1
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Khandoori R, Mondal K, Ghosh P. Resource limitation and population fluctuation drive spatiotemporal order in microbial communities. SOFT MATTER 2024; 20:3823-3835. [PMID: 38647378 DOI: 10.1039/d4sm00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Microbial communities display complex spatiotemporal behaviors leading to spatially-structured and ordered organization driven by species interactions and environmental factors. Resource availability plays a pivotal role in shaping the dynamics of bacterial colonies. In this study, we delve into the intricate interplay between resource limitation and the emergent properties of a growing colony of two visually distinct bacterial strains having similar growth and mechanical properties. Employing an agent-based modeling and computer simulations, we analyze the resource-driven effect on segregation and sectoring, cell length regulation and nematic ordering within a growing colony. We introduce a dimensionless parameter referred to as the active layer thickness, derived from nutrient diffusion equations, indicating effective population participation due to local resource availability. Our results reveal that lower values of active layer thickness arising from decreased resource abundance lead to rougher colony fronts, fostering heightened population fluctuations within the colony and faster spatial genetic diversity loss. Our temporal analyses unveil the dynamics of mean cell length and fluctuations, showcasing how initial disturbances evolve as colonies are exposed to nutrients and subsequently settle. Furthermore, examining microscopic details, we find that lower resource levels yield diverse cell lengths and enhanced nematic ordering, driven by the increased prevalence of longer rod-shaped cells. Our investigation sheds light on the multifaceted relationship between resource constraints and bacterial colony dynamics, revealing insights into their spatiotemporal organization.
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Affiliation(s)
- Rohit Khandoori
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India.
| | - Kaustav Mondal
- Center for High-Performance Computing, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India.
- Center for High-Performance Computing, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala 695551, India
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2
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Herrera-Jordan K, Pennington P, Zea L. Reduced Pseudomonas aeruginosa Cell Size Observed on Planktonic Cultures Grown in the International Space Station. Microorganisms 2024; 12:393. [PMID: 38399797 PMCID: PMC10892763 DOI: 10.3390/microorganisms12020393] [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: 12/21/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Bacterial growth and behavior have been studied in microgravity in the past, but little focus has been directed to cell size despite its impact on a myriad of processes, including biofilm formation, which is impactful regarding crew health. To interrogate this characteristic, supernatant aliquots of P. aeruginosa cultured on different materials and media on board the International Space Station (ISS) as part of the Space Biofilms Project were analyzed. For that experiment, P. aeruginosa was grown in microgravity-with matching Earth controls-in modified artificial urine medium (mAUMg-high Pi) or LB Lennox supplemented with KNO3, and its formation of biofilms on six different materials was assessed. After one, two, and three days of incubation, the ISS crew terminated subsets of the experiment by fixation in paraformaldehyde, and aliquots of the supernatant were used for the planktonic cell size study presented here. The measurements were obtained post-flight through the use of phase contrast microscopy under oil immersion, a Moticam 10+ digital camera, and the FIJI image analysis program. Statistical comparisons were conducted to identify which treatments caused significant differences in cell dimensions using the Kruskal-Wallis and Dunn tests. There were statistically significant differences as a function of material present in the culture in both LBK and mAUMg-high Pi. Along with this, the data were also grouped by gravitational condition, media, and days of incubation. Comparison of planktonic cells cultured in microgravity showed reduced cell length (from 4% to 10% depending on the material) and diameter (from 1% to 10% depending on the material) with respect to their matching Earth controls, with the caveat that the cultures may have been at different points in their growth curve at a given time. In conclusion, smaller cells were observed on the cultures grown in microgravity, and cell size changed as a function of incubation time and the material upon which the culture grew. We describe these changes here and possible implications for human space travel in terms of crew health and potential applications.
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Affiliation(s)
- Katherinne Herrera-Jordan
- Department of Biochemistry and Microbiology, Universidad del Valle de Guatemala, Guatemala City 01015, Guatemala;
| | - Pamela Pennington
- Research Institute, Universidad del Valle de Guatemala, Guatemala City 01015, Guatemala;
| | - Luis Zea
- Aerospace Engineering Sciences Department, University of Colorado, Boulder, CO 80309, USA
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3
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Donachie WD. The Nordström Question. Life (Basel) 2023; 13:1442. [PMID: 37511817 PMCID: PMC10381616 DOI: 10.3390/life13071442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
It is suggested that the absolute dimensions of cells of Escherichia coli may be set by the separation distance between newly completed sister nucleoids.
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Affiliation(s)
- William D Donachie
- Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3FD, Scotland, UK
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4
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Cayron J, Dedieu-Berne A, Lesterlin C. Bacterial filaments recover by successive and accelerated asymmetric divisions that allow rapid post-stress cell proliferation. Mol Microbiol 2023; 119:237-251. [PMID: 36527185 DOI: 10.1111/mmi.15016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Filamentation is a reversible morphological change triggered in response to various stresses that bacteria might encounter in the environment, during host infection or antibiotic treatments. Here we re-visit the dynamics of filament formation and recovery using a consistent framework based on live-cells microscopy. We compare the fate of filamentous Escherichia coli induced by cephalexin that inhibits cell division or by UV-induced DNA-damage that additionally perturbs chromosome segregation. We show that both filament types recover by successive and accelerated rounds of divisions that preferentially occur at the filaments' tip, thus resulting in the rapid production of multiple daughter cells with tightly regulated size. The DNA content, viability and further division of the daughter cells essentially depends on the coordination between chromosome segregation and division within the mother filament. Septum positioning at the filaments' tip depends on the Min system, while the nucleoid occlusion protein SlmA regulates the timing of division to prevent septum closure on unsegregated chromosomes. Our results not only recapitulate earlier conclusions but provide a higher level of detail regarding filaments division and the fate of the daughter cells. Together with previous reports, this work uncovers how filamentation recovery allows for a rapid cell proliferation after stress treatment.
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Affiliation(s)
- Julien Cayron
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
| | - Annick Dedieu-Berne
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
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5
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Barry RG, Hill NA, Stewart PS. Continuum soft tissue models from upscaling of arrays of hyperelastic cells. Proc Math Phys Eng Sci 2022. [DOI: 10.1098/rspa.2022.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Constitutive models for soft tissue mechanics are typically constructed by fitting phenomenological models to experimental measurements. However, a significant challenge is to rationally construct soft tissue models that encode the properties of the constituent cells and their extracellular matrix. This work presents a framework to derive multiscale soft tissue models that incorporate properties of individual cells without assuming homogeneity or periodicity at the cell level. We consider a viscoelastic model for each cell (which can deform, grow and divide), that we couple to form a network description of a one-dimensional line of cells. We use a discrete-to-continuum approach to form (nonlinear) continuum partial differential equation models for the tissue. These models elucidate the contrasting role of the two forms of dissipation: substrate dissipation localizes the deformation to the neighbourhood of the free boundary and inhibits morphoelastic growth, whereas internal cell dissipation promotes spatial uniformity and does not influence the elongation length. Furthermore, cell division is shown to increase the rate of elongation of the array compared with growth alone, provided the substrate dissipation is proportional to the cell surface area.
