1
|
Gudimchuk NB, Alexandrova VV. Measuring and modeling forces generated by microtubules. Biophys Rev 2023; 15:1095-1110. [PMID: 37974983 PMCID: PMC10643784 DOI: 10.1007/s12551-023-01161-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/25/2023] [Indexed: 11/19/2023] Open
Abstract
Tubulins are essential proteins, which are conserved across all eukaryotic species. They polymerize to form microtubules, cytoskeletal components of paramount importance for cellular mechanics. The microtubules combine an extraordinarily high flexural rigidity and a non-equilibrium behavior, manifested in their intermittent assembly and disassembly. These chemically fueled dynamics allow microtubules to generate significant pushing and pulling forces at their ends to reposition intracellular organelles, remodel membranes, bear compressive forces, and transport chromosomes during cell division. In this article, we review classical and recent studies, which have allowed the quantification of microtubule-generated forces. The measurements, to which we owe most of the quantitative information about microtubule forces, were carried out in biochemically reconstituted systems in vitro. We also discuss how mathematical and computational modeling has contributed to the interpretations of these results and shaped our understanding of the mechanisms of force production by tubulin polymerization and depolymerization.
Collapse
Affiliation(s)
- Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
- Pskov State University, Pskov, Russia
| | - Veronika V. Alexandrova
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
| |
Collapse
|
2
|
Carmona B, Marinho HS, Matos CL, Nolasco S, Soares H. Tubulin Post-Translational Modifications: The Elusive Roles of Acetylation. BIOLOGY 2023; 12:biology12040561. [PMID: 37106761 PMCID: PMC10136095 DOI: 10.3390/biology12040561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
Microtubules (MTs), dynamic polymers of α/β-tubulin heterodimers found in all eukaryotes, are involved in cytoplasm spatial organization, intracellular transport, cell polarity, migration and division, and in cilia biology. MTs functional diversity depends on the differential expression of distinct tubulin isotypes and is amplified by a vast number of different post-translational modifications (PTMs). The addition/removal of PTMs to α- or β-tubulins is catalyzed by specific enzymes and allows combinatory patterns largely enriching the distinct biochemical and biophysical properties of MTs, creating a code read by distinct proteins, including microtubule-associated proteins (MAPs), which allow cellular responses. This review is focused on tubulin-acetylation, whose cellular roles continue to generate debate. We travel through the experimental data pointing to α-tubulin Lys40 acetylation role as being a MT stabilizer and a typical PTM of long lived MTs, to the most recent data, suggesting that Lys40 acetylation enhances MT flexibility and alters the mechanical properties of MTs, preventing MTs from mechanical aging characterized by structural damage. Additionally, we discuss the regulation of tubulin acetyltransferases/desacetylases and their impacts on cell physiology. Finally, we analyze how changes in MT acetylation levels have been found to be a general response to stress and how they are associated with several human pathologies.
Collapse
Affiliation(s)
- Bruno Carmona
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
| | - H Susana Marinho
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Catarina Lopes Matos
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Sofia Nolasco
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
- CIISA-Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Helena Soares
- Centro de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096 Lisboa, Portugal
| |
Collapse
|
3
|
Wu YFO, Bryant AT, Nelson NT, Madey AG, Fernandes GF, Goodson HV. Overexpression of the microtubule-binding protein CLIP-170 induces a +TIP network superstructure consistent with a biomolecular condensate. PLoS One 2021; 16:e0260401. [PMID: 34890409 PMCID: PMC8664194 DOI: 10.1371/journal.pone.0260401] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 11/09/2021] [Indexed: 12/02/2022] Open
Abstract
Proper regulation of microtubule (MT) dynamics is critical for cellular processes including cell division and intracellular transport. Plus-end tracking proteins (+TIPs) dynamically track growing MTs and play a key role in MT regulation. +TIPs participate in a complex web of intra- and inter- molecular interactions known as the +TIP network. Hypotheses addressing the purpose of +TIP:+TIP interactions include relieving +TIP autoinhibition and localizing MT regulators to growing MT ends. In addition, we have proposed that the web of +TIP:+TIP interactions has a physical purpose: creating a dynamic scaffold that constrains the structural fluctuations of the fragile MT tip and thus acts as a polymerization chaperone. Here we examine the possibility that this proposed scaffold is a biomolecular condensate (i.e., liquid droplet). Many animal +TIP network proteins are multivalent and have intrinsically disordered regions, features commonly found in biomolecular condensates. Moreover, previous studies have shown that overexpression of the +TIP CLIP-170 induces large “patch” structures containing CLIP-170 and other +TIPs; we hypothesized that these structures might be biomolecular condensates. To test this hypothesis, we used video microscopy, immunofluorescence staining, and Fluorescence Recovery After Photobleaching (FRAP). Our data show that the CLIP-170-induced patches have hallmarks indicative of a biomolecular condensate, one that contains +TIP proteins and excludes other known condensate markers. Moreover, bioinformatic studies demonstrate that the presence of intrinsically disordered regions is conserved in key +TIPs, implying that these regions are functionally significant. Together, these results indicate that the CLIP-170 induced patches in cells are phase-separated liquid condensates and raise the possibility that the endogenous +TIP network might form a liquid droplet at MT ends or other +TIP locations.
