Determining the target protein localization in 3D using the combination of FIB-SEM and APEX2

Yang Shi1, Li Wang2, Jianguo Zhang2, Yujia Zhai1, Fei Sun2
1National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
2Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China

Tóm tắt

Từ khóa


Tài liệu tham khảo

Adams SR, Campbell RE, Gross LA, Martin BR, Walkup GK, Yao Y, Llopis J, Tsien RY (2002) New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J Am Chem Soc 124:6063–6076

Bruggisser J, Käser S, Mani J, Schneider A (2017) Biogenesis of a mitochondrial outer membrane protein in Trypanosoma brucei: targeting signal and dependence on a unique biogenesis factor. J Biol Chem 292:3400–3410

Connolly CN, Futter CE, Gibson A, Hopkins CR, Cutler DF (1994) Transport into and out of the Golgi complex studied by transfecting cells with cDNAs encoding horseradish peroxidase. J Cell Biol 127:641

De Mey J, Moeremans M, Geuens G, Nuydens R, De Brabander M (1981) High resolution light and electron microscopic localization of tubulin with the IGS (immuno gold staining) method. Cell Biol Int Rep 5:889–899

Denk W, Horstmann H (2004) Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol 2:e329

Gaietta G, Deerinck TJ, Adams SR, Bouwer J, Tour O, Laird DW, Sosinsky GE, Tsien RY, Ellisman MH (2002) Multicolor and electron microscopic imaging of connexin trafficking. Science 296:503

Giepmans BNG, Deerinck TJ, Smarr BL, Jones YZ, Ellisman MH (2005) Correlated light and electron microscopic imaging of multiple endogenous proteins using Quantum dots. Nat Methods 2:743–749

Grabenbauer M, Geerts WJC, Fernadez-Rodriguez J, Hoenger A, Koster AJ, Nilsson T (2005) Correlative microscopy and electron tomography of GFP through photooxidation. Nat Methods 2:857–862

Griparic L, van der Wel NN, Orozco IJ, Peters PJ, van der Bliek AM (2004) Loss of the intermembrane space protein Mgm1/OPA1 induces swelling and localized constrictions along the lengths of mitochondria. J Biol Chem 279:18792–18798

Hamer DH (1986) Metallothionein. Annu Rev Biochem 55:913–951

Harris KM, Perry E, Bourne J, Feinberg M, Ostroff L, Hurlburt J (2006) Uniform serial sectioning for transmission electron microscopy. J Neurosci 26:12101

Hart RG (1968) Electron microscopy of unstained biological material: the polytropic montage. Science 159:1464

Hopkins C, Gibson A, Stinchcombe J, Futter C (2000) Chimeric molecules employing horseradish peroxidase as reporter enzyme for protein localization in the electron microscope. In: Jeremy Thorner SDE, John NA (eds) Methods in enzymology, vol 327. Academic Press, New York, pp 35–45

Horstmann H, Körber C, Sätzler K, Aydin D, Kuner T (2012) Serial section scanning electron microscopy (S3EM) on silicon wafers for ultra-structural volume imaging of cells and tissues. PLoS ONE 7:e35172

Huang P, Yu T, Yoon Y (2007) Mitochondrial clustering induced by overexpression of the mitochondrial fusion protein Mfn2 causes mitochondrial dysfunction and cell death. Eur J Cell Biol 86:289–302

James DI, Parone PA, Mattenberger Y, Martinou J-C (2003) hFis1, a novel component of the mammalian mitochondrial fission machinery. J Biol Chem 278:36373–36379

Kagi JH, Schaffer A (1988) Biochemistry of metallothionein. Biochemistry 27:8509–8515

Knott G, Marchman H, Wall D, Lich B (2008) Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. J Neurosci 28:2959

Koshiba T, Detmer SA, Kaiser JT, Chen H, McCaffery JM, Chan DC (2004) Structural basis of mitochondrial tethering by mitofusin complexes. Science 305:858

Koster AJ, Chen H, Sedat JW, Agard DA (1992) Automated microscopy for electron tomography. Ultramicroscopy 46:207–227

Ladinsky MS, Mastronarde DN, McIntosh JR, Howell KE, Staehelin LA (1999) Golgi structure in three dimensions: functional insights from the normal rat kidney cell. J Cell Biol 144:1135

Lam SS, Martell JD, Kamer KJ, Deerinck TJ, Ellisman MH, Mootha VK, Ting AY (2015) Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat Methods 12:51–54

Li J, Wang Y, Chiu S-L, Cline HT (2010) Membrane targeted horseradish peroxidase as a marker for correlative fluorescence and electron microscopy studies. Front Neural Circuits 4:6