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Affiliation(s)
- Roxanna G. Barry
- School of Mathematics and Statistics, University Place, University of Glasgow, Glasgow G12 8QQ, UK
| | - Nicholas A. Hill
- School of Mathematics and Statistics, University Place, University of Glasgow, Glasgow G12 8QQ, UK
| | - Peter S. Stewart
- School of Mathematics and Statistics, University Place, University of Glasgow, Glasgow G12 8QQ, UK
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6
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Mayer Martins J, Wittkowski R. Inertial dynamics of an active Brownian particle. Phys Rev E 2022; 106:034616. [PMID: 36266913 DOI: 10.1103/physreve.106.034616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Active Brownian motion commonly assumes spherical overdamped particles. However, self-propelled particles are often neither symmetric nor overdamped yet underlie random fluctuations from their surroundings. Active Brownian motion has already been generalized to include asymmetric particles. Separately, recent findings have shown the importance of inertial effects for particles of macroscopic size or in low-friction environments. We aim to consolidate the previous findings into the general description of a self-propelled asymmetric particle with inertia. We derive the Langevin equation of such a particle as well as the corresponding Fokker-Planck equation. Furthermore, a formula is presented that allows reconstructing the hydrodynamic resistance matrix of the particle by measuring its trajectory. Numerical solutions of the Langevin equation show that, independently of the particle's shape, the noise-free trajectory at zero temperature starts with an inertial transition phase and converges to a circular helix. We discuss this universal convergence with respect to the helical motion that many microorganisms exhibit.
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Affiliation(s)
- Jonas Mayer Martins
- Institute of Theoretical Physics, Center for Soft Nanoscience, University of Münster, 48149 Münster, Germany
| | - Raphael Wittkowski
- Institute of Theoretical Physics, Center for Soft Nanoscience, University of Münster, 48149 Münster, Germany
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7
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Dimitra Papagianeli S, Lianou A, Aspridou Z, Stathas L, Koutsoumanis K. The magnitude of heterogeneity in individual-cell growth dynamics is an inherent characteristic of Salmonella enterica ser. Typhimurium strains. Food Res Int 2022; 162:111991. [DOI: 10.1016/j.foodres.2022.111991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
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8
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Ajitkumar P, Jakkala K, Paul A, Nair R, Swaminath S, Pradhan A. Growth and division mechanisms by which genetic resisters emerge from the rifampicin-surviving population of differentially antibiotic-susceptible mycobacterial subpopulations. Int J Mycobacteriol 2022; 11:273-286. [DOI: 10.4103/ijmy.ijmy_88_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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9
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Multicellular mechanochemical hybrid cellular Potts model of tissue formation during epithelial‐mesenchymal transition. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021. [DOI: 10.1002/cso2.1031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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10
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Zhang Q, Zhang Z, Shi H. Cell Size Is Coordinated with Cell Cycle by Regulating Initiator Protein DnaA in E. coli. Biophys J 2020; 119:2537-2557. [PMID: 33189684 DOI: 10.1016/j.bpj.2020.10.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022] Open
Abstract
Sixty years ago, bacterial cell size was found to be an exponential function of growth rate. Fifty years ago, a more general relationship was proposed, in which cell mass was equal to the initiation mass multiplied by 2 to the power of the ratio of the total time of C and D periods to the doubling time. This relationship has recently been experimentally confirmed by perturbing doubling time, C period, D period, or initiation mass. However, the underlying molecular mechanism remains unclear. Here, we developed a theoretical model for initiator protein DnaA mediating DNA replication initiation in Escherichia coli. We introduced an initiation probability function for competitive binding of DnaA-ATP and DnaA-ADP at oriC. We established a kinetic description of regulatory processes (e.g., expression regulation, titration, inactivation, and reactivation) of DnaA. Cell size as a spatial constraint also participates in the regulation of DnaA. By simulating DnaA kinetics, we obtained a regular DnaA oscillation coordinated with cell cycle and a converged cell size that matches replication initiation frequency to the growth rate. The relationship between the simulated cell size and growth rate, C period, D period, or initiation mass reproduces experimental results. The model also predicts how DnaA number and initiation mass vary with perturbation parameters, comparable with experimental data. The results suggest that 1) when growth rate, C period, or D period changes, the regulation of DnaA determines the invariance of initiation mass; 2) ppGpp inhibition of replication initiation may be important for the growth rate independence of initiation mass because three possible mechanisms therein produce different DnaA dynamics, which is experimentally verifiable; and 3) perturbation of some DnaA regulatory process causes a changing initiation mass or even an abnormal cell cycle. This study may provide clues for concerted control of cell size and cell cycle in synthetic biology.
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Affiliation(s)
- Qing Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China.
| | - Zhichao Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Hualin Shi
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China.
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11
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Galego L, Barahona S, Romão CV, Arraiano CM. Phosphorylation status of BolA affects its role in transcription and biofilm development. FEBS J 2020; 288:961-979. [PMID: 32535996 DOI: 10.1111/febs.15447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Accepted: 06/08/2020] [Indexed: 11/30/2022]
Abstract
BolA has been characterized as an important transcriptional regulator, which is induced in stationary phase of growth, and in response to several stresses. In Escherichia coli, its cellular function is associated with cell wall synthesis and division, morphology, permeability, motility and biofilm formation. Phosphorylation has been widely described as one of the most important events involved in the modulation of the activity of many transcription factors. In the present work, we have demonstrated in vivo and by mass spectrometry that BolA is phosphorylated in four highly conserved protein positions: S26, S45, T81 and S95. S95 is located in the C terminus unstructured region of the protein, and the other three sites are in the DNA-binding domain. These positions were mutated to nonphosphorylated residues, and their effects were investigated on different known BolA functions. Using northern blot experiments, we showed that the regulation of the expression of these Ser/Thr BolA mutants is performed at the post-translational level. Western blot results revealed that the stability/turnover of the mutated BolA proteins is differently affected depending on the dephosphorylated residue. Moreover, we provide evidences that phosphorylation events are crucial in the modulation of BolA activity as a transcription factor and as a regulator of cell morphology and biofilm development. Here, we propose that phosphorylation affects BolA downstream functions and discuss the possible significance of these phosphoresidues in the protein structure, stability, dimerization and function as a transcription factor.
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Affiliation(s)
- Lisete Galego
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana Barahona
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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12
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Ojkic N, Serbanescu D, Banerjee S. Surface-to-volume scaling and aspect ratio preservation in rod-shaped bacteria. eLife 2019; 8:e47033. [PMID: 31456563 PMCID: PMC6742476 DOI: 10.7554/elife.47033] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
Rod-shaped bacterial cells can readily adapt their lengths and widths in response to environmental changes. While many recent studies have focused on the mechanisms underlying bacterial cell size control, it remains largely unknown how the coupling between cell length and width results in robust control of rod-like bacterial shapes. In this study we uncover a conserved surface-to-volume scaling relation in Escherichia coli and other rod-shaped bacteria, resulting from the preservation of cell aspect ratio. To explain the mechanistic origin of aspect-ratio control, we propose a quantitative model for the coupling between bacterial cell elongation and the accumulation of an essential division protein, FtsZ. This model reveals a mechanism for why bacterial aspect ratio is independent of cell size and growth conditions, and predicts cell morphological changes in response to nutrient perturbations, antibiotics, MreB or FtsZ depletion, in quantitative agreement with experimental data.
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Affiliation(s)
- Nikola Ojkic
- Department of Physics and Astronomy, Institute for the Physics of Living SystemsUniversity College LondonLondonUnited Kingdom
| | - Diana Serbanescu
- Department of Physics and Astronomy, Institute for the Physics of Living SystemsUniversity College LondonLondonUnited Kingdom
| | - Shiladitya Banerjee
- Department of Physics and Astronomy, Institute for the Physics of Living SystemsUniversity College LondonLondonUnited Kingdom
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13
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Allen RJ, Waclaw B. Bacterial growth: a statistical physicist's guide. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:016601. [PMID: 30270850 PMCID: PMC6330087 DOI: 10.1088/1361-6633/aae546] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Bacterial growth presents many beautiful phenomena that pose new theoretical challenges to statistical physicists, and are also amenable to laboratory experimentation. This review provides some of the essential biological background, discusses recent applications of statistical physics in this field, and highlights the potential for future research.
