51
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Micali G, Grilli J, Marchi J, Osella M, Cosentino Lagomarsino M. Dissecting the Control Mechanisms for DNA Replication and Cell Division in E. coli. Cell Rep 2018; 25:761-771.e4. [DOI: 10.1016/j.celrep.2018.09.061] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/22/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022] Open
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52
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Mückl A, Schwarz-Schilling M, Fischer K, Simmel FC. Filamentation and restoration of normal growth in Escherichia coli using a combined CRISPRi sgRNA/antisense RNA approach. PLoS One 2018; 13:e0198058. [PMID: 30204770 PMCID: PMC6133276 DOI: 10.1371/journal.pone.0198058] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/26/2018] [Indexed: 12/31/2022] Open
Abstract
CRISPR interference (CRISPRi) using dCas9-sgRNA is a powerful tool for the exploration and manipulation of gene functions. Here we quantify the reversible switching of a central process of the bacterial cell cycle by CRISPRi and an antisense RNA mechanism. Reversible induction of filamentous growth in E. coli has been recently demonstrated by controlling the expression levels of the bacterial cell division proteins FtsZ/FtsA via CRISPRi. If FtsZ falls below a critical level, cells cannot divide. However, the cells remain metabolically active and continue with DNA replication. We surmised that this makes them amenable to an inducible antisense RNA strategy to counteract FtsZ inhibition. We show that both static and inducible thresholds can adjust the characteristics of the switching process. Combining bulk data with single cell measurements, we characterize the efficiency of the switching process. Successful restoration of division is found to occur faster in the presence of antisense sgRNAs than upon simple termination of CRISPRi induction.
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Affiliation(s)
- Andrea Mückl
- Physics Department, Technische Universität München, Garching, Bavaria, Germany
| | | | - Katrin Fischer
- Physics Department, Technische Universität München, Garching, Bavaria, Germany
| | - Friedrich C. Simmel
- Physics Department, Technische Universität München, Garching, Bavaria, Germany
- Nanosystems Initiative Munich, Munich, Bavaria Germany
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53
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Grilli J, Cadart C, Micali G, Osella M, Cosentino Lagomarsino M. The Empirical Fluctuation Pattern of E. coli Division Control. Front Microbiol 2018; 9:1541. [PMID: 30105006 PMCID: PMC6077223 DOI: 10.3389/fmicb.2018.01541] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/20/2018] [Indexed: 11/30/2022] Open
Abstract
In physics, it is customary to represent the fluctuations of a stochastic system at steady state in terms of linear response to small random perturbations. Previous work has shown that the same framework describes effectively the trade-off between cell-to-cell variability and correction in the control of cell division of single E. coli cells. However, previous analyses were motivated by specific models and limited to a subset of the measured variables. For example, most analyses neglected the role of growth rate variability. Here, we take a comprehensive approach and consider several sets of available data from both microcolonies and microfluidic devices in different growth conditions. We evaluate all the coupling coefficients between the three main measured variables (interdivision times, cell sizes and individual-cell growth rates). The linear-response framework correctly predicts consistency relations between a priori independent experimental measurements, which confirms its validity. Additionally, the couplings between the cell-specific growth rate and the other variables are typically non zero. Finally, we use the framework to detect signatures of mechanisms in experimental data involving growth rate fluctuations, finding that (1) noise-generating coupling between size and growth rate is a consequence of inter-generation growth rate correlations and (2) the correlation patterns agree with a near-adder model where the added size has a dependence on the single-cell growth rate. Our findings define relevant constraints that any theoretical description should reproduce, and will help future studies aiming to falsify some of the competing models of the cell cycle existing today in the literature.
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Affiliation(s)
| | - Clotilde Cadart
- Centre National de la Recherche Scientifique, Institut Curie, PSL Research University, UMR 144, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, Paris, France
| | - Gabriele Micali
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Matteo Osella
- Physics Department, University of Turin, Turin, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Torino, Turin, Italy
| | - Marco Cosentino Lagomarsino
- Sorbonne Université, Paris, France
- Centre National de la Recherche Scientifique, UMR 7238, Paris, France
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
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54
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Kleckner NE, Chatzi K, White MA, Fisher JK, Stouf M. Coordination of Growth, Chromosome Replication/Segregation, and Cell Division in E. coli. Front Microbiol 2018; 9:1469. [PMID: 30038602 PMCID: PMC6046412 DOI: 10.3389/fmicb.2018.01469] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial cells growing in steady state maintain a 1:1:1 relationship between an appropriate mass increase, a round of DNA replication plus sister chromosome segregation, and cell division. This is accomplished without the cell cycle engine found in eukaryotic cells. We propose here a formal logic, and an accompanying mechanism, for how such coordination could be provided in E. coli. Completion of chromosomal and divisome-related events would lead, interactively, to a “progression control complex” (PCC) which provides integrated physical coupling between sister terminus regions and the nascent septum. When a cell has both (i) achieved a sufficient mass increase, and (ii) the PCC has developed, a conformational change in the PCC occurs. This change results in “progression permission,” which triggers both onset of cell division and release of terminus regions. Release of the terminus region, in turn, directly enables a next round of replication initiation via physical changes transmitted through the nucleoid. Division and initiation are then implemented, each at its own rate and timing, according to conditions present. Importantly: (i) the limiting step for progression permission may be either completion of the growth requirement or the chromosome/divisome processes required for assembly of the PCC; and, (ii) the outcome of the proposed process is granting of permission to progress, not determination of the absolute or relative timings of downstream events. This basic logic, and the accompanying mechanism, can explain coordination of events in both slow and fast growth conditions; can accommodate diverse variations and perturbations of cellular events; and is compatible with existing mathematical descriptions of the E. coli cell cycle. Also, while our proposition is specifically designed to provide 1:1:1 coordination among basic events on a “per-cell cycle” basis, it is a small step to further envision permission progression is also the target of basic growth rate control. In such a case, the rate of mass accumulation (or its equivalent) would determine the length of the interval between successive permission events and, thus, successive cell divisions and successive replication initiations.
