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Chadha Y, Khurana A, Schmoller KM. Eukaryotic cell size regulation and its implications for cellular function and dysfunction. Physiol Rev 2024; 104:1679-1717. [PMID: 38900644 PMCID: PMC11495193 DOI: 10.1152/physrev.00046.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/24/2024] [Accepted: 06/19/2024] [Indexed: 06/22/2024] Open
Abstract
Depending on cell type, environmental inputs, and disease, the cells in the human body can have widely different sizes. In recent years, it has become clear that cell size is a major regulator of cell function. However, we are only beginning to understand how the optimization of cell function determines a given cell's optimal size. Here, we review currently known size control strategies of eukaryotic cells and the intricate link of cell size to intracellular biomolecular scaling, organelle homeostasis, and cell cycle progression. We detail the cell size-dependent regulation of early development and the impact of cell size on cell differentiation. Given the importance of cell size for normal cellular physiology, cell size control must account for changing environmental conditions. We describe how cells sense environmental stimuli, such as nutrient availability, and accordingly adapt their size by regulating cell growth and cell cycle progression. Moreover, we discuss the correlation of pathological states with misregulation of cell size and how for a long time this was considered a downstream consequence of cellular dysfunction. We review newer studies that reveal a reversed causality, with misregulated cell size leading to pathophysiological phenotypes such as senescence and aging. In summary, we highlight the important roles of cell size in cellular function and dysfunction, which could have major implications for both diagnostics and treatment in the clinic.
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Affiliation(s)
- Yagya Chadha
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Arohi Khurana
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
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2
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Tveit AT, Söllinger A, Rainer EM, Didriksen A, Hestnes AG, Motleleng L, Hellinger HJ, Rattei T, Svenning MM. Thermal acclimation of methanotrophs from the genus Methylobacter. THE ISME JOURNAL 2023; 17:502-513. [PMID: 36650275 PMCID: PMC10030640 DOI: 10.1038/s41396-023-01363-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Methanotrophs oxidize most of the methane (CH4) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH4 oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH4 oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH4 is consumed to support growth at different CH4 concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH4 uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH4 oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH4 consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH4 uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH4 emissions.
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Affiliation(s)
- Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Edda Marie Rainer
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alena Didriksen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Liabo Motleleng
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Hans-Jörg Hellinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Thomas Rattei
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
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3
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Lv X, Zhang R, Wang J, Morigen. The absence of CsdA in Escherichia coli increases DNA replication and cell size but decreases growth rate at low temperature. Biochem Biophys Res Commun 2022; 631:41-47. [PMID: 36166952 DOI: 10.1016/j.bbrc.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/26/2022]
Abstract
The CsdA protein is a highly conserved, DEAD-box RNA helicase and assists RNA structural remodeling at low temperature. We show that the fast-growing wild-type (WT) cells contain higher number of replication origins per cell with bigger cell size and the slowly growing cells possess less number of replication origins per cell with smaller cell size. The absence of CsdA leads to production of larger cells with higher number of origins per cell but slower growth at low temperature in an independent-manner of growth media. The phenotypes in ΔcsdA mutant are reversed by ectopic expression of CsdA or RNase R. A global transcription analysis shows that the absence of CsdA leads to significant decreases in transcription of about 200 genes at low temperature. These genes are associated with essential metabolic pathways, flagger assembly and cell division (minDE). It is likely that the slow growth of ΔcsdA cell results from the decreased transcription of essential metabolic genes, and the larger ΔcsdA cell could be a result of decreased transcription of minDE. The increased transcription of the nrdHIEF genes in ΔcsdA mutant is a likely reason that promotes DNA replication. We conclude that CsdA coordinates the cell cycle to growth by stabilizing mRNA of essential metabolic and cell division genes and degrading mRNA for nucleotide metabolic genes at low temperature.
