1
|
Inaba H, Kageyama D, Watari S, Tateishi M, Kakugo A, Matsuura K. Peptide-mediated display of Tau-derived peptide for construction of microtubule superstructures. RSC Chem Biol 2025; 6:737-745. [PMID: 40162136 PMCID: PMC11951922 DOI: 10.1039/d4cb00290c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Accepted: 03/13/2025] [Indexed: 04/02/2025] Open
Abstract
Microtubules are major cytoskeletons involved in various cellular functions, such as regulating cell shape and division and cargo transport via motor proteins. In addition to widely studied singlet microtubules, complex microtubule superstructures, including doublets and bundles, provide unique mechanical and functional properties in vivo. However, a method to construct such superstructures in vitro remains unresolved. This study presents a peptide-based approach for constructing microtubule superstructures by displaying Tau-derived peptides (TP) on the outer surface of microtubules using KA7 peptides as binding units. The KA7-connected TP (KA7-TP) bound to the C-terminal tail on the outer surface of microtubules and induced doublets and bundles by recruiting tubulin. Notably, the outer layers of the doublet microtubules generated by KA7-TP dissociated, highlighting the utility of this approach for studying the formation/dissociation mechanisms of microtubule superstructures. The simple peptide-based approach facilitates our understanding of microtubule superstructures and offers new opportunities for applying microtubule superstructures to nanotechnology.
Collapse
Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry, Tottori University Tottori 680-8552 Japan
| | - Daichi Kageyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University Tottori 680-8552 Japan
| | - Soei Watari
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University Tottori 680-8552 Japan
| | - Mahoko Tateishi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University Tottori 680-8552 Japan
| | - Akira Kakugo
- Department of Physics, Graduate School of Science, Kyoto University Oiwake-cho, Kitashirakawa, Sakyo-ku Kyoto 606-8502 Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University Tottori 680-8552 Japan
- Center for Research on Green Sustainable Chemistry, Tottori University Tottori 680-8552 Japan
| |
Collapse
|
2
|
An J, Imasaki T, Narita A, Niwa S, Sasaki R, Makino T, Nitta R, Kikkawa M. Dimerization of GAS2 mediates crosslinking of microtubules and F-actin. EMBO J 2025; 44:2997-3024. [PMID: 40169809 DOI: 10.1038/s44318-025-00415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 03/05/2025] [Accepted: 03/12/2025] [Indexed: 04/03/2025] Open
Abstract
The spectraplakin family protein GAS2 was originally identified as a growth arrest-specific protein, and recent studies have revealed its involvement in multiple cellular processes. Its dual interaction with actin filaments and microtubules highlights its essential role in cytoskeletal organization, such as cell division, apoptosis, and possibly tumorigenesis. However, the structural basis of cytoskeletal dynamics regulation by GAS2 remains unclear. In this study, we present cryo-electron microscopy structures of the GAS2 type 3 calponin homology domain (CH3) in complex with F-actin at 2.8 Å resolution, thus solving the first type CH3 domain structure bound to F-actin and confirming its actin-binding activity. We also provide the first near-atomic resolution cryo-EM structure of the GAS2-GAR domain bound to microtubules and identify conserved microtubule-binding residues. Our biochemical experiments show that GAS2 promotes microtubule nucleation and polymerization, and that its C-terminal region is essential for dimerization, bundling of both F-actin and microtubules, and microtubule nucleation. As mutations leading to expression of C-terminally truncated GAS2 have been linked to hearing loss, these findings suggest that the disruption of GAS2-dependent cytoskeletal organisation could underlie auditory dysfunction.
Collapse
Affiliation(s)
- Jiancheng An
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Shinsuke Niwa
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryohei Sasaki
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Makino
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Nitta
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
3
|
Vadon C, Magiera MM, Cimarelli A. TRIM Proteins and Antiviral Microtubule Reorganization: A Novel Component in Innate Immune Responses? Viruses 2024; 16:1328. [PMID: 39205302 PMCID: PMC11359181 DOI: 10.3390/v16081328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
TRIM proteins are a family of innate immune factors that play diverse roles in innate immunity and protect the cell against viral and bacterial aggression. As part of this special issue on TRIM proteins, we will take advantage of our findings on TRIM69, which acts by reorganizing the microtubules (MTs) in a manner that is fundamentally antiviral, to more generally discuss how host-pathogen interactions that take place for the control of the MT network represent a crucial facet of the struggle that opposes viruses to their cell environment. In this context, we will present several other TRIM proteins that are known to interact with microtubules in situations other than viral infection, and we will discuss evidence that may suggest a possible contribution to viral control. Overall, the present review will highlight the importance that the control of the microtubule network bears in host-pathogen interactions.
Collapse
Affiliation(s)
- Charlotte Vadon
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69364 Lyon, France
| | - Maria Magda Magiera
- Institut Curie, CNRS, UMR3348, Centre Universitaire, Bat 110, F-91405 Orsay, France
| | - Andrea Cimarelli
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69364 Lyon, France
| |
Collapse
|
4
|
Bajaj T, Kuriyan J, Gee CL. Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis. PLoS One 2023; 18:e0276413. [PMID: 37310965 DOI: 10.1371/journal.pone.0276413] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/28/2023] [Indexed: 06/15/2023] Open
Abstract
Genomic analysis of the unicellular choanoflagellate, Monosiga brevicollis (MB), revealed the remarkable presence of cell signaling and adhesion protein domains that are characteristically associated with metazoans. Strikingly, receptor tyrosine kinases, one of the most critical elements of signal transduction and communication in metazoans, are present in choanoflagellates. We determined the crystal structure at 1.95 Å resolution of the kinase domain of the M. brevicollis receptor tyrosine kinase C8 (RTKC8, a member of the choanoflagellate receptor tyrosine kinase C family) bound to the kinase inhibitor staurospaurine. The chonanoflagellate kinase domain is closely related in sequence to mammalian tyrosine kinases (~ 40% sequence identity to the human Ephrin kinase domain EphA3) and, as expected, has the canonical protein kinase fold. The kinase is structurally most similar to human Ephrin (EphA5), even though the extracellular sensor domain is completely different from that of Ephrin. The RTKC8 kinase domain is in an active conformation, with two staurosporine molecules bound to the kinase, one at the active site and another at the peptide-substrate binding site. To our knowledge this is the first example of staurospaurine binding in the Aurora A activation segment (AAS). We also show that the RTKC8 kinase domain can phosphorylate tyrosine residues in peptides from its C-terminal tail segment which is presumably the mechanism by which it transmits the extracellular stimuli to alter cellular function.
