1
|
Govers SK, Campos M, Tyagi B, Laloux G, Jacobs-Wagner C. Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle. Cell Syst 2024; 15:19-36.e5. [PMID: 38157847 DOI: 10.1016/j.cels.2023.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.
Collapse
Affiliation(s)
- Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; de Duve Institute, UCLouvain, Brussels, Belgium; Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Toulouse, France
| | - Bhavyaa Tyagi
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
2
|
Mao W, Renner LD, Cornilleau C, Li de la Sierra-Gallay I, Afensiss S, Benlamara S, Ah-Seng Y, Van Tilbeurgh H, Nessler S, Bertin A, Chastanet A, Carballido-Lopez R. On the role of nucleotides and lipids in the polymerization of the actin homolog MreB from a Gram-positive bacterium. eLife 2023; 12:e84505. [PMID: 37818717 PMCID: PMC10718530 DOI: 10.7554/elife.84505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/08/2023] [Indexed: 10/12/2023] Open
Abstract
In vivo, bacterial actin MreB assembles into dynamic membrane-associated filamentous structures that exhibit circumferential motion around the cell. Current knowledge of MreB biochemical and polymerization properties in vitro remains limited and is mostly based on MreB proteins from Gram-negative species. In this study, we report the first observation of organized protofilaments by electron microscopy and the first 3D-structure of MreB from a Gram-positive bacterium. We show that Geobacillus stearothermophilus MreB forms straight pairs of protofilaments on lipid surfaces in the presence of ATP or GTP, but not in the presence of ADP, GDP or non-hydrolysable ATP analogs. We demonstrate that membrane anchoring is mediated by two spatially close short hydrophobic sequences while electrostatic interactions also contribute to lipid binding, and show that the population of membrane-bound protofilament doublets is in steady-state. In solution, protofilament doublets were not detected in any condition tested. Instead, MreB formed large sheets regardless of the bound nucleotide, albeit at a higher critical concentration. Altogether, our results indicate that both lipids and ATP are facilitators of MreB polymerization, and are consistent with a dual effect of ATP hydrolysis, in promoting both membrane binding and filaments assembly/disassembly.
Collapse
Affiliation(s)
- Wei Mao
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Lars D Renner
- Leibniz Institute of Polymer Research, and the Max-Bergmann-Center of BiomaterialsDresdenGermany
| | - Charlène Cornilleau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSGif-sur-YvetteFrance
| | - Sana Afensiss
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Sarah Benlamara
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Yoan Ah-Seng
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Herman Van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSGif-sur-YvetteFrance
| | - Sylvie Nessler
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRSGif-sur-YvetteFrance
| | - Aurélie Bertin
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Sorbonne Université, 75005ParisFrance
| | - Arnaud Chastanet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| | - Rut Carballido-Lopez
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis InstituteJouy-en-JosasFrance
| |
Collapse
|
3
|
Knapp BD, Ward MD, Bowman GR, Shi H, Huang KC. Multiple conserved states characterize the twist landscape of the bacterial actin homolog MreB. Comput Struct Biotechnol J 2022; 20:5838-5846. [PMID: 36382191 PMCID: PMC9627593 DOI: 10.1016/j.csbj.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 12/01/2022] Open
Abstract
Filament formation by cytoskeletal proteins is critical to their involvement in myriad cellular processes. The bacterial actin homolog MreB, which is essential for cell-shape determination in many rod-shaped bacteria, has served as a model system for studying the mechanics of cytoskeletal filaments. Previous molecular dynamics (MD) simulations revealed that the twist of MreB double protofilaments is dependent on the bound nucleotide, as well as binding to the membrane or the accessory protein RodZ, and MreB mutations that modulate twist also affect MreB spatial organization and cell shape. Here, we show that MreB double protofilaments can adopt multiple twist states during microsecond-scale MD simulations. A deep learning algorithm trained only on high- and low-twist states robustly identified all twist conformations across most perturbations of ATP-bound MreB, suggesting the existence of a conserved set of states whose occupancy is affected by each perturbation to MreB. Simulations replacing ATP with ADP indicated that twist states were generally stable after hydrolysis. These findings suggest a rich twist landscape that could provide the capacity to tune MreB activity and therefore its effects on cell shape.
Collapse
Affiliation(s)
| | - Michael D. Ward
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63130, USA
- Center for the Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Gregory R. Bowman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63130, USA
- Center for the Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| |
Collapse
|
4
|
Lasker K, Boeynaems S, Lam V, Scholl D, Stainton E, Briner A, Jacquemyn M, Daelemans D, Deniz A, Villa E, Holehouse AS, Gitler AD, Shapiro L. The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems. Nat Commun 2022; 13:5643. [PMID: 36163138 PMCID: PMC9512792 DOI: 10.1038/s41467-022-33221-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Intracellular phase separation is emerging as a universal principle for organizing biochemical reactions in time and space. It remains incompletely resolved how biological function is encoded in these assemblies and whether this depends on their material state. The conserved intrinsically disordered protein PopZ forms condensates at the poles of the bacterium Caulobacter crescentus, which in turn orchestrate cell-cycle regulating signaling cascades. Here we show that the material properties of these condensates are determined by a balance between attractive and repulsive forces mediated by a helical oligomerization domain and an expanded disordered region, respectively. A series of PopZ mutants disrupting this balance results in condensates that span the material properties spectrum, from liquid to solid. A narrow range of condensate material properties supports proper cell division, linking emergent properties to organismal fitness. We use these insights to repurpose PopZ as a modular platform for generating tunable synthetic condensates in human cells.
