1
|
Jentzsch J, Wunderlich H, Thein M, Bechthold J, Brehm L, Krauss SW, Weiss M, Ersfeld K. Microtubule polyglutamylation is an essential regulator of cytoskeletal integrity in Trypanosoma brucei. J Cell Sci 2024; 137:jcs261740. [PMID: 38205672 DOI: 10.1242/jcs.261740] [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: 10/19/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Tubulin polyglutamylation, catalysed by members of the tubulin tyrosine ligase-like (TTLL) protein family, is an evolutionarily highly conserved mechanism involved in the regulation of microtubule dynamics and function in eukaryotes. In the protozoan parasite Trypanosoma brucei, the microtubule cytoskeleton is essential for cell motility and maintaining cell shape. In a previous study, we showed that T. brucei TTLL6A and TTLL12B are required to regulate microtubule dynamics at the posterior cell pole. Here, using gene deletion, we show that the polyglutamylase TTLL1 is essential for the integrity of the highly organised microtubule structure at the cell pole, with a phenotype distinct from that observed in TTLL6A- and TTLL12B-depleted cells. Reduced polyglutamylation in TTLL1-deficient cells also leads to increased levels in tubulin tyrosination, providing new evidence for an interplay between the tubulin tyrosination and detyrosination cycle and polyglutamylation. We also show that TTLL1 acts differentially on specific microtubule doublets of the flagellar axoneme, although the absence of TTLL1 appears to have no measurable effect on cell motility.
Collapse
Affiliation(s)
- Jana Jentzsch
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Hannes Wunderlich
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Marinus Thein
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Julia Bechthold
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Lucas Brehm
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Sebastian W Krauss
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Klaus Ersfeld
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| |
Collapse
|
2
|
Duan D, Lyu W, Chai P, Ma S, Wu K, Wu C, Xiong Y, Sestan N, Zhang K, Koleske AJ. Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation. Curr Biol 2023; 33:4582-4598.e10. [PMID: 37858340 PMCID: PMC10877310 DOI: 10.1016/j.cub.2023.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 10/21/2023]
Abstract
Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation, both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics are unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo liquid-liquid phase separation (LLPS) and form co-condensates with tubulin. Abl2 binds to regions adjacent to MT damage, facilitates MT repair via fresh tubulin recruitment, and increases MT rescue frequency and lifetime. Cryo-EM analyses strongly support a model in which Abl2 engages tubulin C-terminal tails along an extended MT lattice conformation at damage sites to facilitate repair via fresh tubulin recruitment. Abl2Δ688-790, which closely mimics a naturally occurring splice isoform, retains binding to the MT lattice but does not bind tubulin, promote MT nucleation, or increase rescue frequency. In COS-7 cells, MT reassembly after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared with wild-type cells, and these defects are rescued by re-expression of Abl2, but not Abl2Δ688-790. We propose that Abl2 locally concentrates tubulin to promote MT nucleation and recruits it to defects in the MT lattice to enable repair and rescue.
Collapse
Affiliation(s)
- Daisy Duan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Wanqing Lyu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Kuanlin Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA; Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Anthony J Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA; Department of Neuroscience, Yale University, New Haven, CT 06510, USA.
| |
Collapse
|
3
|
Marien J, Prévost C, Sacquin-Mora S. It Takes Tau to Tango: Investigating the Fuzzy Interaction between the R2-Repeat Domain and Tubulin C-Terminal Tails. Biochemistry 2023; 62:2492-2502. [PMID: 37499261 DOI: 10.1021/acs.biochem.3c00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The microtubule-associated protein (MAP) tau plays a key role in the regulation of microtubule assembly and spatial organization. Tau hyperphosphorylation affects its binding on the tubulin surface and has been shown to be involved in several pathologies such as Alzheimer's disease. As the tau binding site on the microtubule lays close to the disordered and highly flexible tubulin C-terminal tails (CTTs), these are likely to impact the tau-tubulin interaction. Since the disordered tubulin CTTs are missing from the available experimental structures, we used homology modeling to build two complete models of tubulin heterotrimers with different isotypes for the β-tubulin subunit (βI/αI/βI and βIII/αI/βIII). We then performed long timescale classical Molecular Dynamics simulations for the tau-R2/tubulin assembly (in systems with and without CTTs) and analyzed the resulting trajectories to obtain a detailed view of the protein interface in the complex and the impact of the CTTs on the stability of this assembly. Additional analyses of the CTT mobility in the presence, or in the absence, of tau also highlight how tau might modulate the CTT activity as hooks that are involved in the recruitment of several MAPs. In particular, we observe a wrapping phenomenon, where the β-tubulin CTTs form a loop over tau-R2, thus stabilizing its interaction with the tubulin surface and simultaneously reducing the CTT availability for interactions with other MAPs.
