1
|
Jia X, Lin L, Guo S, Zhou L, Jin G, Dong J, Xiao J, Xie X, Li Y, He S, Wei Z, Yu C. CLASP-mediated competitive binding in protein condensates directs microtubule growth. Nat Commun 2024; 15:6509. [PMID: 39095354 PMCID: PMC11297316 DOI: 10.1038/s41467-024-50863-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Microtubule organization in cells relies on targeting mechanisms. Cytoplasmic linker proteins (CLIPs) and CLIP-associated proteins (CLASPs) are key regulators of microtubule organization, yet the underlying mechanisms remain elusive. Here, we reveal that the C-terminal domain of CLASP2 interacts with a common motif found in several CLASP-binding proteins. This interaction drives the dynamic localization of CLASP2 to distinct cellular compartments, where CLASP2 accumulates in protein condensates at the cell cortex or the microtubule plus end. These condensates physically contact each other via CLASP2-mediated competitive binding, determining cortical microtubule targeting. The phosphorylation of CLASP2 modulates the dynamics of the condensate-condensate interaction and spatiotemporally navigates microtubule growth. Moreover, we identify additional CLASP-interacting proteins that are involved in condensate contacts in a CLASP2-dependent manner, uncovering a general mechanism governing microtubule targeting. Our findings not only unveil a tunable multiphase system regulating microtubule organization, but also offer general mechanistic insights into intricate protein-protein interactions at the mesoscale level.
Collapse
Affiliation(s)
- Xuanyan Jia
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, 518055, China
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Leishu Lin
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, 518055, China
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Siqi Guo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Lulu Zhou
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Gaowei Jin
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Jiayuan Dong
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, 518055, China
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Jinman Xiao
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Xingqiao Xie
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, 518055, China
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yiming Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Sicong He
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Zhiyi Wei
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Shenzhen, Guangdong, 518055, China.
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Cong Yu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, Guangdong, 518055, China.
| |
Collapse
|
2
|
Volkov VA, Akhmanova A. Phase separation on microtubules: from droplet formation to cellular function? Trends Cell Biol 2024; 34:18-30. [PMID: 37453878 DOI: 10.1016/j.tcb.2023.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Microtubules are cytoskeletal polymers that play important roles in numerous cellular processes, ranging from the control of cell shape and polarity to cell division and intracellular transport. Many of these roles rely on proteins that bind to microtubule ends and shafts, carry intrinsically disordered regions, and form complex multivalent interaction networks. A flurry of recent studies demonstrated that these properties allow diverse microtubule-binding proteins to undergo liquid-liquid phase separation (LLPS) in vitro. It is proposed that LLPS could potentially affect multiple microtubule-related processes, such as microtubule nucleation, control of microtubule dynamics and organization, and microtubule-based transport. Here, we discuss the evidence in favor and against the occurrence of LLPS and its functional significance for microtubule-based processes in cells.
Collapse
Affiliation(s)
- Vladimir A Volkov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.
| |
Collapse
|
3
|
Structure Composition and Intracellular Transport of Clathrin-Mediated Intestinal Transmembrane Tight Junction Protein. Inflammation 2023; 46:18-34. [PMID: 36050591 DOI: 10.1007/s10753-022-01724-y] [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: 05/17/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022]
Abstract
Tight junctions (TJs) are located in the apical region of the junctions between epithelial cells and are widely found in organs such as the brain, retina, intestinal epithelium, and endothelial system. As a mechanical barrier of the intestinal mucosa, TJs can not only maintain the integrity of intestinal epithelial cells but also maintain intestinal mucosal permeability by regulating the entry of ions and molecules into paracellular channels. Therefore, the formation disorder or integrity destruction of TJs can induce damage to the intestinal epithelial barrier, ultimately leading to the occurrence of various gastrointestinal diseases, such as inflammatory bowel disease (IBD), gastroesophageal reflux disease (GERD), and irritable bowel syndrome (IBS). However, a large number of studies have shown that TJs protein transport disorder from the endoplasmic reticulum to the apical membrane can lead to TJs formation disorder, in addition to disruption of TJs integrity caused by external pathological factors and reduction of TJs protein synthesis. In this review, we focus on the structural composition of TJs, the formation of clathrin-coated vesicles containing transmembrane TJs from the Golgi apparatus, and the transport process from the Golgi apparatus to the plasma membrane via microtubules and finally fusion with the plasma membrane. At present, the mechanism of the intracellular transport of TJ proteins remains unclear. More studies are needed in the future to focus on the sorting of TJs protein vesicles, regulation of transport processes, and recycling of TJ proteins, etc.