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Affiliation(s)
- Xiaoli Lv
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; Department of Pharmacology of Pharmaceutical College, Inner Mongolia Medical University, Hohhot, China
| | - Ran Zhang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jing Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Morigen
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
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4
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Bhat D, Hauf S, Plessy C, Yokobayashi Y, Pigolotti S. Speed variations of bacterial replisomes. eLife 2022; 11:75884. [PMID: 35877175 PMCID: PMC9385209 DOI: 10.7554/elife.75884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Replisomes are multi-protein complexes that replicate genomes with remarkable speed and accuracy. Despite their importance, their dynamics is poorly characterized, especially in vivo. In this paper, we present an approach to infer the replisome dynamics from the DNA abundance distribution measured in a growing bacterial population. Our method is sensitive enough to detect subtle variations of the replisome speed along the genome. As an application, we experimentally measured the DNA abundance distribution in Escherichia coli populations growing at different temperatures using deep sequencing. We find that the average replisome speed increases nearly five-fold between 17°C and 37°C. Further, we observe wave-like variations of the replisome speed along the genome. These variations correlate with previously observed variations of the mutation rate, suggesting a common dynamical origin. Our approach has the potential to elucidate replication dynamics in E. coli mutants and in other bacterial species.
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Affiliation(s)
- Deepak Bhat
- Biological Complexity Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Samuel Hauf
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology, Onna, Japan
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5
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Jeon H, Choi E, Hwang J. Identification and characterization of VapBC toxin-antitoxin system in Bosea sp. PAMC 26642 isolated from Arctic lichens. RNA (NEW YORK, N.Y.) 2021; 27:1374-1389. [PMID: 34429367 PMCID: PMC8522696 DOI: 10.1261/rna.078786.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Toxin-antitoxin (TA) systems are genetic modules composed of a toxin interfering with cellular processes and its cognate antitoxin, which counteracts the activity of the toxin. TA modules are widespread in bacterial and archaeal genomes. It has been suggested that TA modules participate in the adaptation of prokaryotes to unfavorable conditions. The Bosea sp. PAMC 26642 used in this study was isolated from the Arctic lichen Stereocaulon sp. There are 12 putative type II TA loci in the genome of Bosea sp. PAMC 26642. Of these, nine functional TA systems have been shown to be toxic in Escherichia coli The toxin inhibits growth, but this inhibition is reversed when the cognate antitoxin genes are coexpressed, indicating that these putative TA loci were bona fide TA modules. Only the BoVapC1 (AXW83_01405) toxin, a homolog of VapC, showed growth inhibition specific to low temperatures, which was recovered by the coexpression of BoVapB1 (AXW83_01400). Microscopic observation and growth monitoring revealed that the BoVapC1 toxin had bacteriostatic effects on the growth of E. coli and induced morphological changes. Quantitative real time polymerase chain reaction and northern blotting analyses showed that the BoVapC1 toxin had a ribonuclease activity on the initiator tRNAfMet, implying that degradation of tRNAfMet might trigger growth arrest in E. coli Furthermore, the BoVapBC1 system was found to contribute to survival against prolonged exposure at 4°C. This is the first study to identify the function of TA systems in cold adaptation.
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Affiliation(s)
- Hyerin Jeon
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Eunsil Choi
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
- Microbiological Resource Research Institute, Pusan National University, Busan 46241, Republic of Korea
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6
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Weber de Melo V, Lowe R, Hurd PJ, Petchey OL. Phenotypic responses to temperature in the ciliate Tetrahymena thermophila. Ecol Evol 2020; 10:7616-7626. [PMID: 32760552 PMCID: PMC7391332 DOI: 10.1002/ece3.6486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 02/28/2020] [Accepted: 05/21/2020] [Indexed: 01/20/2023] Open
Abstract
Understanding the effects of temperature on ecological and evolutionary processes is crucial for generating future climate adaptation scenarios. Using experimental evolution, we evolved the model ciliate Tetrahymena thermophila in an initially novel high temperature environment for more than 35 generations, closely monitoring population dynamics and morphological changes. We observed initially long lag phases in the high temperature environment that over about 26 generations reduced to no lag phase, a strong reduction in cell size and modifications in cell shape at high temperature. When exposing the adapted populations to their original temperature, most phenotypic traits returned to the observed levels in the ancestral populations, indicating phenotypic plasticity is an important component of this species thermal stress response. However, persistent changes in cell size were detected, indicating possible costs related to the adaptation process. Exploring the molecular basis of thermal adaptation will help clarify the mechanisms driving these phenotypic responses.