Collapse
Affiliation(s)
- Keren Lasker
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vinson Lam
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Scholl
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emma Stainton
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam Briner
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, Brisbane, QLD, Australia
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ashok Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth Villa
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
5
|
Precise regulation of the relative rates of surface area and volume synthesis in bacterial cells growing in dynamic environments. Nat Commun 2021; 12:1975. [PMID: 33785742 PMCID: PMC8009875 DOI: 10.1038/s41467-021-22092-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
The steady-state size of bacterial cells correlates with nutrient-determined growth rate. Here, we explore how rod-shaped bacterial cells regulate their morphology during rapid environmental changes. We quantify cellular dimensions throughout passage cycles of stationary-phase cells diluted into fresh medium and grown back to saturation. We find that cells exhibit characteristic dynamics in surface area to volume ratio (SA/V), which are conserved across genetic and chemical perturbations as well as across species and growth temperatures. A mathematical model with a single fitting parameter (the time delay between surface and volume synthesis) is quantitatively consistent with our SA/V experimental observations. The model supports that this time delay is due to differential expression of volume and surface-related genes, and that the first division after dilution occurs at a tightly controlled SA/V. Our minimal model thus provides insight into the connections between bacterial growth rate and cell shape in dynamic environments. Bacterial cells actively change their size and shape in response to external environments. Here, Shi et al. explore how cells regulate their morphology during rapid environmental changes, showing that the characteristic dynamics of surface area-to-volume ratio are conserved across genetic and chemical perturbations, as well as across species and growth temperatures.
Collapse
|
6
|
Jorgenson MA, Bryant JC. A genetic screen to identify factors affected by undecaprenyl phosphate recycling uncovers novel connections to morphogenesis in Escherichia coli. Mol Microbiol 2021; 115:191-207. [PMID: 32979869 PMCID: PMC10568968 DOI: 10.1111/mmi.14609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/11/2020] [Indexed: 01/30/2023]
Abstract
Undecaprenyl phosphate (Und-P) is an essential lipid carrier that ferries cell wall intermediates across the cytoplasmic membrane in bacteria. Und-P is generated by dephosphorylating undecaprenyl pyrophosphate (Und-PP). In Escherichia coli, BacA, PgpB, YbjG, and LpxT dephosphorylate Und-PP and are conditionally essential. To identify vulnerabilities that arise when Und-P metabolism is defective, we developed a genetic screen for synthetic interactions which, in combination with ΔybjG ΔlpxT ΔbacA, are lethal or reduce fitness. The screen uncovered novel connections to cell division, DNA replication/repair, signal transduction, and glutathione metabolism. Further analysis revealed several new morphogenes; loss of one of these, qseC, caused cells to enlarge and lyse. QseC is the sensor kinase component of the QseBC two-component system. Loss of QseC causes overactivation of the QseB response regulator by PmrB cross-phosphorylation. Here, we show that deleting qseB completely reverses the shape defect of ΔqseC cells, as does overexpressing rprA (a small RNA). Surprisingly, deleting pmrB only partially suppressed qseC-related shape defects. Thus, QseB is activated by multiple factors in QseC's absence and prior functions ascribed to QseBC may originate from cell wall defects. Altogether, our findings provide a framework for identifying new determinants of cell integrity that could be targeted in future therapies.
Collapse
Affiliation(s)
- Matthew A. Jorgenson
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Joseph C. Bryant
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| |
Collapse
|
7
|
Zeng Y, Liu B. Self-propelling and rolling of a sessile-motile aggregate of the bacterium Caulobacter crescentus. Commun Biol 2020; 3:587. [PMID: 33067555 PMCID: PMC7568532 DOI: 10.1038/s42003-020-01300-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/15/2020] [Indexed: 11/09/2022] Open
Abstract
Active dispersal of microorganisms is often attributed to the cells' motile organelles. However, much less is known about whether sessile cells can access such motility through aggregation with motile counterparts. Here, we show that the rosette aggregates of the bacterium Caulobacter crescentus, although predominantly sessile, can actively disperse through the flagellar motors of motile members. Comparisons in kinematics between the motile rosettes and solitary swimming cells indicate that the rosettes can be powered by as few as a single motor. We further reconstructed the 3D movements of the rosettes to reveal that their proximity to a solid-liquid interface promotes a wheel-like rolling, as powered by the flagellar torque. This rolling movement also features a sequence of sharp turns, a reorientation mechanism distinct from that of swimming cells. Overall, our study elucidates an unexplored regime of aggregation-based motility that can be widely applied to sessile-motile composites.