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Affiliation(s)
- Nancy E Kleckner
- Department of Molecular and Cellular Biology Harvard University, Cambridge, MA, United States
| | - Katerina Chatzi
- Department of Molecular and Cellular Biology Harvard University, Cambridge, MA, United States
| | - Martin A White
- Department of Molecular and Cellular Biology Harvard University, Cambridge, MA, United States
| | | | - Mathieu Stouf
- Department of Molecular and Cellular Biology Harvard University, Cambridge, MA, United States
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55
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Campos M, Govers SK, Irnov I, Dobihal GS, Cornet F, Jacobs-Wagner C. Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli. Mol Syst Biol 2018; 14:e7573. [PMID: 29941428 PMCID: PMC6018989 DOI: 10.15252/msb.20177573] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cell size, cell growth, and cell cycle events are necessarily intertwined to achieve robust bacterial replication. Yet, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image‐based quantitative screen of the single‐gene knockout collection of Escherichia coli and identify many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics, and cell division. Functional analyses, together with high‐dimensional classification, unveil new associations of morphological and cell cycle phenotypes with specific functions and pathways. Additionally, correlation analysis across ~4,000 genetic perturbations shows that growth rate is surprisingly not predictive of cell size. Growth rate was also uncorrelated with the relative timings of nucleoid separation and cell constriction. Rather, our analysis identifies scaling relationships between cell size and nucleoid size and between nucleoid size and the relative timings of nucleoid separation and cell division. These connections suggest that the nucleoid links cell morphogenesis to the cell cycle.
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Affiliation(s)
- Manuel Campos
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Laboratoire de Microbiologie et Génétique Moléculaires (LMGM; UMR5100), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Genevieve S Dobihal
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM; UMR5100), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT, USA .,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
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56
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Lambert A, Vanhecke A, Archetti A, Holden S, Schaber F, Pincus Z, Laub MT, Goley E, Manley S. Constriction Rate Modulation Can Drive Cell Size Control and Homeostasis in C. crescentus. iScience 2018; 4:180-189. [PMID: 30240739 PMCID: PMC6147026 DOI: 10.1016/j.isci.2018.05.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/04/2018] [Accepted: 05/24/2018] [Indexed: 11/24/2022] Open
Abstract
Rod-shaped bacteria typically grow first via sporadic and dispersed elongation along their lateral walls and then via a combination of zonal elongation and constriction at the division site to form the poles of daughter cells. Although constriction comprises up to half of the cell cycle, its impact on cell size control and homeostasis has rarely been considered. To reveal the roles of cell elongation and constriction in bacterial size regulation during cell division, we captured the shape dynamics of Caulobacter crescentus with time-lapse structured illumination microscopy and used molecular markers as cell-cycle landmarks. We perturbed the constriction rate using a hyperconstriction mutant or fosfomycin ([(2R,3S)-3-methyloxiran-2-yl]phosphonic acid) inhibition. We report that the constriction rate contributes to both size control and homeostasis, by determining elongation during constriction and by compensating for variation in pre-constriction elongation on a single-cell basis. Perturbing constriction rate changes cell length Faster constriction rate results in blunter cell poles Early constriction rate modulation balances elongation before and during constriction We propose that constriction rate is set by the accumulation of precursors during elongation
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Affiliation(s)
- Ambroise Lambert
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Aster Vanhecke
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anna Archetti
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Seamus Holden
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Felix Schaber
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Zachary Pincus
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MassachusettsInstitute of Technology, Cambridge, MA 02139, USA
| | - Erin Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Suliana Manley
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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57
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Harris LK, Theriot JA. Surface Area to Volume Ratio: A Natural Variable for Bacterial Morphogenesis. Trends Microbiol 2018; 26:815-832. [PMID: 29843923 DOI: 10.1016/j.tim.2018.04.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/23/2018] [Accepted: 04/27/2018] [Indexed: 11/16/2022]
Abstract
An immediately observable feature of bacteria is that cell size and shape are remarkably constant and characteristic for a given species in a particular condition, but vary quantitatively with physiological parameters such as growth rate, indicating both genetic and environmental regulation. However, despite decades of research, the molecular mechanisms underlying bacterial morphogenesis have remained incompletely characterized. We recently demonstrated that a wide range of bacterial species exhibit a robust surface area to volume ratio (SA/V) homeostasis. Because cell size, shape, and SA/V are mathematically interconnected, if SA/V is indeed the natural variable that cells actively monitor, this finding has critical implications for our understanding of bacterial morphogenesis, placing fundamental constraints on the sizes and shapes that cells can adopt. In this Opinion article we discuss the broad implications that this novel perspective has for the field of bacterial growth and morphogenesis.
