1
|
Ziegler KF, Joshi K, Wright CS, Roy S, Caruso W, Biswas RR, Iyer-Biswas S. Scaling of stochastic growth and division dynamics: A comparative study of individual rod-shaped cells in the Mother Machine and SChemostat platforms. Mol Biol Cell 2024; 35:ar78. [PMID: 38598301 PMCID: PMC11238078 DOI: 10.1091/mbc.e23-11-0452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/15/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Microfluidic platforms enable long-term quantification of stochastic behaviors of individual bacterial cells under precisely controlled growth conditions. Yet, quantitative comparisons of physiological parameters and cell behaviors of different microorganisms in different experimental and device modalities is not available due to experiment-specific details affecting cell physiology. To rigorously assess the effects of mechanical confinement, we designed, engineered, and performed side-by-side experiments under otherwise identical conditions in the Mother Machine (with confinement) and the SChemostat (without confinement), using the latter as the ideal comparator. We established a protocol to cultivate a suitably engineered rod-shaped mutant of Caulobacter crescentus in the Mother Machine and benchmarked the differences in stochastic growth and division dynamics with respect to the SChemostat. While the single-cell growth rate distributions are remarkably similar, the mechanically confined cells in the Mother Machine experience a substantial increase in interdivision times. However, we find that the division ratio distribution precisely compensates for this increase, which in turn reflects identical emergent simplicities governing stochastic intergenerational homeostasis of cell sizes across device and experimental configurations, provided the cell sizes are appropriately mean-rescaled in each condition. Our results provide insights into the nature of the robustness of the bacterial growth and division machinery.
Collapse
Affiliation(s)
- Karl F. Ziegler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health, Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Kunaal Joshi
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Charles S. Wright
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Shaswata Roy
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Will Caruso
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Rudro R. Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| | - Srividya Iyer-Biswas
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907
| |
Collapse
|
2
|
Kratz JC, Banerjee S. Dynamic proteome trade-offs regulate bacterial cell size and growth in fluctuating nutrient environments. Commun Biol 2023; 6:486. [PMID: 37147517 PMCID: PMC10163005 DOI: 10.1038/s42003-023-04865-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
Bacteria dynamically regulate cell size and growth to thrive in changing environments. While previous studies have characterized bacterial growth physiology at steady-state, a quantitative understanding of bacterial physiology in time-varying environments is lacking. Here we develop a quantitative theory connecting bacterial growth and division rates to proteome allocation in time-varying nutrient environments. In such environments, cell size and growth are regulated by trade-offs between prioritization of biomass accumulation or division, resulting in decoupling of single-cell growth rate from population growth rate. Specifically, bacteria transiently prioritize biomass accumulation over production of division machinery during nutrient upshifts, while prioritizing division over growth during downshifts. When subjected to pulsatile nutrient concentration, we find that bacteria exhibit a transient memory of previous metabolic states due to the slow dynamics of proteome reallocation. This allows for faster adaptation to previously seen environments and results in division control which is dependent on the time-profile of fluctuations.
Collapse
Affiliation(s)
- Josiah C Kratz
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
| |
Collapse
|
3
|
Gupta A, Joshi A, Arora K, Mukhopadhyay S, Guptasarma P. The bacterial nucleoid-associated proteins, HU, and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates. J Biol Chem 2023; 299:104637. [PMID: 36963493 PMCID: PMC10141540 DOI: 10.1016/j.jbc.2023.104637] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
The bacterial chromosome, known as its nucleoid, is an amorphous assemblage of globular nucleoprotein domains. It exists in a state of phase separation from the cell's cytoplasm, as an irregularly-shaped, membrane-less, intracellular compartment. This state (the nature of which remains largely unknown) is maintained through bacterial generations ad infinitum. Here, we show that HU, and Dps, two of the most abundant nucleoid-associated proteins (NAPs) of Escherichia coli, undergo spontaneous complex coacervation with different forms of DNA/RNA, both individually and in each other's presence, to cause accretion and compaction of DNA/RNA into liquid-liquid phase separated (LLPS) condensates in vitro. Upon mixing with nucleic acids, HU-A and HU-B form (a) bi-phasic heterotypic mixed condensates in which HU-B helps to lower the Csat of HU-A; and also (b) multi-phasic heterotypic condensates, with Dps, in which de-mixed domains display different contents of HU and Dps. We believe that these modes of complex coacervation that are seen in vitro can serve as models for the in vivo relationships amongst NAPs in nucleoids, involving local and global variations in the relative abundances of the different NAPs, especially in de-mixed sub-domains that are characterized by differing grades of phase separation. Our results clearly demonstrate some quantitative, and some qualitative, differences in the coacervating abilities of different NAPs with DNA, potentially explaining (i) why E. coli has two isoforms of HU, and (ii) why changes in the abundances of HU and Dps facilitate the lag, logarithmic and stationary phases of E. coli growth.
Collapse
Affiliation(s)
- Archit Gupta
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India.
| | - Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Kanika Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Chemical Sciences; Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, Punjab 140306, India.
| |
Collapse
|
4
|
Tian D, Wang C, Liu Y, Zhang Y, Caliari A, Lu H, Xia Y, Xu B, Xu J, Yomo T. Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution. Int J Mol Sci 2023; 24:ijms24043243. [PMID: 36834655 PMCID: PMC9966196 DOI: 10.3390/ijms24043243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on their optical properties, morphology can be easily determined and tracked during experimental evolution. Furthermore, the directed evolution of new culturable morphological phenotypes can find use in synthetic biology to refine fermentation processes. It remains unknown whether and how fast we can obtain a stable mutant with distinct morphologies using fluorescence-activated cell sorting (FACS)-directed experimental evolution. Taking advantage of FACS and imaging flow cytometry (IFC), we direct the experimental evolution of the E. coli population undergoing continuous passage of sorted cells with specific optical properties. After ten rounds of sorting and culturing, a lineage with large cells resulting from incomplete closure of the division ring was obtained. Genome sequencing highlighted a stop-gain mutation in amiC, leading to a dysfunctional AmiC division protein. The combination of FACS-based selection with IFC analysis to track the evolution of the bacteria population in real-time holds promise to rapidly select and culture new morphologies and association tendencies with many potential applications.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Jian Xu
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
| | - Tetsuya Yomo
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
| |
Collapse
|
5
|
Scott S, Weiss M, Selhuber-Unkel C, Barooji YF, Sabri A, Erler JT, Metzler R, Oddershede LB. Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking. Phys Chem Chem Phys 2023; 25:1513-1537. [PMID: 36546878 DOI: 10.1039/d2cp01384c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A panoply of new tools for tracking single particles and molecules has led to an explosion of experimental data, leading to novel insights into physical properties of living matter governing cellular development and function, health and disease. In this Perspective, we present tools to investigate the dynamics and mechanics of living systems from the molecular to cellular scale via single-particle techniques. In particular, we focus on methods to measure, interpret, and analyse complex data sets that are associated with forces, materials properties, transport, and emergent organisation phenomena within biological and soft-matter systems. Current approaches, challenges, and existing solutions in the associated fields are outlined in order to support the growing community of researchers at the interface of physics and the life sciences. Each section focuses not only on the general physical principles and the potential for understanding living matter, but also on details of practical data extraction and analysis, discussing limitations, interpretation, and comparison across different experimental realisations and theoretical frameworks. Particularly relevant results are introduced as examples. While this Perspective describes living matter from a physical perspective, highlighting experimental and theoretical physics techniques relevant for such systems, it is also meant to serve as a solid starting point for researchers in the life sciences interested in the implementation of biophysical methods.
Collapse
Affiliation(s)
- Shane Scott
- Institute of Physiology, Kiel University, Hermann-Rodewald-Straße 5, 24118 Kiel, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Christine Selhuber-Unkel
- Institute for Molecular Systems Engineering, Heidelberg University, D-69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Younes F Barooji
- Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
| | - Adal Sabri
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Janine T Erler
- BRIC, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Str. 24/25, D-14476 Potsdam, Germany.,Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | | |
Collapse
|
6
|
Marro FC, Laurent F, Josse J, Blocker AJ. Methods to monitor bacterial growth and replicative rates at the single-cell level. FEMS Microbiol Rev 2022; 46:6623663. [PMID: 35772001 PMCID: PMC9629498 DOI: 10.1093/femsre/fuac030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 01/09/2023] Open
Abstract
The heterogeneity of bacterial growth and replicative rates within a population was proposed a century ago notably to explain the presence of bacterial persisters. The term "growth rate" at the single-cell level corresponds to the increase in size or mass of an individual bacterium while the "replicative rate" refers to its division capacity within a defined temporality. After a decades long hiatus, recent technical innovative approaches allow population growth and replicative rates heterogeneity monitoring at the single-cell level resuming in earnest. Among these techniques, the oldest and widely used is time-lapse microscopy, most recently combined with microfluidics. We also discuss recent fluorescence dilution methods informing only on replicative rates and best suited. Some new elegant single cell methods so far only sporadically used such as buoyant mass measurement and stable isotope probing have emerged. Overall, such tools are widely used to investigate and compare the growth and replicative rates of bacteria displaying drug-persistent behaviors to that of bacteria growing in specific ecological niches or collected from patients. In this review, we describe the current methods available, discussing both the type of queries these have been used to answer and the specific strengths and limitations of each method.
