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Keating SS, Bademosi AT, San Gil R, Walker AK. Aggregation-prone TDP-43 sequesters and drives pathological transitions of free nuclear TDP-43. Cell Mol Life Sci 2023; 80:95. [PMID: 36930291 PMCID: PMC10023653 DOI: 10.1007/s00018-023-04739-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023]
Abstract
Aggregation of the RNA-binding protein, TDP-43, is the unifying hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43-related neurodegeneration involves multiple changes to normal physiological TDP-43, which undergoes nuclear depletion, cytoplasmic mislocalisation, post-translational modification, and aberrant liquid-liquid phase separation, preceding inclusion formation. Along with toxic cytoplasmic aggregation, concurrent depletion and dysfunction of normal nuclear TDP-43 in cells with TDP-43 pathology is likely a key potentiator of neurodegeneration, but is not well understood. To define processes driving TDP-43 dysfunction, we used CRISPR/Cas9-mediated fluorescent tagging to investigate how disease-associated stressors and pathological TDP-43 alter abundance, localisation, self-assembly, aggregation, solubility, and mobility dynamics of normal nuclear TDP-43 over time in live cells. Oxidative stress stimulated liquid-liquid phase separation of endogenous TDP-43 into droplet-like puncta, or spherical shell-like anisosomes. Further, nuclear RNA-binding-ablated or acetylation-mimicking TDP-43 readily sequestered and depleted free normal nuclear TDP-43 into dynamic anisosomes, in which recruited endogenous TDP-43 proteins remained soluble and highly mobile. Large, phosphorylated inclusions formed by nuclear or cytoplasmic aggregation-prone TDP-43 mutants also caused sequestration, but rendered endogenous TDP-43 immobile and insoluble, indicating pathological transition. These findings suggest that RNA-binding deficiency and post-translational modifications including acetylation exacerbate TDP-43 aggregation and dysfunction by driving sequestration, mislocalisation, and depletion of normal nuclear TDP-43 in neurodegenerative diseases.
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Affiliation(s)
- Sean S Keating
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Adekunle T Bademosi
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Rebecca San Gil
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Adam K Walker
- Neurodegeneration Pathobiology Laboratory, Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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2
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Liu CY, Jin M, Guo H, Zhao HZ, Hou LN, Yang Y, Wen YJ, Wang FX. Concurrent Gene Insertion, Deletion, and Inversion during the Construction of a Novel Attenuated BoHV-1 Using CRISPR/Cas9 Genome Editing. Vet Sci 2022; 9:vetsci9040166. [PMID: 35448664 PMCID: PMC9029512 DOI: 10.3390/vetsci9040166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/12/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Bovine herpesvirus type I (BoHV-1) is an important pathogen that causes respiratory disease in bovines. The disease is prevalent worldwide, causing huge economic losses to the cattle industry. Gene-deficient vaccines with immunological markers to distinguish them from wild-type infections have become a mainstream in vaccine research and development. In order to knock out the gE gene BoHV-1, we employed the CRISPR/Cas9 system. Interesting phenomena were observed at the single guide RNA (sgRNA) splicing site, including gene insertion, gene deletion, and the inversion of 5′ and 3′ ends of the sgRNA splicing site. In addition to the deletion of the gE gene, the US9 gene, and the non-coding regions of gE and US9, it was found that the US4 sequence, US6 sequence, and part of the US7 sequence were inserted into the EGFP sgRNA splicing site and the 3′ end of the EGFP sequence was deleted. Similar to the BoHV-1 parent, the BoHV-1 mutants induced high neutralizing antibodies titer levels in mice. In summary, we developed a series of recombinant gE-deletion BoHV-1 samples using the CRISPR/Cas9 gene editing system. The mutant viruses with EGFP+ or EGFP− will lay the foundation for research on BoHV-1 and vaccine development in the future.
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Affiliation(s)
- Chun-Yu Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.-Y.L.); (M.J.); (H.G.); (H.-Z.Z.); (L.-N.H.)
| | - Ming Jin
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.-Y.L.); (M.J.); (H.G.); (H.-Z.Z.); (L.-N.H.)
| | - Hao Guo
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.-Y.L.); (M.J.); (H.G.); (H.-Z.Z.); (L.-N.H.)
| | - Hong-Zhe Zhao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.-Y.L.); (M.J.); (H.G.); (H.-Z.Z.); (L.-N.H.)
| | - Li-Na Hou
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.-Y.L.); (M.J.); (H.G.); (H.-Z.Z.); (L.-N.H.)
| | - Yang Yang
- School of Life Sciences, Inner Mongolia University, Hohhot 010018, China;
| | - Yong-Jun Wen
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.-Y.L.); (M.J.); (H.G.); (H.-Z.Z.); (L.-N.H.)
- Correspondence: (Y.-J.W.); (F.-X.W.)
| | - Feng-Xue Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.-Y.L.); (M.J.); (H.G.); (H.-Z.Z.); (L.-N.H.)
- Correspondence: (Y.-J.W.); (F.-X.W.)
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Perfilov MM, Gavrikov AS, Lukyanov KA, Mishin AS. Transient Fluorescence Labeling: Low Affinity-High Benefits. Int J Mol Sci 2021; 22:11799. [PMID: 34769228 PMCID: PMC8583718 DOI: 10.3390/ijms222111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
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Affiliation(s)
| | | | | | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.P.); (A.S.G.); (K.A.L.)