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Affiliation(s)
- Leigh K Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Julie A Theriot
- Department of Biochemistry, Department of Microbiology & Immunology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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58
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Ho PY, Lin J, Amir A. Modeling Cell Size Regulation: From Single-Cell-Level Statistics to Molecular Mechanisms and Population-Level Effects. Annu Rev Biophys 2018. [DOI: 10.1146/annurev-biophys-070317-032955] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most microorganisms regulate their cell size. In this article, we review some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics that they generate. We review the biologically relevant insights obtained from these models. We then describe cell cycle regulation and its molecular implementations, protein number regulation, and population growth, all in relation to size regulation. Finally, we discuss several future directions for developing understanding beyond phenomenological models of cell size regulation.
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Affiliation(s)
- Po-Yi Ho
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jie Lin
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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59
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Abstract
How cells establish, maintain, and modulate size has always been an area of great interest and fascination. Until recently, technical limitations curtailed our ability to understand the molecular basis of bacterial cell size control. In the past decade, advances in microfluidics, imaging, and high-throughput single-cell analysis, however, have led to a flurry of work revealing size to be a highly complex trait involving the integration of three core aspects of bacterial physiology: metabolism, growth, and cell cycle progression.
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Affiliation(s)
- Corey S Westfall
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130; ,
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130; ,
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60
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Jun S, Si F, Pugatch R, Scott M. Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:056601. [PMID: 29313526 PMCID: PMC5897229 DOI: 10.1088/1361-6633/aaa628] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1-3), we review the first 'golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4-7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the 'adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome 'sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.
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Affiliation(s)
- Suckjoon Jun
- Department of Physics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America. Section of Molecular Biology, Division of Biology, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America
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61
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Huls PG, Vischer NOE, Woldringh CL. Different Amounts of DNA in Newborn Cells of Escherichia coli Preclude a Role for the Chromosome in Size Control According to the "Adder" Model. Front Microbiol 2018; 9:664. [PMID: 29675011 PMCID: PMC5895768 DOI: 10.3389/fmicb.2018.00664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
According to the recently-revived adder model for cell size control, newborn cells of Escherichia coli will grow and divide after having added a constant size or length, ΔL, irrespective of their size at birth. Assuming exponential elongation, this implies that large newborns will divide earlier than small ones. The molecular basis for the constant size increment is still unknown. As DNA replication and cell growth are coordinated, the constant ΔL could be based on duplication of an equal amount of DNA, ΔG, present in newborn cells. To test this idea, we measured amounts of DNA and lengths of nucleoids in DAPI-stained cells growing in batch culture at slow and fast rates. Deeply-constricted cells were divided in two subpopulations of longer and shorter lengths than average; these were considered to represent large and small prospective daughter cells, respectively. While at slow growth, large and small prospective daughter cells contained similar amounts of DNA, fast growing cells with multiforked replicating chromosomes, showed a significantly higher amount of DNA (20%) in the larger cells. This observation precludes the hypothesis that ΔL is based on the synthesis of a constant ΔG. Growth curves were constructed for siblings generated by asymmetric division and growing according to the adder model. Under the assumption that all cells at the same growth rate exhibit the same time between initiation of DNA replication and cell division (i.e., constant C+D-period), the constructions predict that initiation occurs at different sizes (Li) and that, at fast growth, large newborn cells transiently contain more DNA than small newborns, in accordance with the observations. Because the state of segregation, measured as the distance between separated nucleoids, was found to be more advanced in larger deeply-constricted cells, we propose that in larger newborns nucleoid separation occurs faster and at a shorter length, allowing them to divide earlier. We propose a composite model in which both differential initiation and segregation leads to an adder-like behavior of large and small newborn cells.
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Affiliation(s)
- Peter G Huls
- Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Norbert O E Vischer
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Conrad L Woldringh
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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62
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Vargas–Garcia CA, Ghusinga KR, Singh A. Cell size control and gene expression homeostasis in single-cells. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 8:109-116. [PMID: 29862376 PMCID: PMC5978733 DOI: 10.1016/j.coisb.2018.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Growth of a cell and its subsequent division into daughters is a fundamental aspect of all cellular living systems. During these processes, how do individual cells correct size aberrations so that they do not grow abnormally large or small? How do cells ensure that the concentration of essential gene products are maintained at desired levels, in spite of dynamic/stochastic changes in cell size during growth and division? Both these questions have fascinated researchers for over a century. We review how advances in singe-cell technologies and measurements are providing unique insights into these questions across organisms from prokaryotes to human cells. More specifically, diverse strategies based on timing of cell-cycle events, regulating growth, and number of daughters are employed to maintain cell size homeostasis. Interestingly, size homeostasis often results in size optimality - proliferation of individual cells in a population is maximized at an optimal cell size. We further discuss how size-dependent expression or gene-replication timing can buffer concentration of a gene product from cell-to-cell size variations within a population. Finally, we speculate on an intriguing hypothesis that specific size control strategies may have evolved as a consequence of gene-product concentration homeostasis.