Collapse
Affiliation(s)
- Teena Bajaj
- Graduate Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, California, United States of America
| | - John Kuriyan
- Graduate Program in Comparative Biochemistry, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Christine L Gee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| |
Collapse
|
5
|
Thakkar PV, Kita K, Castillo UD, Galletti G, Madhukar N, Navarro EV, Barasoain I, Goodson HV, Sackett D, Díaz JF, Lu Y, RoyChoudhury A, Molina H, Elemento O, Shah MA, Giannakakou P. CLIP-170S is a microtubule +TIP variant that confers resistance to taxanes by impairing drug-target engagement. Dev Cell 2021; 56:3264-3275.e7. [PMID: 34672971 PMCID: PMC8665049 DOI: 10.1016/j.devcel.2021.09.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 07/14/2021] [Accepted: 09/24/2021] [Indexed: 01/22/2023]
Abstract
Taxanes are widely used cancer chemotherapeutics. However, intrinsic resistance limits their efficacy without any actionable resistance mechanism. We have discovered a microtubule (MT) plus-end-binding CLIP-170 protein variant, hereafter CLIP-170S, which we found enriched in taxane-resistant cell lines and patient samples. CLIP-170S lacks the first Cap-Gly motif, forms longer comets, and impairs taxane access to its MT luminal binding site. CLIP-170S knockdown reversed taxane resistance in cells and xenografts, whereas its re-expression led to resistance, suggesting causation. Using a computational approach in conjunction with the connectivity map, we unexpectedly discovered that Imatinib was predicted to reverse CLIP-170S-mediated taxane resistance. Indeed, Imatinib treatment selectively depleted CLIP-170S, thus completely reversing taxane resistance. Other RTK inhibitors also depleted CLIP-170S, suggesting a class effect. Herein, we identify CLIP-170S as a clinically prevalent variant that confers taxane resistance, whereas the discovery of Imatinib as a CLIP-170S inhibitor provides novel therapeutic opportunities for future trials.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Isabel Barasoain
- Centro de Investigaciones Biológicas Margarita Salas, Madrid, Spain
| | | | - Dan Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD 20892, USA
| | | | - Yao Lu
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, NY 10065, USA
| | - Arindam RoyChoudhury
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, the Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | | | | | | |
Collapse
|
6
|
MacTaggart B, Kashina A. Posttranslational modifications of the cytoskeleton. Cytoskeleton (Hoboken) 2021; 78:142-173. [PMID: 34152688 DOI: 10.1002/cm.21679] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022]
Abstract
The cytoskeleton plays important roles in many essential processes at the cellular and organismal levels, including cell migration and motility, cell division, and the establishment and maintenance of cell and tissue architecture. In order to facilitate these varied functions, the main cytoskeletal components-microtubules, actin filaments, and intermediate filaments-must form highly diverse intracellular arrays in different subcellular areas and cell types. The question of how this diversity is conferred has been the focus of research for decades. One key mechanism is the addition of posttranslational modifications (PTMs) to the major cytoskeletal proteins. This posttranslational addition of various chemical groups dramatically increases the complexity of the cytoskeletal proteome and helps facilitate major global and local cytoskeletal functions. Cytoskeletal proteins undergo many PTMs, most of which are not well understood. Recent technological advances in proteomics and cell biology have allowed for the in-depth study of individual PTMs and their functions in the cytoskeleton. Here, we provide an overview of the major PTMs that occur on the main structural components of the three cytoskeletal systems-tubulin, actin, and intermediate filament proteins-and highlight the cellular function of these modifications.
Collapse
Affiliation(s)
- Brittany MacTaggart
- School of Veterinary Medicine, Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anna Kashina
- School of Veterinary Medicine, Department of Biomedical Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
7
|
Sun J, He D, Fu Y, Zhang R, Guo H, Wang Z, Wang Y, Gao T, Wei Y, Guo Y, Pang Q, Liu Q. A novel lncRNA ARST represses glioma progression by inhibiting ALDOA-mediated actin cytoskeleton integrity. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:187. [PMID: 34099027 PMCID: PMC8183030 DOI: 10.1186/s13046-021-01977-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/09/2021] [Indexed: 12/03/2022]
Abstract
Background Glioma is one of the most aggressive malignant brain tumors that is characterized with inevitably infiltrative growth and poor prognosis. ARST is a novel lncRNA whose expression level is significantly decreased in the patients with glioblastoma multiforme. However, the exact mechanisms of ARST in gliomagenesis are largely unknown. Methods The expressions of ARST in the glioma samples and cell lines were analyzed by qRT-PCR. FISH was utilized to detect the distribution of ARST in the glioma cells. CCK-8, EdU and flow cytometry were used to examine cellular viability, proliferation and apoptosis. Transwell and wound-healing assays were performed to determine the migratory and invasive abilities of the cells. Intracranial tumorigenesis models were established to explore the roles of ARST in vivo. RNA pulldown assay was used to examine proteins that bound to ARST. The activities of key enzymes in the glycolysis and production of lactate acid were measured by colorimetry. In addition, RIP, Co-IP, western blot and immunofluorescence were used to investigate the interaction and regulation between ARST, F-actin, ALDOA and cofilin. Results In this study, we reported that ARST was downregulated in the gliomas. Overexpression of ARST in the glioma cells significantly suppressed various cellular vital abilities such as cell growth, proliferation, migration and invasion. The tumorigenic capacity of these cells in vivo was reduced as well. We further demonstrated that the tumor suppressive effects of ARST could be mediated by a direct binding to a glycolytic enzyme aldolase A (ALDOA), which together with cofilin, keeping the polymerization and depolymerization of actin filaments in an orderly dynamic equilibrium. Upregulation of ARST interrupted the interaction between ALDOA and actin cytoskeleton, which led to a rapid cofilin-dependent loss of F-actin stress fibers. Conclusions Taken together, it is concluded that ARST performs its function via a non-metabolic pathway associated with ALDOA, which otherwise modifies the morphology and invasive properties of the glioma cells. This has added new perspective to its role in tumorigenesis, thus providing potential target for glioma diagnosis, therapy, and prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01977-9.
Collapse
Affiliation(s)
- Jun Sun
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Dong He
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yibing Fu
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Rui Zhang
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Hua Guo
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Zhaojuan Wang
- Department of Physiology, Shandong Medical College, Jinan, 250012, Shandong, People's Republic of China
| | - Yanan Wang
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Department of Pathology, Tai-an Municipal Hospital, Jinan, 250012, Shandong, People's Republic of China
| | - Taihong Gao
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yanbang Wei
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yuji Guo
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
| | - Qian Liu
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
| |
Collapse
|
8
|
Villari G, Enrico Bena C, Del Giudice M, Gioelli N, Sandri C, Camillo C, Fiorio Pla A, Bosia C, Serini G. Distinct retrograde microtubule motor sets drive early and late endosome transport. EMBO J 2020; 39:e103661. [PMID: 33215754 PMCID: PMC7737607 DOI: 10.15252/embj.2019103661|] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Although subcellular positioning of endosomes significantly impacts on their functions, the molecular mechanisms governing the different steady-state distribution of early endosomes (EEs) and late endosomes (LEs)/lysosomes (LYs) in peripheral and perinuclear eukaryotic cell areas, respectively, are still unsolved. We unveil that such differences arise because, while LE retrograde transport depends on the dynein microtubule (MT) motor only, the one of EEs requires the cooperative antagonism of dynein and kinesin-14 KIFC1, a MT minus end-directed motor involved in cancer progression. Mechanistically, the Ser-x-Ile-Pro (SxIP) motif-mediated interaction of the endoplasmic reticulum transmembrane protein stromal interaction molecule 1 (STIM1) with the MT plus end-binding protein 1 (EB1) promotes its association with the p150Glued subunit of the dynein activator complex dynactin and the distinct location of EEs and LEs/LYs. The peripheral distribution of EEs requires their p150Glued-mediated simultaneous engagement with dynein and SxIP motif-containing KIFC1, via HOOK1 and HOOK3 adaptors, respectively. In sum, we provide evidence that distinct minus end-directed MT motor systems drive the differential transport and subcellular distribution of EEs and LEs in mammalian cells.
