1
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Gogishvili D, Illes-Toth E, Harris MJ, Hopley C, Teunissen CE, Abeln S. Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP). Proteins 2024; 92:649-664. [PMID: 38149328 DOI: 10.1002/prot.26656] [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: 10/04/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Glial fibrillary acidic protein (GFAP) is a promising biomarker for brain and spinal cord disorders. Recent studies have highlighted the differences in the reliability of GFAP measurements in different biological matrices. The reason for these discrepancies is poorly understood as our knowledge of the protein's 3-dimensional conformation, proteoforms, and aggregation remains limited. Here, we investigate the structural properties of GFAP under different conditions. For this, we characterized recombinant GFAP proteins from various suppliers and applied hydrogen-deuterium exchange mass spectrometry (HDX-MS) to provide a snapshot of the conformational dynamics of GFAP in artificial cerebrospinal fluid (aCSF) compared to the phosphate buffer. Our findings indicate that recombinant GFAP exists in various conformational species. Furthermore, we show that GFAP dimers remained intact under denaturing conditions. HDX-MS experiments show an overall decrease in H-bonding and an increase in solvent accessibility of GFAP in aCSF compared to the phosphate buffer, with clear indications of mixed EX2 and EX1 kinetics. To understand possible structural interface regions and the evolutionary conservation profiles, we combined HDX-MS results with the predicted GFAP-dimer structure by AlphaFold-Multimer. We found that deprotected regions with high structural flexibility in aCSF overlap with predicted conserved dimeric 1B and 2B domain interfaces. Structural property predictions combined with the HDX data show an overall deprotection and signatures of aggregation in aCSF. We anticipate that the outcomes of this research will contribute to a deeper understanding of the structural flexibility of GFAP and ultimately shed light on its behavior in different biological matrices.
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Affiliation(s)
- Dea Gogishvili
- Bioinformatics, Computer Science Department, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Eva Illes-Toth
- National Measurement Laboratory at Laboratory of the Government Chemist (LGC), Teddington, UK
| | - Matthew J Harris
- National Measurement Laboratory at Laboratory of the Government Chemist (LGC), Teddington, UK
| | - Christopher Hopley
- National Measurement Laboratory at Laboratory of the Government Chemist (LGC), Teddington, UK
| | - Charlotte E Teunissen
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Sanne Abeln
- Bioinformatics, Computer Science Department, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, The Netherlands
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2
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Kotaich F, Caillol D, Bomont P. Neurofilaments in health and Charcot-Marie-Tooth disease. Front Cell Dev Biol 2023; 11:1275155. [PMID: 38164457 PMCID: PMC10758125 DOI: 10.3389/fcell.2023.1275155] [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: 08/09/2023] [Accepted: 10/02/2023] [Indexed: 01/03/2024] Open
Abstract
Neurofilaments (NFs) are the most abundant component of mature neurons, that interconnect with actin and microtubules to form the cytoskeleton. Specifically expressed in the nervous system, NFs present the particularity within the Intermediate Filament family of being formed by four subunits, the neurofilament light (NF-L), medium (NF-M), heavy (NF-H) proteins and α-internexin or peripherin. Here, we review the current knowledge on NF proteins and neurofilaments, from their domain structures and their model of assembly to the dynamics of their transport and degradation along the axon. The formation of the filament and its behaviour are regulated by various determinants, including post-transcriptional (miRNA and RBP proteins) and post-translational (phosphorylation and ubiquitination) modifiers. Altogether, the complex set of modifications enable the neuron to establish a stable but elastic NF array constituting the structural scaffold of the axon, while permitting the local expression of NF proteins and providing the dynamics necessary to fulfil local demands and respond to stimuli and injury. Thus, in addition to their roles in mechano-resistance, radial axonal outgrowth and nerve conduction, NFs control microtubule dynamics, organelle distribution and neurotransmission at the synapse. We discuss how the studies of neurodegenerative diseases with NF aggregation shed light on the biology of NFs. In particular, the NEFL and NEFH genes are mutated in Charcot-Marie-Tooth (CMT) disease, the most common inherited neurological disorder of the peripheral nervous system. The clinical features of the CMT forms (axonal CMT2E, CMT2CC; demyelinating CMT1F; intermediate I-CMT) with symptoms affecting the central nervous system (CNS) will allow us to further investigate the physiological roles of NFs in the brain. Thus, NF-CMT mouse models exhibit various degrees of sensory-motor deficits associated with CNS symptoms. Cellular systems brought findings regarding the dominant effect of NF-L mutants on NF aggregation and transport, although these have been recently challenged. Neurofilament detection without NF-L in recessive CMT is puzzling, calling for a re-examination of the current model in which NF-L is indispensable for NF assembly. Overall, we discuss how the fundamental and translational fields are feeding each-other to increase but also challenge our knowledge of NF biology, and to develop therapeutic avenues for CMT and neurodegenerative diseases with NF aggregation.
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Affiliation(s)
| | | | - Pascale Bomont
- ERC team, NeuroMyoGene Institute-Pathophysiology and Genetics of Neuron and Muscle, Inserm U1315, CNRS UMR5261, University of Lyon 1, Lyon, France
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3
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Li P, Rietscher K, Jopp H, Magin TM, Omary MB. Posttranslational modifications of keratins and their associated proteins as therapeutic targets in keratin diseases. Curr Opin Cell Biol 2023; 85:102264. [PMID: 37925932 DOI: 10.1016/j.ceb.2023.102264] [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: 06/18/2023] [Revised: 09/04/2023] [Accepted: 09/24/2023] [Indexed: 11/07/2023]
Abstract
The keratin cytoskeleton protects epithelia against mechanical, nonmechanical, and physical stresses, and participates in multiple signaling pathways that regulate cell integrity and resilience. Keratin gene mutations cause multiple rare monoallelic epithelial diseases termed keratinopathies, including the skin diseases Epidermolysis Bullosa Simplex (EBS) and Pachyonychia Congenita (PC), with limited available therapies. The disease-related keratin mutations trigger posttranslational modifications (PTMs) in keratins and their associated proteins that can aggravate the disease. Recent findings of drug high-throughput screening have led to the identification of compounds that may be repurposed, since they are used for other human diseases, to treat keratinopathies. These drugs target unique PTM pathways and sites, including phosphorylation and acetylation of keratins and their associated proteins, and have shed insights into keratin regulation and interactions. They also offer the prospect of testing the use of drug mixtures, with the long view of possible beneficial human use coupled with increased efficacy and lower side effects.
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Affiliation(s)
- Pei Li
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Katrin Rietscher
- Division of Cell and Developmental Biology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Henriette Jopp
- Division of Cell and Developmental Biology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Thomas M Magin
- Division of Cell and Developmental Biology, Institute of Biology, Leipzig University, Leipzig, Germany.
| | - M Bishr Omary
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.
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4
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Karabinos A. The long protostomic-type cytoplasmic intermediate filament (cIF) protein in Branchiostoma supports the phylogenetic transition between the protostomic- and the chordate-type cIFs. PROTOPLASMA 2023; 260:1493-1500. [PMID: 37209173 DOI: 10.1007/s00709-023-01865-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
We identified 23 and 20 cytoplasmic IF (cIF) genes in the two Branchiostoma belcheri and Branchiostoma lanceolatum cephalochordates, respectively. Combining these results with earlier data on the related Branchiostoma floridae, the following conclusions can be drawn. First, the Branchiostoma N4 protein with a long lamin-like coil 1B segment is the only protostomic-type cIF found so far in any analysed chordate or vertebrate organism. Second, Branchiostoma is the only organism known so far containing both the long protostomic- and the short chordate-prototypes of cIFs. This finding provides so far missing molecular evidence for the phylogenetic transition between the protostomic- and the chordate-type IF sequences at the base of the cephalochordates and vertebrates. Third, this finding also brings some support for another hypothesis, that the long protostomic-type cIF is subjected to evolutionary constraints in order to preclude inappropriate interactions with lamin and that the latter complexes might be prevented by a several heptad-long rod deletion, which released the selective constraints on it and promoted, at least in part, its expansion in nematodes, cephalochordates, and in vertebrates. Finally, here-presented data confirmed our previous results that cephalochordates do not have any vertebrate type III or type IV IF homolog.
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Affiliation(s)
- Anton Karabinos
- Medirex, a.s., Kosice, Magnezitarska 2/C, 04013, Kosice, Slovakia.
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5
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Ahn J, Jo I, Jeong S, Lee J, Ha NC. Lamin Filament Assembly Derived from the Atomic Structure of the Antiparallel Four-Helix Bundle. Mol Cells 2023; 46:309-318. [PMID: 37170772 PMCID: PMC10183791 DOI: 10.14348/molcells.2023.2144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 05/13/2023] Open
Abstract
The nucleoskeletal protein lamin is primarily responsible for the mechanical stability of the nucleus. The lamin assembly process requires the A11, A22, and ACN binding modes of the coiled-coil dimers. Although X-ray crystallography and chemical cross-linking analysis of lamin A/C have provided snapshots of A11 and ACN binding modes, the assembly mechanism of the entire filament remains to be explained. Here, we report a crystal structure of a coil 2 fragment, revealing the A22 interaction at the atomic resolution. The structure showed detailed structural features, indicating that two coiled-coil dimers of the coil 2 subdomain are separated and then re-organized into the antiparallel-four-helix bundle. Furthermore, our findings suggest that the ACN binding mode between coil 1a and the C-terminal part of coil 2 when the A11 tetramers are arranged by the A22 interactions. We propose a full assembly model of lamin A/C with the curvature around the linkers, reconciling the discrepancy between the in situ and in vitro observations. Our model accounts for the balanced elasticity and stiffness of the nuclear envelopes, which is essential in protecting the cellular nucleus from external pressure.