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Affiliation(s)
- Cesar A. Vargas–Garcia
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Khem Raj Ghusinga
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
- Department of Mathematical Sciences, University of Delaware, Newark, DE, USA
- Center for Applications of Mathematics in Medicine, University of Delaware, Newark, DE, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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63
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Logsdon MM, Aldridge BB. Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations. Front Microbiol 2018; 9:514. [PMID: 29619019 PMCID: PMC5871693 DOI: 10.3389/fmicb.2018.00514] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/06/2018] [Indexed: 11/24/2022] Open
Abstract
Model bacteria, such as E. coli and B. subtilis, tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity.
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Affiliation(s)
- Michelle M Logsdon
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States.,Department of Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, United States
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States.,Department of Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, United States.,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, United States
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64
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Abstract
For many decades, the wedding of quantitative data with mathematical modeling has been fruitful, leading to important biological insights. Here, we review some of the ongoing efforts to gain insights into problems in microbiology - and, in particular, cell-cycle progression and its regulation - through observation and quantitative analysis of the natural fluctuations in the system. We first illustrate this idea by reviewing a classic example in microbiology - the Luria-Delbrück experiment - and discussing how, in that case, useful information was obtained by looking beyond the mean outcome of the experiment, but instead paying attention to the variability between replicates of the experiment. We then switch gears to the contemporary problem of cell cycle progression and discuss in more detail how insights into cell size regulation and, when relevant, coupling between the cell cycle and the circadian clock, can be gained by studying the natural fluctuations in the system and their statistical properties. We end with a more general discussion of how (in this context) the correct level of phenomenological model should be chosen, as well as some of the pitfalls associated with this type of analysis. Throughout this review the emphasis is not on providing details of the experimental setups or technical details of the models used, but rather, in fleshing out the conceptual structure of this particular approach to the problem. For this reason, we choose to illustrate the framework on a rather broad range of problems, and on organisms from all domains of life, to emphasize the commonality of the ideas and analysis used (as well as their differences).
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Affiliation(s)
- Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
| | - Nathalie Q Balaban
- The Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
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65
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Wehrens M, Ershov D, Rozendaal R, Walker N, Schultz D, Kishony R, Levin PA, Tans SJ. Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells. Curr Biol 2018; 28:972-979.e5. [PMID: 29502951 DOI: 10.1016/j.cub.2018.02.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/07/2017] [Accepted: 02/05/2018] [Indexed: 10/17/2022]
Abstract
Our understanding of bacterial cell size control is based mainly on stress-free growth conditions in the laboratory [1-10]. In the real world, however, bacteria are routinely faced with stresses that produce long filamentous cell morphologies [11-28]. Escherichia coli is observed to filament in response to DNA damage [22-25], antibiotic treatment [11-14, 28], host immune systems [15, 16], temperature [17], starvation [20], and more [18, 19, 21], conditions which are relevant to clinical settings and food preservation [26]. This shape plasticity is considered a survival strategy [27]. Size control in this regime remains largely unexplored. Here we report that E. coli cells use a dynamic size ruler to determine division locations combined with an adder-like mechanism to trigger divisions. As filamentous cells increase in size due to growth, or decrease in size due to divisions, its multiple Fts division rings abruptly reorganize to remain one characteristic cell length away from the cell pole and two such length units away from each other. These rules can be explained by spatiotemporal oscillations of Min proteins. Upon removal of filamentation stress, the cells undergo a sequence of division events, randomly at one of the possible division sites, on average after the time required to grow one characteristic cell size. These results indicate that E. coli cells continuously keep track of absolute length to control size, suggest a wider relevance for the adder principle beyond the control of normally sized cells, and provide a new perspective on the function of the Fts and Min systems.
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Affiliation(s)
| | - Dmitry Ershov
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | | | - Noreen Walker
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Daniel Schultz
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Systems Biology, Harvard Medical School, Boston MA 02138, USA
| | - Roy Kishony
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Systems Biology, Harvard Medical School, Boston MA 02138, USA
| | - Petra Anne Levin
- Department of Biology, Washington University, One Brookings Drive, St. Louis, MO, USA
| | - Sander J Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands; Bionanoscience Department, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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66
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van Teeffelen S, Renner LD. Recent advances in understanding how rod-like bacteria stably maintain their cell shapes. F1000Res 2018; 7:241. [PMID: 29560261 PMCID: PMC5832919 DOI: 10.12688/f1000research.12663.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 01/14/2023] Open
Abstract
Cell shape and cell volume are important for many bacterial functions. In recent years, we have seen a range of experimental and theoretical work that led to a better understanding of the determinants of cell shape and size. The roles of different molecular machineries for cell-wall expansion have been detailed and partially redefined, mechanical forces have been shown to influence cell shape, and new connections between metabolism and cell shape have been proposed. Yet the fundamental determinants of the different cellular dimensions remain to be identified. Here, we highlight some of the recent developments and focus on the determinants of rod-like cell shape and size in the well-studied model organisms
Escherichia coli and
Bacillus subtilis.