Collapse
Affiliation(s)
- Yu Zeng
- Department of Physics, University of California, Merced, Merced, CA, 95343, USA
| | - Bin Liu
- Department of Physics, University of California, Merced, Merced, CA, 95343, USA.
| |
Collapse
|
8
|
Shi H, Quint DA, Grason GM, Gopinathan A, Huang KC. Chiral twisting in a bacterial cytoskeletal polymer affects filament size and orientation. Nat Commun 2020; 11:1408. [PMID: 32179732 PMCID: PMC7075873 DOI: 10.1038/s41467-020-14752-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/24/2020] [Indexed: 12/30/2022] Open
Abstract
In many rod-shaped bacteria, the actin homolog MreB directs cell-wall insertion and maintains cell shape, but it remains unclear how structural changes to MreB affect its organization in vivo. Here, we perform molecular dynamics simulations for Caulobacter crescentus MreB to extract mechanical parameters for inputs into a coarse-grained biophysical polymer model that successfully predicts MreB filament properties in vivo. Our analyses indicate that MreB double protofilaments can exhibit left-handed twisting that is dependent on the bound nucleotide and membrane binding; the degree of twisting correlates with the length and orientation of MreB filaments observed in vitro and in vivo. Our molecular dynamics simulations also suggest that membrane binding of MreB double protofilaments induces a stable membrane curvature of similar magnitude to that observed in vivo. Thus, our multiscale modeling correlates cytoskeletal filament size with conformational changes inferred from molecular dynamics simulations, providing a paradigm for connecting protein filament structure and mechanics to cellular organization and function. The actin homolog MreB directs cell-wall insertion and maintains cell shape in many rod-shaped bacteria. Here, Shi et al. perform molecular dynamics simulations for MreB to extract mechanical parameters for inputs into a coarse-grained biophysical polymer model that predicts MreB filament properties.
Collapse
Affiliation(s)
- Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - David A Quint
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Department of Physics, University of California at Merced, Merced, CA, 95343, USA.,NSF-CREST: Center for Cellular and Biomolecular Machines, University of California at Merced, Merced, CA, 95343, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ajay Gopinathan
- Department of Physics, University of California at Merced, Merced, CA, 95343, USA.,NSF-CREST: Center for Cellular and Biomolecular Machines, University of California at Merced, Merced, CA, 95343, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| |
Collapse
|
9
|
Özbaykal G, Wollrab E, Simon F, Vigouroux A, Cordier B, Aristov A, Chaze T, Matondo M, van Teeffelen S. The transpeptidase PBP2 governs initial localization and activity of the major cell-wall synthesis machinery in E. coli. eLife 2020; 9:50629. [PMID: 32077853 PMCID: PMC7089770 DOI: 10.7554/elife.50629] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
Bacterial shape is physically determined by the peptidoglycan cell wall. The cell-wall-synthesis machinery responsible for rod shape in Escherichia coli is the processive 'Rod complex'. Previously, cytoplasmic MreB filaments were thought to govern formation and localization of Rod complexes based on local cell-envelope curvature. Using single-particle tracking of the transpeptidase and Rod-complex component PBP2, we found that PBP2 binds to a substrate different from MreB. Depletion and localization experiments of other putative Rod-complex components provide evidence that none of those provide the sole rate-limiting substrate for PBP2 binding. Consistently, we found only weak correlations between MreB and envelope curvature in the cylindrical part of cells. Residual correlations do not require curvature-based Rod-complex initiation but can be attributed to persistent rotational motion. We therefore speculate that the local cell-wall architecture provides the cue for Rod-complex initiation, either through direct binding by PBP2 or through an unknown intermediate.
Collapse
Affiliation(s)
- Gizem Özbaykal
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne-Paris-Cité, Paris, France
| | - Eva Wollrab
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Francois Simon
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Antoine Vigouroux
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France.,Synthetic Biology Lab, Institut Pasteur, Paris, France.,Université Paris Descartes, Sorbonne-Paris-Cité, Paris, France
| | - Baptiste Cordier
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Andrey Aristov
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | | | | | | |
Collapse
|
10
|
Ruiz-Herrero T, Fai TG, Mahadevan L. Dynamics of Growth and Form in Prebiotic Vesicles. PHYSICAL REVIEW LETTERS 2019; 123:038102. [PMID: 31386448 DOI: 10.1103/physrevlett.123.038102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 06/10/2023]
Abstract
The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is controlled by physicochemical processes that include the intercalation of amphiphiles into the membrane, fluid flow across the membrane, and elastic deformations of the membrane. To understand prebiotic vesicular forms and their dynamics, we construct a minimal model that couples membrane growth, deformation, and fluid permeation, ultimately couched in terms of two dimensionless parameters that characterize the relative rate of membrane growth and the membrane permeability. Numerical simulations show that our model captures the morphological diversity seen in extant precursor mimics of cellular life, and might provide simple guidelines for the synthesis of these complex shapes from simple ingredients.
Collapse
Affiliation(s)
- Teresa Ruiz-Herrero
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas G Fai
- Department of Mathematics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - L Mahadevan
- John A. Paulson School of Engineering and Applied Sciences, Department of Physics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
11
|
Bacillus subtilis cell diameter is determined by the opposing actions of two distinct cell wall synthetic systems. Nat Microbiol 2019; 4:1294-1305. [PMID: 31086310 PMCID: PMC6656618 DOI: 10.1038/s41564-019-0439-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 03/28/2019] [Indexed: 11/08/2022]
Abstract
Rod-shaped bacteria grow by adding material into their cell wall via the action of two spatially distinct enzymatic systems: the Rod complex moves around the cell circumference, whereas class A penicillin-binding proteins (aPBPs) do not. To understand how the combined action of these two systems defines bacterial dimensions, we examined how each affects the growth and width of Bacillus subtilis as well as the mechanical anisotropy and orientation of material within their sacculi. Rod width is not determined by MreB, rather it depends on the balance between the systems: the Rod complex reduces diameter, whereas aPBPs increase it. Increased Rod-complex activity correlates with an increased density of directional MreB filaments and a greater fraction of directional PBP2a enzymes. This increased circumferential synthesis increases the relative quantity of oriented material within the sacculi, making them more resistant to stretching across their width, thereby reinforcing rod shape. Together, these experiments explain how the combined action of the two main cell wall synthetic systems builds and maintains rods of different widths. Escherichia coli Rod mutants also show the same correlation between width and directional MreB filament density, suggesting this model may be generalizable to bacteria that elongate via the Rod complex.