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Lambert GG, Depernet H, Gotthard G, Schultz DT, Navizet I, Lambert T, Adams SR, Torreblanca-Zanca A, Chu M, Bindels DS, Levesque V, Nero Moffatt J, Salih A, Royant A, Shaner NC. Aequorea's secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing. PLoS Biol 2020; 18:e3000936. [PMID: 33137097 PMCID: PMC7660908 DOI: 10.1371/journal.pbio.3000936] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/12/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022] Open
Abstract
Using mRNA sequencing and de novo transcriptome assembly, we identified, cloned, and characterized 9 previously undiscovered fluorescent protein (FP) homologs from Aequorea victoria and a related Aequorea species, with most sequences highly divergent from A. victoria green fluorescent protein (avGFP). Among these FPs are the brightest green fluorescent protein (GFP) homolog yet characterized and a reversibly photochromic FP that responds to UV and blue light. Beyond green emitters, Aequorea species express purple- and blue-pigmented chromoproteins (CPs) with absorbances ranging from green to far-red, including 2 that are photoconvertible. X-ray crystallography revealed that Aequorea CPs contain a chemically novel chromophore with an unexpected crosslink to the main polypeptide chain. Because of the unique attributes of several of these newly discovered FPs, we expect that Aequorea will, once again, give rise to an entirely new generation of useful probes for bioimaging and biosensing.
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Affiliation(s)
- Gerard G. Lambert
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Hadrien Depernet
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Darrin T. Schultz
- University of California Santa Cruz, Santa Cruz, California, United States of America
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi-Echelle, Université Gustave Eiffel, Université Paris Est Creteil, Marne-la-Vallée, France
| | - Talley Lambert
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen R. Adams
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Albertina Torreblanca-Zanca
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Meihua Chu
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Daphne S. Bindels
- Nikon Imaging Center, University of California San Diego, La Jolla, California, United States of America
| | - Vincent Levesque
- Birch Aquarium at Scripps, La Jolla, California, United States of America
| | | | - Anya Salih
- Confocal Facility, Western Sydney University, Penrith, New South Wales, Australia
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Nathan C. Shaner
- Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego School of Medicine, La Jolla, California, United States of America
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Muslinkina L, Gavrikov AS, Bozhanova NG, Mishin AS, Baranov MS, Meiler J, Pletneva NV, Pletnev VZ, Pletnev S. Structure-Based Rational Design of Two Enhanced Bacterial Lipocalin Blc Tags for Protein-PAINT Super-resolution Microscopy. ACS Chem Biol 2020; 15:2456-2465. [PMID: 32809793 DOI: 10.1021/acschembio.0c00440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Super-resolution fluorescent imaging in living cells remains technically challenging, largely due to the photodecomposition of fluorescent tags. The recently suggested protein-PAINT is the only super-resolution technique available for prolonged imaging of proteins in living cells. It is realized with complexes of fluorogen-activating proteins, expressed as fusions, and solvatochromic synthetic dyes. Once photobleached, the dye in the complex is replaced with a fresh fluorogen available in the sample. With suitable kinetics, this replacement creates fluorescence blinking required for attaining super-resolution and overcomes photobleaching associated with the loss of an irreplaceable fluorophore. Here we report on the rational design of two protein-PAINT tags based on the 1.58 Å crystal structure of the DiB1:M739 complex, an improved green-emitting DiB3/F74V:M739 and a new orange-emitting DiB3/F53L:M739. They outperform previously reported DiB-based tags to become best in class biomarkers for protein-PAINT. The new tags advance protein-PAINT from the proof-of-concept to a reliable tool suitable for prolonged super-resolution imaging of intracellular proteins in fixed and living cells and two-color PAINT-like nanoscopy with a single fluorogen.
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Affiliation(s)
- Liya Muslinkina
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, Illinois 60439, United States
| | - Alexey S. Gavrikov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Nina G. Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Alexander S. Mishin
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Mikhail S. Baranov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Nadya V. Pletneva
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Vladimir Z. Pletnev
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergei Pletnev
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, Illinois 60439, United States
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Oi C, Gidden Z, Holyoake L, Kantelberg O, Mochrie S, Horrocks MH, Regan L. LIVE-PAINT allows super-resolution microscopy inside living cells using reversible peptide-protein interactions. Commun Biol 2020; 3:458. [PMID: 32820217 PMCID: PMC7441314 DOI: 10.1038/s42003-020-01188-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 11/09/2022] Open
Abstract
We present LIVE-PAINT, a new approach to super-resolution fluorescent imaging inside live cells. In LIVE-PAINT only a short peptide sequence is fused to the protein being studied, unlike conventional super-resolution methods, which rely on directly fusing the biomolecule of interest to a large fluorescent protein, organic fluorophore, or oligonucleotide. LIVE-PAINT works by observing the blinking of localized fluorescence as this peptide is reversibly bound by a protein that is fused to a fluorescent protein. We have demonstrated the effectiveness of LIVE-PAINT by imaging a number of different proteins inside live S. cerevisiae. Not only is LIVE-PAINT widely applicable, easily implemented, and the modifications minimally perturbing, but we also anticipate it will extend data acquisition times compared to those previously possible with methods that involve direct fusion to a fluorescent protein.
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Affiliation(s)
- Curran Oi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
| | - Zoe Gidden
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Louise Holyoake
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Owen Kantelberg
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland
| | - Simon Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Mathew H Horrocks
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland.
| | - Lynne Regan
- Center for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland.
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Polyaniline as an On−Off−On bright green fluorescent probe: Solvent directed synthesis, characterization and recognition of chromium through the inner filter effect. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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