms. As seen from yeast cells to mammalian cells, size homeostasis is maintained cell autonomously in the shoot meristem. In developing organs, vacuolization contributes to cell size heterogeneity and may resolve conflicts between growth control at the cellular and organ levels. Molecular mechanisms for cell size control have implications for how cell size responds to changes in ploidy, which are particularly important in plant development and evolution. We also discuss comparatively the functional consequences of cell size and their potential repercussions at higher scales, including genome evolution.
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Affiliation(s)
- Marco D'Ario
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert Sablowski
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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20
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Czajkowski M, Sussman DM, Marchetti MC, Manning ML. Glassy dynamics in models of confluent tissue with mitosis and apoptosis. SOFT MATTER 2019; 15:9133-9149. [PMID: 31674622 DOI: 10.1039/c9sm00916g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy dynamics in some epithelial layers despite continued cell cycling. To address this discrepancy, we quantify the role of cell birth and death on glassy states in confluent tissues using simulations of an active vertex model that includes cell motility, cell division, and cell death. Our simulation data is consistent with a simple ansatz in which the rate of cell-life cycling and the rate of relaxation of the tissue in the absence of cell cycling contribute independently and additively to the overall rate of cell motion. Specifically, we find that a glass-like regime with caging behavior indicated by subdiffusive cell displacements can be achieved in systems with sufficiently low rates of cell cycling.
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Affiliation(s)
- Michael Czajkowski
- Physics Department, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Daniel M Sussman
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - M Cristina Marchetti
- Department of Physics, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
| | - M Lisa Manning
- Physics Department and BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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21
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Abstract
Individual cell types have characteristic sizes, suggesting that size sensing mechanisms may coordinate transcription, translation, and metabolism with cell growth rates. Two types of size-sensing mechanisms have been proposed: spatial sensing of the location or dimensions of a signal, subcellular structure or organelle; or titration-based sensing of the intracellular concentrations of key regulators. Here we propose that size sensing in animal cells combines both titration and spatial sensing elements in a dynamic mechanism whereby microtubule motor-dependent localization of RNA encoding importin β1 and mTOR, coupled with regulated local protein synthesis, enable cytoskeleton length sensing for cell growth regulation.
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Affiliation(s)
- Ida Rishal
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Mike Fainzilber
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel.
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22
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Pickering M, Hollis LN, D'Souza E, Rhind N. Fission yeast cells grow approximately exponentially. Cell Cycle 2019; 18:869-879. [PMID: 30957637 DOI: 10.1080/15384101.2019.1595874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
How the rate of cell growth is influenced by cell size is a fundamental question of cell biology. The simple model that cell growth is proportional to cell size, based on the proposition that larger cells have proportionally greater synthetic capacity than smaller cells, leads to the prediction that the rate of cell growth increases exponentially with cell size. However, other modes of cell growth, including bilinear growth, have been reported. The distinction between exponential and bilinear growth has been explored in particular detail in the fission yeast Schizosaccharomyces pombe. We have revisited the mode of fission yeast cell growth using high-resolution time-lapse microscopy and find, as previously reported, that these two growth models are difficult to distinguish both because of the similarity in shapes between exponential and bilinear curves over the two-fold change in length of a normal cell cycle and because of the substantial biological and experimental noise inherent to these experiments. Therefore, we contrived to have cells grow more than twofold, by holding them in G2 for up to 8 h. Over this extended growth period, in which cells grow up to 5.5-fold, the two growth models diverge to the point that we can confidently exclude bilinear growth as a general model for fission yeast growth. Although the growth we observe is clearly more complicated than predicted by simple exponential growth, we find that exponential growth is a robust approximation of fission yeast growth, both during an unperturbed cell cycle and during extended periods of growth.
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Affiliation(s)
- Mary Pickering
- a Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Lauren Nicole Hollis
- a Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Edridge D'Souza
- a Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Nicholas Rhind
- a Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
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23
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Allard CAH, Decker F, Weiner OD, Toettcher JE, Graziano BR. A size-invariant bud-duration timer enables robustness in yeast cell size control. PLoS One 2018; 13:e0209301. [PMID: 30576342 PMCID: PMC6303054 DOI: 10.1371/journal.pone.0209301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022] Open
Abstract
Cell populations across nearly all forms of life generally maintain a characteristic cell type-dependent size, but how size control is achieved has been a long-standing question. The G1/S boundary of the cell cycle serves as a major point of size control, and mechanisms operating here restrict passage of cells to Start if they are too small. In contrast, it is less clear how size is regulated post-Start, during S/G2/M. To gain further insight into post-Start size control, we prepared budding yeast that can be reversibly blocked from bud initiation. While blocked, cells continue to grow isotropically, increasing their volume by more than an order of magnitude over unperturbed cells. Upon release from their block, giant mothers reenter the cell cycle and their progeny rapidly return to the original unperturbed size. We found this behavior to be consistent with a size-invariant 'timer' specifying the duration of S/G2/M. These results indicate that yeast use at least two distinct mechanisms at different cell cycle phases to ensure size homeostasis.