Collapse
|
4
|
Maan R, Reese L, Volkov VA, King MR, van der Sluis EO, Andrea N, Evers WH, Jakobi AJ, Dogterom M. Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus-ends. Nat Cell Biol 2023; 25:68-78. [PMID: 36536175 PMCID: PMC9859754 DOI: 10.1038/s41556-022-01037-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Growing microtubule ends organize end-tracking proteins into comets of mixed composition. Here using a reconstituted fission yeast system consisting of end-binding protein Mal3, kinesin Tea2 and cargo Tip1, we found that these proteins can be driven into liquid-phase droplets both in solution and at microtubule ends under crowding conditions. In the absence of crowding agents, cryo-electron tomography revealed that motor-dependent comets consist of disordered networks where multivalent interactions may facilitate non-stoichiometric accumulation of cargo Tip1. We found that two disordered protein regions in Mal3 are required for the formation of droplets and motor-dependent accumulation of Tip1, while autonomous Mal3 comet formation requires only one of them. Using theoretical modelling, we explore possible mechanisms by which motor activity and multivalent interactions may lead to the observed enrichment of Tip1 at microtubule ends. We conclude that microtubule ends may act as platforms where multivalent interactions condense microtubule-associated proteins into large multi-protein complexes.
Collapse
Affiliation(s)
- Renu Maan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Louis Reese
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.,Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Vladimir A Volkov
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.,Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Matthew R King
- Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St Louis, MO, USA
| | - Eli O van der Sluis
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nemo Andrea
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Wiel H Evers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands. .,Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA.
| |
Collapse
|
5
|
Jara KA, Loening NM, Reardon PN, Yu Z, Woonnimani P, Brooks C, Vesely CH, Barbar EJ. Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein. eLife 2022; 11:e80217. [PMID: 36416224 PMCID: PMC9771362 DOI: 10.7554/elife.80217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
As the only major retrograde transporter along microtubules, cytoplasmic dynein plays crucial roles in the intracellular transport of organelles and other cargoes. Central to the function of this motor protein complex is dynein intermediate chain (IC), which binds the three dimeric dynein light chains at multivalent sites, and dynactin p150Glued and nuclear distribution protein (NudE) at overlapping sites of its intrinsically disordered N-terminal domain. The disorder in IC has hindered cryo-electron microscopy and X-ray crystallography studies of its structure and interactions. Here we use a suite of biophysical methods to reveal how multivalent binding of the three light chains regulates IC interactions with p150Glued and NudE. Using IC from Chaetomium thermophilum, a tractable species to interrogate IC interactions, we identify a significant reduction in binding affinity of IC to p150Glued and a loss of binding to NudE for constructs containing the entire N-terminal domain as well as for full-length constructs when compared to the tight binding observed with short IC constructs. We attribute this difference to autoinhibition caused by long-range intramolecular interactions between the N-terminal single α-helix of IC, the common site for p150Glued, and NudE binding, and residues closer to the end of the N-terminal domain. Reconstitution of IC subcomplexes demonstrates that autoinhibition is differentially regulated by light chains binding, underscoring their importance both in assembly and organization of IC, and in selection between multiple binding partners at the same site.
