1
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Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. Eur J Cell Biol 2024; 103:151380. [PMID: 38218128 DOI: 10.1016/j.ejcb.2023.151380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/15/2024] Open
Abstract
Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components - or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.
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Affiliation(s)
- Philipp Radler
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria; University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
| | - Martin Loose
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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2
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Cheng X, Ullo MF, Case LB. Reconstitution of Phase-Separated Signaling Clusters and Actin Polymerization on Supported Lipid Bilayers. Front Cell Dev Biol 2022; 10:932483. [PMID: 35959492 PMCID: PMC9361016 DOI: 10.3389/fcell.2022.932483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Liquid-liquid phase separation driven by weak interactions between multivalent molecules contributes to the cellular organization by promoting the formation of biomolecular condensates. At membranes, phase separation can promote the assembly of transmembrane proteins with their cytoplasmic binding partners into micron-sized membrane-associated condensates. For example, phase separation promotes clustering of nephrin, a transmembrane adhesion molecule, resulting in increased Arp2/3 complex-dependent actin polymerization. In vitro reconstitution is a powerful approach to understand phase separation in biological systems. With a bottom-up approach, we can determine the molecules necessary and sufficient for phase separation, map the phase diagram by quantifying de-mixing over a range of molecular concentrations, assess the material properties of the condensed phase using fluorescence recovery after photobleaching (FRAP), and even determine how phase separation impacts downstream biochemical activity. Here, we describe a detailed protocol to reconstitute nephrin clusters on supported lipid bilayers with purified recombinant protein. We also describe how to measure Arp2/3 complex-dependent actin polymerization on bilayers using fluorescence microscopy. These different protocols can be performed independently or combined as needed. These general techniques can be applied to reconstitute and study phase-separated signaling clusters of many different receptors or to generally understand how actin polymerization is regulated at membranes.
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Affiliation(s)
| | | | - Lindsay B. Case
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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3
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Hirst WG, Kiefer C, Abdosamadi MK, Schäffer E, Reber S. In Vitro Reconstitution and Imaging of Microtubule Dynamics by Fluorescence and Label-free Microscopy. STAR Protoc 2020; 1:100177. [PMID: 33377071 PMCID: PMC7757405 DOI: 10.1016/j.xpro.2020.100177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Dynamic microtubules are essential for many processes in the lives of eukaryotic cells. To study and understand the mechanisms of microtubule dynamics and regulation, in vitro reconstitution with purified components has proven a vital approach. Imaging microtubule dynamics can be instructive for a given species, isoform composition, or biochemical modification. Here, we describe two methods that visualize microtubule dynamics at high speed and high contrast: (1) total internal reflection fluorescence microscopy and (2) label-free interference reflection microscopy. For complete details on the use and execution of this protocol, please refer to Hirst et al. (2020).
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Affiliation(s)
- William Graham Hirst
- IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin 10115, Germany
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Christine Kiefer
- Cellular Nanoscience (ZMBP), Universität Tübingen, Tübingen 72076, Germany
| | | | - Erik Schäffer
- Cellular Nanoscience (ZMBP), Universität Tübingen, Tübingen 72076, Germany
| | - Simone Reber
- IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin 10115, Germany
- University of Applied Sciences Berlin, Berlin 13353, Germany
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
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4
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Koch S, Seinen AB, Kamel M, Kuckla D, Monzel C, Kedrov A, Driessen AJM. Single-molecule analysis of dynamics and interactions of the SecYEG translocon. FEBS J 2020; 288:2203-2221. [PMID: 33058437 DOI: 10.1111/febs.15596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/11/2020] [Accepted: 10/12/2020] [Indexed: 12/19/2022]
Abstract
Protein translocation and insertion into the bacterial cytoplasmic membrane are the essential processes mediated by the Sec machinery. The core machinery is composed of the membrane-embedded translocon SecYEG that interacts with the secretion-dedicated ATPase SecA and translating ribosomes. Despite the simplicity and the available structural insights on the system, diverse molecular mechanisms and functional dynamics have been proposed. Here, we employ total internal reflection fluorescence microscopy to study the oligomeric state and diffusion of SecYEG translocons in supported lipid bilayers at the single-molecule level. Silane-based coating ensured the mobility of lipids and reconstituted translocons within the bilayer. Brightness analysis suggested that approx. 70% of the translocons were monomeric. The translocons remained in a monomeric form upon ribosome binding, but partial oligomerization occurred in the presence of nucleotide-free SecA. Individual trajectories of SecYEG in the lipid bilayer revealed dynamic heterogeneity of diffusion, as translocons commonly switched between slow and fast mobility modes with corresponding diffusion coefficients of 0.03 and 0.7 µm2 ·s-1 . Interactions with SecA ATPase had a minor effect on the lateral mobility, while bound ribosome:nascent chain complexes substantially hindered the diffusion of single translocons. Notably, the mobility of the translocon:ribosome complexes was not affected by the solvent viscosity or macromolecular crowding modulated by Ficoll PM 70, so it was largely determined by interactions within the lipid bilayer and at the interface. We suggest that the complex mobility of SecYEG arises from the conformational dynamics of the translocon and protein:lipid interactions.