Collapse
|
12
|
Shi H, Bratton BP, Gitai Z, Huang KC. How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction. Cell 2019. [PMID: 29522748 DOI: 10.1016/j.cell.2018.02.050] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cell shape matters across the kingdoms of life, and cells have the remarkable capacity to define and maintain specific shapes and sizes. But how are the shapes of micron-sized cells determined from the coordinated activities of nanometer-sized proteins? Here, we review general principles that have surfaced through the study of rod-shaped bacterial growth. Imaging approaches have revealed that polymers of the actin homolog MreB play a central role. MreB both senses and changes cell shape, thereby generating a self-organizing feedback system for shape maintenance. At the molecular level, structural and computational studies indicate that MreB filaments exhibit tunable mechanical properties that explain their preference for certain geometries and orientations along the cylindrical cell body. We illustrate the regulatory landscape of rod-shape formation and the connectivity between cell shape, cell growth, and other aspects of cell physiology. These discoveries provide a framework for future investigations into the architecture and construction of microbes.
Collapse
Affiliation(s)
- Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Benjamin P Bratton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
13
|
Kurita K, Shin R, Tabei T, Shiomi D. Relation between rotation of MreB actin and cell width of Escherichia coli. Genes Cells 2019; 24:259-265. [PMID: 30597729 DOI: 10.1111/gtc.12667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 12/27/2022]
Abstract
Bacterial cells, including Escherichia coli and Bacillus subtilis, continuously elongate and divide. Although the cell width is maintained during cell cycle, the molecular mechanisms involved in its regulation remain unknown. MreB has been implicated to play a role in maintaining cell width. Several point mutations in mreB that affect cell width have been identified. The MreB protein forms clusters or polymers in the cell and moves along annular tracks perpendicular to the long axis. This rotation is coupled with peptidoglycan synthesis. Here, we focused on two MreB mutants, MreBA125V and MreBA174T . Cells producing MreBA125V and MreBA174T were thinner and thicker than WT cells, and MreBA125V and MreBA174T rotated faster and slower than WT MreB, respectively. We observed that the rotation rate correlated with the cell wall synthesis rate. Thus, we conclude that the velocity of MreB rotation also affects cell width, that is, the faster the MreB rotates, the thinner the cell width is.
Collapse
Affiliation(s)
- Keisuke Kurita
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Ryota Shin
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Tsutomu Tabei
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| |
Collapse
|
14
|
Özdemir B, Asgharzadeh P, Birkhold AI, Mueller SJ, Röhrle O, Reski R. Cytological analysis and structural quantification of FtsZ1-2 and FtsZ2-1 network characteristics in Physcomitrella patens. Sci Rep 2018; 8:11165. [PMID: 30042487 PMCID: PMC6057934 DOI: 10.1038/s41598-018-29284-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/05/2018] [Indexed: 11/24/2022] Open
Abstract
Although the concept of the cytoskeleton as a cell-shape-determining scaffold is well established, it remains enigmatic how eukaryotic organelles adopt and maintain a specific morphology. The Filamentous Temperature Sensitive Z (FtsZ) protein family, an ancient tubulin, generates complex polymer networks, with striking similarity to the cytoskeleton, in the chloroplasts of the moss Physcomitrella patens. Certain members of this protein family are essential for structural integrity and shaping of chloroplasts, while others are not, illustrating the functional diversity within the FtsZ protein family. Here, we apply a combination of confocal laser scanning microscopy and a self-developed semi-automatic computational image analysis method for the quantitative characterisation and comparison of network morphologies and connectivity features for two selected, functionally dissimilar FtsZ isoforms, FtsZ1-2 and FtsZ2-1. We show that FtsZ1-2 and FtsZ2-1 networks are significantly different for 8 out of 25 structural descriptors. Therefore, our results demonstrate that different FtsZ isoforms are capable of generating polymer networks with distinctive morphological and connectivity features which might be linked to the functional differences between the two isoforms. To our knowledge, this is the first study to employ computational algorithms in the quantitative comparison of different classes of protein networks in living cells.
Collapse
Affiliation(s)
- Bugra Özdemir
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Pouyan Asgharzadeh
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany
- Stuttgart Center for Simulation Science (SimTech), University of Stuttgart, Pfaffenwaldring 5a, 70569, Stuttgart, Germany
| | - Annette I Birkhold
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany
| | - Stefanie J Mueller
- INRES - Chemical Signalling, University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Oliver Röhrle
- Institute of Applied Mechanics, University of Stuttgart, Pfaffenwaldring 7, 70569, Stuttgart, Germany.
- Stuttgart Center for Simulation Science (SimTech), University of Stuttgart, Pfaffenwaldring 5a, 70569, Stuttgart, Germany.
