1
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Aureille J, Prabhu SS, Barnett SF, Farrugia AJ, Arnal I, Lafanechère L, Low BC, Kanchanawong P, Mogilner A, Bershadsky AD. Focal adhesions are controlled by microtubules through local contractility regulation. EMBO J 2024:10.1038/s44318-024-00114-4. [PMID: 38769437 DOI: 10.1038/s44318-024-00114-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Microtubules regulate cell polarity and migration via local activation of focal adhesion turnover, but the mechanism of this process is insufficiently understood. Molecular complexes containing KANK family proteins connect microtubules with talin, the major component of focal adhesions. Here, local optogenetic activation of KANK1-mediated microtubule/talin linkage promoted microtubule targeting to an individual focal adhesion and subsequent withdrawal, resulting in focal adhesion centripetal sliding and rapid disassembly. This sliding is preceded by a local increase of traction force due to accumulation of myosin-II and actin in the proximity of the focal adhesion. Knockdown of the Rho activator GEF-H1 prevented development of traction force and abolished sliding and disassembly of focal adhesions upon KANK1 activation. Other players participating in microtubule-driven, KANK-dependent focal adhesion disassembly include kinases ROCK, PAK, and FAK, as well as microtubules/focal adhesion-associated proteins kinesin-1, APC, and αTAT. Based on these data, we develop a mathematical model for a microtubule-driven focal adhesion disruption involving local GEF-H1/RhoA/ROCK-dependent activation of contractility, which is consistent with experimental data.
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Affiliation(s)
- Julien Aureille
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
| | - Srinivas S Prabhu
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Sam F Barnett
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Aaron J Farrugia
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Isabelle Arnal
- Grenoble institute of Neuroscience, University Grenoble Alpes, INSERM U1216, Grenoble, France
| | - Laurence Lafanechère
- University Grenoble Alpes, INSERM U1209, CNRS UMR5309, Institute for Advanced Biosciences, Grenoble, France
| | - Boon Chuan Low
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Alex Mogilner
- Courant Institute and Department of Biology, New York University, New York, USA
| | - Alexander D Bershadsky
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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2
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Meier SM, Steinmetz MO, Barral Y. Microtubule specialization by +TIP networks: from mechanisms to functional implications. Trends Biochem Sci 2024; 49:318-332. [PMID: 38350804 DOI: 10.1016/j.tibs.2024.01.005] [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: 09/29/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024]
Abstract
To fulfill their actual cellular role, individual microtubules become functionally specialized through a broad range of mechanisms. The 'search and capture' model posits that microtubule dynamics and functions are specified by cellular targets that they capture (i.e., a posteriori), independently of the microtubule-organizing center (MTOC) they emerge from. However, work in budding yeast indicates that MTOCs may impart a functional identity to the microtubules they nucleate, a priori. Key effectors in this process are microtubule plus-end tracking proteins (+TIPs), which track microtubule tips to regulate their dynamics and facilitate their targeted interactions. In this review, we discuss potential mechanisms of a priori microtubule specialization, focusing on recent findings indicating that +TIP networks may undergo liquid biomolecular condensation in different cell types.
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Affiliation(s)
- Sandro M Meier
- Institute of Biochemistry, Department of Biology, and Bringing Materials to Life Initiative, ETH Zürich, Switzerland; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland; Bringing Materials to Life Initiative, ETH Zürich, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland; University of Basel, Biozentrum, CH-4056 Basel, Switzerland.
| | - Yves Barral
- Institute of Biochemistry, Department of Biology, and Bringing Materials to Life Initiative, ETH Zürich, Switzerland; Bringing Materials to Life Initiative, ETH Zürich, Switzerland.
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3
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Gonzalez SJ, Heckel JM, Goldblum RR, Reid TA, McClellan M, Gardner MK. Rapid binding to protofilament edge sites facilitates tip tracking of EB1 at growing microtubule plus-ends. eLife 2024; 13:e91719. [PMID: 38385657 PMCID: PMC10883673 DOI: 10.7554/elife.91719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
EB1 is a key cellular protein that delivers regulatory molecules throughout the cell via the tip-tracking of growing microtubule plus-ends. Thus, it is important to understand the mechanism for how EB1 efficiently tracks growing microtubule plus-ends. It is widely accepted that EB1 binds with higher affinity to GTP-tubulin subunits at the growing microtubule tip, relative to GDP-tubulin along the microtubule length. However, it is unclear whether this difference in affinity alone is sufficient to explain the tip-tracking of EB1 at growing microtubule tips. Previously, we found that EB1 binds to exposed microtubule protofilament-edge sites at a ~70 fold faster rate than to closed-lattice sites, due to diffusional steric hindrance to binding. Thus, we asked whether rapid protofilament-edge binding could contribute to efficient EB1 tip tracking. A computational simulation with differential EB1 on-rates based on closed-lattice or protofilament-edge binding, and with EB1 off-rates that were dependent on the tubulin hydrolysis state, robustly recapitulated experimental EB1 tip tracking. To test this model, we used cell-free biophysical assays, as well as live-cell imaging, in combination with a Designed Ankyrin Repeat Protein (DARPin) that binds exclusively to protofilament-edge sites, and whose binding site partially overlaps with the EB1 binding site. We found that DARPin blocked EB1 protofilament-edge binding, which led to a decrease in EB1 tip tracking on dynamic microtubules. We conclude that rapid EB1 binding to microtubule protofilament-edge sites contributes to robust EB1 tip tracking at the growing microtubule plus-end.
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Affiliation(s)
- Samuel J Gonzalez
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Julia M Heckel
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Rebecca R Goldblum
- Department of Biophysics, Molecular Biology, and Biochemistry, University of Minnesota, Minneapolis, United States
- Medical Scientist Training Program, University of Minnesota, Minneapolis, United States
| | - Taylor A Reid
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Mark McClellan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
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4
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Wieland S, Ramsperger AFRM, Gross W, Lehmann M, Witzmann T, Caspari A, Obst M, Gekle S, Auernhammer GK, Fery A, Laforsch C, Kress H. Nominally identical microplastic models differ greatly in their particle-cell interactions. Nat Commun 2024; 15:922. [PMID: 38297000 PMCID: PMC10830523 DOI: 10.1038/s41467-024-45281-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
Due to the abundance of microplastics in the environment, research about its possible adverse effects is increasing exponentially. Most studies investigating the effect of microplastics on cells still rely on commercially available polystyrene microspheres. However, the choice of these model microplastic particles can affect the outcome of the studies, as even nominally identical model microplastics may interact differently with cells due to different surface properties such as the surface charge. Here, we show that nominally identical polystyrene microspheres from eight different manufacturers significantly differ in their ζ-potential, which is the electrical potential of a particle in a medium at its slipping plane. The ζ-potential of the polystyrene particles is additionally altered after environmental exposure. We developed a microfluidic microscopy platform to demonstrate that the ζ-potential determines particle-cell adhesion strength. Furthermore, we find that due to this effect, the ζ-potential also strongly determines the internalization of the microplastic particles into cells. Therefore, the ζ-potential can act as a proxy of microplastic-cell interactions and may govern adverse effects reported in various organisms exposed to microplastics.
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Affiliation(s)
- Simon Wieland
- Biological Physics, University of Bayreuth, Bayreuth, Germany
- Animal Ecology I and BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Anja F R M Ramsperger
- Biological Physics, University of Bayreuth, Bayreuth, Germany
- Animal Ecology I and BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Wolfgang Gross
- Biological Physics, University of Bayreuth, Bayreuth, Germany
| | - Moritz Lehmann
- Biofluid Simulation and Modeling - Theoretical Physics VI, University of Bayreuth, Bayreuth, Germany
| | - Thomas Witzmann
- Leibniz Institut für Polymerforschung Dresden e. V., Institute of Physical Chemistry and Polymer Physics, Dresden, Germany
| | - Anja Caspari
- Leibniz Institut für Polymerforschung Dresden e. V., Institute of Physical Chemistry and Polymer Physics, Dresden, Germany
| | - Martin Obst
- Experimental Biogeochemistry, BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Stephan Gekle
- Biofluid Simulation and Modeling - Theoretical Physics VI, University of Bayreuth, Bayreuth, Germany
| | - Günter K Auernhammer
- Leibniz Institut für Polymerforschung Dresden e. V., Institute of Physical Chemistry and Polymer Physics, Dresden, Germany
| | - Andreas Fery
- Leibniz Institut für Polymerforschung Dresden e. V., Institute of Physical Chemistry and Polymer Physics, Dresden, Germany
- Physical Chemistry of Polymeric Materials, Technische Universität Dresden, Dresden, Germany
| | - Christian Laforsch
- Animal Ecology I and BayCEER, University of Bayreuth, Bayreuth, Germany.
| | - Holger Kress
- Biological Physics, University of Bayreuth, Bayreuth, Germany.
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5
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Au NPB, Wu T, Chen X, Gao F, Li YTY, Tam WY, Yu KN, Geschwind DH, Coppola G, Wang X, Ma CHE. Genome-wide study reveals novel roles for formin-2 in axon regeneration as a microtubule dynamics regulator and therapeutic target for nerve repair. Neuron 2023; 111:3970-3987.e8. [PMID: 38086376 DOI: 10.1016/j.neuron.2023.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/02/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023]
Abstract
Peripheral nerves regenerate successfully; however, clinical outcome after injury is poor. We demonstrated that low-dose ionizing radiation (LDIR) promoted axon regeneration and function recovery after peripheral nerve injury (PNI). Genome-wide CpG methylation profiling identified LDIR-induced hypermethylation of the Fmn2 promoter, exhibiting injury-induced Fmn2 downregulation in dorsal root ganglia (DRGs). Constitutive knockout or neuronal Fmn2 knockdown accelerated nerve repair and function recovery. Mechanistically, increased microtubule dynamics at growth cones was observed in time-lapse imaging of Fmn2-deficient DRG neurons. Increased HDAC5 phosphorylation and rapid tubulin deacetylation were found in regenerating axons of neuronal Fmn2-knockdown mice after injury. Growth-promoting effect of neuronal Fmn2 knockdown was eliminated by pharmaceutical blockade of HDAC5 or neuronal Hdac5 knockdown, suggesting that Fmn2deletion promotes axon regeneration via microtubule post-translational modification. In silico screening of FDA-approved drugs identified metaxalone, administered either immediately or 24-h post-injury, accelerating function recovery. This work uncovers a novel axon regeneration function of Fmn2 and a small-molecule strategy for PNI.
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Affiliation(s)
| | - Tan Wu
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xinyu Chen
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | - Feng Gao
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | | | - Wing Yip Tam
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China
| | - Kwan Ngok Yu
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Coppola
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Chi Him Eddie Ma
- Department of Neuroscience, City University of Hong Kong, Hong Kong, China.
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6
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Roudot P, Legant WR, Zou Q, Dean KM, Isogai T, Welf ES, David AF, Gerlich DW, Fiolka R, Betzig E, Danuser G. u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions. CELL REPORTS METHODS 2023; 3:100655. [PMID: 38042149 PMCID: PMC10783629 DOI: 10.1016/j.crmeth.2023.100655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/04/2023]
Abstract
We describe u-track3D, a software package that extends the versatile u-track framework established in 2D to address the specific challenges of 3D particle tracking. First, we present the performance of the new package in quantifying a variety of intracellular dynamics imaged by multiple 3D microcopy platforms and on the standard 3D test dataset of the particle tracking challenge. These analyses indicate that u-track3D presents a tracking solution that is competitive to both conventional and deep-learning-based approaches. We then present the concept of dynamic region of interest (dynROI), which allows an experimenter to interact with dynamic 3D processes in 2D views amenable to visual inspection. Third, we present an estimator of trackability that automatically defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track3D provides a complete framework for unbiased studies of molecular processes in complex volumetric sequences.
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Affiliation(s)
- Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA; Aix Marseille University, CNRS, Centrale Marseille, I2M, Turing Centre for Living Systems, Marseille, France.
| | - Wesley R Legant
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Erik S Welf
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ana F David
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Eric Betzig
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
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7
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Schwayer C, Brückner DB. Connecting theory and experiment in cell and tissue mechanics. J Cell Sci 2023; 136:jcs261515. [PMID: 38149871 DOI: 10.1242/jcs.261515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.