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Affiliation(s)
- Sabrina Koch
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Anne-Bart Seinen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands.,Biophysics, AMOLF, Amsterdam, The Netherlands
| | - Michael Kamel
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Daniel Kuckla
- Experimental Medical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Department of Physics, Heinrich Heine University Düsseldorf, Germany
| | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Germany
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
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5
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Hirst WG, Biswas A, Mahalingan KK, Reber S. Differences in Intrinsic Tubulin Dynamic Properties Contribute to Spindle Length Control in Xenopus Species. Curr Biol 2020; 30:2184-2190.e5. [PMID: 32386526 DOI: 10.1016/j.cub.2020.03.067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/13/2020] [Accepted: 03/26/2020] [Indexed: 01/21/2023]
Abstract
The function of cellular organelles relates not only to their molecular composition but also to their size. However, how the size of dynamic mesoscale structures is established and maintained remains poorly understood [1-3]. Mitotic spindle length, for example, varies several-fold among cell types and among different organisms [4]. Although most studies on spindle size control focus on changes in proteins that regulate microtubule dynamics [5-8], the contribution of the spindle's main building block, the αβ-tubulin heterodimer, has yet to be studied. Apart from microtubule-associated proteins and motors, two factors have been shown to contribute to the heterogeneity of microtubule dynamics: tubulin isoform composition [9, 10] and post-translational modifications [11]. In the past, studying the contribution of tubulin and microtubules to spindle assembly has been limited by the fact that physiologically relevant tubulins were not available. Here, we show that tubulins purified from two closely related frogs, Xenopus laevis and Xenopus tropicalis, have surprisingly different microtubule dynamics in vitro. X. laevis microtubules combine very fast growth and infrequent catastrophes. In contrast, X. tropicalis microtubules grow slower and catastrophe more frequently. We show that spindle length and microtubule mass can be controlled by titrating the ratios of the tubulins from the two frog species. Furthermore, we combine our in vitro reconstitution assay and egg extract experiments with computational modeling to show that differences in intrinsic properties of different tubulins contribute to the control of microtubule mass and therefore set steady-state spindle length.
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Affiliation(s)
- William G Hirst
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Abin Biswas
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | | | - Simone Reber
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Marine Biological Laboratory, Woods Hole, MA 02543, USA; University of Applied Sciences Berlin, 13353 Berlin, Germany.
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6
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Bezeljak U, Loya H, Kaczmarek B, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proc Natl Acad Sci U S A 2020; 117:6540-6549. [PMID: 32161136 PMCID: PMC7104049 DOI: 10.1073/pnas.1921027117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell.
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Affiliation(s)
- Urban Bezeljak
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Hrushikesh Loya
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Beata Kaczmarek
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, Singapore 119077;
- Department of Biological Sciences, National University of Singapore, Singapore 119077
| | - Martin Loose
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria;
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7
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Abstract
The polymerization-depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material.