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Affiliation(s)
- Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
- Present address: Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
- Present address: Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Soyeon Jeong
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
| | - Jinwook Lee
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Korea
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6
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Vermeire PJ, Lilina AV, Hashim HM, Dlabolová L, Fiala J, Beelen S, Kukačka Z, Harvey JN, Novák P, Strelkov SV. Molecular structure of soluble vimentin tetramers. Sci Rep 2023; 13:8841. [PMID: 37258554 DOI: 10.1038/s41598-023-34814-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Intermediate filaments (IFs) are essential constituents of the metazoan cytoskeleton. A vast family of cytoplasmic IF proteins are capable of self-assembly from soluble tetrameric species into typical 10-12 nm wide filaments. The primary structure of these proteins includes the signature central 'rod' domain of ~ 300 residues which forms a dimeric α-helical coiled coil composed of three segments (coil1A, coil1B and coil2) interconnected by non-helical, flexible linkers (L1 and L12). The rod is flanked by flexible terminal head and tail domains. At present, the molecular architecture of mature IFs is only poorly known, limiting our capacity to rationalize the effect of numerous disease-related mutations found in IF proteins. Here we addressed the molecular structure of soluble vimentin tetramers which are formed by two antiparallel, staggered dimers with coil1B domains aligned (A11 tetramers). By examining a series of progressive truncations, we show that the presence of the coil1A domain is essential for the tetramer formation. In addition, we employed a novel chemical cross-linking pipeline including isotope labelling to identify intra- and interdimeric cross-links within the tetramer. We conclude that the tetramer is synergistically stabilized by the interactions of the aligned coil1B domains, the interactions between coil1A and the N-terminal portion of coil2, and the electrostatic attraction between the oppositely charged head and rod domains. Our cross-linking data indicate that, starting with a straight A11 tetramer, flexibility of linkers L1 and L12 enables 'backfolding' of both the coil1A and coil2 domains onto the tetrameric core formed by the coil1B domains. Through additional small-angle X-ray scattering experiments we show that the elongated A11 tetramers dominate in low ionic strength solutions, while there is also a significant structural flexibility especially in the terminal domains.
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Affiliation(s)
| | | | - Hani M Hashim
- Laboratory for Biocrystallography, KU Leuven, 3000, Leuven, Belgium
- Department of Chemistry, KU Leuven, 3000, Leuven, Belgium
| | - Lada Dlabolová
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Jan Fiala
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Steven Beelen
- Laboratory for Biocrystallography, KU Leuven, 3000, Leuven, Belgium
| | - Zdeněk Kukačka
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | | | - Petr Novák
- Department of Biochemistry, Charles University, 12800, Prague, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, KU Leuven, 3000, Leuven, Belgium.
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7
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Stick R, Peter A. CaaX-less lamins: Lophotrochozoa provide a glance at the playground of evolution. PROTOPLASMA 2023; 260:741-756. [PMID: 36102949 PMCID: PMC10125929 DOI: 10.1007/s00709-022-01809-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/01/2022] [Indexed: 05/05/2023]
Abstract
Nuclear lamins are the main components of the nuclear lamina in many eukaryotes. They are members of the intermediate filament (IF) protein family. Lamins differ from cytoplasmic IF proteins by the presence of a nuclear localisation sequence (NLS) and a C-terminal tetrapeptide, the CaaX motif. The CaaX motif is target of post-translational modifications including isoprenylation, proteolytic processing, and carboxyl-methylation. These modifications, in conjunction with the NLS, direct lamins to the inner nuclear membrane where they assemble into filaments. Lamins lacking a CaaX motif are unable to associate independently with nuclear membranes and remain in the nucleoplasm. So far, three species have been reported to exclusively express CaaX-less lamins. All three belong to the lophotrochozoan lineage. To find out whether they represent rare exceptions, we analysed lamins of representatives of 17 lophotrochozoan phyla. Here we report that all four clades of Rotifera as well as individual taxa of Mollusca and Annelida lack CaaX-lamins, but express lamins with alternative C-termini. Of note, the respective mollusc and annelid groups occupy very different phylogenetic ranks. Most of these alternative C-termini are rich in aromatic residues. A possible function of these residues in membrane association is discussed. Alternative splicing of terebellid lamin transcripts gives rise to two lamin variants, one with a CaaX motif and one with an alternative C-terminus. A similar situation is found in Arenicolidae, Opheliidae, Capitellidae, and Echiura. This points a way, how the switch from lamins carrying a CaaX motif to lamins with alternative C-termini may have occurred.
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Affiliation(s)
- Reimer Stick
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany.
| | - Annette Peter
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany
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8
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Lilina AV, Leekens S, Hashim HM, Vermeire P, Harvey JN, Strelkov SV. Stability profile of vimentin rod domain. Protein Sci 2022; 31:e4505. [PMID: 36369679 PMCID: PMC9703591 DOI: 10.1002/pro.4505] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/14/2022]
Abstract
Intermediate filaments (IFs) form an essential part of the metazoan cytoskeleton. Despite a long history of research, a proper understanding of their molecular architecture and assembly process is still lacking. IFs self-assemble from elongated dimers, which are defined by their central "rod" domain. This domain forms an α-helical coiled coil consisting of three segments called coil1A, coil1B, and coil2. It has been hypothesized that the structural plasticity of the dimer, including the unraveling of some coiled-coil regions, is essential for the assembly process. To systematically explore this possibility, we have studied six 50-residue fragments covering the entire rod domain of human vimentin, a model IF protein. After creating in silico models of these fragments, their evaluation using molecular dynamics was performed. Large differences were seen across the six fragments with respect to their structural variability during a 100 ns simulation. Next, the fragments were prepared recombinantly, whereby their correct dimerization was promoted by adding short N- or C-terminal capping motifs. The capped fragments were subjected to circular dichroism measurements at varying temperatures. The obtained melting temperatures reveal the relative stabilities of individual fragments, which correlate well with in silico results. We show that the least stable regions of vimentin rod are coil1A and the first third of coil2, while the structures of coil1B and the rest of coil2 are significantly more robust. These observations are in line with the data obtained using other experimental approaches, and contribute to a better understanding of the molecular mechanisms driving IF assembly.
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Affiliation(s)
| | - Simon Leekens
- Laboratory for BiocrystallographyKU LeuvenLeuvenBelgium
| | - Hani M. Hashim
- Laboratory for BiocrystallographyKU LeuvenLeuvenBelgium
- Department of ChemistryKU LeuvenLeuvenBelgium
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9
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Wasilewska M, Żeliszewska P, Pogoda K, Deptuła P, Bucki R, Adamczyk Z. Human Vimentin Layers on Solid Substrates: Adsorption Kinetics and Corona Formation Investigations. Biomacromolecules 2022; 23:3308-3317. [PMID: 35829774 PMCID: PMC9364323 DOI: 10.1021/acs.biomac.2c00415] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/27/2022] [Indexed: 11/28/2022]
Abstract
Adsorption kinetics of human vimentin on negatively charged substrates (mica, silica, and polymer particles) was analyzed using atomic force microscopy (AFM), quartz microbalance (QCM), and the laser doppler velocimetry (LDV) method. AFM studies realized under diffusion conditions proved that the adsorbed protein layer mainly consisted of aggregates in the form of compact tetramers and hexamers of a size equal to 11-12 nm. These results were consistent with vimentin adsorption kinetics under flow conditions investigated by QCM. It was established that vimentin aggregates efficiently adsorbed on the negatively charged silica sensor at pH 3.5 and 7.4, forming compact layers with the coverage reaching 3.5 mg m-2. Additionally, the formation of the vimentin corona at polymer particles was examined using the LDV method and interpreted in terms of the electrokinetic model. This allowed us to determine the zeta potential of the corona as a function of pH and the electrokinetic charge of aggregates, which was equal to -0.7 e nm-2 at pH 7.4 in a 10 mM NaCl solution. The anomalous adsorption of aggregates exhibiting an average negative charge on the negatively charged substrates was interpreted as a result of a heterogeneous charge distribution. These investigations confirmed that it is feasible to deposit stable vimentin layers both at planar substrates and at carrier particles with well-controlled coverage and zeta potential. They can be used for investigations of vimentin interactions with various ligands including receptors of the innate immune system, immunoglobulins, bacterial virulence factors, and spike proteins of viruses.
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Affiliation(s)
- Monika Wasilewska
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, PL-30239 Krakow, Poland
| | - Paulina Żeliszewska
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, PL-30239 Krakow, Poland
| | - Katarzyna Pogoda
- Institute
of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Piotr Deptuła
- Department
of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, PL-15222 Białystok, Poland
| | - Robert Bucki
- Department
of Medical Microbiology and Nanobiomedical Engineering, Medical University of Białystok, PL-15222 Białystok, Poland
| | - Zbigniew Adamczyk
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, PL-30239 Krakow, Poland
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10
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Infante E, Etienne-Manneville S. Intermediate filaments: Integration of cell mechanical properties during migration. Front Cell Dev Biol 2022; 10:951816. [PMID: 35990612 PMCID: PMC9389290 DOI: 10.3389/fcell.2022.951816] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022] Open
Abstract
Cell migration is a vital and dynamic process required for the development of multicellular organisms and for immune system responses, tissue renewal and wound healing in adults. It also contributes to a variety of human diseases such as cancers, autoimmune diseases, chronic inflammation and fibrosis. The cytoskeleton, which includes actin microfilaments, microtubules, and intermediate filaments (IFs), is responsible for the maintenance of animal cell shape and structural integrity. Each cytoskeletal network contributes its unique properties to dynamic cell behaviour, such as cell polarization, membrane protrusion, cell adhesion and contraction. Hence, cell migration requires the dynamic orchestration of all cytoskeleton components. Among these, IFs have emerged as a molecular scaffold with unique mechanical features and a key player in the cell resilience to mechanical stresses during migration through complex 3D environment. Moreover, accumulating evidence illustrates the participation of IFs in signalling cascades and cytoskeletal crosstalk. Teaming up with actin and microtubules, IFs contribute to the active generation of forces required for cell adhesion and mesenchymal migration and invasion. Here we summarize and discuss how IFs integrate mechanical properties and signalling functions to control cell migration in a wide spectrum of physiological and pathological situations.
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Affiliation(s)
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Université Paris-Cité, Equipe Labellisée Ligue Contre le Cancer, Paris, France
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11
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Jeong S, Ahn J, Jo I, Kang SM, Park BJ, Cho HS, Kim YH, Ha NC. Cyclin-Dependent Kinase 1 depolymerizes nuclear lamin filaments by disrupting the head-to-tail interaction of the lamin central rod domain. J Biol Chem 2022; 298:102256. [PMID: 35839855 PMCID: PMC9400090 DOI: 10.1016/j.jbc.2022.102256] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Nuclear lamins maintain the nuclear envelope structure by forming long linear filaments via two alternating molecular arrangements of coiled-coil dimers, known as A11 and A22 binding modes. The A11 binding mode is characterized by the antiparallel interactions between coil 1b domains, whereas the A22 binding mode is facilitated by interactions between the coil 2 domains of lamin. The junction between A11- and A22-interacting dimers in the lamin tetramer produces another parallel head–tail interaction between coil 1a and the C-terminal region of coil 2, called the ACN interaction. During mitosis, phosphorylation in the lamin N-terminal head region by the cyclin-dependent kinase (CDK) complex triggers depolymerization of lamin filaments, but the associated mechanisms remain unknown at the molecular level. In this study, we revealed using the purified proteins that phosphorylation by the CDK1 complex promotes disassembly of lamin filaments by directly abolishing the ACN interaction between coil 1a and the C-terminal portion of coil 2. We further observed that this interaction was disrupted as a result of alteration of the ionic interactions between coil 1a and coil 2. Combined with molecular modeling, we propose a mechanism for CDK1-dependent disassembly of the lamin filaments. Our results will help to elucidate the cell cycle–dependent regulation of nuclear morphology at the molecular level.