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Affiliation(s)
- Rosalind J Allen
- School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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14
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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: 80] [Impact Index Per Article: 11.4] [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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15
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Transient MutS-Based Hypermutation System for Adaptive Evolution of Lactobacillus casei to Low pH. Appl Environ Microbiol 2017; 83:AEM.01120-17. [PMID: 28802267 DOI: 10.1128/aem.01120-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
This study explored transient inactivation of the gene encoding the DNA mismatch repair enzyme MutS as a tool for adaptive evolution of Lactobacillus casei MutS deletion derivatives of L. casei 12A and ATCC 334 were constructed and subjected to a 100-day adaptive evolution process to increase lactic acid resistance at low pH. Wild-type parental strains were also subjected to this treatment. At the end of the process, the ΔmutS lesion was repaired in representative L. casei 12A and ATCC 334 ΔmutS mutant isolates. Growth studies in broth at pH 4.0 (titrated with lactic acid) showed that all four adapted strains grew more rapidly, to higher cell densities, and produced significantly more lactic acid than untreated wild-type cells. However, the adapted ΔmutS derivative mutants showed the greatest increases in growth and lactic acid production. Further characterization of the L. casei 12A-adapted ΔmutS derivative revealed that it had a significantly smaller cell volume, a rougher cell surface, and significantly better survival at pH 2.5 than parental L. casei 12A. Genome sequence analysis confirmed that transient mutS inactivation decreased DNA replication fidelity in both L. casei strains, and it identified genetic changes that might contribute to the lactic acid-resistant phenotypes of adapted cells. Targeted inactivation of three genes that had acquired nonsense mutations in the adapted L. casei 12A ΔmutS mutant derivative showed that NADH dehydrogenase (ndh), phosphate transport ATP-binding protein PstB (pstB), and two-component signal transduction system (TCS) quorum-sensing histidine protein kinase (hpk) genes act in combination to increase lactic acid resistance in L. casei 12A.IMPORTANCE Adaptive evolution has been applied to microorganisms to increase industrially desirable phenotypes, including acid resistance. We developed a method to increase the adaptability of Lactobacillus casei 12A and ATCC 334 through transient inactivation of the DNA mismatch repair enzyme MutS. Here, we show this method was effective in increasing the resistance of L. casei to lactic acid at low pH. Additionally, we identified three genes that contribute to increased acid resistance in L. casei 12A. These results provide valuable insight on methods to enhance an organism's fitness to complex phenotypes through adaptive evolution and targeted gene inactivation.
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16
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Banerjee S, Lo K, Daddysman MK, Selewa A, Kuntz T, Dinner AR, Scherer NF. Biphasic growth dynamics control cell division in Caulobacter crescentus. Nat Microbiol 2017; 2:17116. [PMID: 28737755 DOI: 10.1038/nmicrobiol.2017.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/06/2017] [Indexed: 11/09/2022]
Abstract
Cell size is specific to each species and impacts cell function. Various phenomenological models for cell size regulation have been proposed, but recent work in bacteria has suggested an 'adder' model, in which a cell increments its size by a constant amount between each division. However, the coupling between cell size, shape and constriction remains poorly understood. Here, we investigate size control and the cell cycle dependence of bacterial growth using multigenerational cell growth and shape data for single Caulobacter crescentus cells. Our analysis reveals a biphasic mode of growth: a relative timer phase before constriction where cell growth is correlated to its initial size, followed by a pure adder phase during constriction. Cell wall labelling measurements reinforce this biphasic model, in which a crossover from uniform lateral growth to localized septal growth is observed. We present a mathematical model that quantitatively explains this biphasic 'mixer' model for cell size control.
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Affiliation(s)
- Shiladitya Banerjee
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.,Department of Physics and Astronomy, University College London, London WC1E 6BT, UK.,Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK
| | - Klevin Lo
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, llinois 60637, USA
| | - Matthew K Daddysman
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, llinois 60637, USA
| | - Alan Selewa
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, llinois 60637, USA.,Biophysical Sciences Graduate Program, The University of Chicago, Chicago, Illinois 60637, USA
| | - Thomas Kuntz
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Aaron R Dinner
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, llinois 60637, USA.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Norbert F Scherer
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, llinois 60637, USA.,Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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17
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Naylor J, Fellermann H, Ding Y, Mohammed WK, Jakubovics NS, Mukherjee J, Biggs CA, Wright PC, Krasnogor N. Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations. ACS Synth Biol 2017; 6:1194-1210. [PMID: 28475309 DOI: 10.1021/acssynbio.6b00315] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Simbiotics is a spatially explicit multiscale modeling platform for the design, simulation and analysis of bacterial populations. Systems ranging from planktonic cells and colonies, to biofilm formation and development may be modeled. Representation of biological systems in Simbiotics is flexible, and user-defined processes may be in a variety of forms depending on desired model abstraction. Simbiotics provides a library of modules such as cell geometries, physical force dynamics, genetic circuits, metabolic pathways, chemical diffusion and cell interactions. Model defined processes are integrated and scheduled for parallel multithread and multi-CPU execution. A virtual lab provides the modeler with analysis modules and some simulated lab equipment, enabling automation of sample interaction and data collection. An extendable and modular framework allows for the platform to be updated as novel models of bacteria are developed, coupled with an intuitive user interface to allow for model definitions with minimal programming experience. Simbiotics can integrate existing standards such as SBML, and process microscopy images to initialize the 3D spatial configuration of bacteria consortia. Two case studies, used to illustrate the platform flexibility, focus on the physical properties of the biosystems modeled. These pilot case studies demonstrate Simbiotics versatility in modeling and analysis of natural systems and as a CAD tool for synthetic biology.
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Affiliation(s)
- Jonathan Naylor
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Harold Fellermann
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Yuchun Ding
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Waleed K. Mohammed
- School of Dental Sciences, Newcastle University, Newcastle upon Tyne NE2 4BW, U.K
| | | | - Joy Mukherjee
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S10 2TN, U.K
| | - Catherine A. Biggs
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S10 2TN, U.K
| | - Phillip C. Wright
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Natalio Krasnogor
- Interdisciplinary
Computing and Complex Biosystems (ICOS) research group, School of
Computing Science, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
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18
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Abstract
When deprived of FtsZ, Escherichia coli cells (VIP205) grown in liquid form long nonseptated filaments due to their inability to assemble an FtsZ ring and their failure to recruit subsequent divisome components. These filaments fail to produce colonies on solid medium, in which synthesis of FtsZ is induced, upon being diluted by a factor greater than 4. However, once the initial FtsZ levels are recovered in liquid culture, they resume division, and their plating efficiency returns to normal. The potential septation sites generated in the FtsZ-deprived filaments are not annihilated, and once sufficient FtsZ is accumulated, they all become active and divide to produce cells of normal length. FtsZ-deprived cells accumulate defects in their physiology, including an abnormally high number of unsegregated nucleoids that may result from the misplacement of FtsK. Their membrane integrity becomes compromised and the amount of membrane proteins, such as FtsK and ZipA, increases. FtsZ-deprived cells also show an altered expression pattern, namely, transcription of several genes responding to DNA damage increases, whereas transcription of some ribosomal or global transcriptional regulators decreases. We propose that the changes caused by the depletion of FtsZ, besides stopping division, weaken the cell, diminishing its resiliency to minor challenges, such as dilution stress. Our results suggest a role for FtsZ, in addition to its already known effect in the constriction of E. coli, in protecting the nondividing cells against minor stress. This protection can even be exerted when an inactive FtsZ is produced, but it is lost when the protein is altogether absent. These results have implications in fields like synthetic biology or antimicrobial discovery. The construction of synthetic divisomes in the test tube may need to preserve unsuspected roles, such as this newly found FtsZ property, to guarantee the stability of artificial containers. Whereas the effects on viability caused by inhibiting the activity of FtsZ may be partly overcome by filamentation, the absence of FtsZ is not tolerated by E. coli, an observation that may help in the design of effective antimicrobial compounds.