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- BIOSS - Centre for Biological Signalling Research, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
| |
Collapse
|
15
|
Campos M, Govers SK, Irnov I, Dobihal GS, Cornet F, Jacobs-Wagner C. Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli. Mol Syst Biol 2018; 14:e7573. [PMID: 29941428 PMCID: PMC6018989 DOI: 10.15252/msb.20177573] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cell size, cell growth, and cell cycle events are necessarily intertwined to achieve robust bacterial replication. Yet, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image‐based quantitative screen of the single‐gene knockout collection of Escherichia coli and identify many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics, and cell division. Functional analyses, together with high‐dimensional classification, unveil new associations of morphological and cell cycle phenotypes with specific functions and pathways. Additionally, correlation analysis across ~4,000 genetic perturbations shows that growth rate is surprisingly not predictive of cell size. Growth rate was also uncorrelated with the relative timings of nucleoid separation and cell constriction. Rather, our analysis identifies scaling relationships between cell size and nucleoid size and between nucleoid size and the relative timings of nucleoid separation and cell division. These connections suggest that the nucleoid links cell morphogenesis to the cell cycle.
Collapse
Affiliation(s)
- Manuel Campos
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Laboratoire de Microbiologie et Génétique Moléculaires (LMGM; UMR5100), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Sander K Govers
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Genevieve S Dobihal
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM; UMR5100), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT, USA .,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
16
|
Harris LK, Theriot JA. Surface Area to Volume Ratio: A Natural Variable for Bacterial Morphogenesis. Trends Microbiol 2018; 26:815-832. [PMID: 29843923 DOI: 10.1016/j.tim.2018.04.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/23/2018] [Accepted: 04/27/2018] [Indexed: 11/16/2022]
Abstract
An immediately observable feature of bacteria is that cell size and shape are remarkably constant and characteristic for a given species in a particular condition, but vary quantitatively with physiological parameters such as growth rate, indicating both genetic and environmental regulation. However, despite decades of research, the molecular mechanisms underlying bacterial morphogenesis have remained incompletely characterized. We recently demonstrated that a wide range of bacterial species exhibit a robust surface area to volume ratio (SA/V) homeostasis. Because cell size, shape, and SA/V are mathematically interconnected, if SA/V is indeed the natural variable that cells actively monitor, this finding has critical implications for our understanding of bacterial morphogenesis, placing fundamental constraints on the sizes and shapes that cells can adopt. In this Opinion article we discuss the broad implications that this novel perspective has for the field of bacterial growth and morphogenesis.
Collapse
Affiliation(s)
- Leigh K Harris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Julie A Theriot
- Department of Biochemistry, Department of Microbiology & Immunology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
17
|
Pende N, Wang J, Weber PM, Verheul J, Kuru E, Rittmann SKMR, Leisch N, VanNieuwenhze MS, Brun YV, den Blaauwen T, Bulgheresi S. Host-Polarized Cell Growth in Animal Symbionts. Curr Biol 2018; 28:1039-1051.e5. [PMID: 29576473 PMCID: PMC6611161 DOI: 10.1016/j.cub.2018.02.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 12/13/2017] [Accepted: 02/15/2018] [Indexed: 01/16/2023]
Abstract
To determine the fundamentals of cell growth, we must extend cell biological studies to non-model organisms. Here, we investigated the growth modes of the only two rods known to widen instead of elongating, Candidatus Thiosymbion oneisti and Thiosymbion hypermnestrae. These bacteria are attached by one pole to the surface of their respective nematode hosts. By incubating live Ca. T. oneisti and T. hypermnestrae with a peptidoglycan metabolic probe, we observed that the insertion of new cell wall starts at the poles and proceeds inward, concomitantly with FtsZ-based membrane constriction. Remarkably, in Ca. T. hypermnestrae, the proximal, animal-attached pole grows before the distal, free pole, indicating that the peptidoglycan synthesis machinery is host oriented. Immunostaining of the symbionts with an antibody against the actin homolog MreB revealed that it was arranged medially-that is, parallel to the cell long axis-throughout the symbiont life cycle. Given that depolymerization of MreB abolished newly synthesized peptidoglycan insertion and impaired divisome assembly, we conclude that MreB function is required for symbiont widening and division. In conclusion, our data invoke a reassessment of the localization and function of the bacterial actin homolog.
Collapse
Affiliation(s)
- Nika Pende
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | - Jinglan Wang
- Bacterial Cell Biology and Physiology Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan 1108, 1081 Amsterdam, the Netherlands
| | - Philipp M Weber
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | - Jolanda Verheul
- Bacterial Cell Biology and Physiology Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan 1108, 1081 Amsterdam, the Netherlands
| | - Erkin Kuru
- Department of Genetics, Harvard Medical School NRB, 77 Avenue Louis Pasteur, Boston, MA, USA
| | - Simon K-M R Rittmann
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | - Nikolaus Leisch
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | | | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan 1108, 1081 Amsterdam, the Netherlands
| | - Silvia Bulgheresi
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria.
| |
Collapse
|
18
|
van Teeffelen S, Renner LD. Recent advances in understanding how rod-like bacteria stably maintain their cell shapes. F1000Res 2018; 7:241. [PMID: 29560261 PMCID: PMC5832919 DOI: 10.12688/f1000research.12663.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 01/14/2023] Open
Abstract
Cell shape and cell volume are important for many bacterial functions. In recent years, we have seen a range of experimental and theoretical work that led to a better understanding of the determinants of cell shape and size. The roles of different molecular machineries for cell-wall expansion have been detailed and partially redefined, mechanical forces have been shown to influence cell shape, and new connections between metabolism and cell shape have been proposed. Yet the fundamental determinants of the different cellular dimensions remain to be identified. Here, we highlight some of the recent developments and focus on the determinants of rod-like cell shape and size in the well-studied model organisms
Escherichia coli and
Bacillus subtilis.