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Affiliation(s)
- Cornelia Schwayer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - David B Brückner
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
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8
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Menduti G, Boido M. Recent Advances in High-Content Imaging and Analysis in iPSC-Based Modelling of Neurodegenerative Diseases. Int J Mol Sci 2023; 24:14689. [PMID: 37834135 PMCID: PMC10572296 DOI: 10.3390/ijms241914689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of neurodegenerative pathologies, the platforms for disease modelling based on patient-derived induced pluripotent stem cells (iPSCs) represent a valuable molecular diagnostic/prognostic tool. Indeed, they paved the way for the in vitro recapitulation of the pathological mechanisms underlying neurodegeneration and for characterizing the molecular heterogeneity of disease manifestations, also enabling drug screening approaches for new therapeutic candidates. A major challenge is related to the choice and optimization of the morpho-functional study designs in human iPSC-derived neurons to deeply detail the cell phenotypes as markers of neurodegeneration. In recent years, the specific combination of high-throughput screening with subcellular resolution microscopy for cell-based high-content imaging (HCI) screening allowed in-depth analyses of cell morphology and neurite trafficking in iPSC-derived neuronal cells by using specific cutting-edge microscopes and automated computational assays. The present work aims to describe the main recent protocols and advances achieved with the HCI analysis in iPSC-based modelling of neurodegenerative diseases, highlighting technical and bioinformatics tips and tricks for further uses and research. To this end, microscopy requirements and the latest computational pipelines to analyze imaging data will be explored, while also providing an overview of the available open-source high-throughput automated platforms.
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Affiliation(s)
- Giovanna Menduti
- Department of Neuroscience “Rita Levi Montalcini”, Neuroscience Institute Cavalieri Ottolenghi, University of Turin, Regione Gonzole 10, Orbassano, 10043 Turin, TO, Italy;
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9
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Ansari S, Gergely ZR, Flynn P, Li G, Moore JK, Betterton MD. Quantifying Yeast Microtubules and Spindles Using the Toolkit for Automated Microtubule Tracking (TAMiT). Biomolecules 2023; 13:939. [PMID: 37371519 DOI: 10.3390/biom13060939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 06/29/2023] Open
Abstract
Fluorescently labeled proteins absorb and emit light, appearing as Gaussian spots in fluorescence imaging. When fluorescent tags are added to cytoskeletal polymers such as microtubules, a line of fluorescence and even non-linear structures results. While much progress has been made in techniques for imaging and microscopy, image analysis is less well-developed. Current analysis of fluorescent microtubules uses either manual tools, such as kymographs, or automated software. As a result, our ability to quantify microtubule dynamics and organization from light microscopy remains limited. Despite the development of automated microtubule analysis tools for in vitro studies, analysis of images from cells often depends heavily on manual analysis. One of the main reasons for this disparity is the low signal-to-noise ratio in cells, where background fluorescence is typically higher than in reconstituted systems. Here, we present the Toolkit for Automated Microtubule Tracking (TAMiT), which automatically detects, optimizes, and tracks fluorescent microtubules in living yeast cells with sub-pixel accuracy. Using basic information about microtubule organization, TAMiT detects linear and curved polymers using a geometrical scanning technique. Images are fit via an optimization problem for the microtubule image parameters that are solved using non-linear least squares in Matlab. We benchmark our software using simulated images and show that it reliably detects microtubules, even at low signal-to-noise ratios. Then, we use TAMiT to measure monopolar spindle microtubule bundle number, length, and lifetime in a large dataset that includes several S. pombe mutants that affect microtubule dynamics and bundling. The results from the automated analysis are consistent with previous work and suggest a direct role for CLASP/Cls1 in bundling spindle microtubules. We also illustrate automated tracking of single curved astral microtubules in S. cerevisiae, with measurement of dynamic instability parameters. The results obtained with our fully-automated software are similar to results using hand-tracked measurements. Therefore, TAMiT can facilitate automated analysis of spindle and microtubule dynamics in yeast cells.
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Affiliation(s)
- Saad Ansari
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Zachary R Gergely
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Patrick Flynn
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Gabriella Li
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Meredith D Betterton
- Department of Physics, University of Colorado Boulder, Boulder, CO 80309, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
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10
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Kassouf T, Shrivastava R, Meszka I, Bailly A, Polanowska J, Trauchessec H, Mandrioli J, Carra S, Xirodimas DP. Targeting the NEDP1 enzyme to ameliorate ALS phenotypes through stress granule disassembly. SCIENCE ADVANCES 2023; 9:eabq7585. [PMID: 37000881 PMCID: PMC10065448 DOI: 10.1126/sciadv.abq7585] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
The elimination of aberrant inclusions is regarded as a therapeutic approach in neurodegeneration. In amyotrophic lateral sclerosis (ALS), mutations in proteins found within cytoplasmic condensates called stress granules (SGs) are linked to the formation of pathological SGs, aberrant protein inclusions, and neuronal toxicity. We found that inhibition of NEDP1, the enzyme that processes/deconjugates the ubiquitin-like molecule NEDD8, promotes the disassembly of physiological and pathological SGs. Reduction in poly(ADP-ribose) polymerase1 activity through hyper-NEDDylation is a key mechanism for the observed phenotype. These effects are related to improved cell survival in human cells, and in C. elegans, nedp1 deletion ameliorates ALS phenotypes related to animal motility. Our studies reveal NEDP1 as potential therapeutic target for ALS, correlated to the disassembly of pathological SGs.
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Affiliation(s)
| | | | - Igor Meszka
- CRBM, Univ. Montpellier, CNRS, Montpellier, France
| | | | | | | | - Jessica Mandrioli
- Neurology Unit, Azienda Ospedaliero Universitaria di Modena, 41126 Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia,G. Campi 287, 41125 Modena, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia,G. Campi 287, 41125 Modena, Italy
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11
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Ansari S, Gergely ZR, Flynn P, Li G, Moore JK, Betterton MD. Quantifying yeast microtubules and spindles using the Toolkit for Automated Microtubule Tracking (TAMiT). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527544. [PMID: 36798368 PMCID: PMC9934621 DOI: 10.1101/2023.02.07.527544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Fluorescently labeled proteins absorb and emit light, appearing as Gaussian spots in fluorescence imaging. When fluorescent tags are added to cytoskeletal polymers such as microtubules, a line of fluorescence and even non-linear structures results. While much progress has been made in techniques for imaging and microscopy, image analysis is less well developed. Current analysis of fluorescent microtubules uses either manual tools, such as kymographs, or automated software. As a result, our ability to quantify microtubule dynamics and organization from light microscopy remains limited. Despite development of automated microtubule analysis tools for in vitro studies, analysis of images from cells often depends heavily on manual analysis. One of the main reasons for this disparity is the low signal-to-noise ratio in cells, where background fluorescence is typically higher than in reconstituted systems. Here, we present the Toolkit for Automated Microtubule Tracking (TAMiT), which automatically detects, optimizes and tracks fluorescent microtubules in living yeast cells with sub-pixel accuracy. Using basic information about microtubule organization, TAMiT detects linear and curved polymers using a geometrical scanning technique. Images are fit via an optimization problem for the microtubule image parameters that is solved using non-linear least squares in Matlab. We benchmark our software using simulated images and show that it reliably detects microtubules, even at low signal-to-noise ratios. Then, we use TAMiT to measure monopolar spindle microtubule bundle number, length, and lifetime in a large dataset that includes several S. pombe mutants that affect microtubule dynamics and bundling. The results from the automated analysis are consistent with previous work, and suggest a direct role for CLASP/Cls1 in bundling spindle microtubules. We also illustrate automated tracking of single curved astral microtubules in S. cerevisiae , with measurement of dynamic instability parameters. The results obtained with our fully-automated software are similar to results using hand-tracked measurements. Therefore, TAMiT can facilitate automated analysis of spindle and microtubule dynamics in yeast cells.
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12
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Lopes D, Seabra AL, Orr B, Maiato H. α-Tubulin detyrosination links the suppression of MCAK activity with taxol cytotoxicity. J Cell Biol 2023; 222:213730. [PMID: 36459065 PMCID: PMC9723805 DOI: 10.1083/jcb.202205092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/24/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
α/β-Tubulin posttranslational modifications (PTMs) generate microtubule diversity, but whether they account for cancer cell resistance to microtubule-targeting drugs remains unknown. Here, we performed a pilot dissection of the "cancer tubulin code" using the NCI-60 cancer cell panel. We found that acetylated, detyrosinated, and ∆2-α-tubulin that typically accumulate on stable microtubules were uncoupled in many cancer cells. Acetylated α-tubulin did not affect microtubule dynamics, whereas its levels correlated with, but were not required for, taxol-induced cytotoxicity. In contrast, experimental increase of α-tubulin detyrosination, and/or depletion of the detyrosination-sensitive microtubule-depolymerizing enzyme MCAK, enhanced taxol-induced cytotoxicity by promoting cell death in mitosis and the subsequent interphase, without causing a cumulative effect. Interestingly, only increased detyrosinated α-tubulin aggravated taxol-induced spindle multipolarity. Overall, we identified high α-tubulin acetylation as a potential biomarker for cancer cell response to taxol and uncovered a mechanistic link between α-tubulin detyrosination and the suppression of MCAK activity in taxol-induced cytotoxicity, likely by promoting chromosome missegregation, regardless of spindle defects.
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Affiliation(s)
- Danilo Lopes
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandre L Seabra
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Bernardo Orr
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Helder Maiato
- Chromosome Instability & Dynamics Group, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,Cell Division Group, Department of Biomedicine, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
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13
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Houston DW, Elliott KL, Coppenrath K, Wlizla M, Horb ME. Maternal Wnt11b regulates cortical rotation during Xenopus axis formation: analysis of maternal-effect wnt11b mutants. Development 2022; 149:dev200552. [PMID: 35946588 PMCID: PMC9515810 DOI: 10.1242/dev.200552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/01/2022] [Indexed: 12/13/2022]
Abstract
Asymmetric signalling centres in the early embryo are essential for axis formation in vertebrates. These regions (e.g. amphibian dorsal morula, mammalian anterior visceral endoderm) require stabilised nuclear β-catenin, but the role of localised Wnt ligand signalling activity in their establishment remains unclear. In Xenopus, dorsal β-catenin is initiated by vegetal microtubule-mediated symmetry breaking in the fertilised egg, known as 'cortical rotation'. Localised wnt11b mRNA and ligand-independent activators of β-catenin have been implicated in dorsal β-catenin activation, but the extent to which each contributes to axis formation in this paradigm remains unclear. Here, we describe a CRISPR-mediated maternal-effect mutation in Xenopus laevis wnt11b.L. We find that wnt11b is maternally required for robust dorsal axis formation and for timely gastrulation, and zygotically for left-right asymmetry. Importantly, we show that vegetal microtubule assembly and cortical rotation are reduced in wnt11b mutant eggs. In addition, we show that activated Wnt coreceptor Lrp6 and Dishevelled lack behaviour consistent with roles in early β-catenin stabilisation, and that neither is regulated by Wnt11b. This work thus implicates Wnt11b in the distribution of putative dorsal determinants rather than in comprising the determinants themselves. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Douglas W. Houston
- Department of Biology, The University of Iowa, 257 BB, Iowa City, IA 52242-1324, USA
| | - Karen L. Elliott
- Department of Biology, The University of Iowa, 257 BB, Iowa City, IA 52242-1324, USA
| | - Kelsey Coppenrath
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Marcin Wlizla
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Marko E. Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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14
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Quintana J, Arboleda D, Hu H, Scott E, Luthria G, Pai S, Parangi S, Weissleder R, Miller MA. Radiation Cleaved Drug-Conjugate Linkers Enable Local Payload Release. Bioconjug Chem 2022; 33:1474-1484. [PMID: 35833631 PMCID: PMC9390333 DOI: 10.1021/acs.bioconjchem.2c00174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conjugation of therapeutic payloads to biologics including antibodies and albumin can enhance the selectively of drug delivery to solid tumors. However, achieving activity in tumors while avoiding healthy tissues remains a challenge, and payload activity in off-target tissues can cause toxicity for many such drug-conjugates. Here, we address this issue by presenting a drug-conjugate linker strategy that releases an active therapeutic payload upon exposure to ionizing radiation. Localized X-ray irradiation at clinically relevant doses (8 Gy) yields 50% drug (doxorubicin or monomethyl auristatin E, MMAE) release under hypoxic conditions that are traditionally associated with radiotherapy resistance. As proof-of-principle, we apply the approach to antibody- and albumin-drug conjugates and achieve >2000-fold enhanced MMAE cytotoxicity upon irradiation. Overall, this work establishes ionizing radiation as a strategy for spatially localized cancer drug delivery.