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Gupta A, Lloyd-Price J, Ribeiro AS. In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. In Silico Biol 2016; 12:9-21. [PMID: 25318468 PMCID: PMC4923715 DOI: 10.3233/isb-140462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent evidence suggests that cells employ functionally asymmetric partitioning schemes in division to cope with aging. We explore various schemes in silico, with a stochastic model of Escherichia coli that includes gene expression, non-functional proteins generation, aggregation and polar retention, and molecule partitioning in division. The model is implemented in SGNS2, which allows stochastic, multi-delayed reactions within hierarchical, transient, interlinked compartments. After setting parameter values of non-functional proteins’ generation and effects that reproduce realistic intracellular and population dynamics, we investigate how the spatial organization of non-functional proteins affects mean division times of cell populations in lineages and, thus, mean cell numbers over time. We find that division times decrease for increasingly asymmetric partitioning. Also, increasing the clustering of non-functional proteins decreases division times. Increasing the bias in polar segregation further decreases division times, particularly if the bias favors the older pole and aggregates’ polar retention is robust. Finally, we show that the non-energy consuming retention of inherited non-functional proteins at the older pole via nucleoid occlusion is a source of functional asymmetries and, thus, is advantageous. Our results suggest that the mechanisms of intracellular organization of non-functional proteins, including clustering and polar retention, affect the vitality of E. coli populations.
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Affiliation(s)
| | | | - Andre S. Ribeiro
- Corresponding author: Andre S. Ribeiro, Department of Signal Processing, Tampere University of Technology, P.O. Box 553, 33101 Tampere, Finland. Tel.: +358 408490736; Fax: +358 331154989;
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20
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Blanchard AE, Lu T. Bacterial social interactions drive the emergence of differential spatial colony structures. BMC SYSTEMS BIOLOGY 2015; 9:59. [PMID: 26377684 PMCID: PMC4573487 DOI: 10.1186/s12918-015-0188-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/08/2015] [Indexed: 12/25/2022]
Abstract
Background Social interactions have been increasingly recognized as one of the major factors that contribute to the dynamics and function of bacterial communities. To understand their functional roles and enable the design of robust synthetic consortia, one fundamental step is to determine the relationship between the social interactions of individuals and the spatiotemporal structures of communities. Results We present a systematic computational survey on this relationship for two-species communities by developing and utilizing a hybrid computational framework that combines discrete element techniques with reaction-diffusion equations. We found that deleterious interactions cause an increased variance in relative abundance, a drastic decrease in surviving lineages, and a rough expanding front. In contrast, beneficial interactions contribute to a reduced variance in relative abundance, an enhancement in lineage number, and a smooth expanding front. We also found that mutualism promotes spatial homogeneity and population robustness while competition increases spatial segregation and population fluctuations. To examine the generality of these findings, a large set of initial conditions with varying density and species abundance was tested and analyzed. In addition, a simplified mathematical model was developed to provide an analytical interpretation of the findings. Conclusions This work advances our fundamental understanding of bacterial social interactions and population structures and, simultaneously, benefits synthetic biology for facilitated engineering of artificial microbial consortia. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0188-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew E Blanchard
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, 61801, USA.
| | - Ting Lu
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, 61801, USA. .,Department of Bioengineering, University of Illinois at Urbana-Champaign, 1304 West Springfield Avenue, Urbana, 61801, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, 61801, USA.
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21
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Abstract
UNLABELLED Although Escherichia coli is a very small (1- to 2-μm) rod-shaped cell, here we describe an E. coli mutant that forms enormously long cells in rich media such as Luria broth, as long indeed as 750 μm. These extremely elongated (eel) cells are as long as the longest bacteria known and have no internal subdivisions. They are metabolically competent, elongate rapidly, synthesize DNA, and distribute cell contents along this length. They lack only the ability to divide. The concentration of the essential cell division protein FtsZ is reduced in these eel cells, and increasing this concentration restores division. IMPORTANCE Escherichia coli is usually a very small bacterium, 1 to 2 μm long. We have isolated a mutant that forms enormously long cells, 700 times longer than the usual E. coli cell. E. coli filaments that form under other conditions usually die within a few hours, whereas our mutant is fully viable even when it reaches such lengths. This mutant provides a useful tool for the study of aspects of E. coli physiology that are difficult to investigate with small cells.
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22
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Gupta A, Lloyd-Price J, Oliveira SMD, Yli-Harja O, Muthukrishnan AB, Ribeiro AS. Robustness of the division symmetry inEscherichia coliand functional consequences of symmetry breaking. Phys Biol 2014; 11:066005. [DOI: 10.1088/1478-3975/11/6/066005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Breaking through the stress barrier: the role of BolA in Gram-negative survival. World J Microbiol Biotechnol 2014; 30:2559-66. [PMID: 25038865 DOI: 10.1007/s11274-014-1702-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/11/2014] [Indexed: 10/25/2022]
Abstract
The morphogene bolA plays a significant role in the adaptation of Escherichia coli to general stresses. In general, bacteria can thrive and persist under harsh conditions, counteracting external stresses by using varied mechanisms, including biofilm formation, changes in cell shape, size and protein content, together with alterations in the cell wall structure, thickness and permeability. In E. coli, an increased expression of bolA occurs mainly under stress challenges and when bacterial morphology changes from rod-like to spherical. Moreover, BolA is able to induce biofilm formation and changes in the outer membrane, making it less permeable to harmful agents. Although there has been substantial progress in the description of BolA activity, its role on global cell physiology is still incomplete. Proteins with strong homology to BolA have been found in most living organisms, in many cases also exerting a regulatory role. In this review we summarize current knowledge on the role of BolA, mainly in E. coli, and discuss its implication in global regulation in relation to stress.
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24
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Belgrave AMT, Wolgemuth CW. Elasticity and biochemistry of growth relate replication rate to cell length and cross-link density in rod-shaped bacteria. Biophys J 2014; 104:2607-11. [PMID: 23790368 DOI: 10.1016/j.bpj.2013.04.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/28/2013] [Accepted: 04/11/2013] [Indexed: 01/13/2023] Open
Abstract
In rod-shaped bacteria, cell morphology is correlated with the replication rate. For a given species, cells that replicate faster are longer and have less cross-linked cell walls. Here, we propose a simple mechanochemical model that explains the dependence of cell length and cross-linking on the replication rate. Our model shows good agreement with existing experimental data and provides further evidence that cell wall synthesis is mediated by multienzyme complexes; however, our results suggest that these synthesis complexes only mediate glycan insertion and cross-link severing, whereas recross-linking is performed independently.
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Affiliation(s)
- Akeisha M T Belgrave
- University of Connecticut Health Center, Department of Cell Biology and Center for Cell Analysis and Modeling, Farmington, Connecticut, USA
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25
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Stochasticity in colonial growth dynamics of individual bacterial cells. Appl Environ Microbiol 2013; 79:2294-301. [PMID: 23354712 DOI: 10.1128/aem.03629-12] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conventional bacterial growth studies rely on large bacterial populations without considering the individual cells. Individual cells, however, can exhibit marked behavioral heterogeneity. Here, we present experimental observations on the colonial growth of 220 individual cells of Salmonella enterica serotype Typhimurium using time-lapse microscopy videos. We found a highly heterogeneous behavior. Some cells did not grow, showing filamentation or lysis before division. Cells that were able to grow and form microcolonies showed highly diverse growth dynamics. The quality of the videos allowed for counting the cells over time and estimating the kinetic parameters lag time (λ) and maximum specific growth rate (μmax) for each microcolony originating from a single cell. To interpret the observations, the variability of the kinetic parameters was characterized using appropriate probability distributions and introduced to a stochastic model that allows for taking into account heterogeneity using Monte Carlo simulation. The model provides stochastic growth curves demonstrating that growth of single cells or small microbial populations is a pool of events each one of which has its own probability to occur. Simulations of the model illustrated how the apparent variability in population growth gradually decreases with increasing initial population size (N(0)). For bacterial populations with N(0) of >100 cells, the variability is almost eliminated and the system seems to behave deterministically, even though the underlying law is stochastic. We also used the model to demonstrate the effect of the presence and extent of a nongrowing population fraction on the stochastic growth of bacterial populations.