Collapse
Affiliation(s)
- Yueh-Fu O. Wu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, United States of America
| | - Annamarie T. Bryant
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, United States of America
| | - Nora T. Nelson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Alexander G. Madey
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Gail F. Fernandes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Holly V. Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- * E-mail:
| |
Collapse
|
4
|
Regulation of microtubule dynamics, mechanics and function through the growing tip. Nat Rev Mol Cell Biol 2021; 22:777-795. [PMID: 34408299 DOI: 10.1038/s41580-021-00399-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Microtubule dynamics and their control are essential for the normal function and division of all eukaryotic cells. This plethora of functions is, in large part, supported by dynamic microtubule tips, which can bind to various intracellular targets, generate mechanical forces and couple with actin microfilaments. Here, we review progress in the understanding of microtubule assembly and dynamics, focusing on new information about the structure of microtubule tips. First, we discuss evidence for the widely accepted GTP cap model of microtubule dynamics. Next, we address microtubule dynamic instability in the context of structural information about assembly intermediates at microtubule tips. Three currently discussed models of microtubule assembly and dynamics are reviewed. These are considered in the context of established facts and recent data, which suggest that some long-held views must be re-evaluated. Finally, we review structural observations about the tips of microtubules in cells and describe their implications for understanding the mechanisms of microtubule regulation by associated proteins, by mechanical forces and by microtubule-targeting drugs, prominently including cancer chemotherapeutics.
Collapse
|
5
|
Semenova I, Gupta D, Usui T, Hayakawa I, Cowan A, Rodionov V. Stimulation of microtubule-based transport by nucleation of microtubules on pigment granules. Mol Biol Cell 2017; 28:1418-1425. [PMID: 28381426 PMCID: PMC5449142 DOI: 10.1091/mbc.e16-08-0571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 11/11/2022] Open
Abstract
In Xenopus melanophores, nucleation of microtubules on pigment granules provides a positive feedback loop that enhances their transport to the cell center during pigment aggregation. Microtubule (MT)-based transport can be regulated through changes in organization of MT transport tracks, but the mechanisms that regulate these changes are poorly understood. In Xenopus melanophores, aggregation of pigment granules in the cell center involves their capture by the tips of MTs growing toward the cell periphery, and granule aggregation signals facilitate capture by increasing the number of growing MT tips. This increase could be explained by stimulation of MT nucleation either on the centrosome or on the aggregate of pigment granules that gradually forms in the cell center. We blocked movement of pigment granules to the cell center and compared the MT-nucleation activity of the centrosome in the same cells in two signaling states. We found that granule aggregation signals did not stimulate MT nucleation on the centrosome but did increase MT nucleation activity of pigment granules. Elevation of MT-nucleation activity correlated with the recruitment to pigment granules of a major component of MT-nucleation templates, γ-tubulin, and was suppressed by γ-tubulin inhibitors. We conclude that generation of new MT transport tracks by concentration of the leading pigment granules provides a positive feedback loop that enhances delivery of trailing granules to the cell center.