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Affiliation(s)
- Vanessa Weber de Melo
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Robert Lowe
- The Blizard InstituteQueen Mary University of LondonLondonUK
| | - Paul J. Hurd
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Owen L. Petchey
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
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7
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Wickramasinghe NN, Ravensdale JT, Coorey R, Dykes GA, Scott Chandry P. In situ characterisation of biofilms formed by psychrotrophic meat spoilage pseudomonads. BIOFOULING 2019; 35:840-855. [PMID: 31558055 DOI: 10.1080/08927014.2019.1669021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Psychrotrophic Pseudomonas species form biofilms on meat during refrigerated and temperature abuse conditions. Biofilm growth leads to slime formation on meat which is a key organoleptic degradation characteristic. Limited research has been undertaken characterising biofilms grown on meat during chilled aerobic storage. In this work, biofilms formed by two key meat spoilage organisms, Pseudomonas fragi and Pseudomonas lundensis were studied in situ using five strains from each species. Biofilm structures were studied using confocal microscope images, cellular arrangement, cell counts and biomass quantifications. This work demonstrated that highly dense, compact biofilms are a characteristic of P. fragi strains. P. lundensis formed biofilms with loosely arranged cells. The cells in P. fragi biofilm appear to be vertically oriented whereas this characteristic was absent in P. lundensis biofilms formed under identical conditions. Despite the continued access to nutrients, biofilms formed on meat by proteolytic Pseudomonas species dispersed after a population maximum was reached.
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Affiliation(s)
- Nirmani N Wickramasinghe
- School of Public Health, Curtin University, Bentley, Western Australia, Australia
- Agriculture and Food, CSIRO, Werribee, Victoria, Australia
| | - Joshua T Ravensdale
- School of Public Health, Curtin University, Bentley, Western Australia, Australia
| | - Ranil Coorey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Gary A Dykes
- School of Public Health, Curtin University, Bentley, Western Australia, Australia
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8
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Tonyali B, McDaniel A, Trinetta V, Yucel U. Evaluation of heating effects on the morphology and membrane structure of Escherichia coli using electron paramagnetic resonance spectroscopy. Biophys Chem 2019; 252:106191. [PMID: 31177024 DOI: 10.1016/j.bpc.2019.106191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 01/14/2023]
Abstract
Bacterial cell characteristics, such as size, morphology, and membrane integrity, are affected by environmental conditions. Thermal treatment results in related structural changes, extent of which is determined by the microorganism's survival skills and inactivation kinetics. The objective of this study was to characterize changes in cell structure of Escherichia coli during heating using the combined analysis of dynamic light scattering (DLS), electron paramagnetic resonance (EPR) spectroscopy, and transmission electron microscopy (TEM) techniques. The size of E. coli cells increased from 2.3 μm to 3.0 μm with heating up to 50 °C followed by a shrinkage with further heating up to 70 °C. The morphological changes were verified using transmission electron microscopy. Related changes in membrane integrity was quantified via the mobility of 16-doxylstearic acid (16-DSA) spin probe using EPR spectroscopy. Two order parameters S1 and S2 defined on x- and y-axes, respectively, decreased with increasing temperature indicating loss of membrane integrity. The combined techniques as in this study can be used to further understand factors that play role in survival behavior of microorganisms.
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Affiliation(s)
- Bade Tonyali
- Food Science Institute, Kansas State University, Manhattan, KS 66506, United States of America
| | - Austin McDaniel
- Food Science Institute, Kansas State University, Manhattan, KS 66506, United States of America
| | - Valentina Trinetta
- Food Science Institute, Kansas State University, Manhattan, KS 66506, United States of America; Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, United States of America
| | - Umut Yucel
- Food Science Institute, Kansas State University, Manhattan, KS 66506, United States of America; Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, United States of America.
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9
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Jun S, Si F, Pugatch R, Scott M. Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:056601. [PMID: 29313526 PMCID: PMC5897229 DOI: 10.1088/1361-6633/aaa628] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1-3), we review the first 'golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4-7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the 'adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome 'sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.