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Affiliation(s)
- Sven van Teeffelen
- Department of Microbiology, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01069 Dresden, Germany
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67
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Westfall CS, Levin PA. Comprehensive analysis of central carbon metabolism illuminates connections between nutrient availability, growth rate, and cell morphology in Escherichia coli. PLoS Genet 2018; 14:e1007205. [PMID: 29432413 PMCID: PMC5825171 DOI: 10.1371/journal.pgen.1007205] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/23/2018] [Accepted: 01/17/2018] [Indexed: 01/23/2023] Open
Abstract
Bacterial morphology is a complex trait that is highly sensitive to changes in the environment. For heterotrophic organisms, such as Escherichia coli, increases in nutrient levels are frequently accompanied by several-fold increases in both size and growth rate. Despite the dramatic nature of these changes, how alterations in nutrient availability translate into changes in growth and morphology remains a largely open question. To understand the signaling networks coupling nutrient availability with size and shape, we examined the impact of deletions in the entirety of non-essential central carbon metabolic genes on E. coli growth rate and cell size. Our data reveal the presence of multiple metabolic nodes that play important yet distinctive roles in dictating biosynthetic capacity and shaping cell morphology. Specifically, perturbations of acetyl-CoA metabolism impact cell size and division through changes in fatty acid synthesis. Additionally, we identify a genetic pathway linking glucose levels to cell width through the signaling molecule cyclic-AMP. Together our findings highlight a surprising diversity of factors and mechanisms contributing to growth potential and cell morphology, providing a foundation for further studies. Often taken for granted, the shape of bacterial cells is a complex trait that is highly sensitive to environmental perturbations. Nutrients in particular, strongly impact bacterial morphology together with growth rate. The ubiquitous, rod-shaped bacteria Escherichia coli increases both length and width several fold upon a shift from nutrient poor to nutrient rich medium, a change accompanied by an equally dramatic increase in growth rate. Central carbon metabolism is an obvious site for the integration of nutrient dependent signals that dictate cell size and shape. To develop a clearer picture of the molecular mechanisms coupling nutrient assimilation with cell growth and morphology, we screened the entirety of non-essential carbon metabolic genes for their contribution to growth rate and cell shape. Our data reveal the presence of multiple regulatory circuits coordinating different metabolic pathways with specific aspects of cell growth and morphology. Together, these data firmly establish a role for central carbon metabolism as an environmentally sensitive sculptor of bacterial cells.
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Affiliation(s)
- Corey S. Westfall
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
| | - Petra Anne Levin
- Department of Biology, Washington University, St. Louis, Missouri, United States of America
- * E-mail:
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68
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Nguyen HV, Meile JC, Lebrun M, Caruso D, Chu-Ky S, Sarter S. Litsea cubeba leaf essential oil from Vietnam: chemical diversity and its impacts on antibacterial activity. Lett Appl Microbiol 2018; 66:207-214. [PMID: 29266378 DOI: 10.1111/lam.12837] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 01/22/2023]
Abstract
The threat of bacterial resistance to antibiotics has created an urgent need to develop new antimicrobials. The aim of this study was to characterize the chemical diversity of Litsea cubeba leaf essential oil (EO) and its impacts on the antibacterial activity against pathogenic bacteria. Essential oils collected from seven provinces in North Vietnam (n = 25) were characterized by their high content in either 1,8-cineole or linalool. Linalool-type EOs were more effective against the eight bacterial strains tested than 1,8-cineole-type. Oil samples, LC19 (50% 1,8-cineole) and BV27 (94% linalool), were selected to investigate their antibacterial mechanisms against Escherichia coli. A strong bactericidal effect was observed after 4 and 2 h of exposure respectively. Microscopic analysis of treated E. coli cultures clearly showed that EOs caused changes in cell morphology, loss of integrity and permeability of the cell membrane, as well as DNA loss. However, the effects of both EOs were distinct. LC19 mostly affected cell membrane, led to a significant cell filamentation rate and altered cell width, whereas BV27 damaged cell membrane integrity leading to cell permeabilization and altered nucleoid morphology with the appearance of spot and visibly altered compaction. SIGNIFICANCE AND IMPACT OF THE STUDY This study aimed to characterize the chemical diversity of Litsea cubeba leaf essential oil (EO) and its impacts on its antibacterial activity. Two major chemotypes (1,8-cineole or linalool rich) were identified in North Vietnam and both were bactericidal against several pathogenic bacteria. A distinct inhibitory effect of EO samples on Escherichia coli was observed. 1,8-cineole-rich sample (LC19) affected cell membrane, led to cell filamentation and perturbation of cell width, while the linalool-rich one (BV27) induced damages in the cell membrane and changes in the nucleoid morphology. The study demonstrates the importance of considering chemotype variations in terms of chemical composition as well as the mode of action.