Collapse
Affiliation(s)
- Florian C Marro
- Evotec ID Lyon, In Vitro Biology, Infectious Diseases and Antibacterials Unit, Gerland, 69007 Lyon, France,CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France
| | - Frédéric Laurent
- CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France,Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1, Lyon, France,Centre de Référence pour la prise en charge des Infections ostéo-articulaires complexes (CRIOAc Lyon; www.crioac-lyon.fr), Hospices Civils de Lyon, Lyon, France,Laboratoire de bactériologie, Institut des Agents Infectieux, French National Reference Center for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - Jérôme Josse
- CIRI – Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, F-69007 Lyon, France,Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1, Lyon, France,Centre de Référence pour la prise en charge des Infections ostéo-articulaires complexes (CRIOAc Lyon; www.crioac-lyon.fr), Hospices Civils de Lyon, Lyon, France
| | - Ariel J Blocker
- Corresponding author. Evotec ID Lyon, In Vitro Biology, Infectious Diseases and Antibacterials Unit, France. E-mail:
| |
Collapse
|
7
|
Asymmetric peptidoglycan editing generates cell curvature in Bdellovibrio predatory bacteria. Nat Commun 2022; 13:1509. [PMID: 35314810 PMCID: PMC8938487 DOI: 10.1038/s41467-022-29007-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractPeptidoglycan hydrolases contribute to the generation of helical cell shape in Campylobacter and Helicobacter bacteria, while cytoskeletal or periskeletal proteins determine the curved, vibrioid cell shape of Caulobacter and Vibrio. Here, we identify a peptidoglycan hydrolase in the vibrioid-shaped predatory bacterium Bdellovibrio bacteriovorus which invades and replicates within the periplasm of Gram-negative prey bacteria. The protein, Bd1075, generates cell curvature in B. bacteriovorus by exerting LD-carboxypeptidase activity upon the predator cell wall as it grows inside spherical prey. Bd1075 localizes to the outer convex face of B. bacteriovorus; this asymmetric localization requires a nuclear transport factor 2-like (NTF2) domain at the protein C-terminus. We solve the crystal structure of Bd1075, which is monomeric with key differences to other LD-carboxypeptidases. Rod-shaped Δbd1075 mutants invade prey more slowly than curved wild-type predators and stretch invaded prey from within. We therefore propose that the vibrioid shape of B. bacteriovorus contributes to predatory fitness.
Collapse
|
8
|
Lao-Martil D, Verhagen KJA, Schmitz JPJ, Teusink B, Wahl SA, van Riel NAW. Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities. Metabolites 2022; 12:74. [PMID: 35050196 PMCID: PMC8779790 DOI: 10.3390/metabo12010074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
Central carbon metabolism comprises the metabolic pathways in the cell that process nutrients into energy, building blocks and byproducts. To unravel the regulation of this network upon glucose perturbation, several metabolic models have been developed for the microorganism Saccharomyces cerevisiae. These dynamic representations have focused on glycolysis and answered multiple research questions, but no commonly applicable model has been presented. This review systematically evaluates the literature to describe the current advances, limitations, and opportunities. Different kinetic models have unraveled key kinetic glycolytic mechanisms. Nevertheless, some uncertainties regarding model topology and parameter values still limit the application to specific cases. Progressive improvements in experimental measurement technologies as well as advances in computational tools create new opportunities to further extend the model scale. Notably, models need to be made more complex to consider the multiple layers of glycolytic regulation and external physiological variables regulating the bioprocess, opening new possibilities for extrapolation and validation. Finally, the onset of new data representative of individual cells will cause these models to evolve from depicting an average cell in an industrial fermenter, to characterizing the heterogeneity of the population, opening new and unseen possibilities for industrial fermentation improvement.
Collapse
Affiliation(s)
- David Lao-Martil
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
| | - Koen J. A. Verhagen
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Joep P. J. Schmitz
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands;
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands;
| | - S. Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, FAU Erlangen-Nürnberg, 91052 Erlangen, Germany; (K.J.A.V.); (S.A.W.)
| | - Natal A. W. van Riel
- Department of Biomedical Engineering, Eindhoven University of Technology, Groene Loper 5, 5612 AE Eindhoven, The Netherlands;
- Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| |
Collapse
|
9
|
Levin PA, Janakiraman A. Localization, Assembly, and Activation of the Escherichia coli Cell Division Machinery. EcoSal Plus 2021; 9:eESP00222021. [PMID: 34910577 PMCID: PMC8919703 DOI: 10.1128/ecosalplus.esp-0022-2021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023]
Abstract
Decades of research, much of it in Escherichia coli, have yielded a wealth of insight into bacterial cell division. Here, we provide an overview of the E. coli division machinery with an emphasis on recent findings. We begin with a short historical perspective into the discovery of FtsZ, the tubulin homolog that is essential for division in bacteria and archaea. We then discuss assembly of the divisome, an FtsZ-dependent multiprotein platform, at the midcell septal site. Not simply a scaffold, the dynamic properties of polymeric FtsZ ensure the efficient and uniform synthesis of septal peptidoglycan. Next, we describe the remodeling of the cell wall, invagination of the cell envelope, and disassembly of the division apparatus culminating in scission of the mother cell into two daughter cells. We conclude this review by highlighting some of the open questions in the cell division field, emphasizing that much remains to be discovered, even in an organism as extensively studied as E. coli.
Collapse
Affiliation(s)
- Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Anuradha Janakiraman
- Department of Biology, The City College of New York, New York, New York, USA
- Programs in Biology and Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
| |
Collapse
|
10
|
Nieto C, Vargas-García C, Pedraza JM. Continuous rate modeling of bacterial stochastic size dynamics. Phys Rev E 2021; 104:044415. [PMID: 34781449 DOI: 10.1103/physreve.104.044415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022]
Abstract
Bacterial division is an inherently stochastic process with effects on fluctuations of protein concentration and phenotype variability. Current modeling tools for the stochastic short-term cell-size dynamics are scarce and mainly phenomenological. Here we present a general theoretical approach based on the Chapman-Kolmogorov equation incorporating continuous growth and division events as jump processes. This approach allows us to include different division strategies, noisy growth, and noisy cell splitting. Considering bacteria synchronized from their last division, we predict oscillations in both the central moments of the size distribution and its autocorrelation function. These oscillations, barely discussed in past studies, can arise as a consequence of the discrete time displacement invariance of the system with a period of one doubling time, and they do not disappear when including stochasticity on either division times or size heterogeneity on the starting population but only after inclusion of noise in either growth rate or septum position. This result illustrates the usefulness of having a solid mathematical description that explicitly incorporates the inherent stochasticity in various biological processes, both to understand the process in detail and to evaluate the effect of various sources of variability when creating simplified descriptions.
Collapse
Affiliation(s)
- César Nieto
- Department of Physics, Universidad de los Andes, Bogotá 111711, Colombia.,Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - César Vargas-García
- Corporacion Colombiana de Investigación Agropecuaria AGROSAVIA, Mosquera 250047, Colombia
| | - Juan M Pedraza
- Department of Physics, Universidad de los Andes, Bogotá 111711, Colombia
| |
Collapse
|
11
|
Qiu L, Zhang L, Horowitz GL, Turzhitsky V, Coughlan MF, Glyavina M, Khan U, Zakharov YN, Vitkin E, Itzkan I, Perelman LT. Rapid detection and identification of bacteria directly from whole blood with light scattering spectroscopy based biosensor. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 346:130489. [PMID: 34483482 PMCID: PMC8415441 DOI: 10.1016/j.snb.2021.130489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial infections are one of the major causes of death worldwide. The identification of a bacterial species that is the source of an infection generally takes a long time, and often exceeds the treatment window for seriously ill patients. Many of these deaths are preventable if the bacterial species can be identified quickly. Here we present an optical spectroscopic method for rapid detection and identification of bacteria directly from whole blood using a light scattering spectroscopy technique. This technique was originally developed to detect pre-cancerous changes in epithelial tissues, characterize changes in tissue on the cellular scale, and characterize biological structures comparable to or smaller than a single wavelength. We demonstrate here that not only can an inexpensive light scattering spectroscopy-based biosensor rapidly detect and identify four bacteria species in the blood, responsible for the majority of death causing infections, but that species-level identification can potentially be made based on approximately one thousand bacterial cells per milliliter of blood. Observing entire colonies or performing susceptibility testing is therefore not required.