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Affiliation(s)
- Suckjoon Jun
- Department of Physics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America. Section of Molecular Biology, Division of Biology, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, United States of America
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10
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Gangan MS, Athale CA. Threshold effect of growth rate on population variability of Escherichia coli cell lengths. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160417. [PMID: 28386413 PMCID: PMC5367290 DOI: 10.1098/rsos.160417] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 01/23/2017] [Indexed: 05/24/2023]
Abstract
A long-standing question in biology is the effect of growth on cell size. Here, we estimate the effect of Escherichia coli growth rate (r) on population cell size distributions by estimating the coefficient of variation of cell lengths (CVL) from image analysis of fixed cells in DIC microscopy. We find that the CVL is constant at growth rates less than one division per hour, whereas above this threshold, CVL increases with an increase in the growth rate. We hypothesize that stochastic inhibition of cell division owing to replication stalling by a RecA-dependent mechanism, combined with the growth rate threshold of multi-fork replication (according to Cooper and Helmstetter), could form the basis of such a threshold effect. We proceed to test our hypothesis by increasing the frequency of stochastic stalling of replication forks with hydroxyurea (HU) treatment and find that cell length variability increases only when the growth rate exceeds this threshold. The population effect is also reproduced in single-cell studies using agar-pad cultures and 'mother machine'-based experiments to achieve synchrony. To test the role of RecA, critical for the repair of stalled replication forks, we examine the CVL of E. coli ΔrecA cells. We find cell length variability in the mutant to be greater than wild-type, a phenotype that is rescued by plasmid-based RecA expression. Additionally, we find that RecA-GFP protein recruitment to nucleoids is more frequent at growth rates exceeding the growth rate threshold and is further enhanced on HU treatment. Thus, we find growth rates greater than a threshold result in increased E. coli cell lengths in the population, and this effect is, at least in part, mediated by RecA recruitment to the nucleoid and stochastic inhibition of division.
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11
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Gangan MS, Athale CA. Threshold effect of growth rate on population variability of Escherichia coli cell lengths. ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 28386413 DOI: 10.5061/dryad.2bs69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A long-standing question in biology is the effect of growth on cell size. Here, we estimate the effect of Escherichia coli growth rate (r) on population cell size distributions by estimating the coefficient of variation of cell lengths (CVL) from image analysis of fixed cells in DIC microscopy. We find that the CVL is constant at growth rates less than one division per hour, whereas above this threshold, CVL increases with an increase in the growth rate. We hypothesize that stochastic inhibition of cell division owing to replication stalling by a RecA-dependent mechanism, combined with the growth rate threshold of multi-fork replication (according to Cooper and Helmstetter), could form the basis of such a threshold effect. We proceed to test our hypothesis by increasing the frequency of stochastic stalling of replication forks with hydroxyurea (HU) treatment and find that cell length variability increases only when the growth rate exceeds this threshold. The population effect is also reproduced in single-cell studies using agar-pad cultures and 'mother machine'-based experiments to achieve synchrony. To test the role of RecA, critical for the repair of stalled replication forks, we examine the CVL of E. coli ΔrecA cells. We find cell length variability in the mutant to be greater than wild-type, a phenotype that is rescued by plasmid-based RecA expression. Additionally, we find that RecA-GFP protein recruitment to nucleoids is more frequent at growth rates exceeding the growth rate threshold and is further enhanced on HU treatment. Thus, we find growth rates greater than a threshold result in increased E. coli cell lengths in the population, and this effect is, at least in part, mediated by RecA recruitment to the nucleoid and stochastic inhibition of division.
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Affiliation(s)
- Manasi S Gangan
- Division of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr Homi Bhabha Road, Pashan, Pune 411008 , India
| | - Chaitanya A Athale
- Division of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr Homi Bhabha Road, Pashan, Pune 411008 , India
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12
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Skibinski B, Müller P, Uhl W. Rejection of submicron sized particles from swimming pool water by a monolithic SiC microfiltration membrane: Relevance of steric and electrostatic interactions. J Memb Sci 2016. [DOI: 10.1016/j.memsci.2015.10.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Yu H, Lim KP, Xiong S, Tan LP, Shim W. Functional morphometric analysis in cellular behaviors: shape and size matter. Adv Healthc Mater 2013; 2:1188-97. [PMID: 23713066 DOI: 10.1002/adhm.201300053] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Indexed: 12/20/2022]
Abstract
Cellular morphogenesis in response to biophysical and topographical cues provides insights into cytoskeletal status, biointerface communications, and phenotypic adaptations in an incessant signaling feedback that governs cellular fate. Morphometric characterization is an important element in the study of the dynamic cellular behaviors, in their interactive response to environmental influence exerted by culture system. They collectively serve to reflect cellular proliferation, migration, and differentiation, which may serve as prognostic indices for clinical and pathological diagnosis. Various parameters are proposed to categorize morphological adaptations in relation to cellular function. In this review, the underlying principles, assumptions, and limitations of morphological characterizations are discussed. The significance, challenges, and implications of quantitative morphometric characterization of cell shapes and sizes in determining cellular functions are discussed.