Collapse
Affiliation(s)
- Jules Marien
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prévost
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Sacquin-Mora
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|
4
|
Iwanski MK, Kapitein LC. Cellular cartography: Towards an atlas of the neuronal microtubule cytoskeleton. Front Cell Dev Biol 2023; 11:1052245. [PMID: 37035244 PMCID: PMC10073685 DOI: 10.3389/fcell.2023.1052245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
Microtubules, one of the major components of the cytoskeleton, play a crucial role during many aspects of neuronal development and function, such as neuronal polarization and axon outgrowth. Consequently, the microtubule cytoskeleton has been implicated in many neurodevelopmental and neurodegenerative disorders. The polar nature of microtubules is quintessential for their function, allowing them to serve as tracks for long-distance, directed intracellular transport by kinesin and dynein motors. Most of these motors move exclusively towards either the plus- or minus-end of a microtubule and some have been shown to have a preference for either dynamic or stable microtubules, those bearing a particular post-translational modification or those decorated by a specific microtubule-associated protein. Thus, it becomes important to consider the interplay of these features and their combinatorial effects on transport, as well as how different types of microtubules are organized in the cell. Here, we discuss microtubule subsets in terms of tubulin isotypes, tubulin post-translational modifications, microtubule-associated proteins, microtubule stability or dynamicity, and microtubule orientation. We highlight techniques used to study these features of the microtubule cytoskeleton and, using the information from these studies, try to define the composition, role, and organization of some of these subsets in neurons.
Collapse
Affiliation(s)
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
5
|
Kubo S, Bui KH. Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by MD simulation. Sci Rep 2023; 13:1477. [PMID: 36702893 PMCID: PMC9879972 DOI: 10.1038/s41598-023-28026-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Intraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific to the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e., "tubulin code", for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the landing behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.
Collapse
Affiliation(s)
- Shintaroh Kubo
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, H3A 0C7, Canada. .,Department of Biological Science, Grad. Sch. of Sci, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montréal, Québec, H3A 0C7, Canada. .,Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, H3A 0C7, Canada.
| |
Collapse
|
6
|
Bigman LS, Iwahara J, Levy Y. Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes. J Mol Biol 2022; 434:167660. [PMID: 35659505 DOI: 10.1016/j.jmb.2022.167660] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/12/2023]
Abstract
Intrinsically disordered regions (IDRs) of proteins are often characterized by a high fraction of charged residues, but differ in their overall net charge and in the organization of the charged residues. The function-encoding information stored via IDR charge composition and organization remains elusive. Here, we aim to decipher the sequence-function relationship in IDRs by presenting a comprehensive bioinformatic analysis of the charge properties of IDRs in the human, mouse, and yeast proteomes. About 50% of the proteins comprise at least a single IDR, which is either positively or negatively charged. Highly negatively charged IDRs are longer and possess greater net charge per residue compared with highly positively charged IDRs. A striking difference between positively and negatively charged IDRs is the characteristics of the repeated units, specifically, of consecutive Lys or Arg residues (K/R repeats) and Asp or Glu (D/E repeats) residues. D/E repeats are found to be about five times longer than K/R repeats, with the longest found containing 49 residues. Long stretches of consecutive D and E are found to be more prevalent in nucleic acid-related proteins. They are less common in prokaryotes, and in eukaryotes their abundance increases with genome size. The functional role of D/E repeats and the profound differences between them and K/R repeats are discussed.
Collapse
Affiliation(s)
- Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel. https://twitter.com/LaviBigman
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
7
|
Khabudaev KV, Petrova DP, Bedoshvili YD, Likhoshway YV, Grachev MA. Molecular Evolution of Tubulins in Diatoms. Int J Mol Sci 2022; 23:618. [PMID: 35054799 PMCID: PMC8776100 DOI: 10.3390/ijms23020618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 01/29/2023] Open
Abstract
Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the problem of elucidating the molecular mechanisms of genetically programmed morphogenesis, the structure and evolution of diatom tubulins have not been studied previously. Based on available genomic and transcriptome data, we analyzed the phylogeny of the predicted amino acid sequences of diatom α-, β- and γ-tubulins and identified five groups for α-tubulins, six for β-tubulins and four for γ-tubulins. We identified characteristic amino acids of each of these groups and also analyzed possible posttranslational modification sites of diatom tubulins. According to our results, we assumed what changes occurred in the diatom tubulin structures during their evolution. We also identified which tubulin groups are inherent in large diatom taxa. The similarity between the evolution of diatom tubulins and the evolution of diatoms suggests that molecular changes in α-, β- and γ-tubulins could be one of the factors in the formation of a high morphological diversity of diatoms.