Collapse
Affiliation(s)
- Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | | | - Patrick N Reardon
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
- Oregon State University NMR FacilityCorvallisUnited States
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Prajna Woonnimani
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Coban Brooks
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Cat H Vesely
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| |
Collapse
|
6
|
Tension of plus-end tracking protein Clip170 confers directionality and aggressiveness during breast cancer migration. Cell Death Dis 2022; 13:856. [PMID: 36209218 PMCID: PMC9547975 DOI: 10.1038/s41419-022-05306-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022]
Abstract
The microtubule (MT) plus-end binding protein Clip170 is associated closely with breast cancer invasion and migration. In this study, Clip170 tension observed by a newly designed cpstFRET tension probe was suggested to be positive related to breast cancer aggressiveness, which could be regulated by α-tubulin detyrosination-induced MT disassembly. Clip170 phosphorylation induced by Ribosomal protein S6 kinase (RSK) could also increase its tension and promote the conversion of a discrete comet-like Clip-170 distribution into a spotty pattern during cancer metastasis. Heightened Clip170 tension was correlated with the formation of cortactin-associated filopodia and lamellipodia, and then promoted invasion and metastasis both in vitro and in vivo. Meanwhile, Clip170 tension enhanced at the leading edge in directional migration, accompanying with IQGAP1 subcellular distribution variation. Our work indicates that the malignancy and directionality during breast cancer migration depend on the magnitude and polarization of Clip170 tension, and we suggest Clip170 tension as a new potential drug target for breast cancer therapy.
Collapse
|
7
|
Wattanathamsan O, Pongrakhananon V. Emerging role of microtubule-associated proteins on cancer metastasis. Front Pharmacol 2022; 13:935493. [PMID: 36188577 PMCID: PMC9515585 DOI: 10.3389/fphar.2022.935493] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/29/2022] [Indexed: 12/29/2022] Open
Abstract
The major cause of death in cancer patients is strongly associated with metastasis. While much remains to be understood, microtubule-associated proteins (MAPs) have shed light on metastatic progression’s molecular mechanisms. In this review article, we focus on the role of MAPs in cancer aggressiveness, particularly cancer metastasis activity. Increasing evidence has shown that a growing number of MAP member proteins might be fundamental regulators involved in altering microtubule dynamics, contributing to cancer migration, invasion, and epithelial-to-mesenchymal transition. MAP types have been established according to their microtubule-binding site and function in microtubule-dependent activities. We highlight that altered MAP expression was commonly found in many cancer types and related to cancer progression based on available evidence. Furthermore, we discuss and integrate the relevance of MAPs and related molecular signaling pathways in cancer metastasis. Our review provides a comprehensive understanding of MAP function on microtubules. It elucidates how MAPs regulate cancer progression, preferentially in metastasis, providing substantial scientific information on MAPs as potential therapeutic targets and prognostic markers for cancer management.