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Affiliation(s)
- Corey A. H. Allard
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Dept. of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Franziska Decker
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Max Planck Institute for the Physics of Complex Systems, Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden, Dresden, Germany
| | - Orion D. Weiner
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Cardiovascular Research Institute and Dept. of Biochemistry and Biophysics, UC San Francisco, San Francisco, United States of America
| | - Jared E. Toettcher
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Brian R. Graziano
- Marine Biological Laboratory, Woods Hole, MA, United States of America
- Cardiovascular Research Institute and Dept. of Biochemistry and Biophysics, UC San Francisco, San Francisco, United States of America
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24
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Björklund M. Cell size homeostasis: Metabolic control of growth and cell division. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:409-417. [PMID: 30315834 DOI: 10.1016/j.bbamcr.2018.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/25/2018] [Accepted: 10/03/2018] [Indexed: 12/14/2022]
Abstract
Joint regulation of growth rate and cell division rate determines cell size. Here we discuss how animal cells achieve cell size homeostasis potentially involving multiple signaling pathways converging at metabolic regulation of growth rate and cell cycle progression. While several models have been developed to explain cell size control, comparison of the two predominant models shows that size homeostasis is dependent on the ability to adjust cellular growth rate based on cell size. Consequently, maintenance of size homeostasis requires that larger cells can grow slower than small cells in relative terms. We review recent experimental evidence showing that such size adjustment occurs primarily at or immediately before the G1/S transition of the cell cycle. We further propose that bidirectional feedback between growth rate and size results in cell size sensing and discuss potential mechanisms how this may be accomplished.
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Affiliation(s)
- Mikael Björklund
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University School of Medicine, International Campus, 718 East Haizhou Rd., Haining, Zhejiang 314400, PR China.
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25
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Cadart C, Monnier S, Grilli J, Sáez PJ, Srivastava N, Attia R, Terriac E, Baum B, Cosentino-Lagomarsino M, Piel M. Size control in mammalian cells involves modulation of both growth rate and cell cycle duration. Nat Commun 2018; 9:3275. [PMID: 30115907 PMCID: PMC6095894 DOI: 10.1038/s41467-018-05393-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/30/2018] [Indexed: 02/04/2023] Open
Abstract
Despite decades of research, how mammalian cell size is controlled remains unclear because of the difficulty of directly measuring growth at the single-cell level. Here we report direct measurements of single-cell volumes over entire cell cycles on various mammalian cell lines and primary human cells. We find that, in a majority of cell types, the volume added across the cell cycle shows little or no correlation to cell birth size, a homeostatic behavior called "adder". This behavior involves modulation of G1 or S-G2 duration and modulation of growth rate. The precise combination of these mechanisms depends on the cell type and the growth condition. We have developed a mathematical framework to compare size homeostasis in datasets ranging from bacteria to mammalian cells. This reveals that a near-adder behavior is the most common type of size control and highlights the importance of growth rate modulation to size control in mammalian cells.
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Affiliation(s)
- Clotilde Cadart
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Sylvain Monnier
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - Jacopo Grilli
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
| | - Pablo J Sáez
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Nishit Srivastava
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Rafaele Attia
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Emmanuel Terriac
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- INM-Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, UCL, London, WC1E 6BT, UK
- Institute of Physics of Living Systems, UCL, London, WC1E 6BT, UK
| | - Marco Cosentino-Lagomarsino
- Sorbonne Universités, Université Pierre et Marie Curie, Paris, F-75005, France.
- CNRS, UMR 7238 Computational and Quantitative Biology, Paris, F-75005, France.
- FIRC Institute of Molecular Oncology (IFOM), Milan, 20139, Italy.
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France.
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France.
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26
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Perez Gonzalez N, Tao J, Rochman ND, Vig D, Chiu E, Wirtz D, Sun SX. Cell tension and mechanical regulation of cell volume. Mol Biol Cell 2018; 29:0. [PMID: 30113884 PMCID: PMC6254581 DOI: 10.1091/mbc.e18-04-0213] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Animal cells use an unknown mechanism to control their growth and physical size. Here, using the fluorescence exclusion method, we measure cell volume for adherent cells on substrates of varying stiffness. We discover that the cell volume has a complex dependence on substrate stiffness and is positively correlated with the size of the cell adhesion to the substrate. From a mechanical force–balance condition that determines the geometry of the cell surface, we find that the observed cell volume variation can be predicted quantitatively from the distribution of active myosin through the cell cortex. To connect cell mechanical tension with cell size homeostasis, we quantified the nuclear localization of YAP/TAZ, a transcription factor involved in cell growth and proliferation. We find that the level of nuclear YAP/TAZ is positively correlated with the average cell volume. Moreover, the level of nuclear YAP/TAZ is also connected to cell tension, as measured by the amount of phosphorylated myosin. Cells with greater apical tension tend to have higher levels of nuclear YAP/TAZ and a larger cell volume. These results point to a size-sensing mechanism based on mechanical tension: the cell tension increases as the cell grows, and increasing tension feeds back biochemically to growth and proliferation control.