Collapse
Affiliation(s)
| | | | - Yekaterina D. Bedoshvili
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, 664033 Irkutsk, Russia; (K.V.K.); (D.P.P.); (Y.V.L.); (M.A.G.)
| | | | | |
Collapse
|
8
|
Moroz LL, Nikitin MA, Poličar PG, Kohn AB, Romanova DY. Evolution of glutamatergic signaling and synapses. Neuropharmacology 2021; 199:108740. [PMID: 34343611 PMCID: PMC9233959 DOI: 10.1016/j.neuropharm.2021.108740] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
Glutamate (Glu) is the primary excitatory transmitter in the mammalian brain. But, we know little about the evolutionary history of this adaptation, including the selection of l-glutamate as a signaling molecule in the first place. Here, we used comparative metabolomics and genomic data to reconstruct the genealogy of glutamatergic signaling. The origin of Glu-mediated communications might be traced to primordial nitrogen and carbon metabolic pathways. The versatile chemistry of L-Glu placed this molecule at the crossroad of cellular biochemistry as one of the most abundant metabolites. From there, innovations multiplied. Many stress factors or injuries could increase extracellular glutamate concentration, which led to the development of modular molecular systems for its rapid sensing in bacteria and archaea. More than 20 evolutionarily distinct families of ionotropic glutamate receptors (iGluRs) have been identified in eukaryotes. The domain compositions of iGluRs correlate with the origins of multicellularity in eukaryotes. Although L-Glu was recruited as a neuro-muscular transmitter in the early-branching metazoans, it was predominantly a non-neuronal messenger, with a possibility that glutamatergic synapses evolved more than once. Furthermore, the molecular secretory complexity of glutamatergic synapses in invertebrates (e.g., Aplysia) can exceed their vertebrate counterparts. Comparative genomics also revealed 15+ subfamilies of iGluRs across Metazoa. However, most of this ancestral diversity had been lost in the vertebrate lineage, preserving AMPA, Kainate, Delta, and NMDA receptors. The widespread expansion of glutamate synapses in the cortical areas might be associated with the enhanced metabolic demands of the complex brain and compartmentalization of Glu signaling within modular neuronal ensembles.
Collapse
Affiliation(s)
- Leonid L Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Mikhail A Nikitin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Pavlin G Poličar
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Faculty of Computer and Information Science, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Andrea B Kohn
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA
| | - Daria Y Romanova
- Cellular Neurobiology of Learning Lab, Institute of Higher Nervous Activity and Neurophysiology, Moscow, 117485, Russia.
| |
Collapse
|
9
|
Sacquin-Mora S, Prévost C. When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes. Biomolecules 2021; 11:1529. [PMID: 34680162 PMCID: PMC8533853 DOI: 10.3390/biom11101529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
The degree of proteins structural organization ranges from highly structured, compact folding to intrinsic disorder, where each degree of self-organization corresponds to specific functions: well-organized structural motifs in enzymes offer a proper environment for precisely positioned functional groups to participate in catalytic reactions; at the other end of the self-organization spectrum, intrinsically disordered proteins act as binding hubs via the formation of multiple, transient and often non-specific interactions. This review focusses on cases where structurally organized proteins or domains associate with highly disordered protein chains, leading to the formation of interfaces with varying degrees of fuzziness. We present a review of the computational methods developed to provide us with information on such fuzzy interfaces, and how they integrate experimental information. The discussion focusses on two specific cases, microtubules and homologous recombination nucleoprotein filaments, where a network of intrinsically disordered tails exerts regulatory function in recruiting partner macromolecules, proteins or DNA and tuning the atomic level association. Notably, we show how computational approaches such as molecular dynamics simulations can bring new knowledge to help bridging the gap between experimental analysis, that mostly concerns ensemble properties, and the behavior of individual disordered protein chains that contribute to regulation functions.