Collapse
Affiliation(s)
- Le Qiu
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Lei Zhang
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Gary L. Horowitz
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University, Boston, Massachusetts 02111 USA
| | - Vladimir Turzhitsky
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Mark F. Coughlan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Maria Glyavina
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Umar Khan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Yuri N. Zakharov
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Edward Vitkin
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Irving Itzkan
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
| | - Lev T. Perelman
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard University, Boston, Massachusetts 02215 USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, Massachusetts 02115 USA
| |
Collapse
|
12
|
Männik J, Teshima TF, Wolfrum B, Yang D. Lab-on-a-chip based mechanical actuators and sensors for single-cell and organoid culture studies. JOURNAL OF APPLIED PHYSICS 2021; 129:210905. [PMID: 34103765 PMCID: PMC8175090 DOI: 10.1063/5.0051875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/10/2021] [Indexed: 05/04/2023]
Abstract
All living cells constantly experience and respond to mechanical stresses. The molecular networks that activate in cells in response to mechanical stimuli are yet not well-understood. Our limited knowledge stems partially from the lack of available tools that are capable of exerting controlled mechanical stress to individual cells and at the same time observing their responses at subcellular to molecular resolution. Several tools such as rheology setups, micropipetes, and magnetic tweezers have been used in the past. While allowing to quantify short-time viscoelastic responses, these setups are not suitable for long-term observations of cells and most of them have low throughput. In this Perspective, we discuss lab-on-a-chip platforms that have the potential to overcome these limitations. Our focus is on devices that apply shear, compressive, tensile, and confinement derived stresses to single cells and organoid cultures. We compare different design strategies for these devices and highlight their advantages, drawbacks, and future potential. While the majority of these devices are used for fundamental research, some of them have potential applications in medical diagnostics and these applications are also discussed.
Collapse
Affiliation(s)
- Jaan Männik
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee 37996, USA
- Author to whom correspondence should be addressed:
| | | | | | - Da Yang
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee 37996, USA
| |
Collapse
|
13
|
Biochip with multi-planar electrodes geometry for differentiation of non-spherical bioparticles in a microchannel. Sci Rep 2021; 11:11880. [PMID: 34088942 PMCID: PMC8178319 DOI: 10.1038/s41598-021-91109-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/21/2021] [Indexed: 02/04/2023] Open
Abstract
A biosensor capable of differentiating cells or other microparticles based on morphology finds significant biomedical applications. Examples may include morphological determination in the cellular division process, differentiation of bacterial cells, and cellular morphological variation in inflammation and cancer etc. Here, we present a novel integrated multi-planar microelectrodes geometry design that can distinguish a non-spherical individual particle flowing along a microchannel based on its electrical signature. We simulated multi-planar electrodes design in COMSOL Multiphysics and have shown that the changes in electrical field intensity corresponding to multiple particle morphologies can be distinguished. Our initial investigation has shown that top-bottom electrodes configuration produces significantly enhanced signal strength for a spherical particle as compared to co-planar configuration. Next, we integrated the co-planar and top-bottom configurations to develop a multi-planar microelectrode design capable of electrical impedance measurement at different spatial planes inside a microchannel by collecting multiple output signatures. We tested our integrated multi-planar electrode design with particles of different elliptical morphologies by gradually changing spherical particle dimensions to the non-spherical. The computed electrical signal ratio of non-spherical to spherical particle shows a very good correlation to predict the particle morphology. The biochip sensitivity is also found be independent of orientation of the particle flowing in the microchannel. Our integrated design will help develop the technology that will allow morphological analysis of various bioparticles in a microfluidic channel in the future.
Collapse
|
14
|
Huang W, Luo S, Yang D, Zhang S. Applications of smartphone-based near-infrared (NIR) imaging, measurement, and spectroscopy technologies to point-of-care (POC) diagnostics. J Zhejiang Univ Sci B 2021; 22:171-189. [PMID: 33719223 DOI: 10.1631/jzus.b2000388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The role of point-of-care (POC) diagnostics is important in public health. With the support of smartphones, POC diagnostic technologies can be greatly improved. This opportunity has arisen from not only the large number and fast spread of cell-phones across the world but also their improved imaging/diagnostic functions. As a tool, the smartphone is regarded as part of a compact, portable, and low-cost system for real-time POC, even in areas with few resources. By combining near-infrared (NIR) imaging, measurement, and spectroscopy techniques, pathogens can be detected with high sensitivity. The whole process is rapid, accurate, and low-cost, and will set the future trend for POC diagnostics. In this review, the development of smartphone-based NIR fluorescent imaging technology was described, and the quality and potential of POC applications were discussed.
Collapse
Affiliation(s)
- Wenjing Huang
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, China.,Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Shenglin Luo
- Institute of Combined Injury, State Key Laboratory of Trauma, Burn and Combined Injury, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China.,Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown 02129, USA
| | - Dong Yang
- Division of Biomedical Engineering, Renal Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge 02139, USA
| | - Sheng Zhang
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, China. .,State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, China.
| |
Collapse
|
15
|
Kohram M, Vashistha H, Leibler S, Xue B, Salman H. Bacterial Growth Control Mechanisms Inferred from Multivariate Statistical Analysis of Single-Cell Measurements. Curr Biol 2021; 31:955-964.e4. [PMID: 33357764 DOI: 10.1016/j.cub.2020.11.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022]
Abstract
Analysis of single-cell measurements of bacterial growth and division often relied on testing preconceived models of cell size control mechanisms. Such an approach could limit the scope of data analysis and prevent us from uncovering new information. Here, we take an "agnostic" approach by applying regression methods to multiple simultaneously measured cellular variables, which allow us to infer dependencies among those variables from their apparent correlations. Besides previously observed correlations attributed to particular cell size control mechanisms, we identify dependencies that point to potentially new mechanisms. In particular, cells born smaller than their sisters tend to grow faster and make up for the size difference acquired during division. We also find that sister cells are correlated beyond what single-cell, size-control models predict. These trends are consistently found in repeat experiments, although the dependencies vary quantitatively. Such variation highlights the sensitivity of cell growth to environmental variations and the limitation of currently used experimental setups.
Collapse
Affiliation(s)
- Maryam Kohram
- Department of Physics and Astronomy, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Harsh Vashistha
- Department of Physics and Astronomy, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Stanislas Leibler
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA; Laboratory of Living Matter and Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - BingKan Xue
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA; Laboratory of Living Matter and Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Hanna Salman
- Department of Physics and Astronomy, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| |
Collapse
|
16
|
Liang B, Quan B, Li J, Loton C, Bredeche MF, Lindner AB, Xu L. Artificial modulation of cell width significantly affects the division time of Escherichia coli. Sci Rep 2020; 10:17847. [PMID: 33082450 PMCID: PMC7576201 DOI: 10.1038/s41598-020-74778-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Bacterial cells have characteristic spatial and temporal scales. For instance, Escherichia coli, the typical rod-shaped bacteria, always maintains a relatively constant cell width and cell division time. However, whether the external physical perturbation of cell width has an impact on cell division time remains largely unexplored. In this work, we developed two microchannel chips, namely straight channels and ‘necked’ channels, to precisely regulate the width of E. coli cells and to investigate the correlation between cell width and division time of the cells. Our results show that, in the straight channels, the wide cells divide much slower than narrow cells. In the ‘necked’ channels, the cell division is remarkably promoted compared to that in straight channels with the same width. Besides, fluorescence time-lapse microscopy imaging of FtsZ dynamics shows that the cell pre-constriction time is more sensitive to cell width perturbation than cell constriction time. Finally, we revealed a significant anticorrelation between the death rate and the division rate of cell populations with different widths. Our work provides new insights into the correlation between the geometrical property and division time of E. coli cells and sheds new light on the future study of spatial–temporal correlation in cell physiology.
Collapse
Affiliation(s)
- Baihui Liang
- Center for Nano and Micro Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Baogang Quan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Junjie Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Songshan Lake Materials Laboratory, Dongguan, 523808, Guangdong, People's Republic of China
| | - Chantal Loton
- Systems Engineering and Evolution Dynamics Lab, INSERM U1001, Paris Descartes University, 75014, Paris, France.,Faculty of Medicine, Paris Descartes University, 75014, Paris, France
| | - Marie-Florence Bredeche
- Systems Engineering and Evolution Dynamics Lab, INSERM U1001, Paris Descartes University, 75014, Paris, France.,Faculty of Medicine, Paris Descartes University, 75014, Paris, France
| | - Ariel B Lindner
- Systems Engineering and Evolution Dynamics Lab, INSERM U1001, Paris Descartes University, 75014, Paris, France.,Faculty of Medicine, Paris Descartes University, 75014, Paris, France.,Centre for Research and Interdisciplinarity (CRI), Paris Descartes University, 75014, Paris, France
| | - Luping Xu
- Center for Nano and Micro Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, People's Republic of China.
| |
Collapse
|
17
|
Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32894477 DOI: 10.1007/978-3-030-46886-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The internal spatial organization of prokaryotic organisms, including Escherichia coli, is essential for the proper functioning of processes such as cell division. One source of this organization in E. coli is the nucleoid, which causes the exclusion of macromolecules - e.g. protein aggregates and the chemotaxis network - from midcell. Similarly, following DNA replication, the nucleoid(s) assist in placing the Z-ring at midcell. These processes need to be efficient in optimal conditions and robust to suboptimal conditions. After reviewing recent findings on these topics, we make use of past data to study the efficiency of the spatial constraining of Z-rings, chemotaxis networks, and protein aggregates, as a function of the nucleoid(s) morphology. Also, we compare the robustness of these processes to nonoptimal temperatures. We show that Z-rings, Tsr clusters, and protein aggregates have temperature-dependent spatial distributions along the major cell axis that are consistent with the nucleoid(s) morphology and the volume-exclusion phenomenon. Surprisingly, the consequences of the changes in nucleoid size with temperature are most visible in the kurtosis of these spatial distributions, in that it has a statistically significant linear correlation with the mean nucleoid length and, in the case of Z-rings, with the distance between nucleoids prior to cell division. Interestingly, we also find a negative, statistically significant linear correlation between the efficiency of these processes at the optimal condition and their robustness to suboptimal conditions, suggesting a trade-off between these traits.