Collapse
Affiliation(s)
- Sven van Teeffelen
- Department of Microbiology, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01069 Dresden, Germany
| |
Collapse
|
19
|
Hussain S, Wivagg CN, Szwedziak P, Wong F, Schaefer K, Izoré T, Renner LD, Holmes MJ, Sun Y, Bisson-Filho AW, Walker S, Amir A, Löwe J, Garner EC. MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis. eLife 2018; 7:32471. [PMID: 29469806 PMCID: PMC5854468 DOI: 10.7554/elife.32471] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/21/2018] [Indexed: 12/26/2022] Open
Abstract
MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape of Bacillus subtilis. MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomes in vitro, orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape. Many bacteria are surrounded by both a cell membrane and a cell wall – a rigid outer covering made of sugars and short protein chains. The cell wall often determines which of a variety of shapes – such as rods or spheres – the bacteria grow into. One protein required to form the rod shape is called MreB. This protein forms filaments that bind to the bacteria’s cell membrane and associate with the enzymes that build the cell wall. Together, these filament-enzyme complexes rotate around the cell to build and reinforce the cell wall in a hoop-like manner. But how do the MreB filaments know how to move around the circumference of the rod, instead of moving in any other direction? Using a technique called total internal reflection microscopy to study how MreB filaments move across bacteria cells, Hussain, Wivagg et al. show that the filaments sense the shape of a bacterium by orienting along the direction of greatest curvature. As a result, the filaments in rod-shaped cells orient and move around the rod, while in spherical bacteria they move in all directions. However, spherical bacteria can regenerate into rods from small surface ‘bulges’. The MreB filaments in the bulges move in an oriented way, helping them to generate the rod shape. Hussain, Wivagg et al. also found that forcing cells that lack a cell wall into a rod shape caused the MreB filaments bound to the cell membrane to orient and circle around the rod. This shows that the organization of the filaments is sufficient to shape the cell wall. In the future, determining what factors control the activity of the MreB filaments and the enzymes they associate with might reveal new targets for antibiotics that disrupt the cell wall and so kill the bacteria. This will require higher resolution microscopes to be used to examine the cell wall in more detail. The activity of all the proteins involved in building cell walls will also need to be extensively characterized.
Collapse
Affiliation(s)
- Saman Hussain
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Carl N Wivagg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Piotr Szwedziak
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Felix Wong
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, United States
| | - Kaitlin Schaefer
- Department of Microbiology and Immunology, Harvard University, Cambridge, United States
| | - Thierry Izoré
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Lars D Renner
- Leibniz Institute of Polymer Research, Dresden, Germany
| | - Matthew J Holmes
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Yingjie Sun
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | | | - Suzanne Walker
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Ariel Amir
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, United States
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| |
Collapse
|
20
|
|
21
|
Wong F, Renner LD, Özbaykal G, Paulose J, Weibel DB, van Teeffelen S, Amir A. Mechanical strain sensing implicated in cell shape recovery in Escherichia coli. Nat Microbiol 2017; 2:17115. [PMID: 28737752 PMCID: PMC5540194 DOI: 10.1038/nmicrobiol.2017.115] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 06/16/2017] [Indexed: 12/16/2022]
Abstract
The shapes of most bacteria are imparted by the structures of their peptidoglycan cell walls, which are determined by many dynamic processes that can be described on various length-scales ranging from short-range glycan insertions to cellular-scale elasticity.1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 Understanding the mechanisms that maintain stable, rod-like morphologies in certain bacteria has proved to be challenging due to an incomplete understanding of the feedback between growth and the elastic and geometric properties of the cell wall.3, 4, 12, 13, 14 Here we probe the effects of mechanical strain on cell shape by modeling the mechanical strains caused by bending and differential growth of the cell wall. We show that the spatial coupling of growth to regions of high mechanical strain can explain the plastic response of cells to bending4 and quantitatively predict the rate at which bent cells straighten. By growing filamentous E. coli cells in donut-shaped microchambers, we find that the cells recovered their straight, native rod-shaped morphologies when released from captivity at a rate consistent with the theoretical prediction. We then measure the localization of MreB, an actin homolog crucial to cell wall synthesis, inside confinement and during the straightening process and find that it cannot explain the plastic response to bending or the observed straightening rate. Our results implicate mechanical strain-sensing, implemented by components of the elongasome yet to be fully characterized, as an important component of robust shape regulation in E. coli.