Collapse
Affiliation(s)
- Giulia Villari
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | - Chiara Enrico Bena
- Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly,IIGM ‐ Italian Institute for Genomic MedicineCandioloItaly,Present address:
Sorbonne UniversitéCNRS, Institut de Biologie Paris‐SeineLaboratoire Jean Perrin (LJP)ParisFrance
| | - Marco Del Giudice
- Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly,IIGM ‐ Italian Institute for Genomic MedicineCandioloItaly
| | - Noemi Gioelli
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | - Chiara Sandri
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | - Chiara Camillo
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | | | - Carla Bosia
- IIGM ‐ Italian Institute for Genomic MedicineCandioloItaly,Department of Applied Science and TechnologyPolytechnic of TorinoTorinoItaly
| | - Guido Serini
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| |
Collapse
|
9
|
Villari G, Enrico Bena C, Del Giudice M, Gioelli N, Sandri C, Camillo C, Fiorio Pla A, Bosia C, Serini G. Distinct retrograde microtubule motor sets drive early and late endosome transport. EMBO J 2020; 39:e103661. [PMID: 33215754 PMCID: PMC7737607 DOI: 10.15252/embj.2019103661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 11/23/2022] Open
Abstract
Although subcellular positioning of endosomes significantly impacts on their functions, the molecular mechanisms governing the different steady‐state distribution of early endosomes (EEs) and late endosomes (LEs)/lysosomes (LYs) in peripheral and perinuclear eukaryotic cell areas, respectively, are still unsolved. We unveil that such differences arise because, while LE retrograde transport depends on the dynein microtubule (MT) motor only, the one of EEs requires the cooperative antagonism of dynein and kinesin‐14 KIFC1, a MT minus end‐directed motor involved in cancer progression. Mechanistically, the Ser‐x‐Ile‐Pro (SxIP) motif‐mediated interaction of the endoplasmic reticulum transmembrane protein stromal interaction molecule 1 (STIM1) with the MT plus end‐binding protein 1 (EB1) promotes its association with the p150Glued subunit of the dynein activator complex dynactin and the distinct location of EEs and LEs/LYs. The peripheral distribution of EEs requires their p150Glued‐mediated simultaneous engagement with dynein and SxIP motif‐containing KIFC1, via HOOK1 and HOOK3 adaptors, respectively. In sum, we provide evidence that distinct minus end‐directed MT motor systems drive the differential transport and subcellular distribution of EEs and LEs in mammalian cells.
Collapse
Affiliation(s)
- Giulia Villari
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Enrico Bena
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy
| | - Marco Del Giudice
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy
| | - Noemi Gioelli
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Sandri
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Camillo
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Alessandra Fiorio Pla
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Carla Bosia
- IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy.,Department of Applied Science and Technology, Polytechnic of Torino, Torino, Italy
| | - Guido Serini
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| |
Collapse
|
10
|
Fourel G, Boscheron C. Tubulin mutations in neurodevelopmental disorders as a tool to decipher microtubule function. FEBS Lett 2020; 594:3409-3438. [PMID: 33064843 DOI: 10.1002/1873-3468.13958] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023]
Abstract
Malformations of cortical development (MCDs) are a group of severe brain malformations associated with intellectual disability and refractory childhood epilepsy. Human missense heterozygous mutations in the 9 α-tubulin and 10 β-tubulin isoforms forming the heterodimers that assemble into microtubules (MTs) were found to cause MCDs. However, how a single mutated residue in a given tubulin isoform can perturb the entire microtubule population in a neuronal cell remains a crucial question. Here, we examined 85 MCD-associated tubulin mutations occurring in TUBA1A, TUBB2, and TUBB3 and their location in a three-dimensional (3D) microtubule cylinder. Mutations hitting residues exposed on the outer microtubule surface are likely to alter microtubule association with partners, while alteration of intradimer contacts may impair dimer stability and straightness. Other types of mutations are predicted to alter interdimer and lateral contacts, which are responsible for microtubule cohesion, rigidity, and dynamics. MCD-associated tubulin mutations surprisingly fall into all categories, thus providing unexpected insights into how a single mutation may impair microtubule function and elicit dominant effects in neurons.
Collapse
|
11
|
The tubulin code and its role in controlling microtubule properties and functions. Nat Rev Mol Cell Biol 2020; 21:307-326. [PMID: 32107477 DOI: 10.1038/s41580-020-0214-3] [Citation(s) in RCA: 499] [Impact Index Per Article: 99.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Microtubules are core components of the eukaryotic cytoskeleton with essential roles in cell division, shaping, motility and intracellular transport. Despite their functional heterogeneity, microtubules have a highly conserved structure made from almost identical molecular building blocks: the tubulin proteins. Alternative tubulin isotypes and a variety of post-translational modifications control the properties and functions of the microtubule cytoskeleton, a concept known as the 'tubulin code'. Here we review the current understanding of the molecular components of the tubulin code and how they impact microtubule properties and functions. We discuss how tubulin isotypes and post-translational modifications control microtubule behaviour at the molecular level and how this translates into physiological functions at the cellular and organism levels. We then go on to show how fine-tuning of microtubule function by some tubulin modifications can affect homeostasis and how perturbation of this fine-tuning can lead to a range of dysfunctions, many of which are linked to human disease.