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Affiliation(s)
- Jeremy
M. Quintana
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
| | - David Arboleda
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
| | - Huiyu Hu
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
- Department
of Surgery, Massachusetts General Hospital
and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ella Scott
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
| | - Gaurav Luthria
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
| | - Sara Pai
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
- Department
of Surgery, Massachusetts General Hospital
and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Sareh Parangi
- Department
of Surgery, Massachusetts General Hospital
and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Ralph Weissleder
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
- Department
of Radiology, Massachusetts General Hospital
and Harvard Medical School, Boston, Massachusetts 02114, United States
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Miles A. Miller
- Center
for Systems Biology, Massachusetts General
Hospital Research Institute, Boston, Massachusetts 02114, United States
- Department
of Radiology, Massachusetts General Hospital
and Harvard Medical School, Boston, Massachusetts 02114, United States
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15
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Hoff KJ, Aiken JE, Gutierrez MA, Franco SJ, Moore JK. Tubulinopathy mutations in TUBA1A that disrupt neuronal morphogenesis and migration override XMAP215/Stu2 regulation of microtubule dynamics. eLife 2022; 11:76189. [PMID: 35511030 PMCID: PMC9236607 DOI: 10.7554/elife.76189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Heterozygous, missense mutations in α- or β-tubulin genes are associated with a wide range of human brain malformations, known as tubulinopathies. We seek to understand whether a mutation’s impact at the molecular and cellular levels scale with the severity of brain malformation. Here, we focus on two mutations at the valine 409 residue of TUBA1A, V409I, and V409A, identified in patients with pachygyria or lissencephaly, respectively. We find that ectopic expression of TUBA1A-V409I/A mutants disrupt neuronal migration in mice and promote excessive neurite branching and a decrease in the number of neurite retraction events in primary rat neuronal cultures. These neuronal phenotypes are accompanied by increased microtubule acetylation and polymerization rates. To determine the molecular mechanisms, we modeled the V409I/A mutants in budding yeast and found that they promote intrinsically faster microtubule polymerization rates in cells and in reconstitution experiments with purified tubulin. In addition, V409I/A mutants decrease the recruitment of XMAP215/Stu2 to plus ends in budding yeast and ablate tubulin binding to TOG (tumor overexpressed gene) domains. In each assay tested, the TUBA1A-V409I mutant exhibits an intermediate phenotype between wild type and the more severe TUBA1A-V409A, reflecting the severity observed in brain malformations. Together, our data support a model in which the V409I/A mutations disrupt microtubule regulation typically conferred by XMAP215 proteins during neuronal morphogenesis and migration, and this impact on tubulin activity at the molecular level scales with the impact at the cellular and tissue levels. Proteins are molecules made up of long chains of building blocks called amino acids. When a mutation changes one of these amino acids, it can lead to the protein malfunctioning, which can have many effects at the cell and tissue level. Given that human proteins are made up of 20 different amino acids, each building block in a protein could mutate to any of the other 19 amino acids, and each mutations could have different effects. Tubulins are proteins that form microtubules, thin tubes that help give cells their shape and allow them to migrate. These proteins are added or removed to microtubules depending on the cell’s needs, meaning that microtubules can grow or shrink depending on the situation. Mutations in the tubulin proteins have been linked to malformations of varying severities involving the formation of ridges and folds on the surface of the brain, including lissencephaly, pachygyria or polymicrogyria. Hoff et al. wanted to establish links between tubulin mutations and the effects observed at both cell and tissue level in the brain. They focused on two mutations in the tubulin protein TUBA1A that affect the amino acid in position 409 in the protein, which is normally a valine. One of the mutations turns this valine into an amino acid called isoleucine. This mutation is associated with pachygyria, which leads to the brain developing few ridges that are broad and flat. The second mutation turns the valine into an alanine, and is linked to lissencephaly, a more severe condition in which the brain develops no ridges, appearing smooth. Hoff et al. found that both mutations interfere with the development of the brain by stopping neurons from migrating properly, which prevents them from forming the folds in the brain correctly. At the cellular level, the mutations lead to tubulins becoming harder to remove from microtubules, making microtubules more stable than usual. This results in longer microtubules that are harder for the cell to shorten or destroy as needed. Additionally, Hoff et al. showed that the mutant versions of TUBA1A have weaker interactions with a protein called XMAP215, which controls the addition of tubulin to microtubules. This causes the microtubules to grow uncontrollably. Hoff et al. also established that the magnitude of the effects of each mutation on microtubule growth scale with the severity of the disorder they cause. Specifically, cells in which TUBA1A is not mutated have microtubules that grow at a normal rate, and lead to typical brain development. Meanwhile, cells carrying the mutation that turns a valine into an alanine, which is linked to the more severe condition lissencephaly, have microtubules that grow very fast. Finally, cells in which the valine is mutated to an isoleucine – the mutation associated with the less severe malformation pachygyria – have microtubules that grow at an intermediate rate. These findings provide a link between mutations in tubulin proteins and larger effects on cell movement that lead to brain malformations. Additionally, they also link the severity of the malformation to the severity of the microtubule defect caused by each mutation. Further work could examine whether microtubule stabilization is also seen in other similar diseases, which, in the long term, could reveal ways to detect and treat these illnesses.
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Affiliation(s)
- Katelyn J Hoff
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Jayne E Aiken
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Mark A Gutierrez
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Santos J Franco
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Jeffrey K Moore
- University of Colorado School of Medicine, Aurora, United States
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16
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Merenich D, Nakos K, Pompan T, Donovan SJ, Gill A, Patel P, Spiliotis ET, Myers KA. Septins guide noncentrosomal microtubules to promote focal adhesion disassembly in migrating cells. Mol Biol Cell 2022; 33:ar40. [PMID: 35274967 PMCID: PMC9282018 DOI: 10.1091/mbc.e21-06-0334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/07/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022] Open
Abstract
Endothelial cell migration is critical for vascular angiogenesis and is compromised to facilitate tumor metastasis. The migratory process requires the coordinated assembly and disassembly of focal adhesions (FA), actin, and microtubules (MT). MT dynamics at FAs deliver vesicular cargoes and enhance actomyosin contractility to promote FA turnover and facilitate cell advance. Noncentrosomal (NC) MTs regulate FA dynamics and are sufficient to drive cell polarity, but how NC MTs target FAs to control FA turnover is not understood. Here, we show that Rac1 induces the assembly of FA-proximal septin filaments that promote NC MT growth into FAs and inhibit mitotic centromere-associated kinesin (MCAK)-associated MT disassembly, thereby maintaining intact MT plus ends proximal to FAs. Septin-associated MT rescue is coupled with accumulation of Aurora-A kinase and cytoplasmic linker-associated protein (CLASP) localization to the MT between septin and FAs. In this way, NC MTs are strategically positioned to undergo MCAK- and CLASP-regulated bouts of assembly and disassembly into FAs, thereby regulating FA turnover and cell migration.
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Affiliation(s)
- Daniel Merenich
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
| | | | - Taylor Pompan
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
| | - Samantha J. Donovan
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
| | - Amrik Gill
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
| | - Pranav Patel
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
| | | | - Kenneth A. Myers
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
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17
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Ramazi S, Mohammadi N, Allahverdi A, Khalili E, Abdolmaleki P. A review on antimicrobial peptides databases and the computational tools. Database (Oxford) 2022; 2022:6550847. [PMID: 35305010 PMCID: PMC9216472 DOI: 10.1093/database/baac011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 12/29/2022]
Abstract
Antimicrobial Peptides (AMPs) have been considered as potential alternatives for infection therapeutics since antibiotic resistance has been raised as a global problem. The AMPs are a group of natural peptides that play a crucial role in the immune system in various organisms AMPs have features such as a short length and efficiency against microbes. Importantly, they have represented low toxicity in mammals which makes them potential candidates for peptide-based drugs. Nevertheless, the discovery of AMPs is accompanied by several issues which are associated with labour-intensive and time-consuming wet-lab experiments. During the last decades, numerous studies have been conducted on the investigation of AMPs, either natural or synthetic type, and relevant data are recently available in many databases. Through the advancement of computational methods, a great number of AMP data are obtained from publicly accessible databanks, which are valuable resources for mining patterns to design new models for AMP prediction. However, due to the current flaws in assessing computational methods, more interrogations are warranted for accurate evaluation/analysis. Considering the diversity of AMPs and newly reported ones, an improvement in Machine Learning algorithms are crucial. In this review, we aim to provide valuable information about different types of AMPs, their mechanism of action and a landscape of current databases and computational tools as resources to collect AMPs and beneficial tools for the prediction and design of a computational model for new active AMPs.
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Affiliation(s)
- Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| | - Neda Mohammadi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Hemmat Highway, Tehran 1449614535, Iran,Institute of Pharmacology and Toxicology, University of Bonn, Biomedical Center, Venusberg Campus 1, Bonn 53127, Germany
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| | - Elham Khalili
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
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18
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Krajka V, Vulinovic F, Genova M, Tanzer K, Jijumon AS, Bodakuntla S, Tennstedt S, Mueller-Fielitz H, Meier B, Janke C, Klein C, Rakovic A. H-ABC- and dystonia-causing TUBB4A mutations show distinct pathogenic effects. SCIENCE ADVANCES 2022; 8:eabj9229. [PMID: 35275727 PMCID: PMC8916731 DOI: 10.1126/sciadv.abj9229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Mutations in the brain-specific β-tubulin 4A (TUBB4A) gene cause a broad spectrum of diseases, ranging from dystonia (DYT-TUBB4A) to hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC). Currently, the mechanisms of how TUBB4A variants lead to this pleiotropic manifestation remain elusive. Here, we investigated whether TUBB4A mutations causing either DYT-TUBB4A (p.R2G and p.Q424H) or H-ABC (p.R2W and p.D249N) exhibit differential effects at the molecular and cellular levels. Using live-cell imaging of disease-relevant oligodendrocytes and total internal reflection fluorescence microscopy of whole-cell lysates, we observed divergent impact on microtubule polymerization and microtubule integration, partially reflecting the observed pleiotropy. Moreover, in silico simulations demonstrated that the mutants rarely adopted a straight heterodimer conformation in contrast to wild type. In conclusion, for most of the examined variants, we deciphered potential molecular disease mechanisms that may lead to the diverse clinical manifestations and phenotype severity across and within each TUBB4A-related disease.
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Affiliation(s)
- Victor Krajka
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- Institute of Microtechnology (IMT), Technische Universität Braunschweig, Braunschweig 38124, Germany
| | - Franca Vulinovic
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Mariya Genova
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Kerstin Tanzer
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - A. S. Jijumon
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Satish Bodakuntla
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Stephanie Tennstedt
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
- University Heart Center Lübeck, 23562 Lübeck, Germany
| | - Helge Mueller-Fielitz
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Britta Meier
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, 91401 Orsay, France
- Université Paris-Saclay, CNRS UMR3348, 91401 Orsay, France
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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19
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Mahserejian SM, Scripture JP, Mauro AJ, Lawrence EJ, Jonasson EM, Murray KS, Li J, Gardner M, Alber M, Zanic M, Goodson HV. Quantification of Microtubule Stutters: Dynamic Instability Behaviors that are Strongly Associated with Catastrophe. Mol Biol Cell 2022; 33:ar22. [PMID: 35108073 PMCID: PMC9250389 DOI: 10.1091/mbc.e20-06-0348] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Microtubules (MTs) are cytoskeletal fibers that undergo dynamic instability (DI), a remarkable process involving phases of growth and shortening separated by stochastic transitions called catastrophe and rescue. Dissecting DI mechanism(s) requires first characterizing and quantifying these dynamics, a subjective process that often ignores complexity in MT behavior. We present a Statistical Tool for Automated Dynamic Instability Analysis (STADIA) that identifies and quantifies not only growth and shortening, but also a category of intermediate behaviors that we term “stutters.” During stutters, the rate of MT length change tends to be smaller in magnitude than during typical growth or shortening phases. Quantifying stutters and other behaviors with STADIA demonstrates that stutters precede most catastrophes in our in vitro experiments and dimer-scale MT simulations, suggesting that stutters are mechanistically involved in catastrophes. Related to this idea, we show that the anticatastrophe factor CLASP2γ works by promoting the return of stuttering MTs to growth. STADIA enables more comprehensive and data-driven analysis of MT dynamics compared with previous methods. The treatment of stutters as distinct and quantifiable DI behaviors provides new opportunities for analyzing mechanisms of MT dynamics and their regulation by binding proteins.