Collapse
|
18
|
Nolet FE, Vandervelde A, Vanderbeke A, Piñeros L, Chang JB, Gelens L. Nuclei determine the spatial origin of mitotic waves. eLife 2020; 9:e52868. [PMID: 32452767 PMCID: PMC7314552 DOI: 10.7554/elife.52868] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/22/2020] [Indexed: 12/11/2022] Open
Abstract
Traveling waves play an essential role in coordinating mitosis over large distances, but what determines the spatial origin of mitotic waves remains unclear. Here, we show that such waves initiate at pacemakers, regions that oscillate faster than their surroundings. In cell-free extracts of Xenopus laevis eggs, we find that nuclei define such pacemakers by concentrating cell cycle regulators. In computational models of diffusively coupled oscillators that account for nuclear import, nuclear positioning determines the pacemaker location. Furthermore, we find that the spatial dimensions of the oscillatory medium change the nuclear positioning and strongly influence whether a pacemaker is more likely to be at a boundary or an internal region. Finally, we confirm experimentally that increasing the system width increases the proportion of pacemakers at the boundary. Our work provides insight into how nuclei and spatial system dimensions can control local concentrations of regulators and influence the emergent behavior of mitotic waves.
Collapse
Affiliation(s)
- Felix E Nolet
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
| | - Alexandra Vandervelde
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
| | - Arno Vanderbeke
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
- MeBioS - Biosensors Group, Department of Biosystems, KU LeuvenLeuvenBelgium
| | - Liliana Piñeros
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
| | - Jeremy B Chang
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoUnited States
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, Faculty of Medicine, KU LeuvenLeuvenBelgium
| |
Collapse
|
19
|
Nieto-Acuña C, Arias-Castro JC, Vargas-García C, Sánchez C, Pedraza JM. Correlation between protein concentration and bacterial cell size can reveal mechanisms of gene expression. Phys Biol 2020; 17:045002. [PMID: 32289764 DOI: 10.1088/1478-3975/ab891c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Classically, gene expression is modeled as a chemical process with reaction rates dependent on the concentration of the reactants (typically, DNA loci, plasmids, RNA, enzymes, etc). Other variables like cell size are in general ignored. Size dynamics can become an important variable due to the low number of many of these reactants, imperfectly symmetric cell partitioning and molecule segregation. In this work we measure the correlation between size and protein concentration by observing the gene expression of the RpOD gene from a low-copy plasmid in Escherichia coli during balanced growth in different media. A positive correlation was found, and we used it to examine possible models of cell size dynamics and plasmid replication. We implemented a previously developed model describing the full gene expression process including transcription, translation, loci replication, cell division and molecule segregation. By comparing with the observed correlation, we determine that the transcription rate must be proportional to the size times the number of plasmids. We discuss how fluctuations in plasmid segregation, due to the low copy number, can impose limits in this correlation.
Collapse
Affiliation(s)
| | - Juan Carlos Arias-Castro
- Department of Physics, Universidad de los Andes, Bogotá, Colombia.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States of America
| | - César Vargas-García
- Department of Mathematics and Engineering, Fundación universitaria Konrad Lorenz, Bogota, Colombia.,AGROSAVIA, Corporación Colombiana de Investigación Agropecuaria, Mosquera, Bogotá, Colombia
| | - Carlos Sánchez
- Department of Physics, Universidad de los Andes, Bogotá, Colombia.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States of America
| | | |
Collapse
|
20
|
Microfluidic Single-Cell Analytics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:159-189. [PMID: 32737554 DOI: 10.1007/10_2020_134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
What is the impact of cellular heterogeneity on process performance? How do individual cells contribute to averaged process productivity? Single-cell analysis is a key technology for answering such key questions of biotechnology, beyond bulky measurements with populations. The analysis of cellular individuality, its origins, and the dependency of process performance on cellular heterogeneity has tremendous potential for optimizing biotechnological processes in terms of metabolic, reaction, and process engineering. Microfluidics offer unmatched environmental control of the cellular environment and allow massively parallelized cultivation of single cells. However, the analytical accessibility to a cell's physiology is of crucial importance for obtaining the desired information on the single-cell production phenotype. Highly sensitive analytics are required to detect and quantify the minute amounts of target analytes and small physiological changes in a single cell. For their application to biotechnological questions, single-cell analytics must evolve toward the measurement of kinetics and specific rates of the smallest catalytic unit, the single cell. In this chapter, we focus on an introduction to the latest single-cell analytics and their application for obtaining physiological parameters in a biotechnological context from single cells. We present and discuss recent advancements in single-cell analytics that enable the analysis of cell-specific growth, uptake, and production kinetics, as well as the gene expression and regulatory mechanisms at a single-cell level.
Collapse
|
21
|
Wang YK, Krasnopeeva E, Lin SY, Bai F, Pilizota T, Lo CJ. Comparison of Escherichia coli surface attachment methods for single-cell microscopy. Sci Rep 2019; 9:19418. [PMID: 31857669 PMCID: PMC6923479 DOI: 10.1038/s41598-019-55798-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/05/2019] [Indexed: 12/22/2022] Open
Abstract
For in vivo, single-cell imaging bacterial cells are commonly immobilised via physical confinement or surface attachment. Different surface attachment methods have been used both for atomic force and optical microscopy (including super resolution), and some have been reported to affect bacterial physiology. However, a systematic comparison of the effects these attachment methods have on the bacterial physiology is lacking. Here we present such a comparison for bacterium Escherichia coli, and assess the growth rate, size and intracellular pH of cells growing attached to different, commonly used, surfaces. We demonstrate that E. coli grow at the same rate, length and internal pH on all the tested surfaces when in the same growth medium. The result suggests that tested attachment methods can be used interchangeably when studying E. coli physiology.
Collapse
Affiliation(s)
- Yao-Kuan Wang
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, 32001, Republic of China
| | - Ekaterina Krasnopeeva
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Alexander Crum Brown Road, EH9 3FF, Edinburgh, UK
| | - Ssu-Yuan Lin
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, 32001, Republic of China
| | - Fan Bai
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Alexander Crum Brown Road, EH9 3FF, Edinburgh, UK.
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, 32001, Republic of China.
| |
Collapse
|
22
|
Abstract
The notion that graded distributions of signals underlie the spatial organization of biological systems has long been a central pillar in the fields of cell and developmental biology. During morphogenesis, morphogens spread across tissues to guide development of the embryo. Similarly, a variety of dynamic gradients and pattern-forming networks have been discovered that shape subcellular organization. Here we discuss the principles of intracellular pattern formation by these intracellular morphogens and relate them to conceptually similar processes operating at the tissue scale. We will specifically review mechanisms for generating cellular asymmetry and consider how intracellular patterning networks are controlled and adapt to cellular geometry. Finally, we assess the general concept of intracellular gradients as a mechanism for positional control in light of current data, highlighting how the simple readout of fixed concentration thresholds fails to fully capture the complexity of spatial patterning processes occurring inside cells.
Collapse
Affiliation(s)
- Lars Hubatsch
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Nathan W Goehring
- The Francis Crick Institute, London, United Kingdom; Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.
| |
Collapse
|
23
|
Booth S, Lewis RJ. Structural basis for the coordination of cell division with the synthesis of the bacterial cell envelope. Protein Sci 2019; 28:2042-2054. [PMID: 31495975 PMCID: PMC6863701 DOI: 10.1002/pro.3722] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 01/02/2023]
Abstract
Bacteria are surrounded by a complex cell envelope made up of one or two membranes supplemented with a layer of peptidoglycan (PG). The envelope is responsible for the protection of bacteria against lysis in their oft-unpredictable environments and it contributes to cell integrity, morphology, signaling, nutrient/small-molecule transport, and, in the case of pathogenic bacteria, host-pathogen interactions and virulence. The cell envelope requires considerable remodeling during cell division in order to produce genetically identical progeny. Several proteinaceous machines are responsible for the homeostasis of the cell envelope and their activities must be kept coordinated in order to ensure the remodeling of the envelope is temporally and spatially regulated correctly during multiple cycles of cell division and growth. This review aims to highlight the complexity of the components of the cell envelope, but focusses specifically on the molecular apparatuses involved in the synthesis of the PG wall, and the degree of cross talk necessary between the cell division and the cell wall remodeling machineries to coordinate PG remodeling during division. The current understanding of many of the proteins discussed here has relied on structural studies, and this review concentrates particularly on this structural work.