Collapse
|
12
|
Monroy BY, Tan TC, Oclaman JM, Han JS, Simó S, Niwa S, Nowakowski DW, McKenney RJ, Ori-McKenney KM. A Combinatorial MAP Code Dictates Polarized Microtubule Transport. Dev Cell 2020; 53:60-72.e4. [PMID: 32109385 DOI: 10.1016/j.devcel.2020.01.029] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/19/2019] [Accepted: 01/27/2020] [Indexed: 01/14/2023]
Abstract
Many eukaryotic cells distribute their intracellular components asymmetrically through regulated active transport driven by molecular motors along microtubule tracks. While intrinsic and extrinsic regulation of motor activity exists, what governs the overall distribution of activated motor-cargo complexes within cells remains unclear. Here, we utilize in vitro reconstitution of purified motor proteins and non-enzymatic microtubule-associated proteins (MAPs) to demonstrate that MAPs exhibit distinct influences on the motility of the three main classes of transport motors: kinesin-1, kinesin-3, and cytoplasmic dynein. Further, we dissect how combinations of MAPs affect motors and unveil MAP9 as a positive modulator of kinesin-3 motility. From these data, we propose a general "MAP code" that has the capacity to strongly bias directed movement along microtubules and helps elucidate the intricate intracellular sorting observed in highly polarized cells such as neurons.
Collapse
Affiliation(s)
- Brigette Y Monroy
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Tracy C Tan
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Janah May Oclaman
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Jisoo S Han
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Sergi Simó
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Shinsuke Niwa
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | | | - Richard J McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA
| | - Kassandra M Ori-McKenney
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
| |
Collapse
|
13
|
Ustinova K, Novakova Z, Saito M, Meleshin M, Mikesova J, Kutil Z, Baranova P, Havlinova B, Schutkowski M, Matthias P, Barinka C. The disordered N-terminus of HDAC6 is a microtubule-binding domain critical for efficient tubulin deacetylation. J Biol Chem 2020; 295:2614-2628. [PMID: 31953325 DOI: 10.1074/jbc.ra119.011243] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/14/2020] [Indexed: 11/06/2022] Open
Abstract
Histone deacetylase 6 (HDAC6) is a multidomain cytosolic enzyme having tubulin deacetylase activity that has been unequivocally assigned to the second of the tandem catalytic domains. However, virtually no information exists on the contribution of other HDAC6 domains on tubulin recognition. Here, using recombinant protein expression, site-directed mutagenesis, fluorimetric and biochemical assays, microscale thermophoresis, and total internal reflection fluorescence microscopy, we identified the N-terminal, disordered region of HDAC6 as a microtubule-binding domain and functionally characterized it to the single-molecule level. We show that the microtubule-binding motif spans two positively charged patches comprising residues Lys-32 to Lys-58. We found that HDAC6-microtubule interactions are entirely independent of the catalytic domains and are mediated by ionic interactions with the negatively charged microtubule surface. Importantly, a crosstalk between the microtubule-binding domain and the deacetylase domain was critical for recognition and efficient deacetylation of free tubulin dimers both in vitro and in vivo Overall, our results reveal that recognition of substrates by HDAC6 is more complex than previously appreciated and that domains outside the tandem catalytic core are essential for proficient substrate deacetylation.
Collapse
Affiliation(s)
- Kseniya Ustinova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic; Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, Prague 2, Czech Republic
| | - Zora Novakova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Makoto Saito
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
| | - Marat Meleshin
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University, Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Jana Mikesova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Zsofia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Petra Baranova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Barbora Havlinova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University, Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
| |
Collapse
|
14
|
Bodakuntla S, Jijumon AS, Villablanca C, Gonzalez-Billault C, Janke C. Microtubule-Associated Proteins: Structuring the Cytoskeleton. Trends Cell Biol 2019; 29:804-819. [PMID: 31416684 DOI: 10.1016/j.tcb.2019.07.004] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 11/27/2022]
Abstract
Microtubule-associated proteins (MAPs) were initially discovered as proteins that bind to and stabilize microtubules. Today, an ever-growing number of MAPs reveals a more complex picture of these proteins as organizers of the microtubule cytoskeleton that have a large variety of functions. MAPs enable microtubules to participate in a plethora of cellular processes such as the assembly of mitotic and meiotic spindles, neuronal development, and the formation of the ciliary axoneme. Although some subgroups of MAPs have been exhaustively characterized, a strikingly large number of MAPs remain barely characterized other than their interactions with microtubules. We provide a comprehensive view on the currently known MAPs in mammals. We discuss their molecular mechanisms and functions, as well as their physiological role and links to pathologies.
Collapse
Affiliation(s)
- Satish Bodakuntla
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, F-91405 Orsay, France
| | - A S Jijumon
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, F-91405 Orsay, France
| | - Cristopher Villablanca
- Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Christian Gonzalez-Billault
- Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile; Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile.
| | - Carsten Janke
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, F-91405 Orsay, France.
| |
Collapse
|
15
|
Guo C, Williams JC, Polenova T. Conformational Flexibility of p150 Glued(1-191) Subunit of Dynactin Assembled with Microtubules. Biophys J 2019; 117:938-949. [PMID: 31445682 DOI: 10.1016/j.bpj.2019.07.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/12/2019] [Accepted: 07/25/2019] [Indexed: 02/05/2023] Open
Abstract
Microtubule (MT)-associated proteins perform diverse functions in cells. These functions are dependent on their interactions with MTs. Dynactin, a cofactor of dynein motor, assists the binding of dynein to various organelles and is crucial to the long-distance processivity of dynein-based complexes. The largest subunit of dynactin, the p150Glued, contains an N-terminus segment that is responsible for the MT-binding interactions and long-range processivity of dynactin. We employed solution and magic angle spinning NMR spectroscopy to characterize the structure and dynamics of the p150Glued N-terminal region, both free and in complex with polymerized MTs. This 191-residue region encompasses the cytoskeleton-associated protein glycine-rich domain, the basic domain, and serine/proline-rich (SP-rich) domain. We demonstrate that the basic and SP-rich domains are intrinsically disordered in solution and significantly enhance the binding affinity to MTs as these regions contain the second MT-binding site on the p150Glued subunit. The majority of the basic and SP-rich domains are predicted to be random coil, whereas the segments S111-I116, A124-R132, and K144-T146 in the basic domain contain short α-helical or β-sheet structures. These three segments possibly encompass the MT-binding site. Surprisingly, the protein retains a high degree of flexibility upon binding to MTs except for the regions that are directly involved in the binding interactions with MTs. This conformational flexibility may be essential for the biological functions of the p150Glued subunit.