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Affiliation(s)
- Soyeon Jeong
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46241, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 46241, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yong-Hak Kim
- Department of Microbiology, Catholic University of Daegu School of Medicine, Daegu, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea.
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12
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Yang AW, Lin NH, Yeh TH, Snider N, Perng MD. Effects of Alexander disease-associated mutations on the assembly and organization of GFAP intermediate filaments. Mol Biol Cell 2022; 33:ar69. [PMID: 35511821 PMCID: PMC9635275 DOI: 10.1091/mbc.e22-01-0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Alexander disease is a primary genetic disorder of astrocytes caused by dominant mutations in the gene encoding glial fibrillary acidic protein (GFAP). How single-amino-acid changes can lead to cytoskeletal catastrophe and brain degeneration remains poorly understood. In this study, we have analyzed 14 missense mutations located in the GFAP rod domain to investigate how these mutations affect in vitro filament assembly. Whereas the internal rod mutants assembled into filaments that were shorter than those of wild type, the rod end mutants formed structures with one or more of several atypical characteristics, including short filament length, irregular width, roughness of filament surface, and filament aggregation. When transduced into primary astrocytes, GFAP mutants with in vitro assembly defects usually formed cytoplasmic aggregates, which were more resistant to biochemical extraction. The resistance of GFAP to solubilization was also observed in brain tissues of patients with Alexander disease, in which a significant proportion of insoluble GFAP were accumulated in Rosenthal fiber fractions. These findings provide clinically relevant evidence that link GFAP assembly defects to disease pathology at the tissue level and suggest that altered filament assembly and properties as a result of GFAP mutation are critical initiating factors for the pathogenesis of Alexander disease.
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Affiliation(s)
- Ai-Wen Yang
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ni-Hsuan Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ting-Hung Yeh
- Department of Medical Science, College of Life Sciences, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Natasha Snider
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ming-Der Perng
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan,Department of Medical Science, College of Life Sciences, National Tsing Hua University, Hsinchu 30013, Taiwan,*Address correspondence to: Ming-Der Perng ()
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13
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Usman S, Aldehlawi H, Nguyen TKN, Teh MT, Waseem A. Impact of N-Terminal Tags on De Novo Vimentin Intermediate Filament Assembly. Int J Mol Sci 2022; 23:ijms23116349. [PMID: 35683030 PMCID: PMC9181571 DOI: 10.3390/ijms23116349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 02/01/2023] Open
Abstract
Vimentin, a type III intermediate filament protein, is found in most cells along with microfilaments and microtubules. It has been shown that the head domain folds back to associate with the rod domain and this association is essential for filament assembly. The N-terminally tagged vimentin has been widely used to label the cytoskeleton in live cell imaging. Although there is previous evidence that EGFP tagged vimentin fails to form filaments but is able to integrate into a pre-existing network, no study has systematically investigated or established a molecular basis for this observation. To determine whether a tag would affect de novo filament assembly, we used vimentin fused at the N-terminus with two different sized tags, AcGFP (239 residues, 27 kDa) and 3 × FLAG (22 residues; 2.4 kDa) to assemble into filaments in two vimentin-deficient epithelial cells, MCF-7 and A431. We showed that regardless of tag size, N-terminally tagged vimentin aggregated into globules with a significant proportion co-aligning with β-catenin at cell–cell junctions. However, the tagged vimentin aggregates could form filaments upon adding untagged vimentin at a ratio of 1:1 or when introduced into cells containing pre-existing filaments. The resultant filament network containing a mixture of tagged and untagged vimentin was less stable compared to that formed by only untagged vimentin. The data suggest that placing a tag at the N-terminus may create steric hinderance in case of a large tag (AcGFP) or electrostatic repulsion in case of highly charged tag (3 × FLAG) perhaps inducing a conformational change, which deleteriously affects the association between head and rod domains. Taken together our results shows that a free N-terminus is essential for filament assembly as N-terminally tagged vimentin is not only incapable of forming filaments, but it also destabilises when integrated into a pre-existing network.
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Affiliation(s)
- Saima Usman
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK; (S.U.); (T.K.N.N.); (M.-T.T.)
| | - Hebah Aldehlawi
- Department of Oral Diagnostic Sciences, Division of Oral Pathology and Medicine, Faculty of Dentistry, King Abdul Aziz University, Jeddah 21589, Saudi Arabia;
| | - Thuan Khanh Ngoc Nguyen
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK; (S.U.); (T.K.N.N.); (M.-T.T.)
| | - Muy-Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK; (S.U.); (T.K.N.N.); (M.-T.T.)
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Newark Street, London E1 2AT, UK; (S.U.); (T.K.N.N.); (M.-T.T.)
- Centre for Immunobiology and Regenerative Medicine, Blizard Institute, 4 Newark Street, London E1 2AT, UK
- Correspondence: ; Tel.: +44-207-882-2387; Fax: +44-207-882-7137
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14
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Kang YR, Lee SH, Lin NH, Lee SJ, Yang AW, Chandrasekaran G, Kang KW, Jin MS, Kim MK, Perng MD, Choi SY, Nam TS. A novel in-frame GFAP p.E138_L148del mutation in Type II Alexander disease with atypical phenotypes. Eur J Hum Genet 2022; 30:687-694. [PMID: 35246666 DOI: 10.1038/s41431-022-01073-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/29/2022] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
Alexander disease (AxD) is a neurodegenerative astrogliopathy caused by mutation in the glial fibrillary acidic protein (GFAP) gene. A 42-year-old Korean man presented with temporary gait disturbance and psychiatric regression after a minor head trauma in the absence of bulbar symptoms and signs. Magnetic resonance images of the brain and spinal cord showed significant atrophy of the medulla oblongata and the entire spinal cord as well as contrast-enhanced T2 hypointensity in the basal ganglia. DNA sequencing revealed a novel 33-bp in-frame deletion mutation (p.Glu138_Leu148del) within the 1B rod domain of GFAP, which was predicted to be deleterious by PROVEAN analysis. To test whether the deletion mutant is disease-causing, we performed in vitro GFAP assembly and sedimentation assays, and GFAP aggregation assays in human adrenal carcinoma SW13 (Vim-) cells and rat primary astrocytes. All the assays revealed that GFAP p.Glu138_Leu148del is aggregation prone. Based on these findings, we diagnosed the patient with Type II AxD. This is a report that demonstrates the pathogenicity of InDel mutation of GFAP through functional studies. This patient's atypical presentation as well as the discrepancy between clinical symptoms and radiologic findings may extend the scope of AxD.
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Affiliation(s)
- You-Ri Kang
- Department of Neurology, Chonnam National University Medical School and Chonnam National University Hospital, Gwangju, 61469, Republic of Korea
| | - So-Hyun Lee
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Ni-Hsuan Lin
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Seung-Jin Lee
- Department of Radiology, Chonnam National University Hospital, Gwangju, 61469, Republic of Korea
| | - Ai-Wen Yang
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | | | - Kyung Wook Kang
- Department of Neurology, Chonnam National University Medical School and Chonnam National University Hospital, Gwangju, 61469, Republic of Korea
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Myeong-Kyu Kim
- Department of Neurology, Chonnam National University Medical School and Chonnam National University Hospital, Gwangju, 61469, Republic of Korea
| | - Ming-Der Perng
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea.
| | - Tai-Seung Nam
- Department of Neurology, Chonnam National University Medical School and Chonnam National University Hospital, Gwangju, 61469, Republic of Korea.
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15
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Ahn J, Jeong S, Kang SM, Jo I, Park BJ, Ha NC. Crystal structure of progeria mutant S143F lamin A/C reveals increased hydrophobicity driving nuclear deformation. Commun Biol 2022; 5:267. [PMID: 35338226 PMCID: PMC8956589 DOI: 10.1038/s42003-022-03212-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/25/2022] [Indexed: 12/29/2022] Open
Abstract
Lamins are intermediate filaments that form a 3-D meshwork in the periphery of the nuclear envelope. The recent crystal structure of a long fragment of human lamin A/C visualized the tetrameric assembly unit of the central rod domain as a polymerization intermediate. A genetic mutation of S143F caused a phenotype characterized by both progeria and muscular dystrophy. In this study, we determined the crystal structure of the lamin A/C fragment harboring the S143F mutation. The obtained structure revealed the X-shaped interaction between the tetrameric units in the crystals, potentiated by the hydrophobic interactions of the mutated Phe143 residues. Subsequent studies indicated that the X-shaped interaction between the filaments plays a crucial role in disrupting the normal lamin meshwork. Our findings suggest the assembly mechanism of the 3-D meshwork and further provide a molecular framework for understanding the aging process by nuclear deformation.
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Affiliation(s)
- Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soyeon Jeong
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - So-Mi Kang
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bum-Joon Park
- Department of Molecular Biology, College of Natural Science, Pusan National University, Busan, 46241, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul, 08826, Republic of Korea.
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16
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Ostrowska-Podhorodecka Z, Ding I, Norouzi M, McCulloch CA. Impact of Vimentin on Regulation of Cell Signaling and Matrix Remodeling. Front Cell Dev Biol 2022; 10:869069. [PMID: 35359446 PMCID: PMC8961691 DOI: 10.3389/fcell.2022.869069] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Vimentin expression contributes to cellular mechanoprotection and is a widely recognized marker of fibroblasts and of epithelial-mesenchymal transition. But it is not understood how vimentin affects signaling that controls cell migration and extracellular matrix (ECM) remodeling. Recent data indicate that vimentin controls collagen deposition and ECM structure by regulating contractile force application to the ECM and through post-transcriptional regulation of ECM related genes. Binding of cells to the ECM promotes the association of vimentin with cytoplasmic domains of adhesion receptors such as integrins. After initial adhesion, cell-generated, myosin-dependent forces and signals that impact vimentin structure can affect cell migration. Post-translational modifications of vimentin determine its adaptor functions, including binding to cell adhesion proteins like paxillin and talin. Accordingly, vimentin regulates the growth, maturation and adhesive strength of integrin-dependent adhesions, which enables cells to tune their attachment to collagen, regulate the formation of cell extensions and control cell migration through connective tissues. Thus, vimentin tunes signaling cascades that regulate cell migration and ECM remodeling. Here we consider how specific properties of vimentin serve to control cell attachment to the underlying ECM and to regulate mesenchymal cell migration and remodeling of the ECM by resident fibroblasts.