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Affiliation(s)
- Shant M Mahserejian
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, IN 46556.,Pacific Northwest National Laboratory, Richland, WA 99352
| | - Jared P Scripture
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556
| | - Ava J Mauro
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556.,Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst MA, 01003
| | - Elizabeth J Lawrence
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240
| | - Erin M Jonasson
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556.,Department of Natural Sciences, Saint Martin's University, Lacey, WA 98503
| | - Kristopher S Murray
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, IN 46556
| | - Melissa Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Mark Alber
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, IN 46556.,Department of Mathematics, University of California Riverside, Riverside, CA 92521
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235.,Department of Biochemistry, Vanderbilt University, Nashville, TN 37205
| | - Holly V Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, IN 46556
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20
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Wang L, Paudyal SC, Kang Y, Owa M, Liang FX, Spektor A, Knaut H, Sánchez I, Dynlacht BD. Regulators of tubulin polyglutamylation control nuclear shape and cilium disassembly by balancing microtubule and actin assembly. Cell Res 2022; 32:190-209. [PMID: 34782749 PMCID: PMC8807603 DOI: 10.1038/s41422-021-00584-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/05/2021] [Indexed: 02/03/2023] Open
Abstract
Cytoskeletal networks play an important role in regulating nuclear morphology and ciliogenesis. However, the role of microtubule (MT) post-translational modifications in nuclear shape regulation and cilium disassembly has not been explored. Here we identified a novel regulator of the tubulin polyglutamylase complex (TPGC), C11ORF49/CSTPP1, that regulates cytoskeletal organization, nuclear shape, and cilium disassembly. Mechanistically, loss of C11ORF49/CSTPP1 impacts the assembly and stability of the TPGC, which modulates long-chain polyglutamylation levels on microtubules (MTs) and thereby balances the binding of MT-associated proteins and actin nucleators. As a result, loss of TPGC leads to aberrant, enhanced assembly of MTs that penetrate the nucleus, which in turn leads to defects in nuclear shape, and disorganization of cytoplasmic actin that disrupts the YAP/TAZ pathway and cilium disassembly. Further, we showed that C11ORF49/CSTPP1-TPGC plays mechanistically distinct roles in the regulation of nuclear shape and cilium disassembly. Remarkably, disruption of C11ORF49/CSTPP1-TPGC also leads to developmental defects in vivo. Our findings point to an unanticipated nexus that links tubulin polyglutamylation with nuclear shape and ciliogenesis.
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Affiliation(s)
- Lei Wang
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA.
| | - Sharad C Paudyal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuchen Kang
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Mikito Owa
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, NYU Langone Health, New York, NY, USA
| | - Alexander Spektor
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Irma Sánchez
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Brian D Dynlacht
- Department of Pathology, New York University Cancer Institute, New York University School of Medicine, New York, NY, USA.
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21
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Urazbaev A, Serikbaeva A, Tvorogova A, Dusenbayev A, Kauanova S, Vorobjev I. On the Relationship Between EB-3 Profiles and Microtubules Growth in Cultured Cells. Front Mol Biosci 2021; 8:745089. [PMID: 34820422 PMCID: PMC8606533 DOI: 10.3389/fmolb.2021.745089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Microtubules are dynamic structures undergoing rapid growth and shrinkage in living cells and in vitro. The growth of microtubules in vitro was analyzed with subpixel precision (Maurer et al., Current Biology, 2014, 24 (4), 372-384); however, to what extent these results could be applied for microtubules growing in vivo remains largely unknown. Particularly, the question is whether microtubule growth velocity in cells could be sufficiently approximated by a Gaussian distribution or its variability requires a more sophisticated description? Addressing this question, we used time-lapse microscopy and mathematical modeling, and we analyzed EB-3 comets forming on microtubules of cultured cells with subpixel precision. Parameters of comets (shape, form, and velocity) were used as topological characteristics of 3D voxel objects. Using regression analysis, we determined the real positions of the microtubule tips in time-lapse sequences. By exponential decay fitting of the restored comet intensity profile, we found that in vivo EB-3 rapidly exchanges on growing microtubule ends with a decoration time ∼ 2 s. We next developed the model showing that the best correlation between comet length and microtubule end growth velocity is at time intervals close to the decoration time. In the cells, EB comet length positively correlates with microtubule growth velocity in preceding time intervals, while demonstrating no correlation in subsequent time intervals. Correlation between comet length and instantaneous growth velocity of microtubules remains under nocodazole treatment when mean values of both parameters decrease. Our data show that the growth of microtubules in living cells is well-approximated by a constant velocity with large stochastic fluctuations.
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Affiliation(s)
- Arshat Urazbaev
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Anara Serikbaeva
- Laboratory of Biophotonics and Imaging, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Department of Physiology and Biophysics (M/C 901), University of Illinois at Chicago, Chicago, IL, United States
| | - Anna Tvorogova
- A.N.Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Azamat Dusenbayev
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Sholpan Kauanova
- Laboratory of Biophotonics and Imaging, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ivan Vorobjev
- Laboratory of Biophotonics and Imaging, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,A.N.Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
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22
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Yaothak J, Simpson JC, Heffernan LF, Tsai YS, Lin CC. 2D-GolgiTrack-a semi-automated tracking system to quantify morphological changes and dynamics of the Golgi apparatus and Golgi-derived membrane tubules. Med Biol Eng Comput 2021; 60:151-169. [PMID: 34783979 DOI: 10.1007/s11517-021-02460-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 10/07/2021] [Indexed: 11/25/2022]
Abstract
The Golgi apparatus and membrane tubules derived from this organelle play essential roles in membrane trafficking in eukaryotic cells. High-resolution live cell imaging is one highly suitable method for studying the molecular mechanisms of dynamics of organelles during membrane trafficking events. Due to the complex morphological changes and dynamic movements of the Golgi apparatus and associated membrane tubules during membrane trafficking, it is challenging to accurately quantify them. In this study, a semi-automated 2D tracking system, 2D-GolgiTrack, has been established for quantifying morphological changes and movements of Golgi elements, specifically encompassing the Golgi apparatus and its associated tubules, the fission and fusion of Golgi tubules, and the kinetics of formation of Golgi tubules and redistribution of the Golgi-associated protein Rab6A to the endoplasmic reticulum. The Golgi apparatus and associated tubules are segmented by a combination of Otsu's method and adaptive local normalization thresholding. Curvilinear skeletons and tips of skeletons of segmented tubules are used for calculating tubule length by the Geodesic method. The k-nearest neighbor is applied to search the possible candidate objects in the next frame and link the correct objects of adjacent frames by a tracking algorithm to calculate changes in morphological features of each Golgi object or tubule, e.g., number, length, shape, branch point and position, and fission or fusion events. Tracked objects are classified into morphological subtypes, and the Track-Map function of morphological evolution visualizes events of fission and fusion. Our 2D-GolgiTrack not only provides tracking results with 95% accuracy, but also maps morphological evolution for fast visual interpretation of the fission and fusion events. Our tracking system is able to characterize key morphological and dynamic features of the Golgi apparatus and associated tubules, enabling biologists to gain a greater understanding of the molecular mechanisms of membrane traffic involving this essential organelle. Graphical Abstract Overview of the semi-automated 2D tracking system. There are two main parts to the system, namely detection and tracking. The workflow process requires a raw sequence of images (a), which is filtered by the Gaussian filter method (c), and threshold intensity (b) to segment elements of Golgi cisternae (d) and tubules (e). Post-processing outputs are binary images of the cisternae area and tubule skeletons. The tubules are classified into three lengths, namely short, medium, and long tubules (f). Outputs of segmentation are calculated as morphological features (g). The tracking processing starts by loading the segmented outputs (h) and key-inputs of direction reference (i; (DR)) and interval setting of the start ((S)) and end ((E)) frame numbers (j). A tubule of interest is selected by the user (k; (GTinterest, S) as the tubule input ((GTIN)) at the current frame ((i = S)). The tracking algorithm tracks and links the correct tubules at each subsequent frame ((i = i + 1)). The locations of tubule tips are determined for detecting tubule branches using the (DR) to identify the direction of tubule growth (l: (1); (GTtipBr, i); Golgi cisternae: white area; Golgi tubule: white skeleton; tubule tips: green dots; branched tubules: two branches due to the (DR) of growth of the simulated tubule moving from left-to-right away from the Golgi cisternae location). According to the position of the (GTIN), five candidates ((GTcandidates, i)) are searched using the k-nearest neighbor method (l: (2)). Matching of tubules between the (GTIN) and those (GTcandidates, i) uses the bounding box technique to check the amount of tubule-overlap based on the tracking conditions (l: (3)). If there is tubule-overlap, the system collects that tubule as the final output ((GTOUT, i)). By contrast, shape (see the Extent feature in Table reftab:1) and distance features are used to generate the tracked output, which has a priority of a minimum of both of these features ((MinDIST, EXTENT)); otherwise, it is from the minimum of the distance ((MinDIST)). Once a loop of the interval track to the last frame is finished ((i = E + 1)), a Track-Map is generated allowing visualization of the morphological pattern of tubule formation and movement, including identification of fission and fusion events (m). Dynamic features are calculated (n). Related outputs are saved, and all features obtained from the detection and tracking processing are exported as MS Excel files (o).
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Affiliation(s)
- Jindaporn Yaothak
- Department of Biomedical Engineering, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Jeremy C Simpson
- Cell Screening Laboratory, School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin 4, Ireland
| | - Linda F Heffernan
- Cell Screening Laboratory, School of Biology and Environmental Science, Science Centre West, University College Dublin, Dublin 4, Ireland
| | - Yuh-Show Tsai
- Department of Biomedical Engineering, Chung Yuan Christian University, Taoyuan, Taiwan.
| | - Chung-Chih Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.
- Biophotonics Interdisciplinary Research Center, National Yang-Ming University, Taipei, Taiwan.
- Brain Research Center, National Yang-Ming University, Taipei, Taiwan.
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23
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Moon HH, Kreis NN, Friemel A, Roth S, Schulte D, Solbach C, Louwen F, Yuan J, Ritter A. Mitotic Centromere-Associated Kinesin (MCAK/KIF2C) Regulates Cell Migration and Invasion by Modulating Microtubule Dynamics and Focal Adhesion Turnover. Cancers (Basel) 2021; 13:5673. [PMID: 34830827 PMCID: PMC8616312 DOI: 10.3390/cancers13225673] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 01/16/2023] Open
Abstract
The microtubule (MT) cytoskeleton is crucial for cell motility and migration by regulating multiple cellular activities such as transport and endocytosis of key components of focal adhesions (FA). The kinesin-13 family is important in the regulation of MT dynamics and the best characterized member of this family is the mitotic centromere-associated kinesin (MCAK/KIF2C). Interestingly, its overexpression has been reported to be related to increased metastasis in various tumor entities. Moreover, MCAK is involved in the migration and invasion behavior of various cell types. However, the precise molecular mechanisms were not completely clarified. To address these issues, we generated CRISPR/dCas9 HeLa and retinal pigment epithelium (RPE) cell lines overexpressing or downregulating MCAK. Both up- or downregulation of MCAK led to reduced cell motility and poor migration in malignant as well as benign cells. Specifically, it's up- or downregulation impaired FA protein composition and phosphorylation status, interfered with a proper spindle and chromosome segregation, disturbed the assembly and disassembly rate of FA, delayed cell adhesion, and compromised the plus-tip dynamics of MTs. In conclusion, our data suggest MCAK act as an important regulator for cell motility and migration by affecting the actin-MT cytoskeleton dynamics and the FA turnover, providing molecular mechanisms by which deregulated MCAK could promote malignant progression and metastasis of tumor cells.
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Affiliation(s)
- Ha Hyung Moon
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
| | - Nina-Naomi Kreis
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
| | - Alexandra Friemel
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
| | - Susanne Roth
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
| | - Dorothea Schulte
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, J. W. Goethe University, D-60528 Frankfurt, Germany;
| | - Christine Solbach
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
| | - Frank Louwen
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
| | - Juping Yuan
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
| | - Andreas Ritter
- Obstetrics and Prenatal Medicine, Department of Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany; (H.H.M.); (N.-N.K.); (A.F.); (S.R.); (C.S.); (F.L.); (J.Y.)