Collapse
Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - John C Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.
| |
Collapse
|
16
|
Gozes I, Ivashko-Pachima Y, Kapitansky O, Sayas CL, Iram T. Single-cell analysis of cytoskeleton dynamics: From isoelectric focusing to live cell imaging and RNA-seq. J Neurosci Methods 2019; 323:119-124. [DOI: 10.1016/j.jneumeth.2019.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/26/2019] [Accepted: 05/26/2019] [Indexed: 12/31/2022]
|
17
|
The Tubulin Detyrosination Cycle: Function and Enzymes. Trends Cell Biol 2019; 29:80-92. [DOI: 10.1016/j.tcb.2018.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 12/24/2022]
|
18
|
Direct induction of microtubule branching by microtubule nucleation factor SSNA1. Nat Cell Biol 2018; 20:1172-1180. [PMID: 30250060 PMCID: PMC6330057 DOI: 10.1038/s41556-018-0199-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 08/20/2018] [Indexed: 12/22/2022]
Abstract
Microtubules are central elements of the eukaryotic cytoskeleton that often function as part of branched networks. Current models for branching include nucleation of new microtubules from severed microtubule seeds or from gamma-tubulin recruited to the side of a pre-existing microtubule. Here, we found that microtubules can be directly remodeled into branched structures by the microtubule-remodeling factor SSNA1 (or also NA14/DIP13). The branching activity of SSNA1 relies on its ability to self-assemble into fibrils in a head-to-tail fashion. SSNA1 fibrils guide protofilaments of a microtubule to split apart to form daughter microtubules. We further found that SSNA1 localizes at axon branching sites and has a key role in neuronal development. SSNA1 mutants that abolish microtubule branching in vitro also fail to promote axon development and branching when overexpressed in neurons. We have therefore, discovered a mechanism for microtubule-branching and implicated its role in neuronal development.
Collapse
|
19
|
Tan R, Foster PJ, Needleman DJ, McKenney RJ. Cooperative Accumulation of Dynein-Dynactin at Microtubule Minus-Ends Drives Microtubule Network Reorganization. Dev Cell 2018; 44:233-247.e4. [PMID: 29401420 DOI: 10.1016/j.devcel.2017.12.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/10/2017] [Accepted: 12/20/2017] [Indexed: 01/01/2023]
Abstract
Cytoplasmic dynein-1 is a minus-end-directed motor protein that transports cargo over long distances and organizes the intracellular microtubule (MT) network. How dynein motor activity is harnessed for these diverse functions remains unknown. Here, we have uncovered a mechanism for how processive dynein-dynactin complexes drive MT-MT sliding, reorganization, and focusing, activities required for mitotic spindle assembly. We find that motors cooperatively accumulate, in limited numbers, at MT minus-ends. Minus-end accumulations drive MT-MT sliding, independent of MT orientation, resulting in the clustering of MT minus-ends. At a mesoscale level, activated dynein-dynactin drives the formation and coalescence of MT asters. Macroscopically, dynein-dynactin activity leads to bulk contraction of millimeter-scale MT networks, suggesting that minus-end accumulations of motors produce network-scale contractile stresses. Our data provide a model for how localized dynein activity is harnessed by cells to produce contractile stresses within the cytoskeleton, for example, during mitotic spindle assembly.
Collapse
Affiliation(s)
- Ruensern Tan
- Department of Molecular and Cellular Biology, University of California - Davis, Davis, CA 95616, USA
| | - Peter J Foster
- John A. Paulson School of Engineering and Applied Sciences, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Richard J McKenney
- Department of Molecular and Cellular Biology, University of California - Davis, Davis, CA 95616, USA.
| |
Collapse
|
20
|
Monda JK, Whitney IP, Tarasovetc EV, Wilson-Kubalek E, Milligan RA, Grishchuk EL, Cheeseman IM. Microtubule Tip Tracking by the Spindle and Kinetochore Protein Ska1 Requires Diverse Tubulin-Interacting Surfaces. Curr Biol 2017; 27:3666-3675.e6. [PMID: 29153323 DOI: 10.1016/j.cub.2017.10.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/02/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022]
Abstract
The macromolecular kinetochore functions to generate interactions between chromosomal DNA and spindle microtubules [1]. To facilitate chromosome movement and segregation, kinetochores must maintain associations with both growing and shrinking microtubule ends. It is critical to define the proteins and their properties that allow kinetochores to associate with dynamic microtubules. The kinetochore-localized human Ska1 complex binds to microtubules and tracks with depolymerizing microtubule ends [2]. We now demonstrate that the Ska1 complex also autonomously tracks with growing microtubule ends in vitro, a key property that would allow this complex to act at kinetochores to mediate persistent associations with dynamic microtubules. To define the basis for Ska1 complex interactions with dynamic microtubules, we investigated the tubulin-binding properties of the Ska1 microtubule binding domain. In addition to binding to the microtubule lattice and dolastatin-induced protofilament-like structures, we demonstrate that the Ska1 microtubule binding domain can associate with soluble tubulin heterodimers and promote assembly of oligomeric ring-like tubulin structures. We generated mutations on distinct surfaces of the Ska1 microtubule binding domain that disrupt binding to soluble tubulin but do not prevent microtubule binding. These mutants display compromised microtubule tracking activity in vitro and result in defective chromosome alignment and mitotic progression in cells using a CRISPR/Cas9-based replacement assay. Our work supports a model in which multiple surfaces of Ska1 interact with diverse tubulin substrates to associate with dynamic microtubule polymers and facilitate optimal chromosome segregation.
Collapse
Affiliation(s)
- Julie K Monda
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ian P Whitney
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Ekaterina V Tarasovetc
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | | | - Ronald A Milligan
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ekaterina L Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| |
Collapse
|
21
|
Jha R, Roostalu J, Cade NI, Trokter M, Surrey T. Combinatorial regulation of the balance between dynein microtubule end accumulation and initiation of directed motility. EMBO J 2017; 36:3387-3404. [PMID: 29038173 PMCID: PMC5686545 DOI: 10.15252/embj.201797077] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/04/2017] [Accepted: 09/13/2017] [Indexed: 11/14/2022] Open
Abstract
Cytoplasmic dynein is involved in a multitude of essential cellular functions. Dynein's activity is controlled by the combinatorial action of several regulatory proteins. The molecular mechanism of this regulation is still poorly understood. Using purified proteins, we reconstitute the regulation of the human dynein complex by three prominent regulators on dynamic microtubules in the presence of end binding proteins (EBs). We find that dynein can be in biochemically and functionally distinct pools: either tracking dynamic microtubule plus-ends in an EB-dependent manner or moving processively towards minus ends in an adaptor protein-dependent manner. Whereas both dynein pools share the dynactin complex, they have opposite preferences for binding other regulators, either the adaptor protein Bicaudal-D2 (BicD2) or the multifunctional regulator Lissencephaly-1 (Lis1). BicD2 and Lis1 together control the overall efficiency of motility initiation. Remarkably, dynactin can bias motility initiation locally from microtubule plus ends by autonomous plus-end recognition. This bias is further enhanced by EBs and Lis1. Our study provides insight into the mechanism of dynein regulation by dissecting the distinct functional contributions of the individual members of a dynein regulatory network.