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17
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Echarri A. A Multisensory Network Drives Nuclear Mechanoadaptation. Biomolecules 2022; 12:biom12030404. [PMID: 35327596 PMCID: PMC8945967 DOI: 10.3390/biom12030404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have adapted to mechanical forces early in evolution and have developed multiple mechanisms ensuring sensing of, and adaptation to, the diversity of forces operating outside and within organisms. The nucleus must necessarily adapt to all types of mechanical signals, as its functions are essential for virtually all cell processes, many of which are tuned by mechanical cues. To sense forces, the nucleus is physically connected with the cytoskeleton, which senses and transmits forces generated outside and inside the cell. The nuclear LINC complex bridges the cytoskeleton and the nuclear lamina to transmit mechanical information up to the chromatin. This system creates a force-sensing macromolecular complex that, however, is not sufficient to regulate all nuclear mechanoadaptation processes. Within the nucleus, additional mechanosensitive structures, including the nuclear envelope and the nuclear pore complex, function to regulate nuclear mechanoadaptation. Similarly, extra nuclear mechanosensitive systems based on plasma membrane dynamics, mechanotransduce information to the nucleus. Thus, the nucleus has the intrinsic structural components needed to receive and interpret mechanical inputs, but also rely on extra nuclear mechano-sensors that activate nuclear regulators in response to force. Thus, a network of mechanosensitive cell structures ensures that the nucleus has a tunable response to mechanical cues.
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Affiliation(s)
- Asier Echarri
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Mechanoadaptation and Caveolae Biology Laboratory, Areas of Cell & Developmental Biology, Calle Melchor Fernández Almagro, 3, 28029 Madrid, Spain
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18
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Nunes Vicente F, Lelek M, Tinevez JY, Tran QD, Pehau-Arnaudet G, Zimmer C, Etienne-Manneville S, Giannone G, Leduc C. Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging. SCIENCE ADVANCES 2022; 8:eabm2696. [PMID: 35213220 PMCID: PMC8880768 DOI: 10.1126/sciadv.abm2696] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/11/2022] [Indexed: 05/30/2023]
Abstract
Intermediate filaments (IFs) are involved in key cellular functions including polarization, migration, and protection against large deformations. These functions are related to their remarkable ability to extend without breaking, a capacity that should be determined by the molecular organization of subunits within filaments. However, this structure-mechanics relationship remains poorly understood at the molecular level. Here, using super-resolution microscopy (SRM), we show that vimentin filaments exhibit a ~49-nanometer axial repeat both in cells and in vitro. As unit-length filaments (ULFs) were measured at ~59 nanometers, this demonstrates a partial overlap of ULFs during filament assembly. Using an SRM-compatible stretching device, we also provide evidence that the extensibility of vimentin is due to the unfolding of its subunits and not to their sliding, thus establishing a direct link between the structural organization and its mechanical properties. Overall, our results pave the way for future studies of IF assembly, mechanical, and structural properties in cells.
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Affiliation(s)
- Filipe Nunes Vicente
- Institut Interdisciplinaire des Neurosciences, CNRS UMR 5297, Université de Bordeaux, Bordeaux F-33000, France
| | - Mickael Lelek
- Imaging and Modeling Unit, Institut Pasteur, CNRS UMR 3691, Paris F-75015, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, 2RT / DTPS, Institut Pasteur, Paris F-75015 , France
| | - Quang D. Tran
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
- CNRS UMR 7592, Institut Jacques Monod, Université de Paris, Paris F-75013, France
| | - Gerard Pehau-Arnaudet
- CNRS UMR 3528, Institut Pasteur, Paris F-75015, France
- Ultrastructural BioImaging Platform, Institut Pasteur, Paris F-75015, France
| | - Christophe Zimmer
- Imaging and Modeling Unit, Institut Pasteur, CNRS UMR 3691, Paris F-75015, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
| | - Gregory Giannone
- Institut Interdisciplinaire des Neurosciences, CNRS UMR 5297, Université de Bordeaux, Bordeaux F-33000, France
| | - Cécile Leduc
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
- CNRS UMR 7592, Institut Jacques Monod, Université de Paris, Paris F-75013, France
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19
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Ramos-León F, Ramamurthi K. Cytoskeletal proteins: Lessons learned from bacteria. Phys Biol 2022; 19. [PMID: 35081523 DOI: 10.1088/1478-3975/ac4ef0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/26/2022] [Indexed: 11/11/2022]
Abstract
Cytoskeletal proteins are classified as a group that is defined functionally, whose members are capable of polymerizing into higher order structures, either dynamically or statically, to perform structural roles during a variety of cellular processes. In eukaryotes, the most well-studied cytoskeletal proteins are actin, tubulin, and intermediate filaments, and are essential for cell shape and movement, chromosome segregation, and intracellular cargo transport. Prokaryotes often harbor homologs of these proteins, but in bacterial cells, these homologs are usually not employed in roles that can be strictly defined as "cytoskeletal". However, several bacteria encode other proteins capable of polymerizing which, although they do not appear to have a eukaryotic counterpart, nonetheless appear to perform a more traditional "cytoskeletal" function. In this review, we discuss recent reports that cover the structure and functions of prokaryotic proteins that are broadly termed as cytoskeletal, either by sequence homology or by function, to highlight how the enzymatic properties of traditionally studied cytoskeletal proteins may be used for other types of cellular functions; and to demonstrate how truly "cytoskeletal" functions may be performed by uniquely bacterial proteins that do not display homology to eukaryotic proteins.
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Affiliation(s)
- Félix Ramos-León
- National Institutes of Health, 37 Convent Dr., Bldg 37, Room 5132, Bethesda, Maryland, 20892, UNITED STATES
| | - Kumaran Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, 37 Convent Dr, Bldg 37, Room 5132, Bethesda, Maryland, 20892, UNITED STATES
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20
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Schepers AV, Kraxner J, Lorenz C, Köster S. Mechanics of Single Vimentin Intermediate Filaments Under Load. Methods Mol Biol 2022; 2478:677-700. [PMID: 36063338 DOI: 10.1007/978-1-0716-2229-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The eukaryotic cytoskeleton consists of three different types of biopolymers - microtubules, actin filaments, and intermediate filaments - and provides cells with versatile mechanical properties, combining stability and flexibility. The unique molecular structure of intermediate filaments leads to high extensibility and stability under load. With high laser power dual optical tweezers, the mechanical properties of intermediate filaments may be investigated, while monitoring the extension with fluorescence microscopy. Here, we provide detailed protocols for the preparation of single vimentin intermediate filaments and general measurement protocols for (i) stretching experiments, (ii) repeated loading and relaxation cycles, and (iii) force-clamp experiments. We describe methods for the analysis of the experimental data in combination with computational modeling approaches.
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Affiliation(s)
- Anna V Schepers
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany
| | - Julia Kraxner
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany
| | - Charlotta Lorenz
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany
| | - Sarah Köster
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany.
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21
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Vermeire PJ, Stalmans G, Lilina AV, Fiala J, Novak P, Herrmann H, Strelkov SV. Molecular Interactions Driving Intermediate Filament Assembly. Cells 2021; 10:cells10092457. [PMID: 34572105 PMCID: PMC8466517 DOI: 10.3390/cells10092457] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023] Open
Abstract
Given the role of intermediate filaments (IFs) in normal cell physiology and scores of IF-linked diseases, the importance of understanding their molecular structure is beyond doubt. Research into the IF structure was initiated more than 30 years ago, and some important advances have been made. Using crystallography and other methods, the central coiled-coil domain of the elementary dimer and also the structural basis of the soluble tetramer formation have been studied to atomic precision. However, the molecular interactions driving later stages of the filament assembly are still not fully understood. For cytoplasmic IFs, much of the currently available insight is due to chemical cross-linking experiments that date back to the 1990s. This technique has since been radically improved, and several groups have utilized it recently to obtain data on lamin filament assembly. Here, we will summarize these findings and reflect on the remaining open questions and challenges of IF structure. We argue that, in addition to X-ray crystallography, chemical cross-linking and cryoelectron microscopy are the techniques that should enable major new advances in the field in the near future.
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Affiliation(s)
- Pieter-Jan Vermeire
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
| | - Giel Stalmans
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
| | - Anastasia V. Lilina
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
| | - Jan Fiala
- Department of Biochemistry, Charles University, 12800 Prague, Czech Republic; (J.F.); (P.N.)
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novak
- Department of Biochemistry, Charles University, 12800 Prague, Czech Republic; (J.F.); (P.N.)
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Harald Herrmann
- Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
- Correspondence: ; Tel.: +32-1633-0845
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22
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Abstract
Fifty years have passed since the discovery of glial fibrillary acidic protein (GFAP) by Lawrence Eng and colleagues. Now recognized as a member of the intermediate filament family of proteins, it has become a subject for study in fields as diverse as structural biology, cell biology, gene expression, basic neuroscience, clinical genetics and gene therapy. This review covers each of these areas, presenting an overview of current understanding and controversies regarding GFAP with the goal of stimulating continued study of this fascinating protein.
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Affiliation(s)
- Albee Messing
- Waisman Center, University of Wisconsin-Madison.,Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison
| | - Michael Brenner
- Department of Neurobiology, University of Alabama-Birmingham
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23
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Bend, Push, Stretch: Remarkable Structure and Mechanics of Single Intermediate Filaments and Meshworks. Cells 2021; 10:cells10081960. [PMID: 34440729 PMCID: PMC8394331 DOI: 10.3390/cells10081960] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/11/2022] Open
Abstract
The cytoskeleton of the eukaryotic cell provides a structural and functional scaffold enabling biochemical and cellular functions. While actin and microtubules form the main framework of the cell, intermediate filament networks provide unique mechanical properties that increase the resilience of both the cytoplasm and the nucleus, thereby maintaining cellular function while under mechanical pressure. Intermediate filaments (IFs) are imperative to a plethora of regulatory and signaling functions in mechanotransduction. Mutations in all types of IF proteins are known to affect the architectural integrity and function of cellular processes, leading to debilitating diseases. The basic building block of all IFs are elongated α-helical coiled-coils that assemble hierarchically into complex meshworks. A remarkable mechanical feature of IFs is the capability of coiled-coils to metamorphize into β-sheets under stress, making them one of the strongest and most resilient mechanical entities in nature. Here, we discuss structural and mechanical aspects of IFs with a focus on nuclear lamins and vimentin.