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Affiliation(s)
- Nicolas Perez Gonzalez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Jiaxiang Tao
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Nash D Rochman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Dhruv Vig
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Evelyn Chiu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Denis Wirtz
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218.,Physical Sciences in Oncology Center (PSOC), Johns Hopkins University, Baltimore, MD 21218
| | - Sean X Sun
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218.,Physical Sciences in Oncology Center (PSOC), Johns Hopkins University, Baltimore, MD 21218
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27
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Krishna S, Laxman S. A minimal "push-pull" bistability model explains oscillations between quiescent and proliferative cell states. Mol Biol Cell 2018; 29:2243-2258. [PMID: 30044724 PMCID: PMC6249812 DOI: 10.1091/mbc.e18-01-0017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A minimal model for oscillating between quiescent and growth/proliferation states, dependent on the availability of a central metabolic resource, is presented. From the yeast metabolic cycles, metabolic oscillations in oxygen consumption are represented as transitions between quiescent and growth states. We consider metabolic resource availability, growth rates, and switching rates (between states) to model a relaxation oscillator explaining transitions between these states. This frustrated bistability model reveals a required communication between the metabolic resource that determines oscillations and the quiescent and growth state cells. Cells in each state reflect memory, or hysteresis of their current state, and “push–pull” cells from the other state. Finally, a parsimonious argument is made for a specific central metabolite as the controller of switching between quiescence and growth states. We discuss how an oscillator built around the availability of such a metabolic resource is sufficient to generally regulate oscillations between growth and quiescence through committed transitions.
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Affiliation(s)
- Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore 560065, India
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28
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Ginzberg MB, Chang N, D'Souza H, Patel N, Kafri R, Kirschner MW. Cell size sensing in animal cells coordinates anabolic growth rates and cell cycle progression to maintain cell size uniformity. eLife 2018; 7:26957. [PMID: 29889021 PMCID: PMC6031432 DOI: 10.7554/elife.26957] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 06/07/2018] [Indexed: 12/30/2022] Open
Abstract
Cell size uniformity in healthy tissues suggests that control mechanisms might coordinate cell growth and division. We derived a method to assay whether cellular growth rates depend on cell size, by monitoring how variance in size changes as cells grow. Our data revealed that, twice during the cell cycle, growth rates are selectively increased in small cells and reduced in large cells, ensuring cell size uniformity. This regulation was also observed directly by monitoring nuclear growth in live cells. We also detected cell-size-dependent adjustments of G1 length, which further reduce variability. Combining our assays with chemical/genetic perturbations confirmed that cells employ two strategies, adjusting both cell cycle length and growth rate, to maintain the appropriate size. Additionally, although Rb signaling is not required for these regulatory behaviors, perturbing Cdk4 activity still influences cell size, suggesting that the Cdk4 pathway may play a role in designating the cell’s target size. Animal cells come in many different sizes. In humans, for example, egg cells are thousands of times larger than sperm cells. Yet cells of any given type are often strikingly similar in size. The cells that line the surface of organs including the skin and kidneys are especially uniform; in fact a loss of size uniformity in certain tumors is a sign of malignancy. What kind of regulation could enable separate cells within a tissue to have the same size? One possibility is that each type of cell is programmed with a specific target size, and that a cell can sense if it strays from its target and take steps to compensate. Animal cells sensing their own size was first reported in the 1960s, and now Ginzberg et al. confirm that human cells grown in the laboratory do indeed monitor their size and correct deviations from their target. It turns out that two separate and independent processes help to keep all the cells in the population roughly uniform in size. Firstly, proliferating human cells that are smaller than their target size spend longer growing before they divide. Secondly, at two time points between cell divisions, large cells adjust their growth rate such that they grow slower than small cells. To show these processes in action, Ginzberg et al. introduced mutations or chemicals that perturbed the length of time between cell divisions or the rate of a cell’s growth. As expected, most of these perturbations had only a modest influence on cell size, due to the cell’s compensatory strategies. Cells that had less time to grow compensated by more quickly making new protein molecules, meaning that they still had enough material to build two new cells by the time they had to divide. In contrast, if a cell’s division was artificially delayed, it reduced its growth rate to stop it from becoming too large. Similarly, cells grown in conditions that slow the production of proteins extended the time between their cell divisions to give them enough time to accumulate the material required for two new cells. In a recent related study, Liu, Ginzberg et al. identified some of the molecules that a human cell uses to sense its own size. Together these two studies now pave the road to answering a fundamental question in cell biology: what is the elusive cell size sensor? Understanding how cells sense their size will open a window onto how quantitative information is programmed, sensed and communicated within living cells. These findings will shed also new light onto how cells specialize into cell types of different sizes, and what happens when cells lose the ability to sense or regulate their size in diseases like cancers.
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Affiliation(s)
- Miriam Bracha Ginzberg
- Department of Systems Biology, Harvard Medical School, Boston, United States.,Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Nancy Chang
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Heather D'Souza
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Nish Patel
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Ran Kafri
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, United States
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29
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Liu S, Ginzberg MB, Patel N, Hild M, Leung B, Li Z, Chen YC, Chang N, Wang Y, Tan C, Diena S, Trimble W, Wasserman L, Jenkins JL, Kirschner MW, Kafri R. Size uniformity of animal cells is actively maintained by a p38 MAPK-dependent regulation of G1-length. eLife 2018; 7:26947. [PMID: 29595474 PMCID: PMC5876018 DOI: 10.7554/elife.26947] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 12/22/2017] [Indexed: 01/09/2023] Open
Abstract
Animal cells within a tissue typically display a striking regularity in their size. To date, the molecular mechanisms that control this uniformity are still unknown. We have previously shown that size uniformity in animal cells is promoted, in part, by size-dependent regulation of G1 length. To identify the molecular mechanisms underlying this process, we performed a large-scale small molecule screen and found that the p38 MAPK pathway is involved in coordinating cell size and cell cycle progression. Small cells display higher p38 activity and spend more time in G1 than larger cells. Inhibition of p38 MAPK leads to loss of the compensatory G1 length extension in small cells, resulting in faster proliferation, smaller cell size and increased size heterogeneity. We propose a model wherein the p38 pathway responds to changes in cell size and regulates G1 exit accordingly, to increase cell size uniformity.