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24
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Zepeda O J, Bishop LDC, Dutta C, Sarkar-Banerjee S, Leung WW, Landes CF. Untying the Gordian KNOT: Unbiased Single Particle Tracking Using Point Clouds and Adaptive Motion Analysis. J Phys Chem A 2021; 125:8723-8733. [PMID: 34559965 DOI: 10.1021/acs.jpca.1c06100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Achieving mechanistic understanding of transport in complex environments such as inside cells or at polymer interfaces is challenging. We need better ways to image transport in 3-D and better single particle tracking algorithms to determine transport that are not systemically biased toward any classical motion model. Here we present an unbiased single particle tracking algorithm: Knowing Nothing Outside Tracking (KNOT). KNOT uses point clouds provided by iterative deconvolution to educate individual particle localizations and link particle positions between frames to achieve 2-D and 3-D tracking. Information from prior point clouds fuels an independent adaptive motion model for each particle to avoid global models that could introduce biases. KNOT competes with or surpasses other 2-D methods from the 2012 particle tracking challenge while accurately tracking adsorption dynamics of proteins on polymer surfaces and early endosome transport in live cells in 3-D. We apply KNOT to study 3-D endosome transport to reveal new physical insight into locally directed and diffusive transport in live cells. Our analysis demonstrates better accuracy in classifying local motion and its direction compared to previous methods, revealing intricate intracellular transport heterogeneities.
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Affiliation(s)
- Jorge Zepeda O
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States
| | - Logan D C Bishop
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Chayan Dutta
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | | | - Wesley W Leung
- Applied Physics Graduate Program, Smalley-Curl Institute, Rice University, Houston, Texas 77005, United States
| | - Christy F Landes
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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25
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Asthana J, Cade NI, Normanno D, Lim WM, Surrey T. Gradual compaction of the central spindle decreases its dynamicity in PRC1 and EB1 gene-edited cells. Life Sci Alliance 2021; 4:4/12/e202101222. [PMID: 34580180 PMCID: PMC8500333 DOI: 10.26508/lsa.202101222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/24/2022] Open
Abstract
Although different anaphase proteins bind with characteristically different strength to the central spindle, the overall central spindle dynamicity slows down as mitosis proceeds. During mitosis, the spindle undergoes morphological and dynamic changes. It reorganizes at the onset of the anaphase when the antiparallel bundler PRC1 accumulates and recruits central spindle proteins to the midzone. Little is known about how the dynamic properties of the central spindle change during its morphological changes in human cells. Using gene editing, we generated human cells that express from their endogenous locus fluorescent PRC1 and EB1 to quantify their native spindle distribution and binding/unbinding turnover. EB1 plus end tracking revealed a general slowdown of microtubule growth, whereas PRC1, similar to its yeast orthologue Ase1, binds increasingly strongly to compacting antiparallel microtubule overlaps. KIF4A and CLASP1 bind more dynamically to the central spindle, but also show slowing down turnover. These results show that the central spindle gradually becomes more stable during mitosis, in agreement with a recent “bundling, sliding, and compaction” model of antiparallel midzone bundle formation in the central spindle during late mitosis.
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Affiliation(s)
- Jayant Asthana
- The Francis Crick Institute, London, UK.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Davide Normanno
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Wei Ming Lim
- The Francis Crick Institute, London, UK.,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Thomas Surrey
- The Francis Crick Institute, London, UK .,Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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26
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Development of a 2D Automated Tracking System to Characterize Golgi-Derived Membrane Tubule Fission and Fusion Dynamics. J Med Biol Eng 2021. [DOI: 10.1007/s40846-021-00660-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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Masner M, Lujea N, Bisbal M, Acosta C, Kunda P. Linoleic and oleic acids enhance cell migration by altering the dynamics of microtubules and the remodeling of the actin cytoskeleton at the leading edge. Sci Rep 2021; 11:14984. [PMID: 34294745 PMCID: PMC8298526 DOI: 10.1038/s41598-021-94399-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/30/2021] [Indexed: 01/22/2023] Open
Abstract
Fatty acids (FA) have a multitude of biological actions on living cells. A target of their action is cell motility, a process of critical importance during cancer cell dissemination. Here, we studied the effect of unsaturated FA on ovarian cancer cell migration in vitro and its role in regulating cytoskeleton structures that are essential for cell motility. Scratch wound assays on human ovary cancer SKOV-3 cell monolayers revealed that low doses (16 μM) of linoleic acid (LA, 18:2 ω6) and oleic acid (OA; 18:1 ω9) promoted migration, while α-linolenic acid (ALA, 18:3 ω3), showed a migration rate similar to that of the control group. Single cell tracking demonstrated that LA and OA-treated cells migrated faster and were more orientated towards the wound closure than control. In vitro addition of those FA resulted in an increased number, length and protrusion speed of filopodia and also in a prominent and dynamic lamellipodia at the cell leading edge. Using time-lapse video-microscopy and FRAP we observed an increase in both the speed and frequency of actin waves associated with more mobile actin and augmented Rac1 activity. We also observed that FA induced microtubule-organizing center (MTOC)-orientation towards the cell front and affected the dynamics of microtubules (MT) in the direction of cell migration. We propose that environmental cues such as OA and LA present in ascitic fluid, should be taken into account as key factors for the regulation of cell migration.
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Affiliation(s)
- M Masner
- Centro de Investigación en Medicina Traslacional "Severo Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Naciones Unidas 420, Córdoba, Argentina
| | - N Lujea
- Centro de Investigación en Medicina Traslacional "Severo Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Naciones Unidas 420, Córdoba, Argentina
| | - M Bisbal
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - C Acosta
- Instituto de Histología y Embriología de Mendoza (IHEM), Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Patricia Kunda
- Centro de Investigación en Medicina Traslacional "Severo Amuchástegui" (CIMETSA), Instituto Universitario Ciencias Biomédicas Córdoba (IUCBC), Naciones Unidas 420, Córdoba, Argentina.
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28
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Panzade S, Matis M. The Microtubule Minus-End Binding Protein Patronin Is Required for the Epithelial Remodeling in the Drosophila Abdomen. Front Cell Dev Biol 2021; 9:682083. [PMID: 34368132 PMCID: PMC8335404 DOI: 10.3389/fcell.2021.682083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022] Open
Abstract
In the developing Drosophila abdomen, the epithelial tissue displays extensive cytoskeletal remodeling. In stark contrast to the spatio-temporal control of the actin cytoskeleton, the regulation of microtubule architecture during epithelial morphogenesis has remained opaque. In particular, its role in cell motility remains unclear. Here, we show that minus-end binding protein Patronin is required for organizing microtubule arrays in histoblast cells that form the Drosophila abdomen. Loss of Patronin results in a dorsal cleft, indicating the compromised function of histoblasts. We further show that Patronin is polarized in these cells and is required for the formation of highly dynamic non-centrosomal microtubules in the migrating histoblasts. Thus, our study demonstrates that regulation of microtubule cytoskeleton through Patronin mediates epithelium remodeling.
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Affiliation(s)
- Sadhana Panzade
- Interfaculty Centre 'Cells in Motion,' University of Münster, Münster, Germany.,Institute of Cell Biology, Medical Faculty, University of Münster, Münster, Germany
| | - Maja Matis
- Interfaculty Centre 'Cells in Motion,' University of Münster, Münster, Germany.,Institute of Cell Biology, Medical Faculty, University of Münster, Münster, Germany
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29
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Pérez-Martín E, Muñoz-Castañeda R, Moutin MJ, Ávila-Zarza CA, Muñoz-Castañeda JM, Del Pilar C, Alonso JR, Andrieux A, Díaz D, Weruaga E. Oleoylethanolamide Delays the Dysfunction and Death of Purkinje Cells and Ameliorates Behavioral Defects in a Mouse Model of Cerebellar Neurodegeneration. Neurotherapeutics 2021; 18:1748-1767. [PMID: 33829414 PMCID: PMC8609004 DOI: 10.1007/s13311-021-01044-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 02/04/2023] Open
Abstract
Oleoylethanolamide (OEA) is an endocannabinoid that has been proposed to prevent neuronal damage and neuroinflammation. In this study, we evaluated the effects of OEA on the disruption of both cerebellar structure and physiology and on the behavior of Purkinje cell degeneration (PCD) mutant mice. These mice exhibit cerebellar degeneration, displaying microtubule alterations that trigger the selective loss of Purkinje cells and consequent behavioral impairments. The effects of different doses (1, 5, and 10 mg/kg, i.p.) and administration schedules (chronic and acute) of OEA were assessed at the behavioral, histological, cellular, and molecular levels to determine the most effective OEA treatment regimen. Our in vivo results demonstrated that OEA treatment prior to the onset of the preneurodegenerative phase prevented morphological alterations in Purkinje neurons (the somata and dendritic arbors) and decreased Purkinje cell death. This effect followed an inverted U-shaped time-response curve, with acute administration on postnatal day 12 (10 mg/kg, i.p.) being the most effective treatment regimen tested. Indeed, PCD mice that received this specific OEA treatment regimen showed improvements in motor, cognitive and social functions, which were impaired in these mice. Moreover, these in vivo neuroprotective effects of OEA were mediated by the PPARα receptor, as pretreatment with the PPARα antagonist GW6471 (2.5 mg/kg, i.p.) abolished them. Finally, our in vitro results suggested that the molecular effect of OEA was related to microtubule stability and structure since OEA administration normalized some alterations in microtubule features in PCD-like cells. These findings provide strong evidence supporting the use of OEA as a pharmacological agent to limit severe cerebellar neurodegenerative processes.
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Affiliation(s)
- Ester Pérez-Martín
- Laboratory of Neuronal Plasticity and Neurorepair, Institute for Neurosciences of Castile and Leon (INCyL), University of Salamanca, 37007, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
| | - Rodrigo Muñoz-Castañeda
- Laboratory of Neuronal Plasticity and Neurorepair, Institute for Neurosciences of Castile and Leon (INCyL), University of Salamanca, 37007, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
| | - Marie-Jo Moutin
- GIN, Univ. Grenoble Alpes, CNRS, CEA, Grenoble Institute Neurosciences, Inserm, U121638000, Grenoble, France
| | - Carmelo A Ávila-Zarza
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
- Department of Statistics, University of Salamanca, 37007, Salamanca, Spain
| | - José M Muñoz-Castañeda
- Department of Theoretical, Atomic and Optical Physics, University of Valladolid, 47071, Valladolid, Spain
| | - Carlos Del Pilar
- Laboratory of Neuronal Plasticity and Neurorepair, Institute for Neurosciences of Castile and Leon (INCyL), University of Salamanca, 37007, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
| | - José R Alonso
- Laboratory of Neuronal Plasticity and Neurorepair, Institute for Neurosciences of Castile and Leon (INCyL), University of Salamanca, 37007, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
- Universidad de Tarapacá, Arica, Chile
| | - Annie Andrieux
- GIN, Univ. Grenoble Alpes, CNRS, CEA, Grenoble Institute Neurosciences, Inserm, U121638000, Grenoble, France
| | - David Díaz
- Laboratory of Neuronal Plasticity and Neurorepair, Institute for Neurosciences of Castile and Leon (INCyL), University of Salamanca, 37007, Salamanca, Spain.
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain.
| | - Eduardo Weruaga
- Laboratory of Neuronal Plasticity and Neurorepair, Institute for Neurosciences of Castile and Leon (INCyL), University of Salamanca, 37007, Salamanca, Spain.
- Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain.
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30
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Kundu T, Dutta P, Nagar D, Maiti S, Ghose A. Coupling of dynamic microtubules to F-actin by Fmn2 regulates chemotaxis of neuronal growth cones. J Cell Sci 2021; 134:jcs252916. [PMID: 34313311 DOI: 10.1242/jcs.252916] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Dynamic co-regulation of the actin and microtubule subsystems enables the highly precise and adaptive remodelling of the cytoskeleton necessary for critical cellular processes, such as axonal pathfinding. The modes and mediators of this interpolymer crosstalk, however, are inadequately understood. We identify Fmn2, a non-diaphanous-related formin associated with cognitive disabilities, as a novel regulator of cooperative actin-microtubule remodelling in growth cones of both chick and zebrafish neurons. We show that Fmn2 stabilizes microtubules in the growth cones of cultured spinal neurons and in vivo. Super-resolution imaging revealed that Fmn2 facilitates guidance of exploratory microtubules along actin bundles into the chemosensory filopodia. Using live imaging, biochemistry and single-molecule assays, we show that a C-terminal domain in Fmn2 is necessary for the dynamic association between microtubules and actin filaments. In the absence of the cross-bridging function of Fmn2, filopodial capture of microtubules is compromised, resulting in destabilized filopodial protrusions and deficits in growth cone chemotaxis. Our results uncover a critical function for Fmn2 in actin-microtubule crosstalk in neurons and demonstrate that the modulation of microtubule dynamics via associations with F-actin is central to directional motility.