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8
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MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules. Sci Rep 2019; 9:3794. [PMID: 30846705 PMCID: PMC6405942 DOI: 10.1038/s41598-018-37767-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/05/2018] [Indexed: 11/11/2022] Open
Abstract
Microtubules are polar, dynamic filaments fundamental to many cellular processes. In vitro reconstitution approaches with purified tubulin are essential to elucidate different aspects of microtubule behavior. To date, deriving data from fluorescence microscopy images by manually creating and analyzing kymographs is still commonplace. Here, we present MTrack, implemented as a plug-in for the open-source platform Fiji, which automatically identifies and tracks dynamic microtubules with sub-pixel resolution using advanced objection recognition. MTrack provides automatic data interpretation yielding relevant parameters of microtubule dynamic instability together with population statistics. The application of our software produces unbiased and comparable quantitative datasets in a fully automated fashion. This helps the experimentalist to achieve higher reproducibility at higher throughput on a user-friendly platform. We use simulated data and real data to benchmark our algorithm and show that it reliably detects, tracks, and analyzes dynamic microtubules and achieves sub-pixel precision even at low signal-to-noise ratios.
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9
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McKenzie C, Spanova M, Johnson A, Kainrath S, Zheden V, Sitte HH, Janovjak H. Isolation of synaptic vesicles from genetically engineered cultured neurons. J Neurosci Methods 2018; 312:114-121. [PMID: 30496761 DOI: 10.1016/j.jneumeth.2018.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Synaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures. NEW METHOD Here, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus. RESULTS We show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification. COMPARISON WITH EXISTING METHODS Obtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations. CONCLUSIONS These results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts.
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Affiliation(s)
- Catherine McKenzie
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Miroslava Spanova
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Alexander Johnson
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Stephanie Kainrath
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Vanessa Zheden
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Harald H Sitte
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Waehringerstrasse 13A, 1090, Vienna, Austria
| | - Harald Janovjak
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria; Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Melbourne, VIC 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Melbourne, VIC 3800, Australia.
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10
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Pace HP, Hannestad JK, Armonious A, Adamo M, Agnarsson B, Gunnarsson A, Micciulla S, Sjövall P, Gerelli Y, Höök F. Structure and Composition of Native Membrane Derived Polymer-Supported Lipid Bilayers. Anal Chem 2018; 90:13065-13072. [PMID: 30350611 DOI: 10.1021/acs.analchem.8b04110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the last two decades, supported lipid bilayers (SLBs) have been extensively used as model systems to study cell membrane structure and function. While SLBs have been traditionally produced from simple lipid mixtures, there has been a recent surge in compositional complexity to better mimic cellular membranes and thereby bridge the gap between classic biophysical approaches and cell experiments. To this end, native cellular membrane derived SLBs (nSLBs) have emerged as a new category of SLBs. As a new type of biomimetic material, an analytical workflow must be designed to characterize its molecular composition and structure. Herein, we demonstrate how a combination of fluorescence microscopy, neutron reflectometry, and secondary ion mass spectrometry offers new insights on structure, composition, and quality of nSLB systems formed using so-called hybrid vesicles, which are a mixture of native membrane material and synthetic lipids. With this approach, we demonstrate that the nSLB formed a continuous structure with complete mixing of the synthetic and native membrane components and a molecular stoichiometry that essentially mirrors that of the hybrid vesicles. Furthermore, structural investigation of the nSLB revealed that PEGylated lipids do not significantly thicken the hydration layer between the bilayer and substrate when on silicon substrates; however, nSLBs do have more topology than their simpler, purely synthetic counterparts. Beyond new insights regarding the structure and composition of nSLB systems, this work also serves to guide future researchers in producing and characterizing nSLBs from their cellular membrane of choice.