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Affiliation(s)
- Shixuan Liu
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | - Nish Patel
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Marc Hild
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Bosco Leung
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Zhengda Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Yen-Chi Chen
- Department of Statistics, University of Washington, Seattle, United States
| | - Nancy Chang
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Ceryl Tan
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Shulamit Diena
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - William Trimble
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
| | - Larry Wasserman
- Department of Statistics, Carnegie Mellon University, Pittsburgh, United States
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, United States
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Ran Kafri
- Cell Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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30
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Rhind N. Cell Size Control via an Unstable Accumulating Activator and the Phenomenon of Excess Mitotic Delay. Bioessays 2017; 40. [PMID: 29283187 DOI: 10.1002/bies.201700184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/30/2017] [Indexed: 01/21/2023]
Abstract
Unstable Accumulating Activator models for cellular size control propose an activator that accumulates in a size-dependent manner and triggers cell cycle progression once it has reached a certain threshold. Having a short half life makes such an activator responsive to changes in cell size and makes specific predictions for how cells respond to perturbation. In particular, it explains the curious phenomenon of excess mitotic delay. Excess mitotic delay, first observed in Tetrahymena in the '50s, is a phenomenon in which a pulse of protein synthesis inhibition causes a delay in mitotic entry that is longer than the pulse and that gets longer the later in the cell cycle the pulse is delivered. The interpretation of this phenomenon championed by Zeuthen and Mitchison in the '60s and '70s is that an unstable activator of mitosis is degraded during the pulse and has to be resynthesized to a threshold level to trigger mitosis; small cells have more time to resynthesize the activator before mitosis and so suffer less excess delay, whereas, large cells have less time thus suffer greater excess delay. Fifty years later, with our detailed understanding of cell cycle biochemistry, we can identify and test candidate Unstable Accumulating Activators. Here I review the field and further develop this concept.
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Affiliation(s)
- Nicholas Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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31
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Acosta LC, Perez Goncalves GM, Pielak GJ, Gorensek-Benitez AH. Large cosolutes, small cosolutes, and dihydrofolate reductase activity. Protein Sci 2017; 26:2417-2425. [PMID: 28971539 DOI: 10.1002/pro.3316] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/27/2017] [Accepted: 09/27/2017] [Indexed: 11/06/2022]
Abstract
Protein enzymes are the main catalysts in the crowded and complex cellular interior, but their activity is almost always studied in dilute buffered solutions. Studies that attempt to recreate the cellular interior in vitro often utilize synthetic polymers as crowding agents. Here, we report the effects of the synthetic polymer cosolutes Ficoll, dextran, and polyvinylpyrrolidone, and their respective monomers, sucrose, glucose, and 1-ethyl-2-pyrrolidone, on the activity of the 18-kDa monomeric enzyme, Escherichia coli dihydrofolate reductase. At low concentrations, reductase activity increases relative to buffer and monomers, suggesting a macromolecular effect. However, the effect decreases at higher concentrations, approaching, and, in some cases, falling below buffer values. We also assessed activity in terms of volume occupancy, viscosity, and the overlap concentration (where polymers form an interwoven mesh). The trends vary with polymer family, but changes in activity are within threefold of buffer values. We also compiled and analyzed results from previous studies and conclude that alterations of steady-state enzyme kinetics in solutions crowded with synthetic polymers are idiosyncratic with respect to the crowding agent and enzyme.
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Affiliation(s)
| | | | - Gary J Pielak
- Department of Chemistry.,Department of Biochemistry and Biophysics.,Lineberger Comprehensive Cancer Center.,Integrative Program for Biological and Genome Sciences University of North Carolina, Chapel Hill, NC, 27599, USA
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32
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Abriata LA, Spiga E, Peraro MD. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics. Biophys J 2017; 111:743-755. [PMID: 27558718 DOI: 10.1016/j.bpj.2016.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/06/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022] Open
Abstract
Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Enrico Spiga
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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33
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He JH, Yan M, Zuo H, Niu S, Yuan J, Weng SP, He J, Xu X. High reduced/oxidized glutathione ratio in infectious spleen and kidney necrosis virus-infected cells contributes to degradation of VP08R multimers. Vet Microbiol 2017; 207:19-24. [PMID: 28757023 DOI: 10.1016/j.vetmic.2017.05.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 12/29/2022]
Abstract
Infectious spleen and kidney necrosis virus (ISKNV) is the type species of the genus Megalocytivirus, family Iridoviridae. The ISKNV-infected cells in fish tissues are attached by lymphatic endothelial cells (LECs), which is a unique pathological phenomenon of ISKNV infection. The viral proteins VP23R and VP08R and the host protein nidogen-1 constitute the virus-mock basement membrane (VMBM) on the membrane of infected cells to provide attaching sites for LECs. VP08R can form cross-linked multimers via intermolecular disulfide bonds to make VMBM a compact and strong structure. A question is that when the virions mature, how do they penetrate VMBMs to be released from the cells? In this study, the redox state in ISKNV-infected cells was investigated. We demonstrated that the ratio of reduced/oxidized glutathione (GSH/GSSG) was significantly elevated in ISKNV-infected cells, suggesting the increasing of reducing power. Remarkable changes were also observed in activities of many GSH metabolic enzymes and in the ratio of NADPH/NADP. We further exhibited that the high ratio of GSH/GSSG could lead to degradation of the VP08R multimer in vitro. These may suggest that the high GSH/GSSG ratio in infected cells could act on the VP08R multimer to facilitate the disassembly of VMBMs after virus maturation.