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Affiliation(s)
- Tanushree Kundu
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Priyanka Dutta
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Dhriti Nagar
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
| | - Sankar Maiti
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, West Bengal, India
| | - Aurnab Ghose
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
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31
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Deep probabilistic tracking of particles in fluorescence microscopy images. Med Image Anal 2021; 72:102128. [PMID: 34229189 DOI: 10.1016/j.media.2021.102128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 01/16/2023]
Abstract
Tracking of particles in temporal fluorescence microscopy image sequences is of fundamental importance to quantify dynamic processes of intracellular structures as well as virus structures. We introduce a probabilistic deep learning approach for fluorescent particle tracking, which is based on a recurrent neural network that mimics classical Bayesian filtering. Compared to previous deep learning methods for particle tracking, our approach takes into account uncertainty, both aleatoric and epistemic uncertainty. Thus, information about the reliability of the computed trajectories is determined. Manual tuning of tracking parameters is not necessary and prior knowledge about the noise statistics is not required. Short and long-term temporal dependencies of individual object dynamics are exploited for state prediction, and assigned detections are used to update the predicted states. For correspondence finding, we introduce a neural network which computes assignment probabilities jointly across multiple detections as well as determines the probabilities of missing detections. Training requires only simulated data and therefore tedious manual annotation of ground truth is not needed. We performed a quantitative performance evaluation based on synthetic and real 2D as well as 3D fluorescence microscopy images. We used image data of the Particle Tracking Challenge as well as real time-lapse fluorescence microscopy images displaying virus structures and chromatin structures. It turned out that our approach yields state-of-the-art results or improves the tracking results compared to previous methods.
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32
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Erdogan B, Bearce EA, Lowery LA. Live Imaging of Cytoskeletal Dynamics in Embryonic Xenopus laevis Growth Cones and Neural Crest Cells. Cold Spring Harb Protoc 2021; 2021:pdb.prot104463. [PMID: 33272974 DOI: 10.1101/pdb.prot104463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The cytoskeleton is a dynamic, fundamental network that not only provides mechanical strength to maintain a cell's shape but also controls critical events like cell division, polarity, and movement. Thus, how the cytoskeleton is organized and dynamically regulated is critical to our understanding of countless processes. Live imaging of fluorophore-tagged cytoskeletal proteins allows us to monitor the dynamic nature of cytoskeleton components in embryonic cells. Here, we describe a protocol to monitor and analyze cytoskeletal dynamics in primary embryonic neuronal growth cones and neural crest cells obtained from Xenopus laevis embryos.
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Affiliation(s)
- Burcu Erdogan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Elizabeth A Bearce
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Laura Anne Lowery
- Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts 02118, USA
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33
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Sánchez-Huertas C, Bonhomme M, Falco A, Fagotto-Kaufmann C, van Haren J, Jeanneteau F, Galjart N, Debant A, Boudeau J. The +TIP Navigator-1 is an actin-microtubule crosslinker that regulates axonal growth cone motility. J Cell Biol 2021; 219:151835. [PMID: 32497170 PMCID: PMC7480110 DOI: 10.1083/jcb.201905199] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 04/03/2020] [Accepted: 05/08/2020] [Indexed: 12/14/2022] Open
Abstract
Microtubule (MT) plus-end tracking proteins (+TIPs) are central players in the coordination between the MT and actin cytoskeletons in growth cones (GCs) during axon guidance. The +TIP Navigator-1 (NAV1) is expressed in the developing nervous system, yet its neuronal functions remain poorly elucidated. Here, we report that NAV1 controls the dynamics and motility of the axonal GCs of cortical neurons in an EB1-dependent manner and is required for axon turning toward a gradient of netrin-1. NAV1 accumulates in F-actin-rich domains of GCs and binds actin filaments in vitro. NAV1 can also bind MTs independently of EB1 in vitro and crosslinks nonpolymerizing MT plus ends to actin filaments in axonal GCs, preventing MT depolymerization in F-actin-rich areas. Together, our findings pinpoint NAV1 as a key player in the actin-MT crosstalk that promotes MT persistence at the GC periphery and regulates GC steering. Additionally, we present data assigning to NAV1 an important role in the radial migration of cortical projection neurons in vivo.
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Affiliation(s)
- Carlos Sánchez-Huertas
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Marion Bonhomme
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Amandine Falco
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Christine Fagotto-Kaufmann
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Jeffrey van Haren
- Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Freddy Jeanneteau
- Institut de Génomique Fonctionnelle, University of Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam, Netherlands
| | - Anne Debant
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
| | - Jérôme Boudeau
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, Centre National de la Recherche Scientifique, Montpellier, France
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34
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Mimori-Kiyosue Y. Imaging mitotic processes in three dimensions with lattice light-sheet microscopy. Chromosome Res 2021; 29:37-50. [PMID: 33694045 PMCID: PMC8058003 DOI: 10.1007/s10577-021-09656-3] [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: 01/11/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
There are few technologies that can capture mitotic processes occurring in three-dimensional space with the desired spatiotemporal resolution. Due to such technical limitations, our understanding of mitosis, which has been studied since the early 1880s, is still incomplete with regard to mitotic processes and their regulatory mechanisms at a molecular level. A recently developed high-resolution type of light-sheet microscopy, lattice light-sheet microscopy (LLSM), has achieved unprecedented spatiotemporal resolution scans of intracellular spaces at the whole-cell level. This technology enables experiments that were not possible before (e.g., tracking of growth of every spindle microtubule end and discrimination of individual chromosomes in living cells), thus providing a new avenue for the analysis of mitotic processes. Herein, principles of LLSM technology are introduced, as well as experimental techniques that became possible with LLSM. In addition, issues remaining to be solved for use of this technology in mitosis research, big image data problems, are presented to help guide mitosis research into a new era.
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Affiliation(s)
- Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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35
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Rong Y, Yang W, Hao H, Wang W, Lin S, Shi P, Huang Y, Li B, Sun Y, Liu Z, Wu C. The Golgi microtubules regulate single cell durotaxis. EMBO Rep 2021; 22:e51094. [PMID: 33559938 PMCID: PMC7926246 DOI: 10.15252/embr.202051094] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/27/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
Current understandings on cell motility and directionality rely heavily on accumulated investigations of the adhesion-actin cytoskeleton-actomyosin contractility cycles, while microtubules have been understudied in this context. Durotaxis, the ability of cells to migrate up gradients of substrate stiffness, plays a critical part in development and disease. Here, we identify the pivotal role of Golgi microtubules in durotactic migration of single cells. Using high-throughput analysis of microtubule plus ends/focal adhesion interactions, we uncover that these non-centrosomal microtubules actively impart leading edge focal adhesion (FA) dynamics. Furthermore, we designed a new system where islands of higher stiffness were patterned within RGD peptide coated polyacrylamide gels. We revealed that the positioning of the Golgi apparatus is responsive to external mechanical cues and that the Golgi-nucleus axis aligns with the stiffness gradient in durotaxis. Together, our work unveils the cytoskeletal underpinning for single cell durotaxis. We propose a model in which the Golgi-nucleus axis serves both as a compass and as a steering wheel for durotactic migration, dictating cell directionality through the interaction between non-centrosomal microtubules and the FA dynamics.
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Affiliation(s)
- Yingxue Rong
- Institute of Systems BiomedicineSchool of Basic Medical SciencePeking University Health Science CenterBeijingChina
| | - Wenzhong Yang
- Institute of Systems BiomedicineSchool of Basic Medical SciencePeking University Health Science CenterBeijingChina
| | - Huiwen Hao
- State Key Laboratory of Membrane BiologyBiomedical Pioneer Innovation Center (BIOPIC)School of Life SciencesPeking UniversityBeijingChina
| | - Wenxu Wang
- The Institute for Advanced StudiesWuhan UniversityWuhanChina
| | - Shaozhen Lin
- Applied Mechanics LaboratoryDepartment of Engineering MechanicsInstitute of Biomechanics and Medical EngineeringTsinghua UniversityBeijingChina
| | - Peng Shi
- Institute of Systems BiomedicineSchool of Basic Medical SciencePeking University Health Science CenterBeijingChina
| | - Yuxing Huang
- Institute of Systems BiomedicineSchool of Basic Medical SciencePeking University Health Science CenterBeijingChina
| | - Bo Li
- Applied Mechanics LaboratoryDepartment of Engineering MechanicsInstitute of Biomechanics and Medical EngineeringTsinghua UniversityBeijingChina
| | - Yujie Sun
- State Key Laboratory of Membrane BiologyBiomedical Pioneer Innovation Center (BIOPIC)School of Life SciencesPeking UniversityBeijingChina
| | - Zheng Liu
- The Institute for Advanced StudiesWuhan UniversityWuhanChina
| | - Congying Wu
- Institute of Systems BiomedicineSchool of Basic Medical SciencePeking University Health Science CenterBeijingChina
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36
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Feng W, Liu R, Xie X, Diao L, Gao N, Cheng J, Zhang X, Li Y, Bao L. SUMOylation of α-tubulin is a novel modification regulating microtubule dynamics. J Mol Cell Biol 2021; 13:91-103. [PMID: 33394042 PMCID: PMC8104938 DOI: 10.1093/jmcb/mjaa076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/02/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Microtubules (MTs) are regulated by a number of known posttranslational modifications (PTMs) on α/β-tubulin to fulfill diverse cellular functions. Here, we showed that SUMOylation is a novel PTM on α-tubulin in vivo and in vitro. The SUMOylation on α-tubulin mainly occurred at Lys 96 (K96), K166, and K304 of soluble α-tubulin and could be removed by small ubiquitin-related modifier (SUMO)-specific peptidase 1. In vitro experiments showed that tubulin SUMOylation could reduce interprotofilament interaction, promote MT catastrophe, and impede MT polymerization. In cells, mutation of the SUMOylation sites on α-tubulin reduced catastrophe frequency and increased the proportion of polymerized α-tubulin, while upregulation of SUMOylation with fusion of SUMO1 reduced α-tubulin assembly into MTs. Additionally, overexpression of SUMOylation-deficient α-tubulin attenuated the neurite extension in Neuro-2a cells. Thus, SUMOylation on α-tubulin represents a new player in the regulation of MT properties.
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Affiliation(s)
- Wenfeng Feng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Institute of Brain-Intelligence Technology, Zhangjiang Laboratory; Shanghai Research Center for Brain Science & Brain-Inspired Intelligence, Shanghai 201210, China
| | - Rong Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xuan Xie
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Diao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nannan Gao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinke Cheng
- Discipline of Neuroscience and Department of Biochemistry, Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xu Zhang
- Institute of Brain-Intelligence Technology, Zhangjiang Laboratory; Shanghai Research Center for Brain Science & Brain-Inspired Intelligence, Shanghai 201210, China.,Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yong Li
- Discipline of Neuroscience and Department of Biochemistry, Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lan Bao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science/Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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37
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Singh D, Schmidt N, Müller F, Bange T, Bird AW. Destabilization of Long Astral Microtubules via Cdk1-Dependent Removal of GTSE1 from Their Plus Ends Facilitates Prometaphase Spindle Orientation. Curr Biol 2020; 31:766-781.e8. [PMID: 33333009 DOI: 10.1016/j.cub.2020.11.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/25/2020] [Accepted: 11/16/2020] [Indexed: 12/19/2022]
Abstract
The precise regulation of microtubule dynamics over time and space in dividing cells is critical for several mitotic mechanisms that ultimately enable cell proliferation, tissue organization, and development. Astral microtubules, which extend from the centrosome toward the cell cortex, must be present for the mitotic spindle to properly orient, as well as for the faithful execution of anaphase and cytokinesis. However, little is understood about how the dynamic properties of astral microtubules are regulated spatiotemporally, or the contribution of astral microtubule dynamics to spindle positioning. The mitotic regulator Cdk1-CyclinB promotes destabilization of centrosomal microtubules and increased microtubule dynamics as cells enter mitosis, but how Cdk1 activity modulates astral microtubule stability, and whether it impacts spindle positioning, is unknown. Here, we uncover a mechanism revealing that Cdk1 destabilizes astral microtubules in prometaphase and thereby influences spindle reorientation. Phosphorylation of the EB1-dependent microtubule plus-end tracking protein GTSE1 by Cdk1 in early mitosis abolishes its interaction with EB1 and recruitment to microtubule plus ends. Loss of Cdk1 activity, or mutation of phosphorylation sites in GTSE1, induces recruitment of GTSE1 to growing microtubule plus ends in mitosis. This decreases the catastrophe frequency of astral microtubules and causes an increase in the number of long astral microtubules reaching the cell cortex, which restrains the ability of cells to reorient spindles along the long cellular axis in early mitosis. Astral microtubules thus must not only be present but also dynamic to allow the spindle to reorient, a state assisted by selective destabilization of long astral microtubules via Cdk1.