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Affiliation(s)
- H V Nguyen
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - J-C Meile
- CIRAD, UMR Qualisud, Montpellier, France
| | - M Lebrun
- CIRAD, UMR Qualisud, Montpellier, France
| | - D Caruso
- IRD, UMR ISEM, Montpellier, France
| | - S Chu-Ky
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - S Sarter
- CIRAD, UMR ISEM, Montpellier, France
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69
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Eun YJ, Ho PY, Kim M, LaRussa S, Robert L, Renner LD, Schmid A, Garner E, Amir A. Archaeal cells share common size control with bacteria despite noisier growth and division. Nat Microbiol 2017; 3:148-154. [PMID: 29255255 DOI: 10.1038/s41564-017-0082-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 11/21/2017] [Indexed: 01/23/2023]
Abstract
In nature, microorganisms exhibit different volumes spanning six orders of magnitude 1 . Despite their capability to create different sizes, a clonal population in a given environment maintains a uniform size across individual cells. Recent studies in eukaryotic and bacterial organisms showed that this homogeneity in cell size can be accomplished by growing a constant size between two cell cycle events (that is, the adder model 2-6 ). Demonstration of the adder model led to the hypothesis that this phenomenon is a consequence of convergent evolution. Given that archaeal cells share characteristics with both bacteria and eukaryotes, we investigated whether and how archaeal cells exhibit control over cell size. To this end, we developed a soft-lithography method of growing the archaeal cells to enable quantitative time-lapse imaging and single-cell analysis, which would be useful for other microorganisms. Using this method, we demonstrated that Halobacterium salinarum, a hypersaline-adapted archaeal organism, grows exponentially at the single-cell level and maintains a narrow-size distribution by adding a constant length between cell division events. Interestingly, the archaeal cells exhibited greater variability in cell division placement and exponential growth rate across individual cells in a population relative to those observed in Escherichia coli 6-9 . Here, we present a theoretical framework that explains how these larger fluctuations in archaeal cell cycle events contribute to cell size variability and control.
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Affiliation(s)
- Ye-Jin Eun
- Department of Molecular and Cellular Biology, Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Po-Yi Ho
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Minjeong Kim
- Department of Molecular and Cellular Biology, Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | | | - Lydia Robert
- INRA, UMR 1319 Micalis, Jouy-en-Josas, France.,AgroParisTech, UMR Micalis, Jouy-en-Josas, France.,Laboratoire Jean Perrin, UPMC-CNRS, UMR 8237, UPMC, Paris, France
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, Dresden, Germany
| | - Amy Schmid
- Biology Department, Center for Genomics and Computational Biology, Duke University, Durham, NC, USA.
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Center for Systems Biology, Harvard University, Cambridge, MA, USA.
| | - Ariel Amir
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
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70
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Zaritsky A, Rabinovitch A, Liu C, Woldringh CL. Does the eclipse limit bacterial nucleoid complexity and cell width? Synth Syst Biotechnol 2017; 2:267-275. [PMID: 29552651 PMCID: PMC5851910 DOI: 10.1016/j.synbio.2017.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
Cell size of bacteria M is related to 3 temporal parameters: chromosome replication time C, period from replication-termination to subsequent division D, and doubling time τ. Steady-state, bacillary cells grow exponentially by extending length L only, but their constant width W is larger at shorter τ's or longer C's, in proportion to the number of chromosome replication positions n (= C/τ), at least in Escherichia coli and Salmonella typhimurium. Extending C by thymine limitation of fast-growing thyA mutants result in continuous increase of M, associated with rising W, up to a limit before branching. A set of such puzzling observations is qualitatively consistent with the view that the actual cell mass (or volume) at the time of replication-initiation Mi (or Vi), usually relatively constant in growth at varying τ's, rises with time under thymine limitation of fast-growing, thymine-requiring E. coli strains. The hypothesis will be tested that presumes existence of a minimal distance lmin between successive moving replisomes, translated into the time needed for a replisome to reach lmin before a new replication-initiation at oriC is allowed, termed Eclipse E. Preliminary analysis of currently available data is inconsistent with a constant E under all conditions, hence other explanations and ways to test them are proposed in an attempt to elucidate these and other results. The complex hypothesis takes into account much of what is currently known about Bacterial Physiology: the relationships between cell dimensions, growth and cycle parameters, particularly nucleoid structure, replication and position, and the mode of peptidoglycan biosynthesis. Further experiments are mentioned that are necessary to test the discussed ideas and hypotheses.