Collapse
Affiliation(s)
- Rupam Jha
- The Francis Crick Institute, London, UK
| | | | | | | | | |
Collapse
|
22
|
Aiken J, Buscaglia G, Bates EA, Moore JK. The α-Tubulin gene TUBA1A in Brain Development: A Key Ingredient in the Neuronal Isotype Blend. J Dev Biol 2017; 5. [PMID: 29057214 PMCID: PMC5648057 DOI: 10.3390/jdb5030008] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Microtubules are dynamic cytoskeletal polymers that mediate numerous, essential functions such as axon and dendrite growth and neuron migration throughout brain development. In recent years, sequencing has revealed dominant mutations that disrupt the tubulin protein building blocks of microtubules. These tubulin mutations lead to a spectrum of devastating brain malformations, complex neurological and physical phenotypes, and even fatality. The most common tubulin gene mutated is the α-tubulin gene TUBA1A, which is the most prevalent α-tubulin gene expressed in post-mitotic neurons. The normal role of TUBA1A during neuronal maturation, and how mutations alter its function to produce the phenotypes observed in patients, remains unclear. This review synthesizes current knowledge of TUBA1A function and expression during brain development, and the brain malformations caused by mutations in TUBA1A.
Collapse
Affiliation(s)
- Jayne Aiken
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, MS8108, 12801 E 17th Ave, Aurora, CO 80045, USA;
| | - Georgia Buscaglia
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (G.B.); (E.A.B.)
| | - Emily A. Bates
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (G.B.); (E.A.B.)
| | - Jeffrey K. Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, MS8108, 12801 E 17th Ave, Aurora, CO 80045, USA;
- Correspondence: ; Tel.: +1-303-724-6198; Fax: +1-303-724-3420
| |
Collapse
|
23
|
Barbosa DJ, Duro J, Prevo B, Cheerambathur DK, Carvalho AX, Gassmann R. Dynactin binding to tyrosinated microtubules promotes centrosome centration in C. elegans by enhancing dynein-mediated organelle transport. PLoS Genet 2017; 13:e1006941. [PMID: 28759579 PMCID: PMC5552355 DOI: 10.1371/journal.pgen.1006941] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/10/2017] [Accepted: 07/25/2017] [Indexed: 12/01/2022] Open
Abstract
The microtubule-based motor dynein generates pulling forces for centrosome centration and mitotic spindle positioning in animal cells. How the essential dynein activator dynactin regulates these functions of the motor is incompletely understood. Here, we dissect the role of dynactin's microtubule binding activity, located in the p150 CAP-Gly domain and an adjacent basic patch, in the C. elegans zygote. Analysis of p150 mutants engineered by genome editing suggests that microtubule tip tracking of dynein-dynactin is dispensable for targeting the motor to the cell cortex and for generating robust cortical pulling forces. Instead, mutations in p150's CAP-Gly domain inhibit cytoplasmic pulling forces responsible for centration of centrosomes and attached pronuclei. The centration defects are mimicked by mutations of α-tubulin's C-terminal tyrosine, and both p150 CAP-Gly and tubulin tyrosine mutants decrease the frequency of early endosome transport from the cell periphery towards centrosomes during centration. Our results suggest that p150 GAP-Gly domain binding to tyrosinated microtubules promotes initiation of dynein-mediated organelle transport in the dividing one-cell embryo, and that this function of p150 is critical for generating cytoplasmic pulling forces for centrosome centration.
Collapse
Affiliation(s)
- Daniel J. Barbosa
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
| | - Joana Duro
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
| | - Bram Prevo
- Ludwig Institute for Cancer Research/Dept of Cellular & Molecular Medicine UCSD, La Jolla, CA, United States of America
| | - Dhanya K. Cheerambathur
- Ludwig Institute for Cancer Research/Dept of Cellular & Molecular Medicine UCSD, La Jolla, CA, United States of America
| | - Ana X. Carvalho
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
| | - Reto Gassmann
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
| |
Collapse
|
24
|
Baumbach J, Murthy A, McClintock MA, Dix CI, Zalyte R, Hoang HT, Bullock SL. Lissencephaly-1 is a context-dependent regulator of the human dynein complex. eLife 2017; 6. [PMID: 28406398 PMCID: PMC5413349 DOI: 10.7554/elife.21768] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 04/11/2017] [Indexed: 01/19/2023] Open
Abstract
The cytoplasmic dynein-1 (dynein) motor plays a central role in microtubule organisation and cargo transport. These functions are spatially regulated by association of dynein and its accessory complex dynactin with dynamic microtubule plus ends. Here, we elucidate in vitro the roles of dynactin, end-binding protein-1 (EB1) and Lissencephaly-1 (LIS1) in the interaction of end tracking and minus end-directed human dynein complexes with these sites. LIS1 promotes dynactin-dependent tracking of dynein on both growing and shrinking plus ends. LIS1 also increases the frequency and velocity of processive dynein movements that are activated by complex formation with dynactin and a cargo adaptor. This stimulatory effect of LIS1 contrasts sharply with its documented ability to inhibit the activity of isolated dyneins. Collectively, our findings shed light on how mammalian dynein complexes associate with dynamic microtubules and help clarify how LIS1 promotes the plus-end localisation and cargo transport functions of dynein in vivo. DOI:http://dx.doi.org/10.7554/eLife.21768.001
Collapse
Affiliation(s)
- Janina Baumbach
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Andal Murthy
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Mark A McClintock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Carly I Dix
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ruta Zalyte
- Division of Structural Studies, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ha Thi Hoang
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Simon L Bullock
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| |
Collapse
|
25
|
Mechanisms of Chromosome Congression during Mitosis. BIOLOGY 2017; 6:biology6010013. [PMID: 28218637 PMCID: PMC5372006 DOI: 10.3390/biology6010013] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 01/07/2017] [Accepted: 01/28/2017] [Indexed: 12/13/2022]
Abstract
Chromosome congression during prometaphase culminates with the establishment of a metaphase plate, a hallmark of mitosis in metazoans. Classical views resulting from more than 100 years of research on this topic have attempted to explain chromosome congression based on the balance between opposing pulling and/or pushing forces that reach an equilibrium near the spindle equator. However, in mammalian cells, chromosome bi-orientation and force balance at kinetochores are not required for chromosome congression, whereas the mechanisms of chromosome congression are not necessarily involved in the maintenance of chromosome alignment after congression. Thus, chromosome congression and maintenance of alignment are determined by different principles. Moreover, it is now clear that not all chromosomes use the same mechanism for congressing to the spindle equator. Those chromosomes that are favorably positioned between both poles when the nuclear envelope breaks down use the so-called "direct congression" pathway in which chromosomes align after bi-orientation and the establishment of end-on kinetochore-microtubule attachments. This favors the balanced action of kinetochore pulling forces and polar ejection forces along chromosome arms that drive chromosome oscillatory movements during and after congression. The other pathway, which we call "peripheral congression", is independent of end-on kinetochore microtubule-attachments and relies on the dominant and coordinated action of the kinetochore motors Dynein and Centromere Protein E (CENP-E) that mediate the lateral transport of peripheral chromosomes along microtubules, first towards the poles and subsequently towards the equator. How the opposite polarities of kinetochore motors are regulated in space and time to drive congression of peripheral chromosomes only now starts to be understood. This appears to be regulated by position-dependent phosphorylation of both Dynein and CENP-E and by spindle microtubule diversity by means of tubulin post-translational modifications. This so-called "tubulin code" might work as a navigation system that selectively guides kinetochore motors with opposite polarities along specific spindle microtubule populations, ultimately leading to the congression of peripheral chromosomes. We propose an integrated model of chromosome congression in mammalian cells that depends essentially on the following parameters: (1) chromosome position relative to the spindle poles after nuclear envelope breakdown; (2) establishment of stable end-on kinetochore-microtubule attachments and bi-orientation; (3) coordination between kinetochore- and arm-associated motors; and (4) spatial signatures associated with post-translational modifications of specific spindle microtubule populations. The physiological consequences of abnormal chromosome congression, as well as the therapeutic potential of inhibiting chromosome congression are also discussed.