Collapse
Affiliation(s)
- Onsurang Wattanathamsan
- Preclinical Toxicity and Efficacy Assessment of Medicines and Chemicals Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Varisa Pongrakhananon
- Preclinical Toxicity and Efficacy Assessment of Medicines and Chemicals Research Unit, Chulalongkorn University, Bangkok, Thailand
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Varisa Pongrakhananon,
| |
Collapse
|
8
|
Wu YFO, Miller RA, Alberico EO, Huang YAP, Bryant AT, Nelson NT, Jonasson EM, Goodson HV. The CLIP-170 N-terminal domain binds directly to both F-actin and microtubules in a mutually exclusive manner. J Biol Chem 2022; 298:101820. [PMID: 35283190 PMCID: PMC9062740 DOI: 10.1016/j.jbc.2022.101820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/27/2022] Open
Abstract
The cooperation between the actin and microtubule (MT) cytoskeletons is important for cellular processes such as cell migration and muscle cell development. However, a full understanding of how this cooperation occurs has yet to be sufficiently developed. The MT plus-end tracking protein CLIP-170 has been implicated in this actin-MT coordination by associating with the actin-binding signaling protein IQGAP1 and by promoting actin polymerization through binding with formins. Thus far, the interactions of CLIP-170 with actin were assumed to be indirect. Here, we demonstrate using high-speed cosedimentation assays that CLIP-170 can bind to filamentous actin (F-actin) directly. We found that the affinity of this binding is relatively weak but strong enough to be significant in the actin-rich cortex, where actin concentrations can be extremely high. Using CLIP-170 fragments and mutants, we show that the direct CLIP-170-F-actin interaction is independent of the FEED domain, the region that mediates formin-dependent actin polymerization, and that the CLIP-170 F-actin-binding region overlaps with the MT-binding region. Consistent with these observations, in vitro competition assays indicate that CLIP-170-F-actin and CLIP-170-MT interactions are mutually exclusive. Taken together, these observations lead us to speculate that direct CLIP-170-F-actin interactions may function to reduce the stability of MTs in actin-rich regions of the cell, as previously proposed for MT end-binding protein 1.
Collapse
Affiliation(s)
- Yueh-Fu O Wu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA; Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, Indiana, USA
| | - Rachel A Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Emily O Alberico
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yaobing A P Huang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA; Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, Indiana, USA
| | - Annamarie T Bryant
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA; Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nora T Nelson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Erin M Jonasson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Holly V Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA; Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, Indiana, USA; Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA.
| |
Collapse
|
9
|
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
|
10
|
Chen J, Kholina E, Szyk A, Fedorov VA, Kovalenko I, Gudimchuk N, Roll-Mecak A. α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics. Dev Cell 2021; 56:2016-2028.e4. [PMID: 34022132 PMCID: PMC8476856 DOI: 10.1016/j.devcel.2021.05.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Microtubules are non-covalent polymers of αβ-tubulin dimers. Posttranslational processing of the intrinsically disordered C-terminal α-tubulin tail produces detyrosinated and Δ2-tubulin. Although these are widely employed as proxies for stable cellular microtubules, their effect (and of the α-tail) on microtubule dynamics remains uncharacterized. Using recombinant, engineered human tubulins, we now find that neither detyrosinated nor Δ2-tubulin affect microtubule dynamics, while the α-tubulin tail is an inhibitor of microtubule growth. Consistent with the latter, molecular dynamics simulations show the α-tubulin tail transiently occluding the longitudinal microtubule polymerization interface. The marked differential in vivo stabilities of the modified microtubule subpopulations, therefore, must result exclusively from selective effector recruitment. We find that tyrosination quantitatively tunes CLIP-170 density at the growing plus end and that CLIP170 and EB1 synergize to selectively upregulate the dynamicity of tyrosinated microtubules. Modification-dependent recruitment of regulators thereby results in microtubule subpopulations with distinct dynamics, a tenet of the tubulin code hypothesis.
Collapse
Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Ekaterina Kholina
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Agnieszka Szyk
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA
| | - Vladimir A Fedorov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kovalenko
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia; Astrakhan State University, Astrakhan 414056, Russia; Sechenov University, Moscow 119991, Russia
| | - Nikita Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia; Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA; Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, Bethesda, MD 20892, USA.