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Affiliation(s)
- Jian-Hui He
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Muting Yan
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Hongliang Zuo
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, PR China
| | - Shengwen Niu
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Jia Yuan
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Shao-Ping Weng
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, PR China
| | - Jianguo He
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; School of Marine Sciences, Sun Yat-sen University, Guangzhou, PR China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, PR China.
| | - Xiaopeng Xu
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, PR China.
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34
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Aldea M, Jenkins K, Csikász-Nagy A. Growth Rate as a Direct Regulator of the Start Network to Set Cell Size. Front Cell Dev Biol 2017; 5:57. [PMID: 28603712 PMCID: PMC5445111 DOI: 10.3389/fcell.2017.00057] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
Cells are able to adjust their growth and size to external inputs to comply with specific fates and developmental programs. Molecular pathways controlling growth also have an enormous impact in cell size, and bacteria, yeast, or epithelial cells modify their size as a function of growth rate. This universal feature suggests that growth (mass) and proliferation (cell number) rates are subject to general coordinating mechanisms. However, the underlying molecular connections are still a matter of debate. Here we review the current ideas on growth and cell size control, and focus on the possible mechanisms that could link the biosynthetic machinery to the Start network in budding yeast. In particular, we discuss the role of molecular chaperones in a competition framework to explain cell size control by growth at the individual cell level.
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Affiliation(s)
- Martí Aldea
- Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones CientíficasBarcelona, Spain.,Departament de Ciències Bàsiques, Universitat Internacional de CatalunyaBarcelona, Spain
| | - Kirsten Jenkins
- Randall Division of Cell and Molecular Biophysics and Institute of Mathematical and Molecular Biomedicine, King's College LondonLondon, United Kingdom
| | - Attila Csikász-Nagy
- Randall Division of Cell and Molecular Biophysics and Institute of Mathematical and Molecular Biomedicine, King's College LondonLondon, United Kingdom.,Faculty of Information Technology and Bionics, Pázmány Péter Catholic UniversityBudapest, Hungary
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35
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Blasi T, Buettner F, Strasser MK, Marr C, Theis FJ. cgCorrect: a method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics. Phys Biol 2017; 14:036001. [PMID: 28198357 DOI: 10.1088/1478-3975/aa609a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Accessing gene expression at a single-cell level has unraveled often large heterogeneity among seemingly homogeneous cells, which remains obscured when using traditional population-based approaches. The computational analysis of single-cell transcriptomics data, however, still imposes unresolved challenges with respect to normalization, visualization and modeling the data. One such issue is differences in cell size, which introduce additional variability into the data and for which appropriate normalization techniques are needed. Otherwise, these differences in cell size may obscure genuine heterogeneities among cell populations and lead to overdispersed steady-state distributions of mRNA transcript numbers. We present cgCorrect, a statistical framework to correct for differences in cell size that are due to cell growth in single-cell transcriptomics data. We derive the probability for the cell-growth-corrected mRNA transcript number given the measured, cell size-dependent mRNA transcript number, based on the assumption that the average number of transcripts in a cell increases proportionally to the cell's volume during the cell cycle. cgCorrect can be used for both data normalization and to analyze the steady-state distributions used to infer the gene expression mechanism. We demonstrate its applicability on both simulated data and single-cell quantitative real-time polymerase chain reaction (PCR) data from mouse blood stem and progenitor cells (and to quantitative single-cell RNA-sequencing data obtained from mouse embryonic stem cells). We show that correcting for differences in cell size affects the interpretation of the data obtained by typically performed computational analysis.
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Affiliation(s)
- Thomas Blasi
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Department of Mathematics, Technische Universität München, Garching, Germany
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36
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Cell-size dependent progression of the cell cycle creates homeostasis and flexibility of plant cell size. Nat Commun 2017; 8:15060. [PMID: 28447614 PMCID: PMC5414177 DOI: 10.1038/ncomms15060] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/23/2017] [Indexed: 11/09/2022] Open
Abstract
Mean cell size at division is generally constant for specific conditions and cell types, but the mechanisms coupling cell growth and cell cycle control with cell size regulation are poorly understood in intact tissues. Here we show that the continuously dividing fields of cells within the shoot apical meristem of Arabidopsis show dynamic regulation of mean cell size dependent on developmental stage, genotype and environmental signals. We show cell size at division and cell cycle length is effectively predicted using a two-stage cell cycle model linking cell growth and two sequential cyclin dependent kinase (CDK) activities, and experimental results concur in showing that progression through both G1/S and G2/M is size dependent. This work shows that cell-autonomous co-ordination of cell growth and cell division previously observed in unicellular organisms also exists in intact plant tissues, and that cell size may be an emergent rather than directly determined property of cells.