Collapse
Affiliation(s)
- Irina Semenova
- R. D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, UConn Health, Farmington, CT 06030
| | - Dipika Gupta
- R. D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, UConn Health, Farmington, CT 06030
| | - Takeo Usui
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Ichiro Hayakawa
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Ann Cowan
- R. D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, UConn Health, Farmington, CT 06030
| | - Vladimir Rodionov
- R. D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, UConn Health, Farmington, CT 06030
| |
Collapse
|
6
|
Fokin AI, Brodsky IB, Burakov AV, Nadezhdina ES. Interaction of early secretory pathway and Golgi membranes with microtubules and microtubule motors. BIOCHEMISTRY (MOSCOW) 2014; 79:879-93. [DOI: 10.1134/s0006297914090053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
7
|
Semenova I, Ikeda K, Resaul K, Kraikivski P, Aguiar M, Gygi S, Zaliapin I, Cowan A, Rodionov V. Regulation of microtubule-based transport by MAP4. Mol Biol Cell 2014; 25:3119-32. [PMID: 25143402 PMCID: PMC4196864 DOI: 10.1091/mbc.e14-01-0022] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Microtubule (MT)-based transport of organelles driven by the opposing MT motors kinesins and dynein is tightly regulated in cells, but the underlying molecular mechanisms remain largely unknown. Here we tested the regulation of MT transport by the ubiquitous protein MAP4 using Xenopus melanophores as an experimental system. In these cells, pigment granules (melanosomes) move along MTs to the cell center (aggregation) or to the periphery (dispersion) by means of cytoplasmic dynein and kinesin-2, respectively. We found that aggregation signals induced phosphorylation of threonine residues in the MT-binding domain of the Xenopus MAP4 (XMAP4), thus decreasing binding of this protein to MTs. Overexpression of XMAP4 inhibited pigment aggregation by shortening dynein-dependent MT runs of melanosomes, whereas removal of XMAP4 from MTs reduced the length of kinesin-2-dependent runs and suppressed pigment dispersion. We hypothesize that binding of XMAP4 to MTs negatively regulates dynein-dependent movement of melanosomes and positively regulates kinesin-2-based movement. Phosphorylation during pigment aggregation reduces binding of XMAP4 to MTs, thus increasing dynein-dependent and decreasing kinesin-2-dependent motility of melanosomes, which stimulates their accumulation in the cell center, whereas dephosphorylation of XMAP4 during dispersion has an opposite effect.
Collapse
Affiliation(s)
- Irina Semenova
- R.D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030
| | - Kazuho Ikeda
- R.D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030 Quantitative Biology Center, RIKEN, Osaka 565-0874, Japan
| | - Karim Resaul
- R.D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030
| | - Pavel Kraikivski
- R.D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030 Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Mike Aguiar
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Ilya Zaliapin
- Department of Mathematics and Statistics, University of Nevada-Reno, Reno, NV 89557
| | - Ann Cowan
- R.D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030
| | - Vladimir Rodionov
- R.D. Berlin Center for Cell Analysis and Modeling and Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030
| |
Collapse
|
8
|
Zhang J, Qiu R, Arst HN, Peñalva MA, Xiang X. HookA is a novel dynein-early endosome linker critical for cargo movement in vivo. ACTA ACUST UNITED AC 2014; 204:1009-26. [PMID: 24637327 PMCID: PMC3998793 DOI: 10.1083/jcb.201308009] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
HookA is a novel linker protein that binds to endosomes and to dynein–dynactin and promotes dynein–early endosome interaction in Aspergillus. Cytoplasmic dynein transports membranous cargoes along microtubules, but the mechanism of dynein–cargo interaction is unclear. From a genetic screen, we identified a homologue of human Hook proteins, HookA, as a factor required for dynein-mediated early endosome movement in the filamentous fungus Aspergillus nidulans. HookA contains a putative N-terminal microtubule-binding domain followed by coiled-coil domains and a C-terminal cargo-binding domain, an organization reminiscent of cytoplasmic linker proteins. HookA–early endosome interaction occurs independently of dynein–early endosome interaction and requires the C-terminal domain. Importantly, HookA interacts with dynein and dynactin independently of HookA–early endosome interaction but dependent on the N-terminal part of HookA. Both dynein and the p25 subunit of dynactin are required for the interaction between HookA and dynein–dynactin, and loss of HookA significantly weakens dynein–early endosome interaction, causing a virtually complete absence of early endosome movement. Thus, HookA is a novel linker important for dynein–early endosome interaction in vivo.
Collapse
Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | | | | | | | | |
Collapse
|
9
|
Dong C, Dinu CZ. Molecular trucks and complementary tracks for bionanotechnological applications. Curr Opin Biotechnol 2013; 24:612-9. [DOI: 10.1016/j.copbio.2013.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/10/2013] [Accepted: 01/12/2013] [Indexed: 11/28/2022]
|
10
|
A functional link between localized Oskar, dynamic microtubules, and endocytosis. Dev Biol 2012; 367:66-77. [DOI: 10.1016/j.ydbio.2012.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 11/19/2022]
|