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Affiliation(s)
- Haiyang Yu
- Research and Development Unit, National Heart Centre, 9 Hospital Drive, School of Nursing, #05-01, Block C, 169612, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
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14
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Athale CA, Chaudhari H. Population length variability and nucleoid numbers in Escherichia coli. ACTA ACUST UNITED AC 2011; 27:2944-8. [PMID: 21930671 DOI: 10.1093/bioinformatics/btr501] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Cell sizes and shapes are a fundamental defining characteristic of all cellular life. In bacteria like Escherichia coli, the machinery that determines cell length is complex and interconnected, spanning extracellular cues, biosynthesis and cell division. Few tools exist to study cell lengths in a population. We have developed and tested three automated image analysis routines on growing E.coli cultures to simultaneously measure cell lengths and nucleoid numbers in populations of bacteria. We find population profiles changing with culture density-higher density of culture leads to fewer long cells. Additionally, lab strains mutant for recA show a correlation between the number of nucleoids and cell length. CONTACT cathale@iiserpune.ac.in; chaitanya.athale@gmail.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chaitanya A Athale
- Division of Biology, IISER Pune, Central Tower, Sai Trinity, Pashan, Pune 411021, India.
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15
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Buenemann M, Lenz P. A geometrical model for DNA organization in bacteria. PLoS One 2010; 5:e13806. [PMID: 21085464 PMCID: PMC2972204 DOI: 10.1371/journal.pone.0013806] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 10/11/2010] [Indexed: 02/03/2023] Open
Abstract
Recent experimental studies have revealed that bacteria, such as C. crescentus, show a remarkable spatial ordering of their chromosome. A strong linear correlation has been found between the position of genes on the chromosomal map and their spatial position in the cellular volume. We show that this correlation can be explained by a purely geometrical model. Namely, self-avoidance of DNA, specific positioning of one or few DNA loci (such as origin or terminus) together with the action of DNA compaction proteins (that organize the chromosome into topological domains) are sufficient to get a linear arrangement of the chromosome along the cell axis. We develop a Monte-Carlo method that allows us to test our model numerically and to analyze the dependence of the spatial ordering on various physiologically relevant parameters. We show that the proposed geometrical ordering mechanism is robust and universal (i.e. does not depend on specific bacterial details). The geometrical mechanism should work in all bacteria that have compacted chromosomes with spatially fixed regions. We use our model to make specific and experimentally testable predictions about the spatial arrangement of the chromosome in mutants of C. crescentus and the growth-stage dependent ordering in E. coli.