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Affiliation(s)
- Arieh Zaritsky
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84105, Israel
| | - Avinoam Rabinovitch
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva, 84105, Israel
| | - Chenli Liu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen, PR China
| | - Conrad L Woldringh
- Bacterial Cell Biology, SILS, Boelelaan 1108, Amsterdam, The Netherlands
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71
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Manipulating the Bacterial Cell Cycle and Cell Size by Titrating the Expression of Ribonucleotide Reductase. mBio 2017; 8:mBio.01741-17. [PMID: 29138305 PMCID: PMC5686538 DOI: 10.1128/mbio.01741-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Understanding how bacteria coordinate growth with cell cycle events to maintain cell size homeostasis remains a grand challenge in biology. The period of chromosome replication (C period) is a key stage in the bacterial cell cycle. However, the mechanism of in vivo regulation of the C period remains unclear. In this study, we found that titration of the expression of ribonucleotide reductase (RNR), which changes the intracellular deoxynucleoside triphosphate (dNTP) pools, enables significant perturbations of the C period, leading to a substantial change in cell size and DNA content. Our work demonstrates that the intracellular dNTP pool is indeed an important parameter that controls the progression of chromosome replication. Specially, RNR overexpression leads to a shortened C period compared with that of a wild-type strain growing under different nutrient conditions, indicating that the dNTP substrate levels are subsaturated under physiological conditions. In addition, perturbing the C period does not significantly change the D period, indicating that these two processes are largely independent from each other. Overall, titration of ribonucleotide reductase expression can serve as a standard model system for studying the coordination between chromosome replication, cell division, and cell size.IMPORTANCE Bacteria must coordinate growth with cell cycle progression to maintain cell size hemostasis. Cell cycle and cell size regulation is a fundamental concern in biology. The period required for chromosome replication (the C period) is a key stage in the bacterial cell cycle. However, how the C period is controlled in vivo remains largely an open question in this field of bacterial cell cycle regulation. Through introducing a genetic circuit into Escherichia coli for titrating the expression of ribonucleotide reductase, we achieve substantial perturbation of the C period and cell size. Our work demonstrates that the intracellular dNTP pool is an important parameter that controls the progression of chromosome replication. Moreover, our work indicates that bacterial cells manage to maintain subsaturated dNTP levels under different nutrient conditions, leading to a submaximal speed of DNA replication fork movement.
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72
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Barber F, Ho PY, Murray AW, Amir A. Details Matter: Noise and Model Structure Set the Relationship between Cell Size and Cell Cycle Timing. Front Cell Dev Biol 2017; 5:92. [PMID: 29164112 PMCID: PMC5675860 DOI: 10.3389/fcell.2017.00092] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/05/2017] [Indexed: 12/31/2022] Open
Abstract
Organisms across all domains of life regulate the size of their cells. However, the means by which this is done is poorly understood. We study two abstracted “molecular” models for size regulation: inhibitor dilution and initiator accumulation. We apply the models to two settings: bacteria like Escherichia coli, that grow fully before they set a division plane and divide into two equally sized cells, and cells that form a bud early in the cell division cycle, confine new growth to that bud, and divide at the connection between that bud and the mother cell, like the budding yeast Saccharomyces cerevisiae. In budding cells, delaying cell division until buds reach the same size as their mother leads to very weak size control, with average cell size and standard deviation of cell size increasing over time and saturating up to 100-fold higher than those values for cells that divide when the bud is still substantially smaller than its mother. In budding yeast, both inhibitor dilution or initiator accumulation models are consistent with the observation that the daughters of diploid cells add a constant volume before they divide. This “adder” behavior has also been observed in bacteria. We find that in bacteria an inhibitor dilution model produces adder correlations that are not robust to noise in the timing of DNA replication initiation or in the timing from initiation of DNA replication to cell division (the C+D period). In contrast, in bacteria an initiator accumulation model yields robust adder correlations in the regime where noise in the timing of DNA replication initiation is much greater than noise in the C + D period, as reported previously (Ho and Amir, 2015). In bacteria, division into two equally sized cells does not broaden the size distribution.
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Affiliation(s)
- Felix Barber
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
| | - Po-Yi Ho
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States.,FAS Center for Systems Biology, Harvard University, Cambridge, MA, United States
| | - Ariel Amir
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
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73
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Shi H, Colavin A, Bigos M, Tropini C, Monds RD, Huang KC. Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size. Curr Biol 2017; 27:3419-3429.e4. [DOI: 10.1016/j.cub.2017.09.065] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 11/25/2022]
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74
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Lin J, Amir A. The Effects of Stochasticity at the Single-Cell Level and Cell Size Control on the Population Growth. Cell Syst 2017; 5:358-367.e4. [PMID: 28988800 DOI: 10.1016/j.cels.2017.08.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/12/2017] [Accepted: 08/24/2017] [Indexed: 12/20/2022]
Abstract
Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally observed correlations between mother-daughter generation times that are unavoidable when cell size is controlled for, which is essentially always the case. Here, we study population-level growth in the presence of cell size control and corroborate our theory using experimental measurements of single-cell growth rates. We derive a closed formula for the population growth rate and demonstrate that it only depends on the single-cell growth rate variability, not other sources of stochasticity. Our work provides an evolutionary rationale for the narrow growth rate distributions often observed in nature: when single-cell growth rates are less variable but have a fixed mean, the population will exhibit an enhanced population growth rate as long as the correlations between the mother and daughter cells' growth rates are not too strong.