Collapse
Affiliation(s)
- Simon Booth
- Institute for Cell and Molecular Biosciences, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Richard J. Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| |
Collapse
|
24
|
Ramm B, Heermann T, Schwille P. The E. coli MinCDE system in the regulation of protein patterns and gradients. Cell Mol Life Sci 2019; 76:4245-4273. [PMID: 31317204 PMCID: PMC6803595 DOI: 10.1007/s00018-019-03218-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
Molecular self-organziation, also regarded as pattern formation, is crucial for the correct distribution of cellular content. The processes leading to spatiotemporal patterns often involve a multitude of molecules interacting in complex networks, so that only very few cellular pattern-forming systems can be regarded as well understood. Due to its compositional simplicity, the Escherichia coli MinCDE system has, thus, become a paradigm for protein pattern formation. This biological reaction diffusion system spatiotemporally positions the division machinery in E. coli and is closely related to ParA-type ATPases involved in most aspects of spatiotemporal organization in bacteria. The ATPase MinD and the ATPase-activating protein MinE self-organize on the membrane as a reaction matrix. In vivo, these two proteins typically oscillate from pole-to-pole, while in vitro they can form a variety of distinct patterns. MinC is a passenger protein supposedly operating as a downstream cue of the system, coupling it to the division machinery. The MinCDE system has helped to extract not only the principles underlying intracellular patterns, but also how they are shaped by cellular boundaries. Moreover, it serves as a model to investigate how patterns can confer information through specific and non-specific interactions with other molecules. Here, we review how the three Min proteins self-organize to form patterns, their response to geometric boundaries, and how these patterns can in turn induce patterns of other molecules, focusing primarily on experimental approaches and developments.
Collapse
Affiliation(s)
- Beatrice Ramm
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tamara Heermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| |
Collapse
|
25
|
Walsh JC, Angstmann CN, Bisson-Filho AW, Garner EC, Duggin IG, Curmi PMG. Division plane placement in pleomorphic archaea is dynamically coupled to cell shape. Mol Microbiol 2019; 112:785-799. [PMID: 31136034 PMCID: PMC6736733 DOI: 10.1111/mmi.14316] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2019] [Indexed: 12/14/2022]
Abstract
One mechanism for achieving accurate placement of the cell division machinery is via Turing patterns, where nonlinear molecular interactions spontaneously produce spatiotemporal concentration gradients. The resulting patterns are dictated by cell shape. For example, the Min system of Escherichia coli shows spatiotemporal oscillation between cell poles, leaving a mid-cell zone for division. The universality of pattern-forming mechanisms in divisome placement is currently unclear. We examined the location of the division plane in two pleomorphic archaea, Haloferax volcanii and Haloarcula japonica, and showed that it correlates with the predictions of Turing patterning. Time-lapse analysis of H. volcanii shows that divisome locations after successive rounds of division are dynamically determined by daughter cell shape. For H. volcanii, we show that the location of DNA does not influence division plane location, ruling out nucleoid occlusion. Triangular cells provide a stringent test for Turing patterning, where there is a bifurcation in division plane orientation. For the two archaea examined, most triangular cells divide as predicted by a Turing mechanism; however, in some cases multiple division planes are observed resulting in cells dividing into three viable progeny. Our results suggest that the division site placement is consistent with a Turing patterning system in these archaea.
Collapse
Affiliation(s)
- James C. Walsh
- School of Physics, University of New South Wales, Sydney NSW 2052, Australia
- The ithree institute, University of Technology, Sydney NSW 2007, Australia
| | | | | | - Ethan C. Garner
- Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Iain G. Duggin
- The ithree institute, University of Technology, Sydney NSW 2007, Australia
| | - Paul M. G. Curmi
- School of Physics, University of New South Wales, Sydney NSW 2052, Australia
| |
Collapse
|
26
|
Haeusser DP, Levin PA. Keeping replication on par with division in Bacillus. Mol Microbiol 2019; 112:747-750. [PMID: 31254421 DOI: 10.1111/mmi.14338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 11/26/2022]
Abstract
Spatially, division site selection is one of the most precisely controlled processes in bacterial physiology. Despite its obvious importance to the production of properly sized, viable daughter cells, the mechanisms underlying division site selection have remained largely mysterious. Molecular Microbiology, Hajduk et al. provide new insight into this essential process. Overturning previous models, including one of their own, they discover that two factors involved in chromosome remodeling - the ParB-like protein Spo0J, and the nucleoid-associated protein Noc - work together to coordinate early steps in DNA replication with establishment of a medial division site in the Gram-positive bacterium, Bacillus subtilis.
Collapse
Affiliation(s)
- Daniel P Haeusser
- Department of Biology, Canisius College, 2001 Main Street, Buffalo, NY, USA
| | - Petra A Levin
- Department of Biology, Washington University, Box 1137, 1 Brookings Drive, St Louis, MA, USA
| |
Collapse
|
27
|
Vedyaykin AD, Ponomareva EV, Khodorkovskii MA, Borchsenius SN, Vishnyakov IE. Mechanisms of Bacterial Cell Division. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030159] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
28
|
Fanalista F, Birnie A, Maan R, Burla F, Charles K, Pawlik G, Deshpande S, Koenderink GH, Dogterom M, Dekker C. Shape and Size Control of Artificial Cells for Bottom-Up Biology. ACS NANO 2019; 13:5439-5450. [PMID: 31074603 PMCID: PMC6543616 DOI: 10.1021/acsnano.9b00220] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/10/2019] [Indexed: 05/27/2023]
Abstract
Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is increasingly used for the production of minimal artificial containers such as single-emulsion droplets, double-emulsion droplets, and liposomes. Despite the importance of cell morphology on cellular dynamics, current synthetic-cell studies mainly use spherical containers, and methods to actively shape manipulate these have been lacking. In this paper, we describe a microfluidic platform to deform the shape of artificial cells into a variety of shapes (rods and discs) with adjustable cell-like dimensions below 5 μm, thereby mimicking realistic cell morphologies. To illustrate the potential of our method, we reconstitute three biologically relevant protein systems (FtsZ, microtubules, collagen) inside rod-shaped containers and study the arrangement of the protein networks inside these synthetic containers with physiologically relevant morphologies resembling those found in living cells.
Collapse
Affiliation(s)
- Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anthony Birnie
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Renu Maan
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Federica Burla
- Department
of Living Matter, Biological Soft Matter Group, AMOLF, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Kevin Charles
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Grzegorz Pawlik
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Siddharth Deshpande
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Living Matter, Biological Soft Matter Group, AMOLF, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Marileen Dogterom
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
29
|
Reproduction of Large-Scale Bioreactor Conditions on Microfluidic Chips. Microorganisms 2019; 7:microorganisms7040105. [PMID: 31010155 PMCID: PMC6518007 DOI: 10.3390/microorganisms7040105] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 11/17/2022] Open
Abstract
Microbial cells in industrial large-scale bioreactors are exposed to fluctuating conditions, e.g., nutrient concentration, dissolved oxygen, temperature, and pH. These inhomogeneities can influence the cell physiology and metabolism, e.g., decelerate cell growth and product formation. Microfluidic systems offer new opportunities to study such effects in great detail by examining responses to varying environmental conditions at single-cell level. However, the possibility to reproduce large-scale bioreactor conditions in microscale cultivation systems has not yet been systematically investigated. Hence, we apply computational fluid dynamics (CFD) simulations to analyze and compare three commonly used microfluidic single-cell trapping and cultivation devices that are based on (i) mother machines (MM), (ii) monolayer growth chambers (MGC), and (iii) negative dielectrophoresis (nDEP). Several representative time-variant nutrient concentration profiles are applied at the chip entry. Responses to these input signals within the studied microfluidic devices are comparatively evaluated at the positions of the cultivated cells. The results are comprehensively presented in a Bode diagram that illustrates the degree of signal damping depending on the frequency of change in the inlet concentration. As a key finding, the MM can accurately reproduce signal changes that occur within 1 s or slower, which are typical for the environmental conditions observed by single cells in large-scale bioreactors, while faster changes are levelled out. In contrast, the nDEP and MGC are found to level out signal changes occurring within 10 s or faster, which can be critical for the proposed application.
Collapse
|
30
|
Wettmann L, Kruse K. The Min-protein oscillations in Escherichia coli: an example of self-organized cellular protein waves. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0111. [PMID: 29632263 DOI: 10.1098/rstb.2017.0111] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2017] [Indexed: 01/09/2023] Open
Abstract
In the rod-shaped bacterium Escherichia coli, selection of the cell centre as the division site involves pole-to-pole oscillations of the proteins MinC, MinD and MinE. This spatio-temporal pattern emerges from interactions among the Min proteins and with the cytoplasmic membrane. Combining experimental studies in vivo and in vitro together with theoretical analysis has led to a fairly good understanding of Min-protein self-organization. In different geometries, the system can, in addition to standing waves, also produce travelling planar and spiral waves as well as coexisting stable stationary distributions. Today it stands as one of the best-studied examples of cellular self-organization of proteins.This article is part of the theme issue 'Self-organization in cell biology'.