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37
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Cohen RD, Pielak GJ. A cell is more than the sum of its (dilute) parts: A brief history of quinary structure. Protein Sci 2017; 26:403-413. [PMID: 27977883 PMCID: PMC5326556 DOI: 10.1002/pro.3092] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
Most knowledge of protein structure and function is derived from experiments performed with purified protein resuspended in dilute, buffered solutions. However, proteins function in the crowded, complex cellular environment. Although the first four levels of protein structure provide important information, a complete understanding requires consideration of quinary structure. Quinary structure comprises the transient interactions between macromolecules that provides organization and compartmentalization inside cells. We review the history of quinary structure in the context of several metabolic pathways, and the technological advances that have yielded recent insight into protein behavior in living cells. The evidence demonstrates that protein behavior in isolated solutions deviates from behavior in the physiological environment.
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Affiliation(s)
- Rachel D. Cohen
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
| | - Gary J. Pielak
- Department of ChemistryUniversity of North CarolinaChapel HillNorth Carolina27599
- Department of Biochemistry and BiophysicsUniversity of North CarolinaChapel HillNorth Carolina27599
- Lineberger Comprehensive Cancer Center, University of North CarolinaChapel HillNorth Carolina27599
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38
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Evidence of differential mass change rates between human breast cancer cell lines in culture. Biomed Microdevices 2017; 19:10. [DOI: 10.1007/s10544-017-0151-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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39
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40
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Abstract
Schizosaccharomyces pombe is a good model to study cell-size control. These cells integrate size information into cell cycle controls at both the G1/S and G2/M transitions, although the primary control operates at the entry into mitosis. At G2/M there is both a size threshold, demonstrated by the fact that cells divide when they reach 14 μm in length, and also correction around this threshold, evident from the narrow distribution of sizes within a population. This latter property is referred to as size homeostasis. It has been argued that a population of cells accumulating mass in a linear fashion will have size homeostasis in the absence of size control, if cycle time is controlled by a fixed timer. Because fission yeast cells do not grow in a simple linear fashion, they require a size-sensing mechanism. However, current models do not fully describe all aspects of this control, especially the coordination of cell size with ploidy.
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Affiliation(s)
- Elizabeth Wood
- Cell Cycle Laboratory, The Francis Crick Institute, London WC2A 3LY, United Kingdom;
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41
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Horváth A, Rácz-Mónus A, Buchwald P, Sveiczer Á. Cell length growth patterns in fission yeast reveal a novel size control mechanism operating in late G2 phase. Biol Cell 2016; 108:259-77. [DOI: 10.1111/boc.201500066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 04/05/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Anna Horváth
- Department of Applied Biotechnology and Food Science; Budapest University of Technology and Economics; Budapest Hungary
| | - Anna Rácz-Mónus
- Department of Applied Biotechnology and Food Science; Budapest University of Technology and Economics; Budapest Hungary
| | - Peter Buchwald
- Department of Molecular and Cellular Pharmacology; Miller School of Medicine; University of Miami; Miami FL USA
| | - Ákos Sveiczer
- Department of Applied Biotechnology and Food Science; Budapest University of Technology and Economics; Budapest Hungary
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42
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Kaplon J, van Dam L, Peeper D. Two-way communication between the metabolic and cell cycle machineries: the molecular basis. Cell Cycle 2016; 14:2022-32. [PMID: 26038996 DOI: 10.1080/15384101.2015.1044172] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The relationship between cellular metabolism and the cell cycle machinery is by no means unidirectional. The ability of a cell to enter the cell cycle critically depends on the availability of metabolites. Conversely, the cell cycle machinery commits to regulating metabolic networks in order to support cell survival and proliferation. In this review, we will give an account of how the cell cycle machinery and metabolism are interconnected. Acquiring information on how communication takes place among metabolic signaling networks and the cell cycle controllers is crucial to increase our understanding of the deregulation thereof in disease, including cancer.
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Affiliation(s)
- Joanna Kaplon
- a Division of Molecular Oncology; The Netherlands Cancer Institute ; Amsterdam ; The Netherlands
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43
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Abstract
Cells of a given type maintain a characteristic cell size to function efficiently in their ecological or organismal context. They achieve this through the regulation of growth rates or by actively sensing size and coupling this signal to cell division. We focus this review on potential size-sensing mechanisms, including geometric, external cue, and titration mechanisms. Mechanisms that titrate proteins against DNA are of particular interest because they are consistent with the robust correlation of DNA content and cell size. We review the literature, which suggests that titration mechanisms may underlie cell-size sensing in Xenopus embryos, budding yeast, and Escherichia coli, whereas alternative mechanisms may function in fission yeast.