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26
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Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli. Proc Natl Acad Sci U S A 2012; 109:E2561-8. [PMID: 22908292 DOI: 10.1073/pnas.1209742109] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cell size varies greatly among different types of cells, but the range in size that a specific cell type can reach is limited. A long-standing question in biology is how cells control their size. Escherichia coli adjusts size and growth rate according to the availability of nutrients so that it grows larger and faster in nutrient-rich media than in nutrient-poor media. Here, we describe how, using classical genetics, we have isolated a remarkably small E. coli mutant that has undergone a 70% reduction in cell volume with respect to wild type. This mutant lacks FabH, an enzyme involved in fatty acid biosynthesis that previously was thought to be essential for the viability of E. coli. We demonstrate that although FabH is not essential in wild-type E. coli, it is essential in cells that are defective in the production of the small-molecule and global regulator ppGpp. Furthermore, we have found that the loss of FabH causes a reduction in the rate of envelope growth and renders cells unable to regulate cell size properly in response to nutrient excess. Therefore we propose a model in which fatty acid biosynthesis plays a central role in regulating the size of E. coli cells in response to nutrient availability.
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27
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Physiological and proteomic adaptation of "Aromatoleum aromaticum" EbN1 to low growth rates in benzoate-limited, anoxic chemostats. J Bacteriol 2012; 194:2165-80. [PMID: 22366417 DOI: 10.1128/jb.06519-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Aromatoleum aromaticum" EbN1 was cultivated at different growth rates in benzoate-limited chemostats under nitrate-reducing conditions. Physiological characteristics, proteome dynamics, phospholipid-linked fatty acid (PLFA) composition, and poly(3-hydroxybutyrate) (PHB) content were analyzed in steady-state cells at low (μ(low)) (0.036 h(-1)), medium (μ(med)) (0.108 h(-1)), and high (μ(high)) (0.180 h(-1)) growth rates. A positive correlation to growth rate was observed for cellular parameters (cell size, and DNA and protein contents). The free energy consumed for biomass formation steadily increased with growth rate. In contrast, the energy demand for maintenance increased only from μ(low) to μ(med) and then remained constant until μ(high). The most comprehensive proteomic changes were observed at μ(low) compared to μ(high). Uniformly decreased abundances of protein components of the anaerobic benzoyl coenzyme A (benzoyl-CoA) pathway, central carbon metabolism, and information processing agree with a general deceleration of benzoate metabolism and cellular processes in response to slow growth. In contrast, increased abundances were observed at μ(low) for diverse catabolic proteins and components of uptake systems in the absence of the respective substrate (aromatic or aliphatic compounds) and for proteins involved in stress responses. This potential catabolic versatility and stress defense during slow growth may be interpreted as preparation for future needs.
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28
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López-Villarejo J, Diago-Navarro E, Hernández-Arriaga AM, Díaz-Orejas R. Kis antitoxin couples plasmid R1 replication and parD (kis,kid) maintenance modules. Plasmid 2012; 67:118-27. [PMID: 22244926 DOI: 10.1016/j.plasmid.2011.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 12/28/2011] [Accepted: 12/29/2011] [Indexed: 10/14/2022]
Abstract
The coupling between the replication and parD (kis, kid) maintenance modules of R1 has been revisited here by the isolation of a significant collection of conditional replication mutants in the pKN1562 mini-R1 plasmid, and in its derivative, pJLV01, specifically affected in the RNase activity of the Kid toxin. This new analysis aims to identify key factors in this coupling. For this purpose we have quantified and characterized the restriction introduced by parD to isolate conditional replication mutants of this plasmid, a signature of the modular coupling. This restriction depends on the RNase activity of the Kid toxin and it is relieved by either over-expression of the Kis antitoxin or by preventing its degradation by Lon and ClpAP proteases. Based on these data and on the correlation between copy numbers and parD transcriptional levels obtained in the different mutants, it is proposed that a reduction of Kis antitoxin levels in response to inefficient plasmid replication is the key factor for coupling plasmid replication and parD modules.
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Affiliation(s)
- Juan López-Villarejo
- Centro de Investigaciones Biológicas-CSIC, Dept. de Microbiología Molecular y Biología de la Infección, C/Ramiro de Maeztu 9, 28040 Madrid, Spain
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29
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Mendelson NH, Thwaites JJ. Bending, Folding, and Buckling Processes During Bacterial Macrofiber Morphogenesis. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-174-171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractBacterial macrofibers are multicellular structures produced by certain cultures of rod-shaped cells when cells do not separate from one another after septation. Chains of cells arise that twist as they grow. This twisting is thought to reflect either the geometry of assembly of the cell wall polymers or some aspect of their anisotropic behaviour after insertion into the wall. The degree and direction of twisting is controlled by genetic and physiological factors such as growth temperature and the concentration of certain ions and other compounds in the growth medium. Twisting is ultimately responsible for a shape deformation of the cells into double-strand helical forms. The mechanical basis for shape determination and eventually macrofiber morphogenesis involves a folding process, the touching of elongating structures to themselves, blocked rotation, and shape deformation. In normal growth medium, time-lapse films reveal that writhing motions which lead to increased bending result in touching. In media of increased viscosity, bending is suppressed although elongation and rotation are unaffected. Folding occurs but now as a result of buckling. The forces responsible for both processes derive from g–, wth and interaction of the cell surface with the growth medium. The helical shape, once established, is heritable. Whether the shape becomes “set” by cross-linking or other modification of the peptidoglycan remains to be determined. From the perspective of materials science, macrofibers represent a new biodegradable fiber, the mechanical properties of which are governed by cell wall peptidoglycan. Both peptidoglycan and the other major cell wall polymer, teichoic acid, contain many reactive groups to which new constituents can be attached. Thus, there is now the potential to create a range of new materials using bacterial cells as the structural backbone.
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30
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Hanson RB, Shafer D, Ryan T, Pope DH, Lowery HK. Bacterioplankton in antarctic ocean waters during late austral winter: abundance, frequency of dividing cells, and estimates of production. Appl Environ Microbiol 2010; 45:1622-32. [PMID: 16346297 PMCID: PMC242509 DOI: 10.1128/aem.45.5.1622-1632.1983] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterioplankton productivity in Antarctic waters of the eastern South Pacific Ocean and Drake Passage was estimated by direct counts and frequency of dividing cells (FDC). Total bacterioplankton assemblages were enumerated by epifluorescent microscopy. The experimentally determined relationship between in situ FDC and the potential instantaneous growth rate constant (mu) is best described by the regression equation ln mu = 0.081 FDC - 3.73. In the eastern South Pacific Ocean, bacterioplankton abundance (2 x 10 to 3.5 x 10 cells per ml) and FDC (11%) were highest at the Polar Front (Antarctic Convergence). North of the Subantarctic Front, abundance and FDC were between 1 x 10 to 2 x 10 cells per ml and 3 to 5%, respectively, and were vertically homogeneous to a depth of 600 m. In Drake Passage, abundance (10 x 10 cells per ml) and FDC (16%) were highest in waters south of the Polar Front and near the sea ice. Subantarctic waters in Drake Passage contained 4 x 10 cells per ml with 4 to 5% FDC. Instantaneous growth rate constants ranged between 0.029 and 0.088 h. Using estimates of potential mu and measured standing stocks, we estimated productivity to range from 0.62 mug of C per liter . day in the eastern South Pacific Ocean to 17.1 mug of C per liter . day in the Drake Passage near the sea ice.