Li W, Ding W, Ji G, Wang L, Zhang J, Sun F (2016) Three-dimensional visualization of arsenic stimulated mouse liver sinusoidal by FIB-SEM approach. Protein Cell 7:227–232

Liu T, Yu R, Jin S-B, Han L, Lendahl U, Zhao J, Nistér M (2013) The mitochondrial elongation factors MIEF1 and MIEF2 exert partially distinct functions in mitochondrial dynamics. Exp Cell Res 319:2893–2904

Martell JD, Deerinck TJ, Sancak Y, Poulos TL, Mootha VK, Sosinsky GE, Ellisman MH, Ting AY (2012) Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nat Biotechnol 30:1143–1148

McBride HM, Millar DG, Li JM, Shore GC (1992) A signal-anchor sequence selective for the mitochondrial outer membrane. J Cell Biol 119:1451

Meeusen S, McCaffery JM, Nunnari J (2004) Mitochondrial fusion intermediates revealed in vitro. Science 305:1747

Meißlitzer-Ruppitsch C, Vetterlein M, Stangl H, Maier S, Neumüller J, Freissmuth M, Pavelka M, Ellinger A (2008) Electron microscopic visualization of fluorescent signals in cellular compartments and organelles by means of DAB-photoconversion. Histochem Cell Biol 130:407–419

Mercogliano CP, DeRosier DJ (2007) Concatenated metallothionein as a clonable gold label for electron microscopy. J Struct Biol 160:70–82

Morphew MK, O’Toole ET, Page CL, Pagratis M, Meehl J, Giddings T, Gardner JM, Ackerson C, Jaspersen SL, Winey M, Hoenger A, McIntosh JR (2015) Metallothionein as a clonable tag for protein localization by electron microscopy of cells. J Microsc 260:20–29

Mozdy AD, McCaffery JM, Shaw JM (2000) Dnm1p Gtpase-mediated mitochondrial fission is a multi-step process requiring the novel integral membrane component Fis1p. J Cell Biol 151:367–380

Otera H, Wang C, Cleland MM, Setoguchi K, Yokota S, Youle RJ, Mihara K (2010) Mff is an essential factor for mitochondrial recruitment of Drp1 during mitochondrial fission in mammalian cells. J Cell Biol 191:1141–1158

Palmer CS, Osellame LD, Laine D, Koutsopoulos OS, Frazier AE, Ryan MT (2011) MiD49 and MiD51, new components of the mitochondrial fission machinery. EMBO Rep 12:565–573

Peddie CJ, Collinson LM (2014) Exploring the third dimension: volume electron microscopy comes of age. Micron 61:9–19

Rojo M, Legros F, Chateau D, Lombès A (2002) Membrane topology and mitochondrial targeting of mitofusins, ubiquitous mammalian homologs of the transmembrane GTPase Fzo. J Cell Sci 115:1663

Santel A, Fuller MT (2001) Control of mitochondrial morphology by a human mitofusin. J Cell Sci 114:867

Seligman AM, Karnovsky MJ, Wasserkrug HL, Hanker JS (1968) Nondroplet ultrastructural demonstration of cytochrome oxidase activity with a polymerizing osmiophilic reagent, diaminobenzidine (DAB). J Cell Biol 38:1

Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY (2011) A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol 9:e1001041

Smirnova E, Griparic L, Shurland D-L, van der Bliek AM (2001) Dynamin-related protein Drp1 is required for mitochondrial division in mammalian cells. Mol Biol Cell 12:2245–2256

Song Z, Chen H, Fiket M, Alexander C, Chan DC (2007) OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L. J Cell Biol 178:749

Su Y, Nykanen M, Jahn KA, Whan R, Cantrill L, Soon LL, Ratinac KR, Braet F (2010) Multi-dimensional correlative imaging of subcellular events: combining the strengths of light and electron microscopy. Biophys Rev 2:121–135

Waizenegger T, Stan T, Neupert W, Rapaport D (2003) Signal-anchor domains of proteins of the outer membrane of mitochondria: structural and functional characteristics. J Biol Chem 278:42064–42071

Yoon Y, Krueger EW, Oswald BJ, McNiven MA (2003) The mitochondrial protein hFis1 regulates mitochondrial fission in mammalian cells through an interaction with the dynamin-like protein DLP1. Mol Cell Biol 23:5409–5420

Youle RJ, Van Der Bliek AM (2012) Mitochondrial fission, fusion, and stress. Science 337:1062–1065

Zhao J, Liu T, Jin S, Wang X, Qu M, Uhlén P, Tomilin N, Shupliakov O, Lendahl U, Nistér M (2011) Human MIEF1 recruits Drp1 to mitochondrial outer membranes and promotes mitochondrial fusion rather than fission. EMBO J 30:2762–2778