Collapse
Affiliation(s)
- Lukas Wettmann
- Theoretische Physik, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
| | - Karsten Kruse
- Departments of Biochemistry and Theoretical Physics, NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| |
Collapse
|
31
|
Vendel KJA, Tschirpke S, Shamsi F, Dogterom M, Laan L. Minimal in vitro systems shed light on cell polarity. J Cell Sci 2019; 132:132/4/jcs217554. [PMID: 30700498 DOI: 10.1242/jcs.217554] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cell polarity - the morphological and functional differentiation of cellular compartments in a directional manner - is required for processes such as orientation of cell division, directed cellular growth and motility. How the interplay of components within the complexity of a cell leads to cell polarity is still heavily debated. In this Review, we focus on one specific aspect of cell polarity: the non-uniform accumulation of proteins on the cell membrane. In cells, this is achieved through reaction-diffusion and/or cytoskeleton-based mechanisms. In reaction-diffusion systems, components are transformed into each other by chemical reactions and are moving through space by diffusion. In cytoskeleton-based processes, cellular components (i.e. proteins) are actively transported by microtubules (MTs) and actin filaments to specific locations in the cell. We examine how minimal systems - in vitro reconstitutions of a particular cellular function with a minimal number of components - are designed, how they contribute to our understanding of cell polarity (i.e. protein accumulation), and how they complement in vivo investigations. We start by discussing the Min protein system from Escherichia coli, which represents a reaction-diffusion system with a well-established minimal system. This is followed by a discussion of MT-based directed transport for cell polarity markers as an example of a cytoskeleton-based mechanism. To conclude, we discuss, as an example, the interplay of reaction-diffusion and cytoskeleton-based mechanisms during polarity establishment in budding yeast.
Collapse
Affiliation(s)
- Kim J A Vendel
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Sophie Tschirpke
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Fayezeh Shamsi
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Marileen Dogterom
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Liedewij Laan
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| |
Collapse
|
32
|
Affiliation(s)
- Ashoka Chary Taviti
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
- Manipal Academy of Higher Education, Manipal, India
| | - Tushar Kant Beuria
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| |
Collapse
|
33
|
Dewachter L, Verstraeten N, Fauvart M, Michiels J. An integrative view of cell cycle control in Escherichia coli. FEMS Microbiol Rev 2018; 42:116-136. [PMID: 29365084 DOI: 10.1093/femsre/fuy005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/19/2018] [Indexed: 11/14/2022] Open
Abstract
Bacterial proliferation depends on the cells' capability to proceed through consecutive rounds of the cell cycle. The cell cycle consists of a series of events during which cells grow, copy their genome, partition the duplicated DNA into different cell halves and, ultimately, divide to produce two newly formed daughter cells. Cell cycle control is of the utmost importance to maintain the correct order of events and safeguard the integrity of the cell and its genomic information. This review covers insights into the regulation of individual key cell cycle events in Escherichia coli. The control of initiation of DNA replication, chromosome segregation and cell division is discussed. Furthermore, we highlight connections between these processes. Although detailed mechanistic insight into these connections is largely still emerging, it is clear that the different processes of the bacterial cell cycle are coordinated to one another. This careful coordination of events ensures that every daughter cell ends up with one complete and intact copy of the genome, which is vital for bacterial survival.
Collapse
Affiliation(s)
- Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium.,Department of Life Sciences and Imaging, Smart Electronics Unit, imec, B-3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
| |
Collapse
|
34
|
Mohapatra S, Weisshaar JC. Modified Pearson correlation coefficient for two-color imaging in spherocylindrical cells. BMC Bioinformatics 2018; 19:428. [PMID: 30445904 PMCID: PMC6240329 DOI: 10.1186/s12859-018-2444-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/22/2018] [Indexed: 11/10/2022] Open
Abstract
The revolution in fluorescence microscopy enables sub-diffraction-limit ("superresolution") localization of hundreds or thousands of copies of two differently labeled proteins in the same live cell. In typical experiments, fluorescence from the entire three-dimensional (3D) cell body is projected along the z-axis of the microscope to form a 2D image at the camera plane. For imaging of two different species, here denoted "red" and "green", a significant biological question is the extent to which the red and green spatial distributions are positively correlated, anti-correlated, or uncorrelated. A commonly used statistic for assessing the degree of linear correlation between two image matrices R and G is the Pearson Correlation Coefficient (PCC). PCC should vary from - 1 (perfect anti-correlation) to 0 (no linear correlation) to + 1 (perfect positive correlation). However, in the special case of spherocylindrical bacterial cells such as E. coli or B. subtilis, we show that the PCC fails both qualitatively and quantitatively. PCC returns the same + 1 value for 2D projections of distributions that are either perfectly correlated in 3D or completely uncorrelated in 3D. The PCC also systematically underestimates the degree of anti-correlation between the projections of two perfectly anti-correlated 3D distributions. The problem is that the projection of a random spatial distribution within the 3D spherocylinder is non-random in 2D, whereas PCC compares every matrix element of R or G with the constant mean value [Formula: see text] or [Formula: see text]. We propose a modified Pearson Correlation Coefficient (MPCC) that corrects this problem for spherocylindrical cell geometry by using the proper reference matrix for comparison with R and G. Correct behavior of MPCC is confirmed for a variety of numerical simulations and on experimental distributions of HU and RNA polymerase in live E. coli cells. The MPCC concept should be generalizable to other cell shapes.
Collapse
Affiliation(s)
- Sonisilpa Mohapatra
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA. .,Present Address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, 21205, USA.
| | - James C Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| |
Collapse
|
35
|
Söderström B, Badrutdinov A, Chan H, Skoglund U. Cell shape-independent FtsZ dynamics in synthetically remodeled bacterial cells. Nat Commun 2018; 9:4323. [PMID: 30337533 PMCID: PMC6193997 DOI: 10.1038/s41467-018-06887-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/03/2018] [Indexed: 11/26/2022] Open
Abstract
FtsZ is the main regulator of bacterial cell division. It has been implicated in acting as a scaffolding protein for other division proteins, a force generator during constriction, and more recently, as an active regulator of septal cell wall production. FtsZ assembles into a heterogeneous structure coined the Z-ring due to its resemblance to a ring confined by the midcell geometry. Here, to establish a framework for examining geometrical influences on proper Z-ring assembly and dynamics, we sculpted Escherichia coli cells into unnatural shapes using division- and cell wall-specific inhibitors in a micro-fabrication scheme. This approach allowed us to examine FtsZ behavior in engineered Z-squares and Z-hearts. We use stimulated emission depletion (STED) nanoscopy to show that FtsZ clusters in sculpted cells maintain the same dimensions as their wild-type counterparts. Based on our results, we propose that the underlying membrane geometry is not a deciding factor for FtsZ cluster maintenance and dynamics in vivo. The FtsZ protein assembles into a structure known as ‘Z-ring’ at midcell for bacterial cell division. Here, Söderström et al. show that Z-ring assembly and dynamics in E. coli cells with unnatural shapes, such as squares and hearts, are generally similar to those observed in cells with normal shape.
Collapse
Affiliation(s)
- Bill Söderström
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, 904-0495, Okinawa, Japan.
| | - Alexander Badrutdinov
- Mechanical Engineering and Microfabrication Support Section, Okinawa Institute of Science and Technology, 904-0495, Okinawa, Japan
| | - Helena Chan
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, 904-0495, Okinawa, Japan
| | - Ulf Skoglund
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, 904-0495, Okinawa, Japan
| |
Collapse
|
36
|
Effects of geometry and topography on Min-protein dynamics. PLoS One 2018; 13:e0203050. [PMID: 30161173 PMCID: PMC6117030 DOI: 10.1371/journal.pone.0203050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/14/2018] [Indexed: 12/13/2022] Open
Abstract
In the rod-shaped bacterium Escherichia coli, the center is selected by the Min-proteins as the site of cell division. To this end, the proteins periodically translocate between the two cell poles, where they suppress assembly of the cell division machinery. Ample evidence notably obtained from in vitro reconstitution experiments suggests that the oscillatory pattern results from self-organization of the proteins MinD and MinE in presence of a membrane. A mechanism built on cooperative membrane attachment of MinD and persistent MinD removal from the membrane induced by MinE has been shown to be able to reproduce the observed Min-protein patterns in rod-shaped E. coli and on flat supported lipid bilayers. Here, we report our results of a numerical investigation of patterns generated by this mechanism in various geoemtries. Notably, we consider the dynamics on membrane patches of different forms, on topographically structured lipid bilayers, and in closed geometries of various shapes. We find that all previously described patterns can be reproduced by the mechanism. However, it requires different parameter sets for reproducing the patterns in closed and in open geometries.
Collapse
|
37
|
Neeli-Venkata R, Oliveira SMD, Martins L, Startceva S, Bahrudeen M, Fonseca JM, Minoia M, Ribeiro AS. The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures. Phys Biol 2018; 15:056002. [PMID: 29717708 DOI: 10.1088/1478-3975/aac1cb] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cell division in Escherichia coli is morphologically symmetric due to, among other things, the ability of these cells to place the Z-ring at midcell. Studies have reported that, at sub-optimal temperatures, this symmetry decreases at the single-cell level, but the causes remain unclear. Using fluorescence microscopy, we observe FtsZ-GFP and DAPI-stained nucleoids to assess the robustness of the symmetry of Z-ring formation and positioning in individual cells under sub-optimal and critical temperatures. We find the Z-ring formation and positioning to be robust at sub-optimal temperatures, as the Z-ring's mean width, density and displacement from midcell maintain similar levels of correlation to one another as at optimal temperatures. However, at critical temperatures, the Z-ring displacement from midcell is greatly increased. We present evidence showing that this is due to enhanced distance between the replicated nucleoids and, thus, reduced Z-ring density, which explains the weaker precision in setting a morphologically symmetric division site. This also occurs in rich media and is cumulative, i.e. combining richer media and critically high temperatures enhances the asymmetries in division, which is evidence that the causes are biophysical. To further support this, we show that the effects are reversible, i.e. shifting cells from optimal to critical, and then to optimal again, reduces and then enhances the symmetry in Z-ring positioning, respectively, as the width and density of the Z-ring return to normal values. Overall, our findings show that the Z-ring positioning in E. coli is a robust biophysical process under sub-optimal temperatures, and that critical temperatures cause significant asymmetries in division.