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Affiliation(s)
- R B Hanson
- Skidaway Institute of Oceanography, Savannah, Georgia 31406, and Department of Biology & Freshwater Institute, Rensselaer Polytechnic Institute, Troy, New York 12181
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31
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Bell RT, Ahlgren GM, Ahlgren I. Estimating Bacterioplankton Production by Measuring [H]thymidine Incorporation in a Eutrophic Swedish Lake. Appl Environ Microbiol 2010; 45:1709-21. [PMID: 16346304 PMCID: PMC242528 DOI: 10.1128/aem.45.6.1709-1721.1983] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterioplankton abundance, [H]thymidine incorporation, CO(2) uptake in the dark, and fractionated primary production were measured on several occasions between June and August 1982 in eutrophic Lake Norrviken, Sweden. Bacterioplankton abundance and carbon biomass ranged from 0.5 x 10 to 2.4 x 10 cells liter and 7 to 47 mug of C liter, respectively. The average bacterial cell volume was 0.185 mum. [H]thymidine incorporation into cold-trichloroacetic acid-insoluble material ranged from 12 x 10 to 200 x 10 mol liter h. Bacterial carbon production rates were estimated to be 0.2 to 7.1 mug of C liter h. Bacterial production estimates from [H]thymidine incorporation and CO(2) uptake in the dark agreed when activity was high but diverged when activity was low and when blue-green algae (cyanobacteria) dominated the phytoplankton. Size fractionation indicated negligible uptake of [H]thymidine in the >3-mum fraction during a chrysophycean bloom in early June. We found that >50% of the H activity was in the >3-mum fraction in late August; this phenomenon was most likely due to Microcystis spp., their associated bacteria, or both. Over 60% of the CO(2) uptake in the dark was attributed to algae on each sampling occasion. Algal exudate was an important carbon source for planktonic bacteria. Bacterial production was roughly 50% of primary production.
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Affiliation(s)
- R T Bell
- Institute of Limnology, Uppsala University, S-751 22 Uppsala, Sweden
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32
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Abstract
SUMMARYWe calculated the rates of segregation due to plasmid incompatibility under several simple models. A common feature of all the models that we considered is that incompatibility is caused by the inability of the segregation mechanism to distinguish between two incompatible plasmids.We measured the rate of segregation due to incompatibility of a pair of ColE1 derivatives under two conditions: (1) One plasmid was introduced into cells carrying the other by conjugation. (2) Cells carrying both plasmids were maintained by selection and then selection was released.Interpretation of the results was made more difficult by effects of the Plasmids on the host cell's growth rate. These experiments gave results in agreement with the predictions of a random pool replication model. Published results were also in reasonable agreement with this model.
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Freire P, Neves Moreira R, Arraiano CM. BolA Inhibits Cell Elongation and Regulates MreB Expression Levels. J Mol Biol 2009; 385:1345-51. [DOI: 10.1016/j.jmb.2008.12.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 12/05/2008] [Accepted: 12/10/2008] [Indexed: 11/16/2022]
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34
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Reshes G, Vanounou S, Fishov I, Feingold M. Cell shape dynamics in Escherichia coli. Biophys J 2008; 94:251-64. [PMID: 17766333 PMCID: PMC2134870 DOI: 10.1529/biophysj.107.104398] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Accepted: 07/06/2007] [Indexed: 11/18/2022] Open
Abstract
Bacteria are the simplest living organisms. In particular, Escherichia coli has been extensively studied and it has become one of the standard model systems in microbiology. However, optical microscopy studies of single E. coli have been limited by its small size, approximately 1 x 3 microm, not much larger than the optical resolution, approximately 0.25 microm. As a result, not enough quantitative dynamical information on the life cycle of single E. coli is presently available. We suggest that, by careful analysis of images from phase contrast and fluorescence time-lapse microscopy, this limitation can be bypassed. For example, we show that applying this approach to monitoring morphogenesis in individual E. coli leads to a simple, quantitative description of this process. First, we find the time when the formation of the septum starts, tau(c). It occurs much earlier than the time when the constriction can be directly observed by phase contrast. Second, we find that the growth law of single cells is more likely bilinear/trilinear than exponential. This is further supported by the relations that hold between the corresponding growth rates. These methods could be further extended to study the dynamics of cell components, e.g., the nucleoid and the Z-ring.
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Affiliation(s)
- Galina Reshes
- Department of Physics, Ben Gurion University, Beer Sheva, Israel
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35
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Abstract
Phage lambda lyses the host Escherichia coli at a precisely scheduled time after induction. Lysis timing is determined by the action of phage holins, which are small proteins that induce hole formation in the bacterium's cytoplasmic membrane. We present a two-stage nucleation model of lysis timing, with the nucleation of condensed holin rafts on the inner membrane followed by the nucleation of a hole within those rafts. The nucleation of holin rafts accounts for most of the delay of lysis after induction. Our simulations of this model recover the accurate lysis timing seen experimentally and show that the timing accuracy is optimal. An enhanced holin-holin interaction is needed in our model to recover experimental lysis delays after the application of membrane poison, and such early triggering of lysis is possible only after the inner membrane is supersaturated with holin. Antiholin reduces the delay between membrane depolarization and lysis and leads to an earlier time after which triggered lysis is possible.
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Affiliation(s)
- Gillian L Ryan
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, Canada
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36
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Riesenberg D, Erdmann A, Bergter F. Distribution functions of variables characterizing the mycelial morphology of Streptomyces hygtroscopicus
grown in glucose-limited chemostat cultures. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/jobm.19790190705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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37
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Kretschmer S. Kinetics of vegetative growth of Thermoactinomyces vulgaris. J Basic Microbiol 2007. [DOI: 10.1002/jobm.19780181002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Zaritsky A, Woldringh CL, Einav M, Alexeeva S. Use of thymine limitation and thymine starvation to study bacterial physiology and cytology. J Bacteriol 2006; 188:1667-79. [PMID: 16484178 PMCID: PMC1426543 DOI: 10.1128/jb.188.5.1667-1679.2006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Arieh Zaritsky
- Department of Life Sciences, Ben-Gurion University of the Negev, POB 653, Be'er-Sheva 84105, Israel.
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39
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Buchwald P, Sveiczer A. The time-profile of cell growth in fission yeast: model selection criteria favoring bilinear models over exponential ones. Theor Biol Med Model 2006; 3:16. [PMID: 16566825 PMCID: PMC1444923 DOI: 10.1186/1742-4682-3-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 03/27/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is considerable controversy concerning the exact growth profile of size parameters during the cell cycle. Linear, exponential and bilinear models are commonly considered, and the same model may not apply for all species. Selection of the most adequate model to describe a given data-set requires the use of quantitative model selection criteria, such as the partial (sequential) F-test, the Akaike information criterion and the Schwarz Bayesian information criterion, which are suitable for comparing differently parameterized models in terms of the quality and robustness of the fit but have not yet been used in cell growth-profile studies. RESULTS Length increase data from representative individual fission yeast (Schizosaccharomyces pombe) cells measured on time-lapse films have been reanalyzed using these model selection criteria. To fit the data, an extended version of a recently introduced linearized biexponential (LinBiExp) model was developed, which makes possible a smooth, continuously differentiable transition between two linear segments and, hence, allows fully parametrized bilinear fittings. Despite relatively small differences, essentially all the quantitative selection criteria considered here indicated that the bilinear model was somewhat more adequate than the exponential model for fitting these fission yeast data. CONCLUSION A general quantitative framework was introduced to judge the adequacy of bilinear versus exponential models in the description of growth time-profiles. For single cell growth, because of the relatively limited data-range, the statistical evidence is not strong enough to favor one model clearly over the other and to settle the bilinear versus exponential dispute. Nevertheless, for the present individual cell growth data for fission yeast, the bilinear model seems more adequate according to all metrics, especially in the case of wee1Delta cells.