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24
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Weber MS, Eibauer M, Sivagurunathan S, Magin TM, Goldman RD, Medalia O. Structural heterogeneity of cellular K5/K14 filaments as revealed by cryo-electron microscopy. eLife 2021; 10:70307. [PMID: 34323216 PMCID: PMC8360650 DOI: 10.7554/elife.70307] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Keratin intermediate filaments are an essential and major component of the cytoskeleton in epithelial cells. They form a stable yet dynamic filamentous network extending from the nucleus to the cell periphery, which provides resistance to mechanical stresses. Mutations in keratin genes are related to a variety of epithelial tissue diseases. Despite their importance, the molecular structure of keratin filaments remains largely unknown. In this study, we analyzed the structure of keratin 5/keratin 14 filaments within ghost mouse keratinocytes by cryo-electron microscopy and cryo-electron tomography. By averaging a large number of keratin segments, we have gained insights into the helical architecture of the filaments. Two-dimensional classification revealed profound variations in the diameter of keratin filaments and their subunit organization. Computational reconstitution of filaments of substantial length uncovered a high degree of internal heterogeneity along single filaments, which can contain regions of helical symmetry, regions with less symmetry and regions with significant diameter fluctuations. Cross-section views of filaments revealed that keratins form hollow cylinders consisting of multiple protofilaments, with an electron dense core located in the center of the filament. These findings shed light on the complex and remarkable heterogenic architecture of keratin filaments, suggesting that they are highly flexible, dynamic cytoskeletal structures.
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Affiliation(s)
- Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Thomas M Magin
- Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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Multiscale mechanics and temporal evolution of vimentin intermediate filament networks. Proc Natl Acad Sci U S A 2021; 118:2102026118. [PMID: 34187892 DOI: 10.1073/pnas.2102026118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cytoskeleton, an intricate network of protein filaments, motor proteins, and cross-linkers, largely determines the mechanical properties of cells. Among the three filamentous components, F-actin, microtubules, and intermediate filaments (IFs), the IF network is by far the most extensible and resilient to stress. We present a multiscale approach to disentangle the three main contributions to vimentin IF network mechanics-single-filament mechanics, filament length, and interactions between filaments-including their temporal evolution. Combining particle tracking, quadruple optical trapping, and computational modeling, we derive quantitative information on the strength and kinetics of filament interactions. Specifically, we find that hydrophobic contributions to network mechanics enter mostly via filament-elongation kinetics, whereas electrostatics have a direct influence on filament-filament interactions.
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Molecular Insight into the Regulation of Vimentin by Cysteine Modifications and Zinc Binding. Antioxidants (Basel) 2021; 10:antiox10071039. [PMID: 34203497 PMCID: PMC8300659 DOI: 10.3390/antiox10071039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/20/2021] [Accepted: 06/24/2021] [Indexed: 01/11/2023] Open
Abstract
The intermediate filament protein vimentin is involved in essential cellular processes, including cell division and stress responses, as well as in the pathophysiology of cancer, pathogen infection, and autoimmunity. The vimentin network undergoes marked reorganizations in response to oxidative stress, in which modifications of vimentin single cysteine residue, Cys328, play an important role, and is modulated by zinc availability. However, the molecular basis for this regulation is not fully understood. Here, we show that Cys328 displays a low pKa, supporting its reactivity, and is readily alkylated and oxidized in vitro. Moreover, combined oxidation and crosslinking assays and molecular dynamics simulations support that zinc ions interact with Cys328 in its thiolate form, whereas Glu329 and Asp331 stabilize zinc coordination. Vimentin oxidation can induce disulfide crosslinking, implying the close proximity of Cys328 from neighboring dimers in certain vimentin conformations, supported by our computational models. Notably, micromolar zinc concentrations prevent Cys328 alkylation, lipoxidation, and disulfide formation. Moreover, zinc selectively protects vimentin from crosslinking using short-spacer cysteine-reactive but not amine-reactive agents. These effects are not mimicked by magnesium, consistent with a lower number of magnesium ions hosted at the cysteine region, according to molecular dynamics simulations. Importantly, the region surrounding Cys328 is involved in interaction with several drugs targeting vimentin and is conserved in type III intermediate filaments, which include glial fibrillary acidic protein and desmin. Altogether, our results identify this region as a hot spot for zinc binding, which modulates Cys328 reactivity. Moreover, they provide a molecular standpoint for vimentin regulation through the interplay between cysteine modifications and zinc availability.
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Stone EJ, Kolb SJ, Brown A. A review and analysis of the clinical literature on Charcot-Marie-Tooth disease caused by mutations in neurofilament protein L. Cytoskeleton (Hoboken) 2021; 78:97-110. [PMID: 33993654 PMCID: PMC10174713 DOI: 10.1002/cm.21676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023]
Abstract
Charcot-Marie-Tooth disease (CMT) is one of the most common inherited neurological disorders and can be caused by mutations in over 100 different genes. One of the causative genes is NEFL on chromosome 8 which encodes neurofilament light protein (NEFL), one of five proteins that co-assemble to form neurofilaments. At least 34 different CMT-causing mutations in NEFL have been reported which span the head, rod, and tail domains of the protein. The majority of these mutations are inherited dominantly, but some are inherited recessively. The resulting disease is classified variably in clinical reports based on electrodiagnostic studies as either axonal (type 2; CMT2E), demyelinating (type 1; CMT1F), or a form intermediate between the two (dominant intermediate; DI-CMTG). In this article, we first present a brief introduction to CMT and neurofilaments. We then collate and analyze the data from the clinical literature on the disease classification, age of onset and electrodiagnostic test results for the various mutations. We find that mutations in the head, rod, and tail domains can all cause disease with early onset and profound neurological impairment, with a trend toward greater severity for head domain mutations. We also find that the disease classification does not correlate with specific mutation or domain. In fact, different individuals with the same mutation can be classified as having axonal, demyelinating, or dominant intermediate forms of the disease. This suggests that the classification of the disease as CMT2E, CMT1F or DI-CMTG has more to do with variable disease presentation than to differences in the underlying disease mechanism, which is most likely primarily axonal in all cases.
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Affiliation(s)
- Elizabeth J Stone
- Department of Neuroscience, Ohio State University, Columbus, Ohio, USA.,Neuroscience Graduate Program, Ohio State University, Columbus, Ohio, USA
| | - Stephen J Kolb
- Department of Neurology, Ohio State University, Columbus, Ohio, USA.,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, Ohio, USA
| | - Anthony Brown
- Department of Neuroscience, Ohio State University, Columbus, Ohio, USA
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Ostrowska-Podhorodecka Z, McCulloch CA. Vimentin regulates the assembly and function of matrix adhesions. Wound Repair Regen 2021; 29:602-612. [PMID: 33887795 DOI: 10.1111/wrr.12920] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
The intermediate filament protein vimentin is a widely used phenotypic marker for identifying cells of the mesenchymal linkage such as fibroblasts and myofibroblasts, but the full repertoire of vimentin's functional attributes has not been fully explored. Here we consider how vimentin, in addition to its contributions to mechanical stabilization of cell structure, also helps to control the assembly of cell adhesions and migration through collagen matrices. While the assembly and function of matrix adhesions are critical for the differentiation of myofibroblasts and many other types of adherent cells, a potential mechanism that explains how vimentin affects the recruitment and abundance of centrally important proteins in cell adhesions has been elusive. Here we review recent data indicating that vimentin plays a central regulatory role in the assembly of focal adhesions which form in response to the attachment to collagen. We show that in particular, vimentin is a key organizer of the β1 integrin adhesive machinery, which affects cell migration through collagen. This review provides a comprehensive picture of the surprisingly broad array of processes and molecules with which vimentin interacts to affect cell function in the context of fibroblast and myofibroblast adhesion and migration on collagen.
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Perego E, Köster S. Exploring early time points of vimentin assembly in flow by fluorescence fluctuation spectroscopy. LAB ON A CHIP 2021; 21:735-745. [PMID: 33491697 DOI: 10.1039/d0lc00985g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Despite the importance for cellular processes, the dynamics of molecular assembly, especially on fast time scales, is not yet fully understood. To this end, we present a multi-layer microfluidic device and combine it with fluorescence fluctuation spectroscopy. We apply this innovative combination of methods to investigate the early steps in assembly of vimentin intermediate filaments (IFs). These filaments, together with actin filaments and microtubules, constitute the cytoskeleton of cells of mesenchymal origin and greatly influence their mechanical properties. We are able to directly follow the two-step assembly process of vimentin IFs and quantify the time scale of the first lateral step to tens of ms with a lag time of below 3 ms. Although demonstrated for a specific biomolecular system here, our method may potentially be employed for a wide range of fast molecular reactions in biological or, more generally, soft matter systems, as it allows for a precise quantification of the kinetics underlying the aggregation and assembly.
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Affiliation(s)
- Eleonora Perego
- Institute for X-Ray Physics, University of Göttingen, 37077 Göttingen, Germany.
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, 37077 Göttingen, Germany. and Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
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30
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Denz M, Marschall M, Herrmann H, Köster S. Ion type and valency differentially drive vimentin tetramers into intermediate filaments or higher order assemblies. SOFT MATTER 2021; 17:870-878. [PMID: 33237065 DOI: 10.1039/d0sm01659d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Vimentin intermediate filaments, together with actin filaments and microtubules, constitute the cytoskeleton in cells of mesenchymal origin. The mechanical properties of the filaments themselves are encoded in their molecular architecture and depend on their ionic environment. It is thus of great interest to disentangle the influence of both the ion type and their concentration on vimentin assembly. We combine small angle X-ray scattering and fluorescence microscopy and show that vimentin in the presence of the monovalent ions, K+ and Na+, assembles into "standard filaments" with a radius of about 6 nm and 32 monomers per cross-section. In contrast, di- and multivalent ions, independent of type and valency, lead to the formation of thicker filaments associating over time into higher order structures. Hence, our results may indeed be of relevance for living cells, as local ion concentrations in the cytoplasm during certain physiological activities may differ considerably from average intracellular concentrations.