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Affiliation(s)
- Divya Singh
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Nadine Schmidt
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Franziska Müller
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Tanja Bange
- Department for Systems Chronobiology, Institute of Medical Psychology, LMU Munich, Goethestrasse 31/ I, 80336 Munich, Germany
| | - Alexander W Bird
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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38
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Movsisyan N, Pardo LA. Kv10.1 Regulates Microtubule Dynamics during Mitosis. Cancers (Basel) 2020; 12:cancers12092409. [PMID: 32854244 PMCID: PMC7564071 DOI: 10.3390/cancers12092409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022] Open
Abstract
Kv10.1 (potassium voltage-gated channel subfamily H member 1, known as EAG1 or Ether-à-go-go 1), is a voltage-gated potassium channel, prevailingly expressed in the central nervous system. The aberrant expression of Kv10.1 is detected in over 70% of all human tumor tissues and correlates with poorer prognosis. In peripheral tissues, Kv10.1 is expressed almost exclusively during the G2/M phase of the cell cycle and regulates its progression-downregulation of Kv10.1 extends the duration of the G2/M phase both in cancer and healthy cells. Here, using biochemical and imaging techniques, such as live-cell measurements of microtubule growth and of cytosolic calcium, we elucidate the mechanisms of Kv10.1-mediated regulation at the G2/M phase. We show that Kv10.1 has a dual effect on mitotic microtubule dynamics. Through the functional interaction with ORAI1 (calcium release-activated calcium channel protein 1), it modulates cytosolic calcium oscillations, thereby changing microtubule behavior. The inhibition of either Kv10.1 or ORAI1 stabilizes the microtubules. In contrast, the knockdown of Kv10.1 increases the dynamicity of mitotic microtubules, resulting in a stronger spindle assembly checkpoint, greater mitotic spindle angle, and a decrease in lagging chromosomes. Understanding of Kv10.1-mediated modulation of the microtubule architecture will help to comprehend how cancer tissue benefits from the presence of Kv10.1, and thereby increase the efficacy and safety of Kv10.1-directed therapeutic strategies.
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39
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Sankaran DG, Stemm-Wolf AJ, McCurdy BL, Hariharan B, Pearson CG. A semi-automated machine learning-aided approach to quantitative analysis of centrosomes and microtubule organization. J Cell Sci 2020; 133:jcs243543. [PMID: 32591487 PMCID: PMC7406313 DOI: 10.1242/jcs.243543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
Microtubules (MTs) promote important cellular functions including migration, intracellular trafficking, and chromosome segregation. The centrosome, comprised of two centrioles surrounded by the pericentriolar material (PCM), is the cell's central MT-organizing center. Centrosomes in cancer cells are commonly numerically amplified. However, the question of how the amplification of centrosomes alters MT organization capacity is not well studied. We developed a quantitative image-processing and machine learning-aided approach for the semi-automated analysis of MT organization. We designed a convolutional neural network-based approach for detecting centrosomes, and an automated pipeline for analyzing MT organization around centrosomes, encapsulated in a semi-automatic graphical tool. Using this tool, we find that breast cancer cells with supernumerary centrosomes not only have more PCM protein per centrosome, which gradually increases with increasing centriole numbers, but also exhibit expansion in PCM size. Furthermore, cells with amplified centrosomes have more growing MT ends, higher MT density and altered spatial distribution of MTs around amplified centrosomes. Thus, the semi-automated approach developed here enables rapid and quantitative analyses revealing important facets of centrosomal aberrations.
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Affiliation(s)
- Divya Ganapathi Sankaran
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 2801 East 17th Avenue, Aurora, CO 80045-2537, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexander J Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 2801 East 17th Avenue, Aurora, CO 80045-2537, USA
| | - Bailey L McCurdy
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 2801 East 17th Avenue, Aurora, CO 80045-2537, USA
| | - Bharath Hariharan
- Department of Computer Science, Cornell University, Ithaca, NY 14853, USA
| | - Chad G Pearson
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 2801 East 17th Avenue, Aurora, CO 80045-2537, USA
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40
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Montesinos JC, Abuzeineh A, Kopf A, Juanes-Garcia A, Ötvös K, Petrášek J, Sixt M, Benková E. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. EMBO J 2020; 39:e104238. [PMID: 32667089 PMCID: PMC7459425 DOI: 10.15252/embj.2019104238] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/12/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022] Open
Abstract
Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.
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Affiliation(s)
| | - Anas Abuzeineh
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Aglaja Kopf
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Alba Juanes-Garcia
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Krisztina Ötvös
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.,Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Jan Petrášek
- Institute of Experimental Botany, The Czech Academy of Sciences, Praha, Czech Republic
| | - Michael Sixt
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Eva Benková
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
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41
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Luthria G, Li R, Wang S, Prytyskach M, Kohler RH, Lauffenburger DA, Mitchison TJ, Weissleder R, Miller MA. In vivo microscopy reveals macrophage polarization locally promotes coherent microtubule dynamics in migrating cancer cells. Nat Commun 2020; 11:3521. [PMID: 32665556 PMCID: PMC7360550 DOI: 10.1038/s41467-020-17147-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/02/2020] [Indexed: 01/07/2023] Open
Abstract
Microtubules (MTs) mediate mitosis, directional signaling, and are therapeutic targets in cancer. Yet in vivo analysis of cancer cell MT behavior within the tumor microenvironment remains challenging. Here we developed an imaging pipeline using plus-end tip tracking and intravital microscopy to quantify MT dynamics in live xenograft tumor models. Among analyzed features, cancer cells in vivo displayed higher coherent orientation of MT dynamics along their cell major axes compared with 2D in vitro cultures, and distinct from 3D collagen gel cultures. This in vivo MT phenotype was reproduced in vitro when cells were co-cultured with IL4-polarized MΦ. MΦ depletion, MT disruption, targeted kinase inhibition, and altered MΦ polarization via IL10R blockade all reduced MT coherence and/or tumor cell elongation. We show that MT coherence is a defining feature for in vivo tumor cell dynamics and migration, modulated by local signaling from pro-tumor macrophages. The regulation of microtubule (MT) dynamics in cancer cells within the tumor microenvironment is less understood. Here, the authors develop an imaging platform to examine MT dynamics in live xenograft models and show that pro-tumor macrophages modulate MT coherence and alignment to promote cancer cell migration.
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Affiliation(s)
- Gaurav Luthria
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ran Li
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Stephanie Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02181, USA
| | - Mark Prytyskach
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Rainer H Kohler
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02181, USA
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA. .,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02115, USA. .,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA. .,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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42
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Kershaw S, Morgan DJ, Boyd J, Spiller DG, Kitchen G, Zindy E, Iqbal M, Rattray M, Sanderson CM, Brass A, Jorgensen C, Hussell T, Matthews LC, Ray DW. Glucocorticoids rapidly inhibit cell migration through a novel, non-transcriptional HDAC6 pathway. J Cell Sci 2020; 133:jcs242842. [PMID: 32381682 PMCID: PMC7295589 DOI: 10.1242/jcs.242842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Glucocorticoids (GCs) act through the glucocorticoid receptor (GR, also known as NR3C1) to regulate immunity, energy metabolism and tissue repair. Upon ligand binding, activated GR mediates cellular effects by regulating gene expression, but some GR effects can occur rapidly without new transcription. Here, we show that GCs rapidly inhibit cell migration, in response to both GR agonist and antagonist ligand binding. The inhibitory effect on migration is prevented by GR knockdown with siRNA, confirming GR specificity, but not by actinomycin D treatment, suggesting a non-transcriptional mechanism. We identified a rapid onset increase in microtubule polymerisation following GC treatment, identifying cytoskeletal stabilisation as the likely mechanism of action. HDAC6 overexpression, but not knockdown of αTAT1, rescued the GC effect, implicating HDAC6 as the GR effector. Consistent with this hypothesis, ligand-dependent cytoplasmic interaction between GR and HDAC6 was demonstrated by quantitative imaging. Taken together, we propose that activated GR inhibits HDAC6 function, and thereby increases the stability of the microtubule network to reduce cell motility. We therefore report a novel, non-transcriptional mechanism whereby GCs impair cell motility through inhibition of HDAC6 and rapid reorganization of the cell architecture.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Stephen Kershaw
- Systems Oncology, Cancer Research UK Manchester Institute, Manchester, SK10 4TG, UK
| | - David J Morgan
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology and Inflammation University of Manchester, Manchester, M13 9PT, UK
| | - James Boyd
- Division of Cellular and Molecular Physiology, University of Liverpool, Liverpool, L69 3BX, UK
| | - David G Spiller
- Platform Sciences, Enabling Technologies, and Infrastructure, University of Manchester, Manchester, M13 9PT, UK
| | - Gareth Kitchen
- Division of Diabetes, Endocrinology, and Gastroenterology, University of Manchester, Manchester, M13 9PT, UK
| | - Egor Zindy
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Mudassar Iqbal
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Magnus Rattray
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Christopher M Sanderson
- Division of Cellular and Molecular Physiology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Andrew Brass
- Division of Informatics, Imaging, and Data Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Claus Jorgensen
- Systems Oncology, Cancer Research UK Manchester Institute, Manchester, SK10 4TG, UK
| | - Tracy Hussell
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, M13 9PT, UK
- Lydia Becker Institute of Immunology and Inflammation University of Manchester, Manchester, M13 9PT, UK
| | - Laura C Matthews
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - David W Ray
- Division of Diabetes, Endocrinology, and Gastroenterology, University of Manchester, Manchester, M13 9PT, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, OX3 7LE, and NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
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43
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Geisterfer ZM, Zhu DY, Mitchison TJ, Oakey J, Gatlin JC. Microtubule Growth Rates Are Sensitive to Global and Local Changes in Microtubule Plus-End Density. Curr Biol 2020; 30:3016-3023.e3. [PMID: 32531285 DOI: 10.1016/j.cub.2020.05.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/14/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023]
Abstract
The microtubule cytoskeleton plays critically important roles in numerous cellular functions in eukaryotes, and it does so across a functionally diverse and morphologically disparate range of cell types [1]. In these roles, microtubule assemblies must adopt distinct morphologies and physical dimensions to perform specific functions [2-5]. As such, these macromolecular assemblies-as well as the dynamics of the individual microtubule polymers from which they are made-must scale and change in accordance with cell size, geometry, and function. Microtubules in cells typically assemble to a steady state in mass, leaving enough of their tubulin subunits soluble to allow rapid growth and turnover. This suggests some negative feedback that limits the extent of assembly, for example, decrease in growth rate, or increase in catastrophe rate, as the soluble subunit pool decreases. Although these ideas have informed the field for decades, they have not been observed experimentally. Here, we describe the application of an experimental approach that combines cell-free extracts with photo-patterned hydrogel micro-enclosures as a means to investigate microtubule dynamics in cytoplasmic volumes of defined size and shape. Our measurements reveal a negative correlation between microtubule plus-end density and microtubule growth rates and suggest that these rates are sensitive to the presence of nearby growing ends.
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Affiliation(s)
- Zachary M Geisterfer
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA.
| | - Daniel Y Zhu
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA
| | - John Oakey
- Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA; Department of Chemical Engineering, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA
| | - Jesse C Gatlin
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA; Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA.