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Affiliation(s)
- Peter Buchwald
- IVAX Research, Inc., 4400 Biscayne Blvd., Miami, FL 33137, USA
| | - Akos Sveiczer
- Department of Agricultural Chemical Technology, Budapest University of Technology and Economics, 1111 Budapest, Szt. Gellért tér 4., Hungary
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40
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Prozorov AA. The Bacterial Cell Cycle: DNA Replication, Nucleoid Segregation, and Cell Division. Microbiology (Reading) 2005. [DOI: 10.1007/s11021-005-0077-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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41
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Grover NB, Eidelstein E, Koppes LJH. Bacterial shape maintenance: an evaluation of various models. J Theor Biol 2004; 227:547-59. [PMID: 15038989 DOI: 10.1016/j.jtbi.2003.11.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2003] [Revised: 11/05/2003] [Accepted: 11/13/2003] [Indexed: 11/19/2022]
Abstract
In this article, we examine a large number of combinations of growth models, with separate attention to cell volume, cylindrical surface-area, polar caps, nascent poles, onset of constriction, precision of cell division and interdivision-time dispersion, for Escherichia coli cells growing in steady state at various doubling times. Our main conclusion is striking, and quite general: exponential cylindrical surface-area growth is not possible, irrespective of the behaviour of cell volume, the polar regions, the nascent poles, or any other feature of cell growth-such cells never reach steady state. The same is true of linear cylindrical surface-area growth, regardless of when during the cell cycle the doubling in growth rate takes place. Only after the introduction of feedback into the surface-area growth law, do the cultures attain steady state, all of them. The other components of the models contribute only marginally to the properties of the steady state. Thus, whether the feedback applies just to the cylindrical portion of the cell or to its entire surface area affects only the coefficient of variation of cell radius and the radius-volume correlation. The dynamics of old-pole maintenance, constant area or constant shape, influences the radius-length and radius-volume correlations and, to a much lesser extent, the coefficients of variation of cell radius and length; how the nascent poles grow, whether linearly or exponentially, does not seem to matter at all. The absolute dimensions of the cells are set by the growth rate of the culture and have almost no effect when the feedback is taken to apply to the entire cell surface area; when it is limited to the cylindrical portion of the cell, however, both radius-length and radius-volume correlations increase with increasing doubling time. Comparison with published values was inconclusive. The nature of cell surface-area growth has therefore been settled, but whether the volume increases by simple-exponential or by pseudo-exponential growth, or whether the old poles maintain a constant shape or a constant area during the cell cycle, can be determined only with more precise experimental data. The form of nascent-pole growth is not resolvable by present techniques.
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Affiliation(s)
- N B Grover
- Hubert H. Humphrey Center for Experimental Medicine and Cancer Research, The Hebrew University Faculty of Medicine, PO Box 12272, Jerusalem 91120, Israel.
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42
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Abstract
During the cell cycle, major bulk parameters such as volume, dry mass, total protein, and total RNA double and such growth is a fundamental property of the cell cycle. The patterns of growth in volume and total protein or RNA provide an "envelope" that contains and may restrict the gear wheels. The main parameters of cell cycle growth were established in the earlier work when people moved from this field to the reductionist approaches of molecular biology, but very little is known on the patterns of metabolism. Most of the bulk properties of cells show a continuous increase during the cell cycle, although the exact pattern of this increase may vary. Since the earliest days, there have been two popular models, based on an exponential increase and linear increase. In the first, there is no sharp change in the rate of increase through the cycle but a smooth increase by a factor of two. In the second, the rate of increase stays constant through much of the cycle but it doubles sharply at a rate change point (RCP). It is thought that the exponential increase is caused by the steady growth of ribosome numbers and the linear pattern is caused by a doubling of the structural genes during the S period giving an RCP--a "gene dosage" effect. In budding yeast, there are experiments fitting both models but on balance slightly favoring "gene dosage." In fission yeast, there is no good evidence of exponential increase. All the bulk properties, except O2 consumption, appear to follow linear patterns with an RCP during the short S period. In addition, there is in wild-type cells a minor RCP in G2 where the rate increases by 70%. In mammalian cells, there is good but not extensive evidence of exponential increase. In Escherichia coli, exponential increase appears to be the pattern. There are two important points: First, some proteins do not show peaks of periodic synthesis. If they show patterns of exponential increase both they and the total protein pattern will not be cell cycle regulated. However, if the total protein pattern is not exponential, then a majority of the individual proteins will be so regulated. If this majority pattern is linear, then it can be detected from rate measurements on total protein. However, it would be much harder at the level of individual proteins where the methods are at present not sensitive enough to detect a rate change by a factor of two. At a simple level, it is only the exponential increase that is not cell cycle regulated in a synchronous culture. The existence of a "size control" is well known and the control has been studied for a long time, but it has been remarkably resistant to molecular analysis. The attainment of a critical size triggers the periodic events of the cycle such as the S period and mitosis. This control acts as a homeostatic effector that maintains a constant "average" cell size at division through successive cycles in a growing culture. It is a vital link coordinating cell growth with periodic events of the cycle. A size control is present in all the systems and appears to operate near the start of S or of mitosis when the cell has reached a critical size, but the molecular mechanism by which size is measured remains both obscure and a challenge. A simple version might be for the cell to detect a critical concentration of a gene product.
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Affiliation(s)
- J M Mitchison
- Institute for Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
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Graña M, Acerenza L. A model combining cell physiology and population genetics to explain Escherichia coli laboratory evolution. BMC Evol Biol 2003; 1:12. [PMID: 11782284 PMCID: PMC64492 DOI: 10.1186/1471-2148-1-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2001] [Accepted: 12/04/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Laboratory experiments under controlled conditions during thousands of generations are useful tools to assess the processes underlying bacterial evolution. As a result of these experiments, the way in which the traits change in time is obtained. Under these conditions, the bacteria E. coli shows a parallel increase in cell volume and fitness. RESULTS To explain this pattern it is required to consider organismic and population contributions. For this purpose we incorporate relevant information concerning bacterial structure, composition and transformations in a minimal modular model. In the short time scale, the model reproduces the physiological responses of the traits to changes in nutrient concentration. The decay of unused catabolic functions, found experimentally, is introduced in the model using simple population genetics. The resulting curves representing the evolution of volume and fitness in time are in good agreement with those obtained experimentally. CONCLUSIONS This study draws attention on physiology when studying evolution. Moreover, minimal modular models appear to be an adequate strategy to unite these barely related disciplines of biology.
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Affiliation(s)
- Martín Graña
- Sección Biofísica, Facultad de Ciencias Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Luis Acerenza
- Sección Biofísica, Facultad de Ciencias Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
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Hargreaves D, Santos-Sierra S, Giraldo R, Sabariegos-Jareño R, de la Cueva-Méndez G, Boelens R, Díaz-Orejas R, Rafferty JB. Structural and functional analysis of the kid toxin protein from E. coli plasmid R1. Structure 2002; 10:1425-33. [PMID: 12377128 DOI: 10.1016/s0969-2126(02)00856-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have determined the structure of Kid toxin protein from E. coli plasmid R1 involved in stable plasmid inheritance by postsegregational killing of plasmid-less daughter cells. Kid forms a two-component system with its antagonist, Kis antitoxin. Our 1.4 A crystal structure of Kid reveals a 2-fold symmetric dimer that closely resembles the DNA gyrase-inhibitory toxin protein CcdB from E. coli F plasmid despite the lack of any notable sequence similarity. Analysis of nontoxic mutants of Kid suggests a target interaction interface associated with toxicity that is in marked contrast to that proposed for CcdB. A possible region for interaction of Kid with the antitoxin is proposed that overlaps with the target binding site and may explain the mode of antitoxin action.