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Affiliation(s)
- Manuela Denz
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
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31
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Kraxner J, Lorenz C, Menzel J, Parfentev I, Silbern I, Denz M, Urlaub H, Schwappach B, Köster S. Post-translational modifications soften vimentin intermediate filaments. NANOSCALE 2021; 13:380-387. [PMID: 33351020 DOI: 10.1039/d0nr07322a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The mechanical properties of biological cells are determined by the cytoskeleton, a composite biopolymer network consisting of microtubules, actin filaments and intermediate filaments (IFs). By differential expression of cytoskeletal proteins, modulation of the network architecture and interactions between the filaments, cell mechanics may be adapted to varying requirements on the cell. Here, we focus on the intermediate filament protein vimentin and introduce post-translational modifications as an additional, much faster mechanism for mechanical modulation. We study the impact of phosphorylation on filament mechanics by recording force-strain curves using optical traps. Partial phosphorylation softens the filaments. We show that binding of the protein 14-3-3 to phosphorylated vimentin IFs further enhances this effect and speculate that in the cell 14-3-3 may serve to preserve the softening and thereby the altered cell mechanics. We explain our observation by the additional charges introduced during phosphorylation.
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Affiliation(s)
- Julia Kraxner
- Institute for X-Ray Physics, University of Göttingen, 37077 Göttingen, Germany.
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32
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Separation of Coiled-Coil Structures in Lamin A/C Is Required for the Elongation of the Filament. Cells 2020; 10:cells10010055. [PMID: 33396475 PMCID: PMC7824274 DOI: 10.3390/cells10010055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
Intermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, the crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the critical interaction. This study investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in the N-terminal of coil 1a and the C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in the elongation of IF proteins.
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Briot J, Simon M, Méchin MC. Deimination, Intermediate Filaments and Associated Proteins. Int J Mol Sci 2020; 21:E8746. [PMID: 33228136 PMCID: PMC7699402 DOI: 10.3390/ijms21228746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Deimination (or citrullination) is a post-translational modification catalyzed by a calcium-dependent enzyme family of five peptidylarginine deiminases (PADs). Deimination is involved in physiological processes (cell differentiation, embryogenesis, innate and adaptive immunity, etc.) and in autoimmune diseases (rheumatoid arthritis, multiple sclerosis and lupus), cancers and neurodegenerative diseases. Intermediate filaments (IF) and associated proteins (IFAP) are major substrates of PADs. Here, we focus on the effects of deimination on the polymerization and solubility properties of IF proteins and on the proteolysis and cross-linking of IFAP, to finally expose some features of interest and some limitations of citrullinomes.
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Affiliation(s)
| | | | - Marie-Claire Méchin
- UDEAR, Institut National de la Santé Et de la Recherche Médicale, Université Toulouse III Paul Sabatier, Université Fédérale de Toulouse Midi-Pyrénées, U1056, 31059 Toulouse, France; (J.B.); (M.S.)
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Abstract
Simple Summary Cell migration is an essential process from embryogenesis to cell death. This is tightly regulated by numerous proteins that help in proper functioning of the cell. In diseases like cancer, this process is deregulated and helps in the dissemination of tumor cells from the primary site to secondary sites initiating the process of metastasis. For metastasis to be efficient, cytoskeletal components like actin, myosin, and intermediate filaments and their associated proteins should co-ordinate in an orderly fashion leading to the formation of many cellular protrusions-like lamellipodia and filopodia and invadopodia. Knowledge of this process is the key to control metastasis of cancer cells that leads to death in 90% of the patients. The focus of this review is giving an overall understanding of these process, concentrating on the changes in protein association and regulation and how the tumor cells use it to their advantage. Since the expression of cytoskeletal proteins can be directly related to the degree of malignancy, knowledge about these proteins will provide powerful tools to improve both cancer prognosis and treatment. Abstract Successful metastasis depends on cell invasion, migration, host immune escape, extravasation, and angiogenesis. The process of cell invasion and migration relies on the dynamic changes taking place in the cytoskeletal components; actin, tubulin and intermediate filaments. This is possible due to the plasticity of the cytoskeleton and coordinated action of all the three, is crucial for the process of metastasis from the primary site. Changes in cellular architecture by internal clues will affect the cell functions leading to the formation of different protrusions like lamellipodia, filopodia, and invadopodia that help in cell migration eventually leading to metastasis, which is life threatening than the formation of neoplasms. Understanding the signaling mechanisms involved, will give a better insight of the changes during metastasis, which will eventually help targeting proteins for treatment resulting in reduced mortality and longer survival.
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35
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Zhang MY, Han YC, Han Q, Liang Y, Luo Y, Wei L, Yan T, Yang Y, Liu SL, Wang EH. Lamin B2 promotes the malignant phenotype of non-small cell lung cancer cells by upregulating dimethylation of histone 3 lysine 9. Exp Cell Res 2020; 393:112090. [PMID: 32416090 DOI: 10.1016/j.yexcr.2020.112090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/21/2022]
Abstract
The relationship between Lamin B2 and tumor proliferation and migration is unclear. We explored the impact of Lamin B2 on non-small cell lung cancer (NSCLC) cells. Tissue microarray and immunohistochemistry were combined to evaluate Lamin B2 expression and its relationship with the clinicopathological factors found in NSCLC. Western blotting, immunofluorescence analysis, and bioinformatics were used to investigate the effects of Lamin B2 on various regulatory pathways in cancer. Cytological experiments were conducted to evaluate Lamin B2 expression in tumor cells. We conducted co-immunoprecipitation and chromatin immunoprecipitation to explore the molecular mechanisms underlying the relationship between Lamin B2 and NSCLC and evaluate the results of rescue experiments. Lamin B2 was highly expressed in NSCLC and positively correlated with lymph node metastasis. In NSCLC, Lamin B2 interacted with Cyclin D1, upregulating G9α expression, thus increasing H3K9me2 levels. H3K9me2 binds to the promoter region of the E-cadherin gene (CDH1) to induce CDH1 silencing and promotes cancer cell migration. Thus, we found that Lamin B2 was highly expressed in NSCLC cells and promoted their migration by increasing H3K9me2 levels, which induced E-cadherin gene silencing.
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Affiliation(s)
- Mei-Yu Zhang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China.
| | - Yu-Chen Han
- Department of Pathology, Shanghai Jiaotong University Affiliated Chest Hospital, China
| | - Qiang Han
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China; The First Affiliated Hospital of China Medical University, China
| | - Yuan Liang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China
| | - Yuan Luo
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China
| | - Lai Wei
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China
| | - Ting Yan
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China
| | - Yue Yang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China
| | - Shu-Li Liu
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China; The First Affiliated Hospital of China Medical University, China.
| | - En-Hua Wang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, China; The First Affiliated Hospital of China Medical University, China.
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36
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Schepers AV, Lorenz C, Köster S. Tuning intermediate filament mechanics by variation of pH and ion charges. NANOSCALE 2020; 12:15236-15245. [PMID: 32642745 DOI: 10.1039/d0nr02778b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The cytoskeleton is formed by three types of filamentous proteins - microtubules, actin filaments, and intermediate filaments (IFs) - and enables cells to withstand external and internal forces. Vimentin is the most abundant IF protein in humans and assembles into 10 nm diameter filaments with remarkable mechanical properties, such as high extensibility and stability. It is, however, unclear to which extent these properties are influenced by the electrostatic environment. Here, we study the mechanical properties of single vimentin filaments by employing optical trapping combined with microfluidics. Force-strain curves, recorded at varying ion concentrations and pH values, reveal that the mechanical properties of single vimentin IFs are influenced by pH and ion concentration. By combination with Monte Carlo simulations, we relate these altered mechanics to electrostatic interactions of subunits within the filaments. We thus suggest possible mechanisms that allow cells to locally tune their stiffness without remodeling the entire cytoskeleton.
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Affiliation(s)
- Anna V Schepers
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Charlotta Lorenz
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
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37
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Type III intermediate filaments as targets and effectors of electrophiles and oxidants. Redox Biol 2020; 36:101582. [PMID: 32711378 PMCID: PMC7381704 DOI: 10.1016/j.redox.2020.101582] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Intermediate filaments (IFs) play key roles in cell mechanics, signaling and homeostasis. Their assembly and dynamics are finely regulated by posttranslational modifications. The type III IFs, vimentin, desmin, peripherin and glial fibrillary acidic protein (GFAP), are targets for diverse modifications by oxidants and electrophiles, for which their conserved cysteine residue emerges as a hot spot. Pathophysiological examples of these modifications include lipoxidation in cell senescence and rheumatoid arthritis, disulfide formation in cataracts and nitrosation in endothelial shear stress, although some oxidative modifications can also be detected under basal conditions. We previously proposed that cysteine residues of vimentin and GFAP act as sensors for oxidative and electrophilic stress, and as hinges influencing filament assembly. Accumulating evidence indicates that the structurally diverse cysteine modifications, either per se or in combination with other posttranslational modifications, elicit specific functional outcomes inducing distinct assemblies or network rearrangements, including filament stabilization, bundling or fragmentation. Cysteine-deficient mutants are protected from these alterations but show compromised cellular performance in network assembly and expansion, organelle positioning and aggresome formation, revealing the importance of this residue. Therefore, the high susceptibility to modification of the conserved cysteine of type III IFs and its cornerstone position in filament architecture sustains their role in redox sensing and integration of cellular responses. This has deep pathophysiological implications and supports the potential of this residue as a drug target. Type III intermediate filaments can be modified by many oxidants and electrophiles. Oxidative modifications of type III IFs occur in normal and pathological conditions. The conserved cysteine residue acts as a hub for redox/electrophilic modifications. Cysteine modifications elicit structure-dependent type III IF rearrangements. Type III intermediate filaments act as sensors for oxidative and electrophilic stress.