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Affiliation(s)
- Hudson P Pace
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Jonas K Hannestad
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden.,Biosciences and Materials , Research Institutes of Sweden , SE-501 15 Borås , Sweden
| | - Antonious Armonious
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Marco Adamo
- Institute Laue-Langevin , 38000 Grenoble , France.,Department of Chemical Engineering , Imperial College London , London SW7 2AZ , United Kingdom
| | - Bjorn Agnarsson
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Anders Gunnarsson
- Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg , Sweden
| | - Samantha Micciulla
- Institute Laue-Langevin , 38000 Grenoble , France.,Max Planck Institute of Colloids and Interfaces , 14476 Potsdam , Germany
| | - Peter Sjövall
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden.,Biosciences and Materials , Research Institutes of Sweden , SE-501 15 Borås , Sweden
| | - Yuri Gerelli
- Institute Laue-Langevin , 38000 Grenoble , France
| | - Fredrik Höök
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
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11
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de-Carvalho J, Deshpande O, Nabais C, Telley IA. A cell-free system of Drosophila egg explants supporting native mitotic cycles. Methods Cell Biol 2018; 144:233-257. [DOI: 10.1016/bs.mcb.2018.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Nguyen PA, Field CM, Mitchison TJ. Prc1E and Kif4A control microtubule organization within and between large Xenopus egg asters. Mol Biol Cell 2017; 29:304-316. [PMID: 29187577 PMCID: PMC5996955 DOI: 10.1091/mbc.e17-09-0540] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/13/2017] [Accepted: 11/22/2017] [Indexed: 11/11/2022] Open
Abstract
The cleavage furrow in Xenopus zygotes is positioned by two large microtubule asters that grow out from the poles of the first mitotic spindle. Where these asters meet at the midplane, they assemble a disk-shaped interaction zone consisting of anti-parallel microtubule bundles coated with chromosome passenger complex (CPC) and centralspindlin that instructs the cleavage furrow. Here we investigate the mechanism that keeps the two asters separate and forms a distinct boundary between them, focusing on the conserved cytokinesis midzone proteins Prc1 and Kif4A. Prc1E, the egg orthologue of Prc1, and Kif4A were recruited to anti-parallel bundles at interaction zones between asters in Xenopus egg extracts. Prc1E was required for Kif4A recruitment but not vice versa. Microtubule plus-end growth slowed and terminated preferentially within interaction zones, resulting in a block to interpenetration that depended on both Prc1E and Kif4A. Unexpectedly, Prc1E and Kif4A were also required for radial order of large asters growing in isolation, apparently to compensate for the direction-randomizing influence of nucleation away from centrosomes. We propose that Prc1E and Kif4, together with catastrophe factors, promote "anti-parallel pruning" that enforces radial organization within asters and generates boundaries to microtubule growth between asters.
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Affiliation(s)
- P A Nguyen
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Marine Biological Laboratory, Woods Hole, MA 02543
| | - C M Field
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115.,Marine Biological Laboratory, Woods Hole, MA 02543
| | - T J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 .,Marine Biological Laboratory, Woods Hole, MA 02543
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13
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Bermudez JG, Chen H, Einstein LC, Good MC. Probing the biology of cell boundary conditions through confinement of Xenopus cell-free cytoplasmic extracts. Genesis 2017; 55. [PMID: 28132422 DOI: 10.1002/dvg.23013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/04/2016] [Accepted: 12/05/2016] [Indexed: 11/11/2022]
Abstract
Cell-free cytoplasmic extracts prepared from Xenopus eggs and embryos have for decades provided a biochemical system with which to interrogate complex cell biological processes in vitro. Recently, the application of microfabrication and microfluidic strategies in biology has narrowed the gap between in vitro and in vivo studies by enabling formation of cell-size compartments containing functional cytoplasm. These approaches provide numerous advantages over traditional biochemical experiments performed in a test tube. Most notably, the cell-free cytoplasm is confined using a two- or three-dimensional boundary, which mimics the natural configuration of a cell. This strategy enables characterization of the spatial organization of a cell, and the role that boundaries play in regulating intracellular assembly and function. In this review, we describe the marriage of Xenopus cell-free cytoplasm and confinement technologies to generate synthetic cell-like systems, the recent biological insights they have enabled, and the promise they hold for future scientific discovery.
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Affiliation(s)
- Jessica G Bermudez
- Department of Bioengineering, University of Pennsylvania, 421 Curie Blvd, 1151 BRB II/III, Philadelphia, Pennsylvania, 19104
| | - Hui Chen
- Department of Cell and Developmental Biology, University of Pennsylvania, 421 Curie Blvd, 1151 BRB II/III, Philadelphia, Pennsylvania, 19104
| | - Lily C Einstein
- Department of Cell and Developmental Biology, University of Pennsylvania, 421 Curie Blvd, 1151 BRB II/III, Philadelphia, Pennsylvania, 19104
| | - Matthew C Good
- Department of Bioengineering, University of Pennsylvania, 421 Curie Blvd, 1151 BRB II/III, Philadelphia, Pennsylvania, 19104.,Department of Cell and Developmental Biology, University of Pennsylvania, 421 Curie Blvd, 1151 BRB II/III, Philadelphia, Pennsylvania, 19104
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