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Affiliation(s)
- Amanda A Amodeo
- Department of Biology, Stanford University, Stanford, California 94305
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, California 94305
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44
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Popa C, Coll NS, Valls M, Sessa G. Yeast as a Heterologous Model System to Uncover Type III Effector Function. PLoS Pathog 2016; 12:e1005360. [PMID: 26914889 PMCID: PMC4767418 DOI: 10.1371/journal.ppat.1005360] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Type III effectors (T3E) are key virulence proteins that are injected by bacterial pathogens inside the cells of their host to subvert cellular processes and contribute to disease. The budding yeast Saccharomyces cerevisiae represents an important heterologous system for the functional characterisation of T3E proteins in a eukaryotic environment. Importantly, yeast contains eukaryotic processes with low redundancy and are devoid of immunity mechanisms that counteract T3Es and mask their function. Expression in yeast of effectors from both plant and animal pathogens that perturb conserved cellular processes often resulted in robust phenotypes that were exploited to elucidate effector functions, biochemical properties, and host targets. The genetic tractability of yeast and its amenability for high-throughput functional studies contributed to the success of this system that, in recent years, has been used to study over 100 effectors. Here, we provide a critical view on this body of work and describe advantages and limitations inherent to the use of yeast in T3E research. “Favourite” targets of T3Es in yeast are cytoskeleton components and small GTPases of the Rho family. We describe how mitogen-activated protein kinase (MAPK) signalling, vesicle trafficking, membrane structures, and programmed cell death are also often altered by T3Es in yeast and how this reflects their function in the natural host. We describe how effector structure–function studies and analysis of candidate targeted processes or pathways can be carried out in yeast. We critically analyse technologies that have been used in yeast to assign biochemical functions to T3Es, including transcriptomics and proteomics, as well as suppressor, gain-of-function, or synthetic lethality screens. We also describe how yeast can be used to select for molecules that block T3E function in search of new antibacterial drugs with medical applications. Finally, we provide our opinion on the limitations of S. cerevisiae as a model system and its most promising future applications.
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Affiliation(s)
- Crina Popa
- Genetics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Núria S. Coll
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
| | - Marc Valls
- Genetics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Catalonia, Spain
- * E-mail: (GS); (MV)
| | - Guido Sessa
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (GS); (MV)
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45
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Gérard C, Goldbeter A. Dynamics of the mammalian cell cycle in physiological and pathological conditions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 8:140-56. [PMID: 26613368 DOI: 10.1002/wsbm.1325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/22/2015] [Accepted: 10/08/2015] [Indexed: 01/01/2023]
Abstract
A network of cyclin-dependent kinases (Cdks) controls progression along the successive phases G1, S, G2, and M of the mammalian cell cycle. Deregulations in the expression of molecular components in this network often lead to abusive cell proliferation and cancer. Given the complex nature of the Cdk network, it is fruitful to resort to computational models to grasp its dynamical properties. Investigated by means of bifurcation diagrams, a detailed computational model for the Cdk network shows how the balance between quiescence and proliferation is affected by activators (oncogenes) and inhibitors (tumor suppressors) of cell cycle progression, as well as by growth factors and other external factors such as the extracellular matrix (ECM) and cell contact inhibition. Suprathreshold changes in all these factors can trigger a switch in the dynamical behavior of the network corresponding to a bifurcation between a stable steady state, associated with cell cycle arrest, and sustained oscillations of the various cyclin/Cdk complexes, corresponding to cell proliferation. The model for the Cdk network accounts for the dependence or independence of cell proliferation on serum and/or cell anchorage to the ECM. Such computational approach provides an integrated view of the control of cell proliferation in physiological or pathological conditions. Whether the balance is tilted toward cell cycle arrest or cell proliferation depends on the direction in which the threshold associated with the bifurcation is passed once the cell integrates the multiple signals, internal or external to the Cdk network, that promote or impede progression in the cell cycle.
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Affiliation(s)
- Claude Gérard
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Albert Goldbeter
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, South Africa
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46
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Arenas-Mena C, Coffman JA. Developmental control of transcriptional and proliferative potency during the evolutionary emergence of animals. Dev Dyn 2015; 244:1193-201. [PMID: 26173445 PMCID: PMC4705838 DOI: 10.1002/dvdy.24305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 06/18/2015] [Accepted: 07/07/2015] [Indexed: 12/13/2022] Open
Abstract
It is proposed that the evolution of complex animals required repressive genetic mechanisms for controlling the transcriptional and proliferative potency of cells. Unicellular organisms are transcriptionally potent, able to express their full genetic complement as the need arises through their life cycle, whereas differentiated cells of multicellular organisms can only express a fraction of their genomic potential. Likewise, whereas cell proliferation in unicellular organisms is primarily limited by nutrient availability, cell proliferation in multicellular organisms is developmentally regulated. Repressive genetic controls limiting the potency of cells at the end of ontogeny would have stabilized the gene expression states of differentiated cells and prevented disruptive proliferation, allowing the emergence of diverse cell types and functional shapes. We propose that distal cis-regulatory elements represent the primary innovations that set the stage for the evolution of developmental gene regulatory networks and the repressive control of key multipotency and cell-cycle control genes. The testable prediction of this model is that the genomes of extant animals, unlike those of our unicellular relatives, encode gene regulatory circuits dedicated to the developmental control of transcriptional and proliferative potency.