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Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions. Cells 2020; 9:cells9071633. [PMID: 32645958 PMCID: PMC7407374 DOI: 10.3390/cells9071633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022] Open
Abstract
The molecular architecture and assembly mechanism of intermediate filaments have been enigmatic for decades. Among those, lamin filaments are of particular interest due to their universal role in cell nucleus and numerous disease-related mutations. Filament assembly is driven by specific interactions of the elementary dimers, which consist of the central coiled-coil rod domain flanked by non-helical head and tail domains. We aimed to investigate the longitudinal 'head-to-tail' interaction of lamin dimers (the so-called ACN interaction), which is crucial for filament assembly. To this end, we prepared a series of recombinant fragments of human lamin A centred around the N- and C-termini of the rod. The fragments were stabilized by fusions to heterologous capping motifs which provide for a correct formation of parallel, in-register coiled-coil dimers. As a result, we established crystal structures of two N-terminal fragments one of which highlights the propensity of the coiled-coil to open up, and one C-terminal rod fragment. Additional studies highlighted the capacity of such N- and C-terminal fragments to form specific complexes in solution, which were further characterized using chemical cross-linking. These data yielded a molecular model of the ACN complex which features a 6.5 nm overlap of the rod ends.
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39
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Ramos I, Stamatakis K, Oeste CL, Pérez-Sala D. Vimentin as a Multifaceted Player and Potential Therapeutic Target in Viral Infections. Int J Mol Sci 2020; 21:E4675. [PMID: 32630064 PMCID: PMC7370124 DOI: 10.3390/ijms21134675] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022] Open
Abstract
Vimentin is an intermediate filament protein that plays key roles in integration of cytoskeletal functions, and therefore in basic cellular processes such as cell division and migration. Consequently, vimentin has complex implications in pathophysiology. Vimentin is required for a proper immune response, but it can also act as an autoantigen in autoimmune diseases or as a damage signal. Although vimentin is a predominantly cytoplasmic protein, it can also appear at extracellular locations, either in a secreted form or at the surface of numerous cell types, often in relation to cell activation, inflammation, injury or senescence. Cell surface targeting of vimentin appears to associate with the occurrence of certain posttranslational modifications, such as phosphorylation and/or oxidative damage. At the cell surface, vimentin can act as a receptor for bacterial and viral pathogens. Indeed, vimentin has been shown to play important roles in virus attachment and entry of severe acute respiratory syndrome-related coronavirus (SARS-CoV), dengue and encephalitis viruses, among others. Moreover, the presence of vimentin in specific virus-targeted cells and its induction by proinflammatory cytokines and tissue damage contribute to its implication in viral infection. Here, we recapitulate some of the pathophysiological implications of vimentin, including the involvement of cell surface vimentin in interaction with pathogens, with a special focus on its role as a cellular receptor or co-receptor for viruses. In addition, we provide a perspective on approaches to target vimentin, including antibodies or chemical agents that could modulate these interactions to potentially interfere with viral pathogenesis, which could be useful when multi-target antiviral strategies are needed.
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Affiliation(s)
- Irene Ramos
- Department of Neurology and Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Konstantinos Stamatakis
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC. Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain; (K.S.); (C.L.O.)
| | - Clara L. Oeste
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC. Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, 28049 Madrid, Spain; (K.S.); (C.L.O.)
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain
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40
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Odintsova E, Mohammed F, Trieber C, Rodriguez-Zamora P, Al-Jassar C, Huang TH, Fogl C, Knowles T, Sridhar P, Kumar J, Jeeves M, Chidgey M, Overduin M. Binding of the periplakin linker requires vimentin acidic residues D176 and E187. Commun Biol 2020; 3:83. [PMID: 32081916 PMCID: PMC7035337 DOI: 10.1038/s42003-020-0810-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/06/2020] [Indexed: 01/18/2023] Open
Abstract
Plakin proteins form connections that link the cell membrane to the intermediate filament cytoskeleton. Their interactions are mediated by a highly conserved linker domain through an unresolved mechanism. Here analysis of the human periplakin linker domain structure reveals a bi-lobed module transected by an electropositive groove. Key basic residues within the periplakin groove are vital for co-localization with vimentin in human cells and compromise direct binding which also requires acidic residues D176 and E187 in vimentin. We propose a model whereby basic periplakin linker domain residues recognize acidic vimentin side chains and form a complementary binding groove. The model is shared amongst diverse linker domains and can be used to investigate the effects of pathogenic mutations in the desmoplakin linker associated with arrhythmogenic right ventricular cardiomyopathy. Linker modules either act solely or collaborate with adjacent plakin repeat domains to create strong and adaptable tethering within epithelia and cardiac muscle.
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Affiliation(s)
- Elena Odintsova
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Catharine Trieber
- Department of Biochemistry, Faculty of Medicine & Dentistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Penelope Rodriguez-Zamora
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Mexico City, 04510, Mexico
| | - Caezar Al-Jassar
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Tzu-Han Huang
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claudia Fogl
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- The Binding Site, Birmingham, B15 1QT, UK
| | - Timothy Knowles
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jitendra Kumar
- Department of Biochemistry, Faculty of Medicine & Dentistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Martyn Chidgey
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
- Institute of Clinical Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Michael Overduin
- Department of Biochemistry, Faculty of Medicine & Dentistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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41
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Cogné B, Bouameur JE, Hayot G, Latypova X, Pattabiraman S, Caillaud A, Si-Tayeb K, Besnard T, Küry S, Chariau C, Gaignerie A, David L, Bordure P, Kaganovich D, Bézieau S, Golzio C, Magin TM, Isidor B. A dominant vimentin variant causes a rare syndrome with premature aging. Eur J Hum Genet 2020; 28:1218-1230. [PMID: 32066935 PMCID: PMC7609319 DOI: 10.1038/s41431-020-0583-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 12/19/2022] Open
Abstract
Progeroid syndromes are a group of rare genetic disorders, which mimic natural aging. Unraveling the molecular defects in such conditions could impact our understanding of age-related syndromes such as Alzheimer’s or cardiovascular diseases. Here we report a de novo heterozygous missense variant in the intermediate filament vimentin (c.1160 T > C; p.(Leu387Pro)) causing a multisystem disorder associated with frontonasal dysostosis and premature aging in a 39-year-old individual. Human vimentin p.(Leu387Pro) expression in zebrafish perturbed body fat distribution, and craniofacial and peripheral nervous system development. In addition, studies in patient-derived and transfected cells revealed that the variant affects vimentin turnover and its ability to form filaments in the absence of wild-type vimentin. Vimentin p.(Leu387Pro) expression diminished the amount of peripilin and reduced lipid accumulation in differentiating adipocytes, recapitulating key patient’s features in vivo and in vitro. Our data highlight the function of vimentin during development and suggest its contribution to natural aging.
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Affiliation(s)
- Benjamin Cogné
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, France.,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Jamal-Eddine Bouameur
- Division of Cell and Developmental Biology, Institute of Biology, University of Leipzig, Philipp-Rosenthal-Strasse 55, 04103, Leipzig, Germany
| | - Gaëlle Hayot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Xenia Latypova
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, France.,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Sundararaghavan Pattabiraman
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Walweg 33, 37073, Göttingen, Germany
| | - Amandine Caillaud
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Karim Si-Tayeb
- Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Thomas Besnard
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, France.,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Sébastien Küry
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, France.,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Caroline Chariau
- Nantes Université, CHU Nantes, Inserm, CNRS, SFR Santé, FED 4203, Inserm UMS 016, CNRS UMS 3556, F-44000, Nantes, France
| | - Anne Gaignerie
- Nantes Université, CHU Nantes, Inserm, CNRS, SFR Santé, FED 4203, Inserm UMS 016, CNRS UMS 3556, F-44000, Nantes, France
| | - Laurent David
- Nantes Université, CHU Nantes, Inserm, CNRS, SFR Santé, FED 4203, Inserm UMS 016, CNRS UMS 3556, F-44000, Nantes, France.,Nantes Université, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000, Nantes, France
| | - Philippe Bordure
- Centre Hospitalier Universitaire de Nantes, Service Oto-rhino-laryngologie, 9 quai Moncousu, 44093, Nantes, France
| | - Daniel Kaganovich
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Walweg 33, 37073, Göttingen, Germany.,1 Base Pharmaceuticals, 9A Monument Square, #2A, Boston, MA, 02129, USA
| | - Stéphane Bézieau
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, France.,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
| | - Christelle Golzio
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France. .,Université de Strasbourg, Strasbourg, France.
| | - Thomas M Magin
- Division of Cell and Developmental Biology, Institute of Biology, University of Leipzig, Philipp-Rosenthal-Strasse 55, 04103, Leipzig, Germany.
| | - Bertrand Isidor
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes, France. .,Université de Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France.
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42
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Lateral A11 type tetramerization in lamins. J Struct Biol 2020; 209:107404. [DOI: 10.1016/j.jsb.2019.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
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43
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Abstract
Lamin proteins are major constituents of the nuclear lamina. They are required for fundamental nuclear activities, as evidenced by the large number of laminopathies. Mutations in the human lamin A/C gene exhibit a broad spectrum of clinical manifestations. Most non-vertebrates including the nearest relatives of the vertebrates have only a single lamin gene. In jawed vertebrates (Gnathostomata), four lamin subtypes (B1, B2, LIII, and A) are found. Lampreys and hagfish form the two orders of jawless vertebrates, Agnatha, which represent the sister group of the Gnathostomata at the base of the vertebrate lineage. Lamin sequence information of lampreys and hagfish sheds light on the evolution of the lamin protein family at the base of the vertebrate lineage. In the genomes of the lamprey (Petromyzon marinus) and the hagfish (Eptatretus burgeri), only three lamin genes are present, a lamin A gene is lacking. The presence of an LIII gene in both, lampreys and hagfish, proves that the distinguishing features of this gene had been established before the agnathan/gnathostome split. The other two agnathan lamins, LmnI and LmnII, deviate strongly in their sequences from those of the gnathostome lamins. For none of these two agnathan lamins can orthology be established to one of the gnathostome lamin types. In the direct chromosomal neighbourhood of all three hagfish lamin genes, a MARCH3 paralog is found. This can be interpreted as further evidence that the vertebrate lamin genes have arisen in the course of the two rounds of whole genome duplication that took place at the base of the vertebrate lineage.