Collapse
Affiliation(s)
- Felix Wong
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01069 Dresden, Germany.,Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Gizem Özbaykal
- Department of Microbiology, Institut Pasteur, 75724 Paris, France
| | - Jayson Paulose
- Departments of Physics and Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Douglas B Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Ariel Amir
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
22
|
Herrmann J, Jabbarpour F, Bargar PG, Nomellini JF, Li PN, Lane TJ, Weiss TM, Smit J, Shapiro L, Wakatsuki S. Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer. Biophys J 2017; 112:1841-1851. [PMID: 28494955 PMCID: PMC5425405 DOI: 10.1016/j.bpj.2017.04.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 11/23/2022] Open
Abstract
Surface layers (S-layers) are paracrystalline, proteinaceous structures found in most archaea and many bacteria. Often the outermost cell envelope component, S-layers serve diverse functions including aiding pathogenicity and protecting against predators. We report that the S-layer of Caulobacter crescentus exhibits calcium-mediated structural plasticity, switching irreversibly between an amorphous aggregate state and the crystalline state. This finding invalidates the common assumption that S-layers serve only as static wall-like structures. In vitro, the Caulobacter S-layer protein, RsaA, enters the aggregate state at physiological temperatures and low divalent calcium ion concentrations. At higher concentrations, calcium ions stabilize monomeric RsaA, which can then transition to the two-dimensional crystalline state. Caulobacter requires micromolar concentrations of calcium for normal growth and development. Without an S-layer, Caulobacter is even more sensitive to changes in environmental calcium concentration. Therefore, this structurally dynamic S-layer responds to environmental conditions as an ion sensor and protects Caulobacter from calcium deficiency stress, a unique mechanism of bacterial adaptation. These findings provide a biochemical and physiological basis for RsaA's calcium-binding behavior, which extends far beyond calcium's commonly accepted role in aiding S-layer biogenesis or oligomerization and demonstrates a connection to cellular fitness.
Collapse
Affiliation(s)
- Jonathan Herrmann
- Department of Structural Biology, Stanford University, Stanford, California; Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California.
| | - Fatemeh Jabbarpour
- Department of Structural Biology, Stanford University, Stanford, California
| | | | - John F Nomellini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Po-Nan Li
- Department of Electrical Engineering, Stanford University, Stanford, California
| | - Thomas J Lane
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Thomas M Weiss
- Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California
| | - John Smit
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, Stanford, California.
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Stanford, California; Bioscience Division, SLAC National Accelerator Laboratory, Menlo Park, California.
| |
Collapse
|
23
|
Woldemeskel SA, Goley ED. Shapeshifting to Survive: Shape Determination and Regulation in Caulobacter crescentus. Trends Microbiol 2017; 25:673-687. [PMID: 28359631 DOI: 10.1016/j.tim.2017.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/28/2017] [Accepted: 03/06/2017] [Indexed: 01/05/2023]
Abstract
Bacterial cell shape is a genetically encoded and inherited feature that is optimized for efficient growth, survival, and propagation of bacteria. In addition, bacterial cell morphology is adaptable to changes in environmental conditions. Work in recent years has demonstrated that individual features of cell shape, such as length or curvature, arise through the spatial regulation of cell wall synthesis by cytoskeletal proteins. However, the mechanisms by which these different morphogenetic factors are coordinated and how they may be globally regulated in response to cell cycle and environmental cues are only beginning to emerge. Here, we have summarized recent advances that have been made to understand morphology in the dimorphic Gram-negative bacterium Caulobacter crescentus.
Collapse
Affiliation(s)
- Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
24
|
Cytoskeletal Proteins in Caulobacter crescentus: Spatial Orchestrators of Cell Cycle Progression, Development, and Cell Shape. Subcell Biochem 2017; 84:103-137. [PMID: 28500524 DOI: 10.1007/978-3-319-53047-5_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Caulobacter crescentus, an aquatic Gram-negative α-proteobacterium, is dimorphic, as a result of asymmetric cell divisions that give rise to a free-swimming swarmer daughter cell and a stationary stalked daughter. Cell polarity of vibrioid C. crescentus cells is marked by the presence of a stalk at one end in the stationary form and a polar flagellum in the motile form. Progression through the cell cycle and execution of the associated morphogenetic events are tightly controlled through regulation of the abundance and activity of key proteins. In synergy with the regulation of protein abundance or activity, cytoskeletal elements are key contributors to cell cycle progression through spatial regulation of developmental processes. These include: polarity establishment and maintenance, DNA segregation, cytokinesis, and cell elongation. Cytoskeletal proteins in C. crescentus are additionally required to maintain its rod shape, curvature, and pole morphology. In this chapter, we explore the mechanisms through which cytoskeletal proteins in C. crescentus orchestrate developmental processes by acting as scaffolds for protein recruitment, generating force, and/or restricting or directing the motion of molecular machines. We discuss each cytoskeletal element in turn, beginning with those important for organization of molecules at the cell poles and chromosome segregation, then cytokinesis, and finally cell shape.
Collapse
|
25
|
Harris LK, Theriot JA. Relative Rates of Surface and Volume Synthesis Set Bacterial Cell Size. Cell 2016; 165:1479-1492. [PMID: 27259152 DOI: 10.1016/j.cell.2016.05.045] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/18/2016] [Accepted: 05/12/2016] [Indexed: 01/28/2023]
Abstract
Many studies have focused on the mechanisms underlying length and width determination in rod-shaped bacteria. Here, we focus instead on cell surface area to volume ratio (SA/V) and demonstrate that SA/V homeostasis underlies size determination. We propose a model whereby the instantaneous rates of surface and volume synthesis both scale with volume. This model predicts that these relative rates dictate SA/V and that cells approach a new steady-state SA/V exponentially, with a decay constant equal to the volume growth rate. To test this, we exposed diverse bacterial species to sublethal concentrations of a cell wall biosynthesis inhibitor and observed dose-dependent decreases in SA/V. Furthermore, this decrease was exponential and had the expected decay constant. The model also quantitatively describes SA/V alterations induced by other chemical, nutritional, and genetic perturbations. We additionally present evidence for a surface material accumulation threshold underlying division, sensitizing cell length to changes in SA/V requirements.