| |
Collapse
|
11
|
Henrie H, Bakhos-Douaihy D, Cantaloube I, Pilon A, Talantikite M, Stoppin-Mellet V, Baillet A, Poüs C, Benoit B. Stress-induced phosphorylation of CLIP-170 by JNK promotes microtubule rescue. J Cell Biol 2021; 219:151834. [PMID: 32491151 PMCID: PMC7337496 DOI: 10.1083/jcb.201909093] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/17/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023] Open
Abstract
The stress-induced c-Jun N-terminal kinase (JNK) controls microtubule dynamics by enhancing both microtubule growth and rescues. Here, we show that upon cell stress, JNK directly phosphorylates the microtubule rescue factor CLIP-170 in its microtubule-binding domain to increase its rescue-promoting activity. Phosphomimetic versions of CLIP-170 enhance its ability to promote rescue events in vitro and in cells. Furthermore, while phosphomimetic mutations do not alter CLIP-170’s capability to form comets at growing microtubule ends, both phosphomimetic mutations and JNK activation increase the occurrence of CLIP-170 remnants on the microtubule lattice at the rear of comets. As the CLIP-170 remnants, which are potential sites of microtubule rescue, display a shorter lifetime when CLIP-170 is phosphorylated, we propose that instead of acting at the time of rescue occurrence, CLIP-170 would rather contribute in preparing the microtubule lattice for future rescues at these predetermined sites.
Collapse
Affiliation(s)
- Hélène Henrie
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France
| | - Dalal Bakhos-Douaihy
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France
| | - Isabelle Cantaloube
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France
| | - Antoine Pilon
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France.,Département de Biochimie, Hormonologie et Suivi Thérapeutique, Département Médico-Universitaire BioGeM, Assistance Publique - Hôpitaux de Paris Sorbonne Université, Paris, France
| | - Maya Talantikite
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France
| | - Virginie Stoppin-Mellet
- Grenoble Institut des Neurosciences, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1216, Université Grenoble Alpes, Grenoble, France
| | - Anita Baillet
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France
| | - Christian Poüs
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France.,Biochimie-Hormonologie, Assistance Publique - Hôpitaux de Paris Université Paris-Saclay, Clamart, France
| | - Béatrice Benoit
- Université Paris-Saclay, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1193, Châtenay-Malabry, France
| |
Collapse
|
12
|
Karki P, Ke Y, Zhang CO, Li Y, Tian Y, Son S, Yoshimura A, Kaibuchi K, Birukov KG, Birukova AA. SOCS3-microtubule interaction via CLIP-170 and CLASP2 is critical for modulation of endothelial inflammation and lung injury. J Biol Chem 2021; 296:100239. [PMID: 33372035 PMCID: PMC7949054 DOI: 10.1074/jbc.ra120.014232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 11/23/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022] Open
Abstract
Proinflammatory cytokines such as IL-6 induce endothelial cell (EC) barrier disruption and trigger an inflammatory response in part by activating the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway. The protein suppressor of cytokine signaling-3 (SOCS3) is a negative regulator of JAK-STAT, but its role in modulation of lung EC barrier dysfunction caused by bacterial pathogens has not been investigated. Using human lung ECs and EC-specific SOCS3 knockout mice, we tested the hypothesis that SOCS3 confers microtubule (MT)-mediated protection against endothelial dysfunction. SOCS3 knockdown in cultured ECs or EC-specific SOCS3 knockout in mice resulted in exacerbated lung injury characterized by increased permeability and inflammation in response to IL-6 or heat-killed Staphylococcus aureus (HKSA). Ectopic expression of SOCS3 attenuated HKSA-induced EC dysfunction, and this effect required assembled MTs. SOCS3 was enriched in the MT fractions, and treatment with HKSA disrupted SOCS3-MT association. We discovered that-in addition to its known partners gp130 and JAK2-SOCS3 interacts with MT plus-end binding proteins CLIP-170 and CLASP2 via its N-terminal domain. The resulting SOCS3-CLIP-170/CLASP2 complex was essential for maximal SOCS3 anti-inflammatory effects. Both IL-6 and HKSA promoted MT disassembly and disrupted SOCS3 interaction with CLIP-170 and CLASP2. Moreover, knockdown of CLIP-170 or CLASP2 impaired SOCS3-JAK2 interaction and abolished the anti-inflammatory effects of SOCS3. Together, these findings demonstrate for the first time an interaction between SOCS3 and CLIP-170/CLASP2 and reveal that this interaction is essential to the protective effects of SOCS3 in lung endothelium.