Collapse
Affiliation(s)
- Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 Rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| |
Collapse
|
10
|
Bujak Ł, Holanová K, García Marín A, Henrichs V, Barvík I, Braun M, Lánský Z, Piliarik M. Fast Leaps between Millisecond Confinements Govern Ase1 Diffusion along Microtubules. SMALL METHODS 2021; 5:e2100370. [PMID: 34927934 DOI: 10.1002/smtd.202100370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/24/2021] [Indexed: 06/14/2023]
Abstract
Diffusion is the most fundamental mode of protein translocation within cells. Confined diffusion of proteins along the electrostatic potential constituted by the surface of microtubules, although modeled meticulously in molecular dynamics simulations, has not been experimentally observed in real-time. Here, interferometric scattering microscopy is used to directly visualize the movement of the microtubule-associated protein Ase1 along the microtubule surface at nanometer and microsecond resolution. Millisecond confinements of Ase1 and fast leaps between these positions of dwelling preferentially occurring along the microtubule protofilaments are resolved, revealing Ase1's mode of diffusive translocation along the microtubule's periodic surface. The derived interaction potential closely matches the tubulin-dimer periodicity and the distribution of the electrostatic potential on the microtubule lattice. It is anticipated that mapping the interaction landscapes for different proteins on microtubules, finding plausible energetic barriers of different positioning and heights, can provide valuable insights into regulating the dynamics of essential cytoskeletal processes, such as intracellular cargo trafficking, cell division, and morphogenesis, all of which rely on diffusive translocation of proteins along microtubules.
Collapse
Affiliation(s)
- Łukasz Bujak
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
| | - Kristýna Holanová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
| | - Antonio García Marín
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
| | - Verena Henrichs
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 25250, Czech Republic
| | - Ivan Barvík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 2026/5, Prague, 12116, Czech Republic
| | - Marcus Braun
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 25250, Czech Republic
| | - Zdeněk Lánský
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec, 25250, Czech Republic
| | - Marek Piliarik
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 1014/57, Prague, 18251, Czech Republic
| |
Collapse
|
11
|
Abstract
Flexibility in complexes between intrinsically disordered proteins and folded ligands is widespread in nature. However, timescales and spatial amplitudes of such dynamics remained unexplored for most systems. Our results show that the disordered cytoplasmic tail of the cell adhesion protein E-cadherin diffuses across the entire surface of its folded binding partner β-catenin at fast submillisecond timescales. The nanometer amplitude of these motions could allow kinases to access their recognition motifs without requiring a dissociation of the complex. We expect that the rugged energy landscape found in the E-cadherin/β-catenin complex is a defining feature of dynamic and partially disordered protein complexes. Intrinsically disordered proteins often form dynamic complexes with their ligands. Yet, the speed and amplitude of these motions are hidden in classical binding kinetics. Here, we directly measure the dynamics in an exceptionally mobile, high-affinity complex. We show that the disordered tail of the cell adhesion protein E-cadherin dynamically samples a large surface area of the protooncogene β-catenin. Single-molecule experiments and molecular simulations resolve these motions with high resolution in space and time. Contacts break and form within hundreds of microseconds without a dissociation of the complex. The energy landscape of this complex is rugged with many small barriers (3 to 4 kBT) and reconciles specificity, high affinity, and extreme disorder. A few persistent contacts provide specificity, whereas unspecific interactions boost affinity.
Collapse
|
12
|
Bigman LS, Levy Y. Modulating Microtubules: A Molecular Perspective on the Effects of Tail Modifications. J Mol Biol 2021; 433:166988. [PMID: 33865866 DOI: 10.1016/j.jmb.2021.166988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Microtubules (MTs), an essential component of the eukaryotic cytoskeleton, are a lattice of polymerized tubulin dimers and are crucial for various cellular processes. The genetic and chemical diversity of tubulin and their disordered tails gives rise to a "tubulin code". The functional role of tubulin post-translational modifications (PTMs), which contribute to the chemical diversity of the tubulin code, is gradually being unraveled. However, variation in the length and spatial organization of tubulin poly-modifications leads to an enormous combinatorial PTM space, which is difficult to study experimentally. Hence, the impact of the combinatorial tubulin PTM space on the biophysical properties of tubulin tails and their interactions with other proteins remains elusive. Here, we combine all-atom and coarse-grained molecular dynamics simulations to elucidate the biophysical implications of the large combinatorial tubulin PTM space in the context of an MT lattice. We find that tail-body interactions are more dominant in the tubulin dimer than in an MT lattice, and are more significant for the tails of α compared with β tubulin. In addition, polyglutamylation, but not polyglycylation, expands the dimensions of the tubulin tails. Polyglutamylation also leads to a decrease in the diffusion rate of MT-associated protein EB1 on MTs, while polyglycylation often increases diffusion rate. These observations are generally not sensitive to the organization of the polymodifications. The effect of PTMs on MT charge density and tail dynamics are also discussed. Overall, this study presents a molecular quantification of the biophysical properties of tubulin tails and their polymodifications, and provides predictions on the functional importance of tubulin PTMs.