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44
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Masoudi S, Razi A, Wright CHG, Gatlin JC, Bagci U. Instance-Level Microtubule Tracking. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:2061-2075. [PMID: 31905134 DOI: 10.1109/tmi.2019.2963865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We propose a new method of instance-level microtubule (MT) tracking in time-lapse image series using recurrent attention. Our novel deep learning algorithm segments individual MTs at each frame. Segmentation results from successive frames are used to assign correspondences among MTs. This ultimately generates a distinct path trajectory for each MT through the frames. Based on these trajectories, we estimate MT velocities. To validate our proposed technique, we conduct experiments using real and simulated data. We use statistics derived from real time-lapse series of MT gliding assays to simulate realistic MT time-lapse image series in our simulated data. This data set is employed as pre-training and hyperparameter optimization for our network before training on the real data. Our experimental results show that the proposed supervised learning algorithm improves the precision for MT instance velocity estimation drastically to 71.3% from the baseline result (29.3%). We also demonstrate how the inclusion of temporal information into our deep network can reduce the false negative rates from 67.8% (baseline) down to 28.7% (proposed). Our findings in this work are expected to help biologists characterize the spatial arrangement of MTs, specifically the effects of MT-MT interactions.
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45
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Yamashita N, Morita M, Yokota H, Mimori-Kiyosue Y. Digital Spindle: A New Way to Explore Mitotic Functions by Whole Cell Data Collection and a Computational Approach. Cells 2020; 9:E1255. [PMID: 32438637 PMCID: PMC7291015 DOI: 10.3390/cells9051255] [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] [Received: 03/31/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 02/06/2023] Open
Abstract
From cells to organisms, every living system is three-dimensional (3D), but the performance of fluorescence microscopy has been largely limited when attempting to obtain an overview of systems' dynamic processes in three dimensions. Recently, advanced light-sheet illumination technologies, allowing drastic improvement in spatial discrimination, volumetric imaging times, and phototoxicity/photobleaching, have been making live imaging to collect precise and reliable 3D information increasingly feasible. In particular, lattice light-sheet microscopy (LLSM), using an ultrathin light-sheet, enables whole-cell 3D live imaging of cellular processes, including mitosis, at unprecedented spatiotemporal resolution for extended periods of time. This technology produces immense and complex data, including a significant amount of information, raising new challenges for big image data analysis and new possibilities for data utilization. Once the data are digitally archived in a computer, the data can be reused for various purposes by anyone at any time. Such an information science approach has the potential to revolutionize the use of bioimage data, and provides an alternative method for cell biology research in a data-driven manner. In this article, we introduce examples of analyzing digital mitotic spindles and discuss future perspectives in cell biology.
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Affiliation(s)
- Norio Yamashita
- Image Processing Research Team, RIKEN Center for Advanced Photonics, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan; (N.Y.); (M.M.); (H.Y.)
| | - Masahiko Morita
- Image Processing Research Team, RIKEN Center for Advanced Photonics, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan; (N.Y.); (M.M.); (H.Y.)
| | - Hideo Yokota
- Image Processing Research Team, RIKEN Center for Advanced Photonics, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan; (N.Y.); (M.M.); (H.Y.)
| | - Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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46
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Nunes V, Dantas M, Castro D, Vitiello E, Wang I, Carpi N, Balland M, Piel M, Aguiar P, Maiato H, Ferreira JG. Centrosome-nuclear axis repositioning drives the assembly of a bipolar spindle scaffold to ensure mitotic fidelity. Mol Biol Cell 2020; 31:1675-1690. [PMID: 32348198 PMCID: PMC7521851 DOI: 10.1091/mbc.e20-01-0047] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
During the initial stages of cell division, the cytoskeleton is extensively reorganized so that a bipolar mitotic spindle can be correctly assembled. This process occurs through the action of molecular motors, cytoskeletal networks, and the nucleus. How the combined activity of these different components is spatiotemporally regulated to ensure efficient spindle assembly remains unclear. To investigate how cell shape, cytoskeletal organization, and molecular motors cross-talk to regulate initial spindle assembly, we use a combination of micropatterning with high-resolution imaging and 3D cellular reconstruction. We show that during prophase, centrosomes and nucleus reorient so that centrosomes are positioned on the shortest nuclear axis at nuclear envelope (NE) breakdown. We also find that this orientation depends on a combination of centrosome movement controlled by Arp2/3-mediated regulation of microtubule dynamics and Dynein-generated forces on the NE that regulate nuclear reorientation. Finally, we observe this centrosome configuration favors the establishment of an initial bipolar spindle scaffold, facilitating chromosome capture and accurate segregation, without compromising division plane orientation.
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Affiliation(s)
- Vanessa Nunes
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal.,Instituto de Biologia Celular e Molecular (IBMC), 4200-135 Porto, Portugal.,BiotechHealth PhD program, Instituto de Ciências Biomédicas (ICBAS), 4050-313 Porto, Portugal
| | - Margarida Dantas
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal.,Instituto de Biologia Celular e Molecular (IBMC), 4200-135 Porto, Portugal.,BiotechHealth PhD program, Instituto de Ciências Biomédicas (ICBAS), 4050-313 Porto, Portugal
| | - Domingos Castro
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal.,Instituto Nacional de Engenharia Biomédica (INEB), 4200-135 Porto, Portugal
| | - Elisa Vitiello
- Laboratoire Interdisciplinaire de Physique, Université Joseph Fourier (Grenoble 1) 38058, France
| | - Irène Wang
- Laboratoire Interdisciplinaire de Physique, Université Joseph Fourier (Grenoble 1) 38058, France
| | - Nicolas Carpi
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France.,Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
| | - Martial Balland
- Laboratoire Interdisciplinaire de Physique, Université Joseph Fourier (Grenoble 1) 38058, France
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France.,Institut Pierre-Gilles de Gennes, PSL Research University, F-75005 Paris, France
| | - Paulo Aguiar
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal.,Instituto Nacional de Engenharia Biomédica (INEB), 4200-135 Porto, Portugal
| | - Helder Maiato
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal.,Instituto de Biologia Celular e Molecular (IBMC), 4200-135 Porto, Portugal.,Departamento de Biomedicina, Faculdade de Medicina do Porto, 4200-450 Porto, Portugal
| | - Jorge G Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal.,Instituto de Biologia Celular e Molecular (IBMC), 4200-135 Porto, Portugal.,Departamento de Biomedicina, Faculdade de Medicina do Porto, 4200-450 Porto, Portugal
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47
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McElmurry K, Stone JE, Ma D, Lamoureux P, Zhang Y, Steidemann M, Fix L, Huang F, Miller KE, Suter DM. Dynein-mediated microtubule translocation powering neurite outgrowth in chick and Aplysia neurons requires microtubule assembly. J Cell Sci 2020; 133:133/8/jcs232983. [PMID: 32332091 DOI: 10.1242/jcs.232983] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 03/02/2020] [Indexed: 12/22/2022] Open
Abstract
Previously, we have shown that bulk microtubule (MT) movement correlates with neurite elongation, and blocking either dynein activity or MT assembly inhibits both processes. However, whether the contributions of MT dynamics and dynein activity to neurite elongation are separate or interdependent is unclear. Here, we investigated the underlying mechanism by testing the roles of dynein and MT assembly in neurite elongation of Aplysia and chick neurites using time-lapse imaging, fluorescent speckle microscopy, super-resolution imaging and biophysical analysis. Pharmacologically inhibiting either dynein activity or MT assembly reduced neurite elongation rates as well as bulk and individual MT anterograde translocation. Simultaneously suppressing both processes did not have additive effects, suggesting a shared mechanism of action. Single-molecule switching nanoscopy revealed that inhibition of MT assembly decreased the association of dynein with MTs. Finally, inhibiting MT assembly prevented the rise in tension induced by dynein inhibition. Taken together, our results suggest that MT assembly is required for dynein-driven MT translocation and neurite outgrowth.
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Affiliation(s)
- Kristi McElmurry
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jessica E Stone
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Donghan Ma
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Phillip Lamoureux
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yueyun Zhang
- Department of Statistics, Purdue University, West Lafayette, IN 47904, USA
| | - Michelle Steidemann
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Lucas Fix
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Kyle E Miller
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Daniel M Suter
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA .,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA.,Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA.,Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
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48
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Galletti G, Zhang C, Gjyrezi A, Cleveland K, Zhang J, Powell S, Thakkar PV, Betel D, Shah MA, Giannakakou P. Microtubule Engagement with Taxane Is Altered in Taxane-Resistant Gastric Cancer. Clin Cancer Res 2020; 26:3771-3783. [PMID: 32321717 DOI: 10.1158/1078-0432.ccr-19-3018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 02/19/2020] [Accepted: 04/17/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE Although taxane-based therapy is standard treatment for advanced gastric cancer, a majority of patients exhibit intrinsic resistance to taxanes. Here, we aim to identify the molecular basis of taxane resistance in gastric cancer. EXPERIMENTAL DESIGN We performed a post hoc analysis of the TAX-325 clinical trial and molecular interrogation of gastric cancer cell lines to assess the benefit of docetaxel in diffuse (DIF-GC) versus intestinal (INT-GC) gastric cancer. We assessed drug-induced microtubule stabilization in gastric cancer cells and in biopsies of patients with gastric cancer treated with taxanes. We performed transcriptome analysis in taxane-treated gastric cancer cells and patients to identify molecular drivers of taxane resistance. RESULTS Patients with DIF-GC did not derive a clinical benefit from taxane treatment suggesting intrinsic taxane resistance. DIF-GC cell lines displayed intrinsic resistance specific to taxanes because of impaired drug-induced microtubule stabilization, in the absence of tubulin mutations or decreased drug accumulation. Using taxane-treated gastric cancer patient biopsies, we demonstrated that absence of drug-target engagement was correlated with clinical taxane resistance. Taxane-sensitive cell lines displayed faster microtubule dynamics at baseline, implicating proteins that regulate cytoskeletal dynamics in intrinsic taxane resistance. Differential gene expression analysis of untreated and docetaxel-treated gastric cancer lines and patient samples identified kinesins to be associated with taxane sensitivity in vitro and in patient samples. CONCLUSIONS Our data reveal that taxane resistance is more prevalent in patients with DIF-GC, support assessment of drug-target engagement as an early read-out of taxane clinical efficacy, and encourage the investigation of kinesins and other microtubule-associated proteins as potentially targetable mediators of taxane resistance in gastric cancer.
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Affiliation(s)
- Giuseppe Galletti
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, New York, New York
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Ada Gjyrezi
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, New York, New York
| | - Kyle Cleveland
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, New York, New York
| | - Jiaren Zhang
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, New York, New York
| | - Sarah Powell
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, New York, New York
| | - Prashant V Thakkar
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, New York, New York
| | - Doron Betel
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Manish A Shah
- Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, New York, New York
| | - Paraskevi Giannakakou
- Department of Medicine, Weill Cornell Medicine, New York, New York. .,Sandra and Edward Meyer Cancer Center, New York, New York
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49
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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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50
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King MR, Petry S. Phase separation of TPX2 enhances and spatially coordinates microtubule nucleation. Nat Commun 2020; 11:270. [PMID: 31937751 PMCID: PMC6959270 DOI: 10.1038/s41467-019-14087-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 12/10/2019] [Indexed: 12/14/2022] Open
Abstract
Phase separation of substrates and effectors is proposed to enhance biological reaction rates and efficiency. Targeting protein for Xklp2 (TPX2) is an effector of branching microtubule nucleation in spindles and functions with the substrate tubulin by an unknown mechanism. Here we show that TPX2 phase separates into a co-condensate with tubulin, which mediates microtubule nucleation in vitro and in isolated cytosol. TPX2-tubulin co-condensation preferentially occurs on pre-existing microtubules, the site of branching microtubule nucleation, at the endogenous and physiologically relevant concentration of TPX2. Truncation and chimera versions of TPX2 suggest that TPX2-tubulin co-condensation enhances the efficiency of TPX2-mediated branching microtubule nucleation. Finally, the known inhibitor of TPX2, the importin-α/β heterodimer, regulates TPX2 condensation in vitro and, consequently, branching microtubule nucleation activity in isolated cytosol. Our study demonstrates how regulated phase separation can simultaneously enhance reaction efficiency and spatially coordinate microtubule nucleation, which may facilitate rapid and accurate spindle formation.
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Affiliation(s)
- Matthew R King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
- Department of Biomedical Engineering, Washington University, Brauer Hall, One Brookings Drive, Saint Louis, Missouri, 63130, USA
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA.
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