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      FerriTag is a new genetically-encoded inducible tag for correlative light-electron microscopy

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      Nature Communications
      Nature Publishing Group UK

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          Abstract

          A current challenge is to develop tags to precisely visualize proteins in cells by light and electron microscopy. Here, we introduce FerriTag, a genetically-encoded chemically-inducible tag for correlative light-electron microscopy. FerriTag is a fluorescent recombinant electron-dense ferritin particle that can be attached to a protein-of-interest using rapamycin-induced heterodimerization. We demonstrate the utility of FerriTag for correlative light-electron microscopy by labeling proteins associated with various intracellular structures including mitochondria, plasma membrane, and clathrin-coated pits and vesicles. FerriTagging has a good signal-to-noise ratio and a labeling resolution of approximately 10 nm. We demonstrate how FerriTagging allows nanoscale mapping of protein location relative to a subcellular structure, and use it to detail the distribution and conformation of huntingtin-interacting protein 1 related (HIP1R) in and around clathrin-coated pits.

          Abstract

          Correlative light-electron microscopy (CLEM) pairs versatile fluorescence imaging with high resolution electron microscopy. Here, the authors develop a genetically-encoded, chemically-inducible tag that allows acute labeling of single proteins for CLEM.

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          Most cited references26

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          Directed evolution of APEX2 for electron microscopy and proteomics

          APEX is an engineered peroxidase that functions both as an electron microscopy tag, and as a promiscuous labeling enzyme for live-cell proteomics. Because the limited sensitivity of APEX precludes applications requiring low APEX expression, we used yeast display evolution to improve its catalytic efficiency. Our evolved APEX2 is far more active in cells, enabling the superior enrichment of endogenous mitochondrial and endoplasmic reticulum membrane proteins and the use of electron microscopy to resolve the sub-mitochondrial localization of calcium uptake regulatory protein MICU1.
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            Engineered ascorbate peroxidase as a genetically-encoded reporter for electron microscopy

            Electron microscopy (EM) is the standard method for imaging cellular structures with nanometer resolution, but existing genetic tags are inactive in most cellular compartments 1 or require light and are difficult to use 2 . Here we report the development of a simple and robust EM genetic tag, called “APEX,” that is active in all cellular compartments and does not require light. APEX is a monomeric 28 kDa peroxidase that withstands strong EM fixation to give excellent ultrastructural preservation. We demonstrate the utility of APEX for high-resolution EM imaging of a variety of mammalian organelles and specific proteins. We also fused APEX to the N- or C-terminus of the mitochondrial calcium uniporter (MCU), a newly identified channel whose topology is disputed 3,4 . MCU-APEX and APEX-MCU give EM contrast exclusively in the mitochondrial matrix, suggesting that both the N-and C-termini of MCU face the matrix.
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              Protein localization in electron micrographs using fluorescence nanoscopy

              A complete portrait of a cell requires a detailed description of its molecular topography: proteins must be linked to particular organelles. Immuno-electron microscopy can reveal locations of proteins with nanometer resolution but is limited by the quality of fixation, the paucity of antibodies, and the inaccessibility of the antigens. Here, we describe correlative fluorescence electron microscopy for the nanoscopic localization of proteins in electron micrographs. Proteins tagged with Citrine or tdEos were expressed in Caenorhabditis elegans, fixed and embedded. Tagged proteins were imaged from ultrathin sections using stimulated emission depletion microscopy (STED) or photoactivated localization microscopy (PALM). Fluorescence was correlated with organelles imaged in electron micrographs from the same sections. These methods were used to successfully localize histones, a mitochondrial protein, and a presynaptic dense projection protein in electron micrographs.
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                Author and article information

                Contributors
                s.j.royle@warwick.ac.uk
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                4 July 2018
                4 July 2018
                2018
                : 9
                : 2604
                Affiliations
                ISNI 0000 0000 8809 1613, GRID grid.7372.1, Centre for Mechanochemical Cell Biology, , Warwick Medical School, ; Gibbet Hill Road, Coventry, CV4 7AL UK
                Author information
                http://orcid.org/0000-0003-3297-8604
                http://orcid.org/0000-0001-8927-6967
                Article
                4993
                10.1038/s41467-018-04993-0
                6031641
                29973588
                daadde31-3f36-4b87-b671-8d6f66fac720
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 30 June 2017
                : 24 May 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100000289, Cancer Research UK (CRUK);
                Award ID: C25425/A15182
                Award ID: C25425/A16141
                Award Recipient :
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