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Affiliation(s)
- Mathias Buenemann
- Department of Physics and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
- Fachbereich Physik and Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Peter Lenz
- Department of Physics and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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16
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Sherr EB, Sherr BF. Double-staining epifluorescence technique to assess frequency of dividing cells and bacteriovory in natural populations of heterotrophic microprotozoa. Appl Environ Microbiol 2010; 46:1388-93. [PMID: 16346446 PMCID: PMC239580 DOI: 10.1128/aem.46.6.1388-1393.1983] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a double-staining procedure for use with epifluorescence microscopy which allows the detection both of dividing cells and of ingested bacteria in food vacuoles of heterotrophic microprotozoa. Microprotozoan cells are stained sequentially with the DNA-specific fluorochrome DAPI (4',6-diami-dino-2-phenylindole) and the nonspecific protein stain fluorescein isothiocyanate. During microscopic examination, heterotrophic microprotozoan cells are first located with fluorescein isothiocyanate fluorescence and then epifluorescence filter sets are switched to permit inspection under DAPI fluorescence of the cell nuclei and of the contents of food vacuoles. Among in situ populations of estuarine microprotozoa sampled over a tidal cycle, we found from 2.2 to 5.2% of the heterotrophic cells in a recognizable stage of division (nuclei elongated or double). Batch culture growth experiments were also carried out both with natural populations and with two isolated species of estuarine microprotozoa. In these experiments, the frequency of dividing cells ranged from 1.2 to 3.8% and appeared to be negatively correlated with growth rate. Microprotozoan populations sampled in continental shelf waters off Savannah, Ga., had mean frequencies of dividing cells ranging from 2.0 to 5.0%. A large fraction of cells in heterotrophic microprotozoan populations (an average of 27.4 +/- 1.0% in estuarine water and of 30.1 +/- 4.8% in shelf water) had DAPI-stained inclusions, presumably recently ingested bacteria, in their food vacuoles.
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Affiliation(s)
- E B Sherr
- University of Georgia Marine Institute, Sapelo Island, Georgia 31327
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17
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Dens EJ, Bernaerts K, Standaert AR, Kreft JU, Van Impe JF. Cell division theory and individual-based modeling of microbial lag: part II. Modeling lag phenomena induced by temperature shifts. Int J Food Microbiol 2005; 101:319-32. [PMID: 15913823 DOI: 10.1016/j.ijfoodmicro.2004.11.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2004] [Revised: 09/10/2004] [Accepted: 11/19/2004] [Indexed: 11/17/2022]
Abstract
This paper is the second in a series of two, and studies microbial lag in cell number and/or biomass measurements caused by temperature changes with an individual-based modeling approach. For this purpose, the theory of cell division, as discussed in the first part of this series of research papers, was implemented in the individual-based modeling framework BacSim. Simulations of this model are compared with experimental data of Escherichia coli, growing in an aerated, glucose-rich medium and subjected to sudden temperature shifts. The premise of a constant cell volume under changing temperature conditions predicts no lag in cell numbers after the shift, in contrast to the experimental observations. Based on literature research, two biological mechanisms that could be responsible for the observed lag phenomena are proposed. The first assumes that the average cell volume depends on temperature while the second assumes that a lag in biomass growth occurs after the temperature shift. For a lag in cell number caused by an increased average cell volume, the cell biomass always increases at the maximal rate. Therefore, cells are evidently not stressed and do not have to adapt to the new conditions, as opposed to a lag in biomass growth. Implementation and simulation of both mechanisms are found to describe the experimental observations equally well. Therefore, further research is needed to distinguish between the two mechanisms. This can be done by observing, in addition to cell numbers, a measure for the average cell volumes. In conclusion, the individual-based modeling approach is a good methodology to investigate and test biological theories and assumptions. Also, based on the simulations, suggestions for further experimental observations can be made.
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Affiliation(s)
- E J Dens
- Bioprocess Technology and Control, Department of Chemical Engineering, Katholieke Universiteit Leuven, W. De Croylaan 46, B-3001 Leuven, Belgium
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Bernaerts K, Dens E, Vereecken K, Geeraerd AH, Standaert AR, Devlieghere F, Debevere J, Van Impe JF. Concepts and tools for predictive modeling of microbial dynamics. J Food Prot 2004; 67:2041-52. [PMID: 15453600 DOI: 10.4315/0362-028x-67.9.2041] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Description of microbial cell (population) behavior as influenced by dynamically changing environmental conditions intrinsically needs dynamic mathematical models. In the past, major effort has been put into the modeling of microbial growth and inactivation within a constant environment (static models). In the early 1990s, differential equation models (dynamic models) were introduced in the field of predictive microbiology. Here, we present a general dynamic model-building concept describing microbial evolution under dynamic conditions. Starting from an elementary model building block, the model structure can be gradually complexified to incorporate increasing numbers of influencing factors. Based on two case studies, the fundamentals of both macroscopic (population) and microscopic (individual) modeling approaches are revisited. These illustrations deal with the modeling of (i) microbial lag under variable temperature conditions and (ii) interspecies microbial interactions mediated by lactic acid production (product inhibition). Current and future research trends should address the need for (i) more specific measurements at the cell and/or population level, (ii) measurements under dynamic conditions, and (iii) more comprehensive (mechanistically inspired) model structures. In the context of quantitative microbial risk assessment, complexity of the mathematical model must be kept under control. An important challenge for the future is determination of a satisfactory trade-off between predictive power and manageability of predictive microbiology models.