Collapse
Affiliation(s)
- Ramakanth Neeli-Venkata
- Laboratory of Biosystem Dynamics, BioMediTech Institute and Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, 33101, Tampere, Finland
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Yang D, Jennings AD, Borrego E, Retterer ST, Männik J. Analysis of Factors Limiting Bacterial Growth in PDMS Mother Machine Devices. Front Microbiol 2018; 9:871. [PMID: 29765371 PMCID: PMC5938360 DOI: 10.3389/fmicb.2018.00871] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 11/22/2022] Open
Abstract
The microfluidic mother machine platform has attracted much interest for its potential in studies of bacterial physiology, cellular organization, and cell mechanics. Despite numerous experiments and development of dedicated analysis software, differences in bacterial growth and morphology in narrow mother machine channels compared to typical liquid media conditions have not been systematically characterized. Here we determine changes in E. coli growth rates and cell dimensions in different sized dead-end microfluidic channels using high resolution optical microscopy. We find that E. coli adapt to the confined channel environment by becoming narrower and longer compared to the same strain grown in liquid culture. Cell dimensions decrease as the channel length increases and width decreases. These changes are accompanied by increases in doubling times in agreement with the universal growth law. In channels 100 μm and longer, cell doublings can completely stop as a result of frictional forces that oppose cell elongation. Before complete cessation of elongation, mechanical stresses lead to substantial deformation of cells and changes in their morphology. Our work shows that mechanical forces rather than nutrient limitation are the main growth limiting factor for bacterial growth in long and narrow channels.
Collapse
Affiliation(s)
- Da Yang
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, United States
| | - Anna D Jennings
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, United States
| | - Evalynn Borrego
- Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, TN, United States
| | - Scott T Retterer
- Oak Ridge National Laboratory, Center for Nanophase Materials Sciences, Oak Ridge, TN, United States
| | - Jaan Männik
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, United States
| |
Collapse
|
39
|
van Teeffelen S, Renner LD. Recent advances in understanding how rod-like bacteria stably maintain their cell shapes. F1000Res 2018; 7:241. [PMID: 29560261 PMCID: PMC5832919 DOI: 10.12688/f1000research.12663.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 01/14/2023] Open
Abstract
Cell shape and cell volume are important for many bacterial functions. In recent years, we have seen a range of experimental and theoretical work that led to a better understanding of the determinants of cell shape and size. The roles of different molecular machineries for cell-wall expansion have been detailed and partially redefined, mechanical forces have been shown to influence cell shape, and new connections between metabolism and cell shape have been proposed. Yet the fundamental determinants of the different cellular dimensions remain to be identified. Here, we highlight some of the recent developments and focus on the determinants of rod-like cell shape and size in the well-studied model organisms
Escherichia coli and
Bacillus subtilis.
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
|
40
|
ZANG XQ, LI ZY, ZHANG XY, JIANG L, REN NQ, SUN K. Advance in Bacteria Chemotaxis on Microfluidic Devices. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61050-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
41
|
Rosenthal K, Oehling V, Dusny C, Schmid A. Beyond the bulk: disclosing the life of single microbial cells. FEMS Microbiol Rev 2017; 41:751-780. [PMID: 29029257 PMCID: PMC5812503 DOI: 10.1093/femsre/fux044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 09/08/2017] [Indexed: 01/08/2023] Open
Abstract
Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples.
Collapse
Affiliation(s)
- Katrin Rosenthal
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Verena Oehling
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Christian Dusny
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Andreas Schmid
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| |
Collapse
|
42
|
Bisson-Filho AW, Hsu YP, Squyres GR, Kuru E, Wu F, Jukes C, Sun Y, Dekker C, Holden S, VanNieuwenhze MS, Brun YV, Garner EC. Treadmilling by FtsZ filaments drives peptidoglycan synthesis and bacterial cell division. Science 2017; 355:739-743. [PMID: 28209898 DOI: 10.1126/science.aak9973] [Citation(s) in RCA: 377] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/20/2017] [Indexed: 01/18/2023]
Abstract
The mechanism by which bacteria divide is not well understood. Cell division is mediated by filaments of FtsZ and FtsA (FtsAZ) that recruit septal peptidoglycan-synthesizing enzymes to the division site. To understand how these components coordinate to divide cells, we visualized their movements relative to the dynamics of cell wall synthesis during cytokinesis. We found that the division septum was built at discrete sites that moved around the division plane. FtsAZ filaments treadmilled circumferentially around the division ring and drove the motions of the peptidoglycan-synthesizing enzymes. The FtsZ treadmilling rate controlled both the rate of peptidoglycan synthesis and cell division. Thus, FtsZ treadmilling guides the progressive insertion of new cell wall by building increasingly smaller concentric rings of peptidoglycan to divide the cell.
Collapse
Affiliation(s)
- Alexandre W Bisson-Filho
- Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yen-Pang Hsu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Georgia R Squyres
- Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Erkin Kuru
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Fabai Wu
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Netherlands
| | - Calum Jukes
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Yingjie Sun
- Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Netherlands.
| | - Seamus Holden
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK.
| | - Michael S VanNieuwenhze
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA. .,Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Ethan C Garner
- Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
43
|
Modi S, Vargas-Garcia CA, Ghusinga KR, Singh A. Analysis of Noise Mechanisms in Cell-Size Control. Biophys J 2017; 112:2408-2418. [PMID: 28591613 DOI: 10.1016/j.bpj.2017.04.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 03/27/2017] [Accepted: 04/24/2017] [Indexed: 11/15/2022] Open
Abstract
At the single-cell level, noise arises from multiple sources, such as inherent stochasticity of biomolecular processes, random partitioning of resources at division, and fluctuations in cellular growth rates. How these diverse noise mechanisms combine to drive variations in cell size within an isoclonal population is not well understood. Here, we investigate the contributions of different noise sources in well-known paradigms of cell-size control, such as adder (division occurs after adding a fixed size from birth), sizer (division occurs after reaching a size threshold), and timer (division occurs after a fixed time from birth). Analysis reveals that variation in cell size is most sensitive to errors in partitioning of volume among daughter cells, and not surprisingly, this process is well regulated among microbes. Moreover, depending on the dominant noise mechanism, different size-control strategies (or a combination of them) provide efficient buffering of size variations. We further explore mixer models of size control, where a timer phase precedes/follows an adder, as has been proposed in Caulobacter crescentus. Although mixing a timer and an adder can sometimes attenuate size variations, it invariably leads to higher-order moments growing unboundedly over time. This results in a power-law distribution for the cell size, with an exponent that depends inversely on the noise in the timer phase. Consistent with theory, we find evidence of power-law statistics in the tail of C. crescentus cell-size distribution, although there is a discrepancy between the observed power-law exponent and that predicted from the noise parameters. The discrepancy, however, is removed after data reveal that the size added by individual newborns in the adder phase itself exhibits power-law statistics. Taken together, this study provides key insights into the role of noise mechanisms in size homeostasis, and suggests an inextricable link between timer-based models of size control and heavy-tailed cell-size distributions.
Collapse
Affiliation(s)
- Saurabh Modi
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware
| | | | - Khem Raj Ghusinga
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware
| | - Abhyudai Singh
- Department of Biomedical Engineering, University of Delaware, Newark, Delaware; Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware; Department of Mathematical Sciences, University of Delaware, Newark, Delaware.
| |
Collapse
|
44
|
Kinetics of large-scale chromosomal movement during asymmetric cell division in Escherichia coli. PLoS Genet 2017; 13:e1006638. [PMID: 28234902 PMCID: PMC5345879 DOI: 10.1371/journal.pgen.1006638] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/10/2017] [Accepted: 02/15/2017] [Indexed: 11/19/2022] Open
Abstract
Coordination between cell division and chromosome replication is essential for a cell to produce viable progeny. In the commonly accepted view, Escherichia coli realize this coordination via the accurate positioning of its cell division apparatus relative to the nucleoids. However, E. coli lacking proper positioning of its cell division planes can still successfully propagate. Here, we characterize how these cells partition their chromosomes into daughters during such asymmetric divisions. Using quantitative time-lapse imaging, we show that DNA translocase, FtsK, can pump as much as 80% (3.7 Mb) of the chromosome between daughters at an average rate of 1700±800 bp/s. Pauses in DNA translocation are rare, and in no occasions did we observe reversals at experimental time scales of a few minutes. The majority of DNA movement occurs at the latest stages of cell division when the cell division protein ZipA has already dissociated from the septum, and the septum has closed to a narrow channel with a diameter much smaller than the resolution limit of the microscope (~250 nm). Our data suggest that the narrow constriction is necessary for effective translocation of DNA by FtsK. DNA translocases are conserved throughout bacteria. While at atomic and molecular levels they have been well characterized, their ability to partition DNA in vegetatively growing cells has remained less clear. Here we show that E. coli translocase, FtsK, can move as much as 80% (3.7 Mb) of the chromosomal DNA across the closing septum in asymmetrically dividing cells at an average rate of 1700 bp/s. The majority of DNA movement occurs at the latest stages of cell division when the septum has closed to a narrow channel. Our data implies that a narrow septal opening is needed for effective translocation of DNA by FtsK.