Collapse
|
26
|
Xie S, Chen M, Gao S, Zhong T, Zhou P, Li D, Zhou J, Gao J, Liu M. The B-box module of CYLD is responsible for its intermolecular interaction and cytoplasmic localization. Oncotarget 2017; 8:50889-50895. [PMID: 28881612 PMCID: PMC5584213 DOI: 10.18632/oncotarget.15142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/11/2017] [Indexed: 12/26/2022] Open
Abstract
The tumor suppressor protein cylindromatosis (CYLD), as a microtubule-associated deubiquitinase, plays a pivotal role in a wide range of cellular activities, including innate immunity, cell division, and ciliogenesis. Structural characterization reveals a small zinc-binding B-box inserted within the ubiquitin specific protease (USP) domain of CYLD; however, the exact role for this module remains yet to be elucidated. Here we identify a critical role for the B-box in facilitating the intermolecular interaction and subcellular localization of CYLD. By co-immunoprecipitation assays we uncover that CYLD has the ability to form an intermolecular complex. Native gel electrophoresis analysis and pull down assays show that the USP domain of CYLD is essential for its intermolecular interaction. Further investigation reveals that deletion of the B-box from the USP domain disrupts the intermolecular interaction of CYLD. Importantly, although loss of the B-box has no obvious effect on the deubiquitinase activity of CYLD, it abolishes the USP domain-mediated retention of CYLD in the cytoplasm. Collectively, these data demonstrate an important role for the B-box module of CYLD in mediating its assembly and subcellular distribution, which might be related to the functions of CYLD in various biological processes.
Collapse
Affiliation(s)
- Songbo Xie
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan 250014, China
| | - Miao Chen
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan 250014, China
| | - Siqi Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tao Zhong
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan 250014, China
| | - Peng Zhou
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan 250014, China
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jun Zhou
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan 250014, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jinmin Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Min Liu
- Institute of Biomedical Sciences, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan 250014, China
| |
Collapse
|
27
|
Kraatz S, Guichard P, Obbineni JM, Olieric N, Hatzopoulos GN, Hilbert M, Sen I, Missimer J, Gönczy P, Steinmetz MO. The Human Centriolar Protein CEP135 Contains a Two-Stranded Coiled-Coil Domain Critical for Microtubule Binding. Structure 2016; 24:1358-1371. [PMID: 27477386 DOI: 10.1016/j.str.2016.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 11/24/2022]
Abstract
Centrioles are microtubule-based structures that play important roles notably in cell division and cilium biogenesis. CEP135/Bld10p family members are evolutionarily conserved microtubule-binding proteins important for centriole formation. Here, we analyzed in detail the microtubule-binding activity of human CEP135 (HsCEP135). X-ray crystallography and small-angle X-ray scattering in combination with molecular modeling revealed that the 158 N-terminal residues of HsCEP135 (HsCEP135-N) form a parallel two-stranded coiled-coil structure. Biochemical, cryo-electron, and fluorescence microscopy analyses revealed that in vitro HsCEP135-N interacts with tubulin, protofilaments, and microtubules and induces the formation of microtubule bundles. We further identified a 13 amino acid segment spanning residues 96-108, which represents a major microtubule-binding site in HsCEP135-N. Within this segment, we identified a cluster of three lysine residues that contribute to the microtubule bundling activity of HsCEP135-N. Our results provide the first structural information on CEP135/Bld10p proteins and offer insights into their microtubule-binding mechanism.
Collapse
Affiliation(s)
- Sebastian Kraatz
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Paul Guichard
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Jagan M Obbineni
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Georgios N Hatzopoulos
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Manuel Hilbert
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Indrani Sen
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - John Missimer
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), 1015 Lausanne, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland.
| |
Collapse
|
28
|
McKenney RJ, Huynh W, Vale RD, Sirajuddin M. Tyrosination of α-tubulin controls the initiation of processive dynein-dynactin motility. EMBO J 2016; 35:1175-85. [PMID: 26968983 DOI: 10.15252/embj.201593071] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/18/2016] [Indexed: 11/09/2022] Open
Abstract
Post-translational modifications (PTMs) of α/β-tubulin are believed to regulate interactions with microtubule-binding proteins. A well-characterized PTM involves in the removal and re-ligation of the C-terminal tyrosine on α-tubulin, but the purpose of this tyrosination-detyrosination cycle remains elusive. Here, we examined the processive motility of mammalian dynein complexed with dynactin and BicD2 (DDB) on tyrosinated versus detyrosinated microtubules. Motility was decreased ~fourfold on detyrosinated microtubules, constituting the largest effect of a tubulin PTM on motor function observed to date. This preference is mediated by dynactin's microtubule-binding p150 subunit rather than dynein itself. Interestingly, on a bipartite microtubule consisting of tyrosinated and detyrosinated segments, DDB molecules that initiated movement on tyrosinated tubulin continued moving into the segment composed of detyrosinated tubulin. This result indicates that the α-tubulin tyrosine facilitates initial motor-tubulin encounters, but is not needed for subsequent motility. Our results reveal a strong effect of the C-terminal α-tubulin tyrosine on dynein-dynactin motility and suggest that the tubulin tyrosination cycle could modulate the initiation of dynein-driven motility in cells.
Collapse
Affiliation(s)
- Richard J McKenney
- Department of Cellular and Molecular Pharmacology, the Howard Hughes Medical Institute University of California, San Francisco, CA, USA
| | - Walter Huynh
- Department of Cellular and Molecular Pharmacology, the Howard Hughes Medical Institute University of California, San Francisco, CA, USA
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, the Howard Hughes Medical Institute University of California, San Francisco, CA, USA
| | - Minhajuddin Sirajuddin
- Department of Cellular and Molecular Pharmacology, the Howard Hughes Medical Institute University of California, San Francisco, CA, USA
| |
Collapse
|
29
|
Nogales E, Zhang R. Visualizing microtubule structural transitions and interactions with associated proteins. Curr Opin Struct Biol 2016; 37:90-6. [PMID: 26803284 DOI: 10.1016/j.sbi.2015.12.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/14/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022]
Abstract
Microtubules (MTs) have been the subject of cryo-electron microscopy (cryo-EM) studies since the birth of this technique. Although MTs pose some unique challenges, having to do with the presence of a MT seam, lattice variability and disorder, MT cryo-EM reconstructions are steadily improving in resolution and providing exciting new insights into MT structure and function. Recent work has lead to the atomic-detail visualization of lateral contacts between tubulin subunits and the conformational changes that give rise to strain in the MT lattice accompanying GTP hydrolysis. Cryo-EM has also been invaluable in describing the interactions between MTs and MT associated proteins (MAPs), which function to regulate MT dynamic instability, move cargoes, or contribute to other MT cellular processes.