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Affiliation(s)
- Cesar Arenas-Mena
- Department of Biology, College of Staten Island and Graduate Center, The City University of New York (CUNY), Staten Island, New York
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47
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Wu H, Chen J, Xu J, Dong Z, Meyuhas O, Chen JK. Blocking rpS6 Phosphorylation Exacerbates Tsc1 Deletion-Induced Kidney Growth. J Am Soc Nephrol 2015; 27:1145-58. [PMID: 26296742 DOI: 10.1681/asn.2014121264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 07/16/2015] [Indexed: 11/03/2022] Open
Abstract
The molecular mechanisms underlying renal growth and renal growth-induced nephron damage remain poorly understood. Here, we report that in murine models, deletion of the tuberous sclerosis complex protein 1 (Tsc1) in renal proximal tubules induced strikingly enlarged kidneys, with minimal cystogenesis and occasional microscopic tumorigenesis. Signaling studies revealed hyperphosphorylation of eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) and increased phosphorylation of ribosomal protein S6 (rpS6) in activated renal tubules. Notably, knockin of a nonphosphorylatable rpS6 in these Tsc1-mutant mice exacerbated cystogenesis and caused drastic nephron damage and renal fibrosis, leading to kidney failure and a premature death rate of 67% by 9 weeks of age. In contrast, Tsc1 single-mutant mice were all alive and had far fewer renal cysts at this age. Mechanistic studies revealed persistent activation of mammalian target of rapamycin complex 1 (mTORC1) signaling causing hyperphosphorylation and consequent accumulation of 4E-BP1, along with greater cell proliferation, in the renal tubules of Tsc1 and rpS6 double-mutant mice. Furthermore, pharmacologic treatment of Tsc1 single-mutant mice with rapamycin reduced hyperphosphorylation and accumulation of 4E-BP1 but also inhibited phosphorylation of rpS6. Rapamycin also exacerbated cystic and fibrotic lesions and impaired kidney function in these mice, consequently leading to a premature death rate of 40% within 2 weeks of treatment, despite destroying tumors and decreasing kidney size. These findings indicate that Tsc1 prevents aberrant renal growth and tumorigenesis by inhibiting mTORC1 signaling, whereas phosphorylated rpS6 suppresses cystogenesis and fibrosis in Tsc1-deleted kidneys.
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Affiliation(s)
- Huijuan Wu
- Department of Cellular Biology and Anatomy, Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Jianchun Chen
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jinxian Xu
- Department of Cellular Biology and Anatomy, Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Research Department, Charlie Norwood VA Medical Center, Augusta, Georgia; and
| | - Oded Meyuhas
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Jian-Kang Chen
- Department of Cellular Biology and Anatomy, Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia;
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48
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Abstract
Different animal cell types have distinctive and characteristic sizes. How a particular cell size is specified by differentiation programs and physiology remains one of the fundamental unknowns in cell biology. In this Review, we explore the evidence that individual cells autonomously sense and specify their own size. We discuss possible mechanisms by which size-sensing and size-specification may take place. Last, we explore the physiological implications of size control: Why is it important that particular cell types maintain a particular size? We develop these questions through examination of the current literature and pose the questions that we anticipate will guide this field in the upcoming years.
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Affiliation(s)
- Miriam B Ginzberg
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ran Kafri
- The Hospital for Sick Children, Toronto, Canada
| | - Marc Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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49
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Guzmán-Vendrell M, Rincon SA, Dingli F, Loew D, Paoletti A. Molecular control of the Wee1 regulatory pathway by the SAD kinase Cdr2. J Cell Sci 2015; 128:2842-53. [PMID: 26071525 DOI: 10.1242/jcs.173146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/10/2015] [Indexed: 01/14/2023] Open
Abstract
Cell growth and division are tightly coordinated to maintain cell size constant during successive cell cycles. In Schizosaccharomyces pombe, the SAD kinase Cdr2 regulates the cell size at division and the positioning of the division plane. Cdr2 forms nodes on the medial cortex containing factors that constitute an inhibitory pathway for Wee1. This pathway is regulated by polar gradients of the DYRK kinase Pom1, and involves a direct inhibitor of Wee1, the SAD kinase Cdr1. Cdr2 also interacts with the anillin Mid1, which defines the division plane, and with additional components of the medial cortical nodes, including Blt1, which participate in the mitotic-promoting and cytokinetic functions of nodes. Here, we show that the interaction of Cdr2 with Wee1 and Mid1 requires the UBA domain of Cdr2, which is necessary for its kinase activity. In contrast, Cdr1 associates with the C-terminus of Cdr2, which is composed of basic and KA-1 lipid-binding domains. Mid1 also interacts with the C-terminus of Cdr2 and might bridge the N- and C-terminal domains, whereas Blt1 associates with the central spacer region. We propose that the association of Cdr2 effectors with different domains might constrain Cdr1 and Wee1 spatially to promote Wee1 inhibition upon Cdr2 kinase activation.
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Affiliation(s)
- Mercè Guzmán-Vendrell
- Institut Curie, Centre de Recherche, PSL Research University, Paris F-75248, France CNRS UMR144, Paris F-75248, France
| | - Sergio A Rincon
- Institut Curie, Centre de Recherche, PSL Research University, Paris F-75248, France CNRS UMR144, Paris F-75248, France
| | - Florent Dingli
- Institut Curie, Centre de Recherche, PSL Research University, Paris F-75248, France Laboratory of Mass Spectrometry and Proteomics, Paris F-75248, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, PSL Research University, Paris F-75248, France Laboratory of Mass Spectrometry and Proteomics, Paris F-75248, France
| | - Anne Paoletti
- Institut Curie, Centre de Recherche, PSL Research University, Paris F-75248, France CNRS UMR144, Paris F-75248, France
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50
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Polymenis M, Aramayo R. Translate to divide: сontrol of the cell cycle by protein synthesis. MICROBIAL CELL 2015; 2:94-104. [PMID: 28357283 PMCID: PMC5348972 DOI: 10.15698/mic2015.04.198] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein synthesis underpins much of cell growth and, consequently, cell multiplication. Understanding how proliferating cells commit and progress into the cell cycle requires knowing not only which proteins need to be synthesized, but also what determines their rate of synthesis during cell division.
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Affiliation(s)
- Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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