Collapse
Affiliation(s)
- Pratap Karki
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yunbo Ke
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Chen-Ou Zhang
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yue Li
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Yufeng Tian
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Sophia Son
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University, Tokyo, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University, Nagoya, Japan
| | - Konstantin G Birukov
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anna A Birukova
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.
| |
Collapse
|
13
|
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: 21] [Impact Index Per Article: 5.3] [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
|
14
|
Santos da Silva E, Shanmugapriya S, Malikov V, Gu F, Delaney MK, Naghavi MH. HIV-1 capsids mimic a microtubule regulator to coordinate early stages of infection. EMBO J 2020; 39:e104870. [PMID: 32896909 DOI: 10.15252/embj.2020104870] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 01/09/2023] Open
Abstract
While the microtubule end-binding protein, EB1 facilitates early stages of HIV-1 infection, how it does so remains unclear. Here, we show that beyond its effects on microtubule acetylation, EB1 also indirectly contributes to infection by delivering the plus-end tracking protein (+TIP), cytoplasmic linker protein 170 (CLIP170) to the cell periphery. CLIP170 bound to intact HIV-1 cores or in vitro assembled capsid-nucleocapsid complexes, while EB1 did not. Moreover, unlike EB1 and several other +TIPs, CLIP170 enhanced infection independently of effects on microtubule acetylation. Capsid mutants and imaging revealed that CLIP170 bound HIV-1 cores in a manner distinct from currently known capsid cofactors, influenced by pentamer composition or curvature. Structural analyses revealed an EB-like +TIP-binding motif within the capsid major homology region (MHR) that binds SxIP motifs found in several +TIPs, and variability across this MHR sequence correlated with the extent to which different retroviruses engage CLIP170 to facilitate infection. Our findings provide mechanistic insights into the complex roles of +TIPs in mediating early stages of retroviral infection, and reveal divergent capsid-based EB1 mimicry across retroviral species.
Collapse
Affiliation(s)
- Eveline Santos da Silva
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Shanmugapriya Shanmugapriya
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Viacheslav Malikov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Feng Gu
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M Keegan Delaney
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mojgan H Naghavi
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
15
|
Bugge K, Brakti I, Fernandes CB, Dreier JE, Lundsgaard JE, Olsen JG, Skriver K, Kragelund BB. Interactions by Disorder - A Matter of Context. Front Mol Biosci 2020; 7:110. [PMID: 32613009 PMCID: PMC7308724 DOI: 10.3389/fmolb.2020.00110] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Living organisms depend on timely and organized interactions between proteins linked in interactomes of high complexity. The recent increased precision by which protein interactions can be studied, and the enclosure of intrinsic structural disorder, suggest that it is time to zoom out and embrace protein interactions beyond the most central points of physical encounter. The present paper discusses protein-protein interactions in the view of structural disorder with an emphasis on flanking regions and contexts of disorder-based interactions. Context constitutes an overarching concept being of physicochemical, biomolecular, and physiological nature, but it also includes the immediate molecular context of the interaction. For intrinsically disordered proteins, which often function by exploiting short linear motifs, context contributes in highly regulatory and decisive manners and constitute a yet largely unrecognized source of interaction potential in a multitude of biological processes. Through selected examples, this review emphasizes how multivalency, charges and charge clusters, hydrophobic patches, dynamics, energetic frustration, and ensemble redistribution of flanking regions or disordered contexts are emerging as important contributors to allosteric regulation, positive and negative cooperativity, feedback regulation and negative selection in binding. The review emphasizes that understanding context, and in particular the role the molecular disordered context and flanking regions take on in protein interactions, constitute an untapped well of energetic modulation potential, also of relevance to drug discovery and development.
Collapse
Affiliation(s)
- Katrine Bugge
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Inna Brakti
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Catarina B. Fernandes
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesper E. Dreier
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe E. Lundsgaard
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Johan G. Olsen
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Karen Skriver
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B. Kragelund
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|