Collapse
|
45
|
Abstract
Cytokinesis in E. coli is organized by a cytoskeletal element designated the Z ring. The Z ring is formed at midcell by the coalescence of FtsZ filaments tethered to the membrane by interaction of FtsZ's conserved C-terminal peptide (CCTP) with two membrane-associated proteins, FtsA and ZipA. Although interaction between an FtsZ monomer and either of these proteins is of low affinity, high affinity is achieved through avidity - polymerization linked CCTPs interacting with the membrane tethers. The placement of the Z ring at midcell is ensured by antagonists of FtsZ polymerization that are positioned within the cell and target FtsZ filaments through the CCTP. The placement of the ring is reinforced by a protein network that extends from the terminus (Ter) region of the chromosome to the Z ring. Once the Z ring is established, additional proteins are recruited through interaction with FtsA, to form the divisome. The assembled divisome is then activated by FtsN to carry out septal peptidoglycan synthesis, with a dynamic Z ring serving as a guide for septum formation. As the septum forms, the cell wall is split by spatially regulated hydrolases and the outer membrane invaginates in step with the aid of a transenvelope complex to yield progeny cells.
Collapse
Affiliation(s)
- Joe Lutkenhaus
- University of Kansas Medical Center, Kansas City, KS, USA.
| | - Shishen Du
- University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
46
|
Caspi Y, Dekker C. Mapping out Min protein patterns in fully confined fluidic chambers. eLife 2016; 5. [PMID: 27885986 PMCID: PMC5217063 DOI: 10.7554/elife.19271] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/24/2016] [Indexed: 11/13/2022] Open
Abstract
The bacterial Min protein system provides a major model system for studying reaction-diffusion processes in biology. Here we present the first in vitro study of the Min system in fully confined three-dimensional chambers that are lithography-defined, lipid-bilayer coated and isolated through pressure valves. We identify three typical dynamical behaviors that occur dependent on the geometrical chamber parameters: pole-to-pole oscillations, spiral rotations, and traveling waves. We establish the geometrical selection rules and show that, surprisingly, Min-protein spiral rotations govern the larger part of the geometrical phase diagram. Confinement as well as an elevated temperature reduce the characteristic wavelength of the Min patterns, although even for confined chambers with a bacterial-level viscosity, the patterns retain a ~5 times larger wavelength than in vivo. Our results provide an essential experimental base for modeling of intracellular Min gradients in bacterial cell division as well as, more generally, for understanding pattern formation in reaction-diffusion systems. DOI:http://dx.doi.org/10.7554/eLife.19271.001 Some proteins can spontaneously organize themselves into ordered patterns within living cells. One widely studied pattern is made in a rod-shaped bacterium called Escherichia coli by a group of proteins called the Min proteins. The pattern formed by the Min proteins allows an E. coli cell to produce two equally sized daughter cells when it divides by ensuring that the division machinery correctly assembles at the center of the parent cell. These proteins move back and forth between the two ends of the parent cell so that the levels of Min proteins are highest at the ends and lowest in the middle. Since the Min proteins act to inhibit the assembly of the cell division machinery, this machinery only assembles in locations where the level of Min proteins is at its lowest, that is, at the middle of the cell. When Min proteins are purified and placed within an artificial compartment that contains a source of chemical energy and is covered by a membrane similar to the membranes that surround cells, they spontaneously form traveling waves on top of the membrane in many directions along to surface. It is not clear how these waves relate to the oscillations seen in E. coli. Caspi and Dekker now analyze the behavior of purified Min proteins inside chambers of various sizes that are fully enclosed by a membrane. The results show that in narrow chambers, Min proteins move back and forth (i.e. oscillate) from one side to the other. However, in wider containers the wave motion is more common. In containers of medium width the Min proteins rotate in a spiral fashion. Caspi and Dekker propose that the spiral rotations are the underlying pattern formed by Min proteins and that the back and forth motion is caused by spirals being cut short. In other words, if a spiral cannot form because the compartment is too small then the back and forth motion emerges. Similarly, Caspi and Dekker propose that the waves emerge in larger containers when multiple spirals come together. These findings suggest that the different patterns that Min proteins form in bacterial cells and artificial compartments arise from different underlying mechanisms. The next step will be to investigate other differences in how the patterns of Min proteins form in E. coli and in artificial compartments. DOI:http://dx.doi.org/10.7554/eLife.19271.002
Collapse
Affiliation(s)
- Yaron Caspi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| |
Collapse
|
47
|
Marantan A, Amir A. Stochastic modeling of cell growth with symmetric or asymmetric division. Phys Rev E 2016; 94:012405. [PMID: 27575162 DOI: 10.1103/physreve.94.012405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/07/2022]
Abstract
We consider a class of biologically motivated stochastic processes in which a unicellular organism divides its resources (volume or damaged proteins, in particular) symmetrically or asymmetrically between its progeny. Assuming the final amount of the resource is controlled by a growth policy and subject to additive and multiplicative noise, we derive the recursive integral equation describing the evolution of the resource distribution over subsequent generations and use it to study the properties of stable resource distributions. We find conditions under which a unique stable resource distribution exists and calculate its moments for the class of affine linear growth policies. Moreover, we apply an asymptotic analysis to elucidate the conditions under which the stable distribution (when it exists) has a power-law tail. Finally, we use the results of this asymptotic analysis along with the moment equations to draw a stability phase diagram for the system that reveals the counterintuitive result that asymmetry serves to increase stability while at the same time widening the stable distribution. We also briefly discuss how cells can divide damaged proteins asymmetrically between their progeny as a form of damage control. In the appendixes, motivated by the asymmetric division of cell volume in Saccharomyces cerevisiae, we extend our results to the case wherein mother and daughter cells follow different growth policies.
Collapse
Affiliation(s)
- Andrew Marantan
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ariel Amir
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
48
|
Wu F, Halatek J, Reiter M, Kingma E, Frey E, Dekker C. Multistability and dynamic transitions of intracellular Min protein patterns. Mol Syst Biol 2016; 12:873. [PMID: 27279643 PMCID: PMC4923923 DOI: 10.15252/msb.20156724] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/13/2016] [Accepted: 05/14/2016] [Indexed: 11/09/2022] Open
Abstract
Cells owe their internal organization to self-organized protein patterns, which originate and adapt to growth and external stimuli via a process that is as complex as it is little understood. Here, we study the emergence, stability, and state transitions of multistable Min protein oscillation patterns in live Escherichia coli bacteria during growth up to defined large dimensions. De novo formation of patterns from homogenous starting conditions is observed and studied both experimentally and in simulations. A new theoretical approach is developed for probing pattern stability under perturbations. Quantitative experiments and simulations show that, once established, Min oscillations tolerate a large degree of intracellular heterogeneity, allowing distinctly different patterns to persist in different cells with the same geometry. Min patterns maintain their axes for hours in experiments, despite imperfections, expansion, and changes in cell shape during continuous cell growth. Transitions between multistable Min patterns are found to be rare events induced by strong intracellular perturbations. The instances of multistability studied here are the combined outcome of boundary growth and strongly nonlinear kinetics, which are characteristic of the reaction-diffusion patterns that pervade biology at many scales.
Collapse
Affiliation(s)
- Fabai Wu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Jacob Halatek
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, München, Germany
| | - Matthias Reiter
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, München, Germany
| | - Enzo Kingma
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Erwin Frey
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, München, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
49
|
Abstract
We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape with the dynamics of growth and constriction. The model allows us to derive constraints on cell wall mechanical energy based on the observed dynamics of cell shape. We predict that exponential growth in cell size requires a constant amount of cell wall energy to be dissipated per unit volume. We use the model to understand and contrast growth in bacteria with different shapes such as spherical, ellipsoidal, cylindrical and toroidal morphologies. Coupling growth to cell wall constriction, we predict a discontinuous shape transformation, from partial constriction to cell division, as a function of the chemical potential driving cell wall synthesis. Our model for cell wall energy and shape dynamics relates growth kinetics with cell geometry, and provides a unified framework to describe the interplay between shape, growth and division in bacterial cells.
Collapse
|
50
|
In Vivo study of naturally deformed Escherichia coli bacteria. J Bioenerg Biomembr 2016; 48:281-91. [PMID: 27026097 DOI: 10.1007/s10863-016-9658-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
Abstract
A combination of light-microscopy and image processing has been applied to study naturally deformed Escherichia coli under in vivo condition and at the order of sub-pixel high-resolution accuracy. To classify deflagellated non-dividing E. coli cells to the rod-shape and bent-shape, a geometrical approach has been applied. From the analysis of the geometrical data which were obtained of image processing, we estimated the required effective energy for shaping a rod-shape to a bent-shape with the same size. We evaluated the energy of deformation in the naturally deformed bacteria with minimum cell manipulation, under in vivo condition, and with minimum influence of any external force, torque and pressure. Finally, we have also elaborated on the possible scenario to explain how naturally deformed bacteria are formed from initial to final-stage.
Collapse
|