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Affiliation(s)
- Jie Lin
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
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75
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Facchetti G, Chang F, Howard M. Controlling cell size through sizer mechanisms. CURRENT OPINION IN SYSTEMS BIOLOGY 2017; 5:86-92. [PMID: 32984663 PMCID: PMC7493432 DOI: 10.1016/j.coisb.2017.08.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cell size is partly determined through coordination between cell growth and division. How this coordination is achieved mechanistically remains mostly unknown. However, quantitative experiments together with computational modelling have reinvigorated the field and are elucidating underlying molecular processes. Size homeostasis may be achieved through different modes of regulation, including "sizers", "adders" and "timers." For sizer regulation, the cell division cycle does not proceed until a minimal size has been reached, requiring that the cell monitors its own size. Here, we highlight progress in defining sizer mechanisms in fission and budding yeasts showing how accumulation or dilution of key molecules can be used to monitor cell size during growth. We also discuss a potential role for sizers in bacterial size control.
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Affiliation(s)
- Giuseppe Facchetti
- Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Fred Chang
- Dept. of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
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76
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77
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“Living” dynamics of filamentous bacteria on an adherent surface under hydrodynamic exposure. Biointerphases 2017; 12:02C410. [DOI: 10.1116/1.4983150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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78
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Abstract
Environmental perturbations can lead to changes in bacterial cell size that are not predicted by current models. A recent study presents a model that accurately predicts cell size under a variety of environmental conditions, from just a few measurable variables.
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Affiliation(s)
- Stephen Vadia
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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79
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Suppression of the Escherichia coli dnaA46 mutation by changes in the activities of the pyruvate-acetate node links DNA replication regulation to central carbon metabolism. PLoS One 2017; 12:e0176050. [PMID: 28448512 PMCID: PMC5407757 DOI: 10.1371/journal.pone.0176050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
To ensure faithful transmission of genetic material to progeny cells, DNA replication is tightly regulated, mainly at the initiation step. Escherichia coli cells regulate the frequency of initiation according to growth conditions. Results of the classical, as well as the latest studies, suggest that the DNA replication in E. coli starts at a predefined, constant cell volume per chromosome but the mechanisms coordinating DNA replication with cell growth are still not fully understood. Results of recent investigations have revealed a role of metabolic pathway proteins in the control of cell division and a direct link between metabolism and DNA replication has also been suggested both in Bacillus subtilis and E. coli cells. In this work we show that defects in the acetate overflow pathway suppress the temperature-sensitivity of a defective replication initiator–DnaA under acetogenic growth conditions. Transcriptomic and metabolic analyses imply that this suppression is correlated with pyruvate accumulation, resulting from alterations in the pyruvate dehydrogenase (PDH) activity. Consequently, deletion of genes encoding the pyruvate dehydrogenase subunits likewise resulted in suppression of the thermal-sensitive growth of the dnaA46 strain. We propose that the suppressor effect may be directly related to the PDH complex activity, providing a link between an enzyme of the central carbon metabolism and DNA replication.
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80
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Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli. Curr Biol 2017; 27:1278-1287. [PMID: 28416114 DOI: 10.1016/j.cub.2017.03.022] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 12/17/2022]
Abstract
It is generally assumed that the allocation and synthesis of total cellular resources in microorganisms are uniquely determined by the growth conditions. Adaptation to a new physiological state leads to a change in cell size via reallocation of cellular resources. However, it has not been understood how cell size is coordinated with biosynthesis and robustly adapts to physiological states. We show that cell size in Escherichia coli can be predicted for any steady-state condition by projecting all biosynthesis into three measurable variables representing replication initiation, replication-division cycle, and the global biosynthesis rate. These variables can be decoupled by selectively controlling their respective core biosynthesis using CRISPR interference and antibiotics, verifying our predictions that different physiological states can result in the same cell size. We performed extensive growth inhibition experiments, and we discovered that cell size at replication initiation per origin, namely the initiation mass or unit cell, is remarkably invariant under perturbations targeting transcription, translation, ribosome content, replication kinetics, fatty acid and cell wall synthesis, cell division, and cell shape. Based on this invariance and balanced resource allocation, we explain why the total cell size is the sum of all unit cells. These results provide an overarching framework with quantitative predictive power over cell size in bacteria.
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81
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Step by Step, Cell by Cell: Quantification of the Bacterial Cell Cycle. Trends Microbiol 2017; 25:250-256. [DOI: 10.1016/j.tim.2016.12.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/09/2016] [Accepted: 12/12/2016] [Indexed: 11/22/2022]
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82
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Abstract
All organisms control the size of their cells. We focus here on the question of size regulation in bacteria, and suggest that the quantitative laws governing cell size and its dependence on growth rate may arise as byproducts of a regulatory mechanism which evolved to support multiple DNA replication forks. In particular, we show that the increase of bacterial cell size during Lenski’s long-term evolution experiments is a natural outcome of this proposal. This suggests that, in the context of evolution, cell size may be a 'spandrel' DOI:http://dx.doi.org/10.7554/eLife.22186.001
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Affiliation(s)
- Ariel Amir
- School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
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