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Affiliation(s)
- David Hargreaves
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, United Kingdom
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45
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Santos JM, Lobo M, Matos APA, De Pedro MA, Arraiano CM. The gene bolA regulates dacA (PBP5), dacC (PBP6) and ampC (AmpC), promoting normal morphology in Escherichia coli. Mol Microbiol 2002; 45:1729-40. [PMID: 12354237 DOI: 10.1046/j.1365-2958.2002.03131.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The gene bolA has been shown to trigger the formation of osmotically stable round cells when overexpressed in stationary phase. We show that in poor growth conditions bolA is essential for normal cell morphology in stationary phase and under conditions of starvation. During exponential growth bolA promotes round morphology through a mechanism that is strictly dependent on the two main Escherichia colid,d-carboxypeptidases, PBP5 and PBP6. The results show that bolA controls the levels of transcription of dacA (PBP5), dacC (PBP6) and ampC (AmpC), a class C beta-lactamase, thus connecting for the first time penicillin binding proteins (PBPs) and beta-lactamases at the level of gene regulation. Furthermore, PBP5 and PBP6 are shown to be independently regulated and to have distinct effects on the peptidoglycan layer. The evidence presented demonstrates that bolA is a regulator of cell wall biosynthetic enzymes with different roles in cell morphology and cell division.
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Affiliation(s)
- Jorge M Santos
- Instituto de Technologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Addinall SG, Holland B. The tubulin ancestor, FtsZ, draughtsman, designer and driving force for bacterial cytokinesis. J Mol Biol 2002; 318:219-36. [PMID: 12051832 DOI: 10.1016/s0022-2836(02)00024-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We discuss in this review the regulation of synthesis and action of FtsZ, its structure in relation to tubulin and microtubules, and the mechanism of polymerization and disassembly (contraction) of FtsZ rings from a specific nucleation site (NS) at mid cell. These topics are considered in the light of recent immunocytological studies, high resolution structures of some division proteins and results indicating how bacteria may measure their mid cell point.
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Affiliation(s)
- Stephen G Addinall
- School of Biological Sciences, University Manchester, 2.205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
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de Pedro MA, Donachie WD, Höltje JV, Schwarz H. Constitutive septal murein synthesis in Escherichia coli with impaired activity of the morphogenetic proteins RodA and penicillin-binding protein 2. J Bacteriol 2001; 183:4115-26. [PMID: 11418550 PMCID: PMC95299 DOI: 10.1128/jb.183.14.4115-4126.2001] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pattern of peptidoglycan (murein) segregation in cells of Escherichia coli with impaired activity of the morphogenetic proteins penicillin-binding protein 2 and RodA has been investigated by the D-cysteine-biotin immunolabeling technique (M. A. de Pedro, J. C. Quintela, J.-V. Höltje, and H. Schwarz, J. Bacteriol. 179:2823-2834, 1997). Inactivation of these proteins either by amdinocillin treatment or by mutations in the corresponding genes, pbpA and rodA, respectively, leads to the generation of round, osmotically stable cells. In normal rod-shaped cells, new murein precursors are incorporated all over the lateral wall in a diffuse manner, being mixed up homogeneously with preexisting material, except during septation, when strictly localized murein synthesis occurs. In contrast, in rounded cells, incorporation of new precursors is apparently a zonal process, localized at positions at which division had previously taken place. Consequently, there is no mixing of new and old murein. Old murein is preserved for long periods of time in large, well-defined areas. We propose that the observed patterns are the result of a failure to switch off septal murein synthesis at the end of septation events. Furthermore, the segregation results confirm that round cells of rodA mutants do divide in alternate, perpendicular planes as previously proposed (K. J. Begg and W. D. Donachie, J. Bacteriol. 180:2564-2567, 1998).
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Affiliation(s)
- M A de Pedro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain.
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48
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Abstract
A discussion of some aspects of the regulation of chromosome replication, segregation and cell division in Escherichia coli.
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Affiliation(s)
- W D Donachie
- Department of Molecular Biology, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, UK
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49
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Grover NB, Woldringh CL. Dimensional regulation of cell-cycle events in Escherichia coli during steady-state growth. MICROBIOLOGY (READING, ENGLAND) 2001; 147:171-81. [PMID: 11160811 DOI: 10.1099/00221287-147-1-171] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two opposing models have been put forward in the literature to describe the changes in the shape of individual Escherichia coli cells in steady-state growth that take place during the cell cycle: the Length model, which maintains that the regulating dimension is cell length, and the Volume model, which asserts it to be cell volume. In addition, the former model envisages cell diameter as decreasing with length up to constriction whereas the latter sees it as being constrained by the rigid cell wall. These two models differ in the correlations they predict between the various cellular dimensions (diameter, length, volume) not only across the entire population of bacteria but also, and especially, within subpopulations that define specific cell-cycle events (division, for example, or onset of constriction); the coefficients of variation at these specific events are also expected to be very different. Observations from cells prepared for electron microscopy (air-dried) and for phase-contrast microscopy (hydrated) appeared qualitatively largely in accordance with the predictions of the Length model. To obtain a more quantitative comparison, simulations were carried out of populations defined by each of the models; again, the results favoured the Length model. Finally, in age-selected cells using membrane elution, the diameter-length and diameter-volume correlations were in complete agreement with the Length model, as were the coefficients of variation. It is concluded that, at least with respect to cell-cycle events such as onset of constriction and cell division, length rather than volume is the controlling dimension.
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Affiliation(s)
- N B Grover
- Hubert H. Humphrey Center for Experimental Medicine and Cancer Research, Hebrew University, Faculty of Medicine, PO Box 12272, Jerusalem 91120, Israel
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Lu C, Stricker J, Erickson HP. FtsZ from Escherichia coli, Azotobacter vinelandii, and Thermotoga maritima--quantitation, GTP hydrolysis, and assembly. CELL MOTILITY AND THE CYTOSKELETON 2000; 40:71-86. [PMID: 9605973 DOI: 10.1002/(sici)1097-0169(1998)40:1<71::aid-cm7>3.0.co;2-i] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have cloned the ftsZ genes from Thermotoga maritima and Azotobacter vinelandii and expressed the proteins (TmFtsZ and AzFtsZ) in Escherichia coli. We compared these proteins to E. coli FtsZ (EcFtsZ), and found that several remarkable features of their GTPase activities were similar for all three species, implying that these characteristics may be universal among FtsZs. Using a calibrated protein assay, we found that all three FtsZs bound 1 mole guanine nucleotide per mole FtsZ and hydrolyzed GTP at high rates (> 2 GTP per FtsZ per min). All three required magnesium and a monovalent cation for GTP hydrolysis. Previous reports showed that EcFtsZ (and some other species) required potassium. We confirmed this specificity for EcFtsZ but found that potassium and sodium both worked for Az- and TmFtsZ. Specific GTPase activity had a striking dependence on FtsZ concentration: activity (per FtsZ molecule) was absent or low below 50 microg/ml, rose steeply from 50 to 300 microg/ml and plateaued at a constant high value above 300 microg/ml. This finding suggests that the active state requires a polymer that is assembled cooperatively at 50-300 microg/ml. A good candidate for the active polymer was visualized by negative stain electron microscopy--straight protofilaments and protofilament pairs were seen under all conditions with active GTPase. We suggest that the GTP hydrolysis of FtsZ may be coupled to assembly, as it is for tubulin, with hydrolysis occurring shortly after an FtsZ monomer associates onto a protofilament end. As a part of this study, we determined the concentration of EcFtsZ and TmFtsZ by quantitative amino acid analysis and used this to standardize the bicinchonic acid colorimetric assay. This is the first accurate determination of FtsZ concentration. Using this standard and quantitative Western blotting, we determined that the average E. coli cell has 15,000 molecules of FtsZ, at a concentration of 400 microg/ml. This is just above the plateau for full GTPase activity in vitro.
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Affiliation(s)
- C Lu
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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