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Affiliation(s)
- Kristel Bernaerts
- BioTeC--Bioprocess Technology and Control, Department of Chemical Engineering, Katholieke Universiteit Leuven, W de Croylaan 46, B-3001 Leuven, Belgium
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19
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Zimmerman SB. Studies on the compaction of isolated nucleoids from Escherichia coli. J Struct Biol 2004; 147:146-58. [PMID: 15193643 DOI: 10.1016/j.jsb.2004.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 02/06/2004] [Indexed: 12/01/2022]
Abstract
The genomic DNA of Escherichia coli is contained in one or two compact bodies known as nucleoids. Isolation of typically shaped nucleoids requires control of DNA expansion, accomplished here by a modification of the polylysine-spermidine procedure. The ability to control expansion of in vitro nucleoids has application in nucleoid purification and in preparation of samples for high-resolution imaging, and may allow an increased resolution in gene localization studies. Polylysine of relatively low average molecular weight (approximately 3 kDa) is used to produce lysates containing nucleoids that are several-fold expanded relative to the sizes of in vivo nucleoids. These expanded forms can be converted to compact forms similar in dimensions to the cellular nucleoids by either a further addition of polylysine or by incubation of diluted lysates at 37 degrees C. The incubation at 37 degrees C is accompanied by autolytic degradation of most ribosomal RNA. Hyperchromism and circular dichroism spectra indicate that polylysine-DNA complexes are modified during the incubation. Compact forms of the nucleoid can be progressively reexpanded by exposure to salt solutions. Nucleoid compaction was similar in lysates made from rapidly or slowly growing cells or from cells that had been briefly treated with chloramphenicol to reduce linkages between DNA and cell envelope.
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Affiliation(s)
- Steven B Zimmerman
- Laboratory of Molecular Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0560, USA.
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20
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Umehara S, Wakamoto Y, Inoue I, Yasuda K. On-chip single-cell microcultivation assay for monitoring environmental effects on isolated cells. Biochem Biophys Res Commun 2003; 305:534-40. [PMID: 12763026 DOI: 10.1016/s0006-291x(03)00794-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have developed a on-chip single-cell microcultivation assay as a means of observing the adaptation process of single bacterial cells during nutrient concentration changes. This assay enables the direct observation of single cells captured in microchambers made on thin glass slides and having semipermeable membrane lids, in which cells were kept isolated with optical tweezers. After changing a medium of 0.2% (w/v) glucose concentration to make it nutrient-free 0.9% NaCl medium, the growth of all cells inserted into the medium stopped within 20 min, irrespective of their cell cycles. When a nutrient-rich medium was restored, the cells started to grow again, even after the medium had remained nutrient-free for 42 h. The results indicate that the cell's growth and division are directly related to their nutrient condition. The growth curve also indicates that the cells keep their memory of what their growth and division had been before they stopped growing.
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Affiliation(s)
- Senkei Umehara
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
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Helmstetter CE, Leonard AC, Grimwade JE. Relationships between chromosome segregation, cell shape and temperature in Escherichia coli. J Theor Biol 1992; 159:261-6. [PMID: 1294848 DOI: 10.1016/s0022-5193(05)80705-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The partitioning of chromosomes into daughter cells during the division of Escherichia coli is non-random. As a result, the chromosome containing the older template DNA strand has a higher probability of segregating toward the old cell pole than toward the new cell pole. The numerical value of this probability is a function of the incubation temperature. It is shown here that a recent model for explaining the physiological basis for non-random chromosome segregation also explains the temperature dependence of the segregation process.