Collapse
Affiliation(s)
- Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
13
|
Bigman LS, Greenblatt HM, Levy Y. What Are the Molecular Requirements for Protein Sliding along DNA? J Phys Chem B 2021; 125:3119-3131. [PMID: 33754737 PMCID: PMC8041311 DOI: 10.1021/acs.jpcb.1c00757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
DNA-binding proteins rely on linear
diffusion along the longitudinal
DNA axis, supported by their nonspecific electrostatic affinity for
DNA, to search for their target recognition sites. One may therefore
expect that the ability to engage in linear diffusion along DNA is
universal to all DNA-binding proteins, with the detailed biophysical
characteristics of that diffusion differing between proteins depending
on their structures and functions. One key question is whether the
linear diffusion mechanism is defined by translation coupled with
rotation, a mechanism that is often termed sliding. We conduct coarse-grained
and atomistic molecular dynamics simulations to investigate the minimal
requirements for protein sliding along DNA. We show that coupling,
while widespread, is not universal. DNA-binding proteins that slide
along DNA transition to uncoupled translation–rotation (i.e.,
hopping) at higher salt concentrations. Furthermore, and consistently
with experimental reports, we find that the sliding mechanism is the
less dominant mechanism for some DNA-binding proteins, even at low
salt concentrations. In particular, the toroidal PCNA protein is shown
to follow the hopping rather than the sliding mechanism.
Collapse
Affiliation(s)
- Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
14
|
Biased Brownian Motion of KIF1A and the Role of Tubulin's C-Terminal Tail Studied by Molecular Dynamics Simulation. Int J Mol Sci 2021; 22:ijms22041547. [PMID: 33557020 PMCID: PMC7913626 DOI: 10.3390/ijms22041547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/29/2022] Open
Abstract
KIF1A is a kinesin family protein that moves over a long distance along the microtubule (MT) to transport synaptic vesicle precursors in neurons. A single KIF1A molecule can move toward the plus-end of MT in the monomeric form, exhibiting the characteristics of biased Brownian motion. However, how the bias is generated in the Brownian motion of KIF1A has not yet been firmly established. To elucidate this, we conducted a set of molecular dynamics simulations and observed the binding of KIF1A to MT. We found that KIF1A exhibits biased Brownian motion along MT as it binds to MT. Furthermore, we show that the bias toward the plus-end is generated by the ratchet-like energy landscape for the KIF1A-MT interaction, in which the electrostatic interaction and the negatively-charged C-terminal tail (CTT) of tubulin play an essential role. The relevance to the post-translational modifications of CTT is also discussed.
Collapse
|
15
|
Inhibition of Histone Deacetylase 6 by Tubastatin A Attenuates the Progress of Osteoarthritis via Improving Mitochondrial Function. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:2376-2386. [DOI: 10.1016/j.ajpath.2020.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/01/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022]
|
16
|
Li J, Snyder EY, Tang FHF, Pasqualini R, Arap W, Sidman RL. Nna1 gene deficiency triggers Purkinje neuron death by tubulin hyperglutamylation and ER dysfunction. JCI Insight 2020; 5:136078. [PMID: 33004692 PMCID: PMC7566705 DOI: 10.1172/jci.insight.136078] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Posttranslational glutamylation/deglutamylation balance in tubulins influences dendritic maturation and neuronal survival of cerebellar Purkinje neurons (PNs). PNs and some additional neuronal types degenerate in several spontaneous, independently occurring Purkinje cell degeneration (pcd) mice featuring mutant neuronal nuclear protein induced by axotomy (Nna1), a deglutamylase gene. This defective deglutamylase allows glutamylases to form hyperglutamylated tubulins. In pcd, all PNs die during postnatal “adolescence.” Neurons in some additional brain regions also die, mostly later than PNs. We show in laser capture microdissected single PNs, in cerebellar granule cell neuronal clusters, and in dissected hippocampus and substantia nigra that deglutamase mRNA and protein were virtually absent before pcd PNs degenerated, whereas glutaminase mRNA and protein remained normal. Hyperglutamylated microtubules and dimeric tubulins accumulated in pcd PNs and were involved in pcd PN death by glutamylase/deglutamylase imbalance. Importantly, treatment with a microtubule depolymerizer corrected the glutamylation/deglutamylation ratio, increasing PN survival. Further, before onset of neuronal death, pcd PNs displayed prominent basal polylisosomal masses rich in ER. We propose a “seesaw” metamorphic model summarizing mutant Nna1-induced tubulin hyperglutamylation, the pcd’s PN phenotype, and report that the neuronal disorder involved ER stress, unfolded protein response, and protein synthesis inhibition preceding PN death by apoptosis/necroptosis. Purkinje cell degeneration is due to ER stress, unfolded protein response, and protein synthesis inhibition preceding Purkinje neuron death by apoptosis/necroptosis.