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44
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Stone EJ, Uchida A, Brown A. Charcot-Marie-Tooth disease Type 2E/1F mutant neurofilament proteins assemble into neurofilaments. Cytoskeleton (Hoboken) 2019; 76:423-439. [PMID: 31574566 DOI: 10.1002/cm.21566] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 11/12/2022]
Abstract
Charcot-Marie-Tooth disease Type 2E/1F (CMT2E/1F) is a peripheral neuropathy caused by mutations in neurofilament protein L (NFL), which is one of five neurofilament subunit proteins that co-assemble to form neurofilaments in vivo. Prior studies on cultured cells have shown that CMT2E/1F mutations disrupt neurofilament assembly and lead to protein aggregation, suggesting a possible disease mechanism. However, electron microscopy of axons in peripheral nerve biopsies from patients has revealed accumulations of neurofilament polymers of normal appearance and no evidence of protein aggregates. To reconcile these observations, we reexamined the assembly of seven CMT2E/1F NFL mutants in cultured cells. None of the mutants assembled into homopolymers in SW13vim- cells, but P8R, P22S, L268/269P, and P440/441L mutant NFL assembled into heteropolymers in the presence of neurofilament protein M (NFM) alone, and N98S, Q332/333P, and E396/397K mutant NFL assembled in the presence of NFM and peripherin. P8R, P22S, N98S, L268/269P, E396/397K, and P440/441L mutant NFL co-assembled into neurofilaments with endogenous NFL, NFM, and α-internexin in cultured neurons, although the N98S and E396/397K mutants showed reduced filament incorporation, and the Q332/333P mutant showed limited incorporation. We conclude that all the mutants are capable of assembling into neurofilaments, but for some of the mutants this was dependent on the identity of the other neurofilament proteins available for co-assembly, and most likely also their relative expression level. Thus, caution should be exercised when drawing conclusions about the assembly capacity of CMT2E/1F mutants based on transient transfections in cultured cells.
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Affiliation(s)
- Elizabeth J Stone
- Department of Neuroscience, Ohio State University, Columbus, Ohio.,Neuroscience Graduate Program, Ohio State University, Columbus, Ohio
| | - Atsuko Uchida
- Department of Neuroscience, Ohio State University, Columbus, Ohio
| | - Anthony Brown
- Department of Neuroscience, Ohio State University, Columbus, Ohio
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45
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Gae DD, Budamagunta MS, Hess JF, McCarrick RM, Lorigan GA, FitzGerald PG, Voss JC. Completion of the Vimentin Rod Domain Structure Using Experimental Restraints: A New Tool for Exploring Intermediate Filament Assembly and Mutations. Structure 2019; 27:1547-1560.e4. [PMID: 31402219 PMCID: PMC6774864 DOI: 10.1016/j.str.2019.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/23/2019] [Accepted: 07/22/2019] [Indexed: 11/28/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy of full-length vimentin and X-ray crystallography of vimentin peptides has provided concordant structural data for nearly the entire central rod domain of the protein. In this report, we use a combination of EPR spectroscopy and molecular modeling to determine the structure and dynamics of the missing region and unite the separate elements into a single structure. Validation of the linker 1-2 (L1-2) modeling approach is demonstrated by the close correlation between EPR and X-ray data in the previously solved regions. Importantly, molecular dynamic (MD) simulation of the constructed model agrees with spin label motion as determined by EPR. Furthermore, MD simulation shows L1-2 heterogeneity, with a concerted switching of states among the dimer chains. These data provide the first ever experimentally driven model of a complete intermediate filament rod domain, providing research tools for further modeling and assembly studies.
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Affiliation(s)
- David D Gae
- Department of Surgery, School of Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Madhu S Budamagunta
- Department of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - John F Hess
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Paul G FitzGerald
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California Davis, Davis, CA 95616, USA.
| | - John C Voss
- Department of Biochemistry & Molecular Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA.
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46
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Abstract
Lamins are evolutionarily conserved nuclear intermediate filament proteins. They provide structural support for the nucleus and help regulate many other nuclear activities. Mutations in human lamin genes, and especially in the LMNA gene, cause numerous diseases, termed laminopathies, including muscle, cardiac, metabolic, neuronal and early aging diseases. Most laminopathies arise from autosomal dominant missense mutations. Many of the mutant residues are conserved in the lamin genes of the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster. Our current understanding of the mechanisms leading to these diseases is mostly based on patients cell lines and animal models including C. elegans and D. melanogaster. The simpler lamin system and the powerful genetic tools offered by these invertebrate organisms greatly contributed to such studies. Here we provide an overview of the studies of laminopathies in Drosophila and C. elegans models.
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Affiliation(s)
- Ryszard Rzepecki
- a Laboratory of Nuclear Proteins, Faculty of Biotechnology , University of Wroclaw , Fryderyka Joliot-Curie, Wroclaw , Poland
| | - Yosef Gruenbaum
- a Laboratory of Nuclear Proteins, Faculty of Biotechnology , University of Wroclaw , Fryderyka Joliot-Curie, Wroclaw , Poland.,b Department of Genetics , Institute of Life Sciences, Hebrew University of Jerusalem , Jerusalem , Israel
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47
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Structural basis for lamin assembly at the molecular level. Nat Commun 2019; 10:3757. [PMID: 31434876 PMCID: PMC6704074 DOI: 10.1038/s41467-019-11684-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/26/2019] [Indexed: 12/02/2022] Open
Abstract
Nuclear structure and function are governed by lamins, which are intermediate filaments that mostly consist of α-helices. Different lamin assembly models have been proposed based on low resolution and fragmented structures. However, their assembly mechanisms are still poorly understood at the molecular level. Here, we present the crystal structure of a long human lamin fragment at 3.2 Å resolution that allows the visualization of the features of the full-length protein. The structure shows an anti-parallel arrangement of the two coiled-coil dimers, which is important for the assembly process. We further discover an interaction between the lamin dimers by using chemical cross-linking and mass spectrometry analysis. Based on these two interactions, we propose a molecular mechanism for lamin assembly that is in agreement with a recent model representing the native state and could explain pathological mutations. Our findings also provide the molecular basis for assembly mechanisms of other intermediate filaments. Lamins are intermediate filaments and the major component of the nuclear lamina. Here the authors determine the crystal structure of a construct comprising the N-terminal half of human lamin A/C and use their structure and cross-linking and biochemical experiments to discuss lamin assembly.
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48
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D'Amore C, Salizzato V, Borgo C, Cesaro L, Pinna LA, Salvi M. A Journey through the Cytoskeleton with Protein Kinase CK2. Curr Protein Pept Sci 2019; 20:547-562. [PMID: 30659536 DOI: 10.2174/1389203720666190119124846] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/21/2018] [Accepted: 01/09/2019] [Indexed: 01/15/2023]
Abstract
Substrate pleiotropicity, a very acidic phosphorylation consensus sequence, and an apparent uncontrolled activity, are the main features of CK2, a Ser/Thr protein kinase that is required for a plethora of cell functions. Not surprisingly, CK2 appears to affect cytoskeletal structures and correlated functions such as cell shape, mechanical integrity, cell movement and division. This review outlines our current knowledge of how CK2 regulates cytoskeletal structures, and discusses involved pathways and molecular mechanisms.
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Affiliation(s)
- Claudio D'Amore
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Valentina Salizzato
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.,CNR Institute of Neurosciences, Via U. Bassi 58/B, Padova, Italy
| | - Christian Borgo
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Luca Cesaro
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy.,CNR Institute of Neurosciences, Via U. Bassi 58/B, Padova, Italy
| | - Mauro Salvi
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, Padova, Italy
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49
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Eldirany SA, Ho M, Hinbest AJ, Lomakin IB, Bunick CG. Human keratin 1/10-1B tetramer structures reveal a knob-pocket mechanism in intermediate filament assembly. EMBO J 2019; 38:embj.2018100741. [PMID: 31036554 PMCID: PMC6545558 DOI: 10.15252/embj.2018100741] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 01/07/2023] Open
Abstract
To characterize keratin intermediate filament assembly mechanisms at atomic resolution, we determined the crystal structure of wild-type human keratin-1/keratin-10 helix 1B heterotetramer at 3.0 Å resolution. It revealed biochemical determinants for the A11 mode of axial alignment in keratin filaments. Four regions on a hydrophobic face of the K1/K10-1B heterodimer dictated tetramer assembly: the N-terminal hydrophobic pocket (defined by L227K1, Y230K1, F231K1, and F234K1), the K10 hydrophobic stripe, K1 interaction residues, and the C-terminal anchoring knob (formed by F314K1 and L318K1). Mutation of both knob residues to alanine disrupted keratin 1B tetramer and full-length filament assembly. Individual knob residue mutant F314AK1, but not L318AK1, abolished 1B tetramer formation. The K1-1B knob/pocket mechanism is conserved across keratins and many non-keratin intermediate filaments. To demonstrate how pathogenic mutations cause skin disease by altering filament assembly, we additionally determined the 2.39 Å structure of K1/10-1B containing a S233LK1 mutation linked to epidermolytic palmoplantar keratoderma. Light scattering and circular dichroism measurements demonstrated enhanced aggregation of K1S233L/K10-1B in solution without affecting secondary structure. The K1S233L/K10-1B octamer structure revealed S233LK1 causes aberrant hydrophobic interactions between 1B tetramers.
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Affiliation(s)
| | - Minh Ho
- Department of DermatologyYale UniversityNew HavenCTUSA
| | | | - Ivan B Lomakin
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
| | - Christopher G Bunick
- Department of DermatologyYale UniversityNew HavenCTUSA,Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
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50
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Hirve N, Rajanikanth V, Hogan PG, Gudlur A. Coiled-Coil Formation Conveys a STIM1 Signal from ER Lumen to Cytoplasm. Cell Rep 2019; 22:72-83. [PMID: 29298434 DOI: 10.1016/j.celrep.2017.12.030] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/07/2017] [Accepted: 12/10/2017] [Indexed: 10/18/2022] Open
Abstract
STIM1 and STIM2 are endoplasmic reticulum (ER) membrane proteins that sense decreases in ER-luminal free Ca2+ and, through a conformational change in the STIM cytoplasmic domain, control gating of the plasma membrane Ca2+ channel ORAI1. To determine how STIM1 conveys a signal from the ER lumen to the cytoplasm, we studied the Ca2+-dependent conformational change of engineered STIM1 proteins in isolated ER membranes and, in parallel, physiological activation of these proteins in cells. We find that conserved "sentinel" features of the CC1 region help to prevent activation while Ca2+ is bound to STIM ER-luminal domains. Reduced ER-luminal Ca2+ drives a concerted conformational change, in which STIM luminal domains rearrange and the STIM transmembrane helices and initial parts of the CC1 regions pair in an extended coiled coil. This intradimer rearrangement overcomes the relatively weak CC1-SOAR/CAD interactions that hold STIM in an inactive conformation, releasing the SOAR/CAD domain to activate ORAI channels.
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Affiliation(s)
- Nupura Hirve
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Vangipurapu Rajanikanth
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Patrick G Hogan
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; Program in Immunology, University of California, San Diego, La Jolla, CA 92037, USA.
| | - Aparna Gudlur
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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