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Affiliation(s)
- C E Helmstetter
- Department of Biological Sciences, Florida Institute of Technology, Melbourne 32901
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van Bakel M, Vischer N, Tixador R, Gasset G, Woldringh C. Influence of low-temperature storage and glucose starvation on growth recovery in Escherichia coli relA and relA+ strains. J Biotechnol 1991; 19:159-72. [PMID: 1367237 DOI: 10.1016/0168-1656(91)90056-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To study the influence of microgravity on bacterial growth behavior during a space mission, the special experimental conditions and the hardware environment necessitate storage of cells at low temperature, and permit a relatively short experimental period. Before this experimental period, cells have to recover their condition of steady-state growth, because it is only in this condition that the growth behavior of the flight and ground populations can be adequately compared. To meet these requirements and to obtain cells which recover rapidly their steady-state growth, we analyzed the size and shape of Escherichia coli cells during storage at 4 degrees C, with and without previous glucose starvation of the cells. It appeared that cells stored at low temperature in the presence of glucose continued to increase in average mass and assumed ovoid shapes. In addition, upon restoration of maximal growth rate at 37 degrees C, they continued to increase in size and showed a transient overshoot of their final steady-state value, which was reached after about 5 h. Cells previously starved for glucose, however, maintained their average size and rod-shape during low-temperature storage. Recovery of the starved cells was most rapid in the relA+ strain which, contrary to the isogenic relA strain, showed no overshoot and reached its final steady-state size within 2 h.
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Affiliation(s)
- M van Bakel
- University of Amsterdam, Department of Molecular Cell Biology, The Netherlands
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Cooper S. The constrained hoop: an explanation of the overshoot in cell length during a shift-up of Escherichia coli. J Bacteriol 1989; 171:5239-43. [PMID: 2676969 PMCID: PMC210357 DOI: 10.1128/jb.171.10.5239-5243.1989] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- S Cooper
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
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Dicker DT, Higgins ML. Cell cycle changes in the buoyant density of exponential-phase cells of Streptococcus faecium. J Bacteriol 1987; 169:1200-4. [PMID: 3818544 PMCID: PMC211919 DOI: 10.1128/jb.169.3.1200-1204.1987] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cell buoyant densities were determined by centrifugation in Percoll gradients containing exponential-phase cells of Streptococcus faecium ATCC 9790 grown at a mass doubling time of about 33 min. This bacterium showed the highest average density values (1.13 g/ml) measured to date for any eucaryotic or procaryotic organism. Fractions having the highest densities were enriched with cells that were in the process of dividing or had just divided. These high-density fractions were also enriched with cells that had newly initiated sites of cell wall growth. It appears that S. faecium shows minimum cell densities in the midportion of its cycle.
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Golosow L, Hulme R, Cho S, Vermeulen CW. Isopycnography of intact cells. VI: Effect of temperature on steady state Escherichia coli. Biochem Biophys Res Commun 1986; 135:708-12. [PMID: 3516147 DOI: 10.1016/0006-291x(86)90986-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Steady state cultures of Escherichia coli W3110 possess constant cellular concentrations of ribosomes while above 22 C as measured isopycnographically. Below 22 C, ribosome levels are significantly diminished, equivalent to those found in dormant cells. Concommitantly, the energy of activation of steady state population growth in E. coli remains at a constant 18.6 kcal between 22 C and 37 C. This suggests that the thermal stability of the protein synthesis apparatus may play an important role in pathogenesis as well as in other areas of ecological niche acquisition and dominance.
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Zaritsky A, Parola AH, Abdah M, Masalha H. Homeoviscous adaptation, growth rate, and morphogenesis in bacteria. Biophys J 1985; 48:337-9. [PMID: 3902110 PMCID: PMC1329326 DOI: 10.1016/s0006-3495(85)83788-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Fluorescence polarization, P, of 1,6-diphenyl-1,3,5-hexatriene was studied in Escherichia coli B/r. Modification of nutritional conditions was not compensated by homeoviscous adaptation, demonstrated to exist for temperature variations. Cell diameter, which is known also to vary with nutrition but not with temperature, was found to be positively correlated with 1/P, and may therefore be regulated by membrane lipid order and fluidity.
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27
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Molin G, Nilsson I. Effect of different environmental parameters on the biofilm build-up of Pseudomonas putida ATCC 11172 in chemostat. ACTA ACUST UNITED AC 1983. [DOI: 10.1007/bf00500834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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