Collapse
Affiliation(s)
- Jianxue Li
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Evan Y Snyder
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Fenny HF Tang
- Rutgers Cancer Institute of New Jersey and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey and Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Richard L Sidman
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
17
|
Jentzsch J, Sabri A, Speckner K, Lallinger-Kube G, Weiss M, Ersfeld K. Microtubule polyglutamylation is important for regulating cytoskeletal architecture and motility in Trypanosoma brucei. J Cell Sci 2020; 133:jcs248047. [PMID: 32843576 DOI: 10.1242/jcs.248047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/30/2020] [Indexed: 11/20/2022] Open
Abstract
The shape of kinetoplastids, such as Trypanosoma brucei, is precisely defined during the stages of the life cycle and governed by a stable subpellicular microtubule cytoskeleton. During the cell cycle and transitions between life cycle stages, this stability has to transiently give way to a dynamic behaviour to enable cell division and morphological rearrangements. How these opposing requirements of the cytoskeleton are regulated is poorly understood. Two possible levels of regulation are activities of cytoskeleton-associated proteins and microtubule post-translational modifications (PTMs). Here, we investigate the functions of two putative tubulin polyglutamylases in T. brucei, TTLL6A and TTLL12B. Depletion of both proteins leads to a reduction in tubulin polyglutamylation in situ and is associated with disintegration of the posterior cell pole, loss of the microtubule plus-end-binding protein EB1 and alterations of microtubule dynamics. We also observe a reduced polyglutamylation of the flagellar axoneme. Quantitative motility analysis reveals that the PTM imbalance correlates with a transition from directional to diffusive cell movement. These data show that microtubule polyglutamylation has an important role in regulating cytoskeletal architecture and motility in the parasite T. bruceiThis article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Jana Jentzsch
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Adal Sabri
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Konstantin Speckner
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Gertrud Lallinger-Kube
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, Department of Physics, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| | - Klaus Ersfeld
- Molecular Parasitology, Department of Biology, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
| |
Collapse
|
18
|
Bigman LS, Levy Y. Protein Diffusion on Charged Biopolymers: DNA versus Microtubule. Biophys J 2020; 118:3008-3018. [PMID: 32492371 DOI: 10.1016/j.bpj.2020.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/28/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023] Open
Abstract
Protein diffusion in lower-dimensional spaces is used for various cellular functions. For example, sliding on DNA is essential for proteins searching for their target sites, and protein diffusion on microtubules is important for proper cell division and neuronal development. On the one hand, these linear diffusion processes are mediated by long-range electrostatic interactions between positively charged proteins and negatively charged biopolymers and have similar characteristic diffusion coefficients. On the other hand, DNA and microtubules have different structural properties. Here, using computational approaches, we studied the mechanism of protein diffusion along DNA and microtubules by exploring the diffusion of both protein types on both biopolymers. We found that DNA-binding and microtubule-binding proteins can diffuse on each other's substrates; however, the adopted diffusion mechanism depends on the molecular properties of the diffusing proteins and the biopolymers. On the protein side, only DNA-binding proteins can perform rotation-coupled diffusion along DNA, with this being due to their higher net charge and its spatial organization at the DNA recognition helix. By contrast, the lower net charge on microtubule-binding proteins enables them to diffuse more quickly than DNA-binding proteins on both biopolymers. On the biopolymer side, microtubules possess intrinsically disordered, negatively charged C-terminal tails that interact with microtubule-binding proteins, thus supporting their diffusion. Thus, although both DNA-binding and microtubule-binding proteins can diffuse on the negatively charged biopolymers, the unique molecular features of the biopolymers and of their natural substrates are essential for function.
Collapse
Affiliation(s)
- Lavi S Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|