Collapse
Affiliation(s)
- Leigh K Harris
- Biophysics Program, Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Julie A Theriot
- Biophysics Program, Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
26
|
Bratton BP, Shaevitz JW. Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System. PLoS One 2015; 10:e0134616. [PMID: 26270960 PMCID: PMC4536040 DOI: 10.1371/journal.pone.0134616] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/12/2015] [Indexed: 11/23/2022] Open
Abstract
Three-dimensional optical microscopy is often complicated by a refractive index mismatch between the sample and objective lens. This mismatch causes focal shift, a difference between sample motion and focal-plane motion, that hinders the accuracy of 3D reconstructions. We present two methods for measuring focal shift using fluorescent beads of different sizes and ring-stained fluorescent beads. These simple methods are applicable to most situations, including total internal reflection objectives and samples very close to the interface. For distances 0-1.5 μm into an aqueous environment, our 1.49-NA objective has a relative focal shift of 0.57 ± 0.02, significantly smaller than the simple n2/n1 approximation of 0.88. We also expand on a previous sub-critical angle theory by means of a simple polynomial extrapolation. We test the validity of this extrapolation by measuring the apparent focal shift in samples where the refractive index is between 1.33 and 1.45 and with objectives with numerical apertures between 1.25 and 1.49.
Collapse
Affiliation(s)
- Benjamin P. Bratton
- Department of Physics, Princeton University, Princeton, NJ, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States of America
| | - Joshua W. Shaevitz
- Department of Physics, Princeton University, Princeton, NJ, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States of America
| |
Collapse
|
27
|
Randich AM, Brun YV. Molecular mechanisms for the evolution of bacterial morphologies and growth modes. Front Microbiol 2015; 6:580. [PMID: 26106381 PMCID: PMC4460556 DOI: 10.3389/fmicb.2015.00580] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 12/13/2022] Open
Abstract
Bacteria exhibit a rich diversity of morphologies. Within this diversity, there is a uniformity of shape for each species that is replicated faithfully each generation, suggesting that bacterial shape is as selectable as any other biochemical adaptation. We describe the spatiotemporal mechanisms that target peptidoglycan synthesis to different subcellular zones to generate the rod-shape of model organisms Escherichia coli and Bacillus subtilis. We then demonstrate, using the related genera Caulobacter and Asticcacaulis as examples, how the modularity of the core components of the peptidoglycan synthesis machinery permits repositioning of the machinery to achieve different growth modes and morphologies. Finally, we highlight cases in which the mechanisms that underlie morphological evolution are beginning to be understood, and how they depend upon the expansion and diversification of the core components of the peptidoglycan synthesis machinery.
Collapse
Affiliation(s)
- Amelia M Randich
- Department of Biology, Indiana University , Bloomington, IN, USA
| | - Yves V Brun
- Department of Biology, Indiana University , Bloomington, IN, USA
| |
Collapse
|
28
|
Eun YJ, Kapoor M, Hussain S, Garner EC. Bacterial Filament Systems: Toward Understanding Their Emergent Behavior and Cellular Functions. J Biol Chem 2015; 290:17181-9. [PMID: 25957405 DOI: 10.1074/jbc.r115.637876] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria use homologs of eukaryotic cytoskeletal filaments to conduct many different tasks, controlling cell shape, division, and DNA segregation. These filaments, combined with factors that regulate their polymerization, create emergent self-organizing machines. Here, we summarize the current understanding of the assembly of these polymers and their spatial regulation by accessory factors, framing them in the context of being dynamical systems. We highlight how comparing the in vivo dynamics of the filaments with those measured in vitro has provided insight into the regulation, emergent behavior, and cellular functions of these polymeric systems.
Collapse
Affiliation(s)
- Ye-Jin Eun
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Mrinal Kapoor
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Saman Hussain
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Ethan C Garner
- From the Molecular and Cellular Biology Department and Faculty of Arts and Sciences (FAS) Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| |
Collapse
|
29
|
A constant size extension drives bacterial cell size homeostasis. Cell 2015; 159:1433-46. [PMID: 25480302 DOI: 10.1016/j.cell.2014.11.022] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/20/2014] [Accepted: 11/13/2014] [Indexed: 12/13/2022]
Abstract
Cell size control is an intrinsic feature of the cell cycle. In bacteria, cell growth and division are thought to be coupled through a cell size threshold. Here, we provide direct experimental evidence disproving the critical size paradigm. Instead, we show through single-cell microscopy and modeling that the evolutionarily distant bacteria Escherichia coli and Caulobacter crescentus achieve cell size homeostasis by growing, on average, the same amount between divisions, irrespective of cell length at birth. This simple mechanism provides a remarkably robust cell size control without the need of being precise, abating size deviations exponentially within a few generations. This size homeostasis mechanism is broadly applicable for symmetric and asymmetric divisions, as well as for different growth rates. Furthermore, our data suggest that constant size extension is implemented at or close to division. Altogether, our findings provide fundamentally distinct governing principles for cell size and cell-cycle control in bacteria.
Collapse
|