Collapse
Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department and QB3 Institute, UC Berkeley, CA 94720, United States; Howard Hughes Medical Institute, UC Berkeley, CA 94720, United States; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
| | - Rui Zhang
- Howard Hughes Medical Institute, UC Berkeley, CA 94720, United States; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| |
Collapse
|
30
|
Yan S, Guo C, Hou G, Zhang H, Lu X, Williams JC, Polenova T. Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A 2015; 112:14611-6. [PMID: 26604305 PMCID: PMC4664305 DOI: 10.1073/pnas.1509852112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.
Collapse
Affiliation(s)
- Si Yan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Huilan Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - John Charles Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716;
| |
Collapse
|
31
|
Mittelmeier TM, Thompson MD, Lamb MR, Lin H, Dieckmann CL. MLT1 links cytoskeletal asymmetry to organelle placement in chlamydomonas. Cytoskeleton (Hoboken) 2015; 72:113-23. [PMID: 25809438 DOI: 10.1002/cm.21220] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 11/08/2022]
Abstract
Asymmetric placement of the photosensory eyespot organelle in Chlamydomonas is patterned by mother-daughter differences between the two basal bodies, which template the anterior flagella. Each basal body is associated with two bundled microtubule rootlets, one with two microtubules and one with four, forming a cruciate pattern. In wild-type cells, the single eyespot is positioned at the equator in close proximity to the plus end of the daughter rootlet comprising four microtubules, the D4. Here we identify mutations in two linked loci, MLT1 and MLT2, which cause multiple eyespots. Antiserum raised against MLT1 localized the protein along the D4 rootlet microtubules, from the basal bodies to the eyespot. MLT1 associates immediately with the new D4 as it extends during cell division, before microtubule acetylation. MLT1 is a low-complexity protein of over 300,000 Daltons. The expression or stability of MLT1 is dependent on MLT2, predicted to encode a second large, low-complexity protein. MLT1 was not restricted to the D4 rootlet in cells with the vfl2-220 mutation in the gene encoding the basal body-associated protein centrin. The cumulative data highlight the role of mother-daughter basal body differences in establishing asymmetry in associated rootlets, and suggest that eyespot components are directed to the correct location by MLT1 on the D4 microtubules.
Collapse
Affiliation(s)
- Telsa M Mittelmeier
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona
| | | | | | | | | |
Collapse
|
32
|
Crevenna AH, Arciniega M, Dupont A, Mizuno N, Kowalska K, Lange OF, Wedlich-Söldner R, Lamb DC. Side-binding proteins modulate actin filament dynamics. eLife 2015; 4. [PMID: 25706231 PMCID: PMC4375888 DOI: 10.7554/elife.04599] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 02/20/2015] [Indexed: 01/10/2023] Open
Abstract
Actin filament dynamics govern many key physiological processes from cell motility to tissue morphogenesis. A central feature of actin dynamics is the capacity of filaments to polymerize and depolymerize at their ends in response to cellular conditions. It is currently thought that filament kinetics can be described by a single rate constant for each end. In this study, using direct visualization of single actin filament elongation, we show that actin polymerization kinetics at both filament ends are strongly influenced by the binding of proteins to the lateral filament surface. We also show that the pointed-end has a non-elongating state that dominates the observed filament kinetic asymmetry. Estimates of flexibility as well as effects on fragmentation and growth suggest that the observed kinetic diversity arises from structural alteration. Tuning elongation kinetics by exploiting the malleability of the filament structure may be a ubiquitous mechanism to generate a rich variety of cellular actin dynamics. DOI:http://dx.doi.org/10.7554/eLife.04599.001 Actin is one of the most abundant proteins in cells. It forms networks of filaments that provide structural support and generate the forces needed for cell movement, division, and many other processes in cells. Filaments of actin continuously change in length as actin molecules are added or removed at the ends. One end of an actin filament—called the barbed-end—grows much faster than the other, known as the pointed-end. Many other proteins also help the actin filaments to form. Some of these proteins bind to the ends of the filaments, where they directly control the growth of the filaments. Other proteins bind along the length of the filaments, but how these ‘side-binding’ proteins influence the growth of filaments is not clear. In this study, Crevenna et al. used a technique called ‘total internal reflection fluorescence (TIRF) microscopy’ to study how several side-binding proteins affect the growth of actin filaments in an artificial system. The growth of the barbed-ends was strongly influenced by which side-binding protein was interacting with the filament. For example, the barbed-end grew rapidly when a protein called VASP was present but grew more slowly in the presence of the protein α-actinin. Although the growth at the pointed-end was generally slow and sporadic, the side-binding proteins also had noticeable effects. Crevenna et al. found that when the side-binding proteins were present at low levels, filament growth was similar for all proteins studied. It was only when the proteins were present at higher levels that the growth of the actin filaments was altered depending on the specific side-binding protein present. One side-binding protein called α-actinin also altered the shape of the actin filament so that when it was present at high levels, the filaments curved in a particular direction. Together, these results suggest that the growth, structure, and flexibility of actin filaments can be strongly influenced by the various proteins that bind along the length of the filaments. The next challenges are to understand the precise details of how these side-binding proteins are able to alter the growth and shape of actin and investigate how they influence other processes that control the structure of actin networks in cells. DOI:http://dx.doi.org/10.7554/eLife.04599.002
Collapse
Affiliation(s)
- Alvaro H Crevenna
- Physical Chemistry, Department of Chemistry and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany.,Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marcelino Arciniega
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Chemistry, Technische Universität München, Garching, Germany
| | - Aurélie Dupont
- Physical Chemistry, Department of Chemistry and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany.,NanoSystems Initiative Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Naoko Mizuno
- Cellular and Membrane Trafficking, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kaja Kowalska
- Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Oliver F Lange
- Department of Chemistry, Technische Universität München, Garching, Germany.,Biomolecular NMR and Munich Center for Integrated Protein Science, Technische Universität München, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Roland Wedlich-Söldner
- Cellular Dynamics and Cell Patterning, Max Planck Institute of Biochemistry, Martinsried, Germany.,Institute of Cell Dynamics and Imaging, Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry and Center for Nanoscience, Ludwig-Maximilians-Universität München, Munich, Germany.,NanoSystems Initiative Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|