1932

Abstract

Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen–hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.

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2017-06-20
2024-06-13
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Literature Cited

  1. Ruska E. 1.  1987. Nobel lecture. The development of the electron microscope and of electron microscopy. Biosci. Rep. 7:607–29 [Google Scholar]
  2. Kisielowski C, Freitag B, Bischoff M, van Lin H, Lazar S. 2.  et al. 2008. Detection of single atoms and buried defects in three dimensions by aberration-corrected electron microscope with 0.5-Å information limit. Microsc. Microanal. 14:469–77 [Google Scholar]
  3. Porter KR, Kallman FL. 3.  1952. Significance of cell particulates as seen by electron microscopy. Ann. NY Acad. Sci. 54:882–91 [Google Scholar]
  4. Pilhofer M, Ladinsky MS, McDowall AW, Jensen GJ. 4.  2010. Bacterial TEM: new insights from cryo-microscopy. Methods Cell Biol 96:21–45 [Google Scholar]
  5. Dubochet J, Adrian M, Chang JJ, Homo JC, Lepault J. 5.  et al. 1988. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21:129–228 [Google Scholar]
  6. Tivol WF, Briegel A, Jensen GJ. 6.  2008. An improved cryogen for plunge freezing. Microsc. Microanal. 14:375–79 [Google Scholar]
  7. Koster AJ, Grimm R, Typke D, Hegerl R, Stoschek A. 7.  et al. 1997. Perspectives of molecular and cellular electron tomography. J. Struct. Biol. 120:276–308 [Google Scholar]
  8. Schur FK, Obr M, Hagen WJ, Wan W, Jakobi AJ. 8.  et al. 2016. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science 353:506–8 [Google Scholar]
  9. Gan L, Jensen GJ. 9.  2012. Electron tomography of cells. Q. Rev. Biophys. 45:27–56 [Google Scholar]
  10. Lučić V, Rigort A, Baumeister W. 10.  2013. Cryo-electron tomography: the challenge of doing structural biology in situ. J. Cell Biol. 202:407–19 [Google Scholar]
  11. Butan C, Hartnell LM, Fenton AK, Bliss D, Sockett RE. 11.  et al. 2011. Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus. J. Bacteriol. 193:1341–50 [Google Scholar]
  12. Raddi G, Morado DR, Yan J, Haake DA, Yang XF, Liu J. 12.  2012. Three-dimensional structures of pathogenic and saprophytic Leptospira species revealed by cryo-electron tomography. J. Bacteriol. 194:1299–306 [Google Scholar]
  13. Jasnin M, Asano S, Gouin E, Hegerl R, Plitzko JM. 13.  et al. 2013. Three-dimensional architecture of actin filaments in Listeria monocytogenes comet tails. PNAS 110:20521–26 [Google Scholar]
  14. Mahamid J, Pfeffer S, Schaffer M, Villa E, Danev R. 14.  et al. 2016. Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 351:969–72 [Google Scholar]
  15. Jasnin M, Ecke M, Baumeister W, Gerisch G. 15.  2016. Actin organization in cells responding to a perforated surface, revealed by live imaging and cryo-electron tomography. Structure 24:1031–43 [Google Scholar]
  16. Urban E, Jacob S, Nemethova M, Resch GP, Small JV. 16.  2010. Electron tomography reveals unbranched networks of actin filaments in lamellipodia. Nat. Cell Biol. 12:429–35 [Google Scholar]
  17. Tee YH, Shemesh T, Thiagarajan V, Hariadi RF, Anderson KL. 17.  et al. 2015. Cellular chirality arising from the self-organization of the actin cytoskeleton. Nat. Cell Biol. 17:445–57 [Google Scholar]
  18. Mourao MA, Hakim JB, Schnell S. 18.  2014. Connecting the dots: the effects of macromolecular crowding on cell physiology. Biophys. J. 107:2761–66 [Google Scholar]
  19. Murphy GE, Leadbetter JR, Jensen GJ. 19.  2006. In situ structure of the complete Treponema primitia flagellar motor. Nature 442:1062–64 [Google Scholar]
  20. Liu J, Lin T, Botkin DJ, McCrum E, Winkler H, Norris SJ. 20.  2009. Intact flagellar motor of Borrelia burgdorferi revealed by cryo-electron tomography: evidence for stator ring curvature and rotor/C-ring assembly flexion. J. Bacteriol. 191:5026–36 [Google Scholar]
  21. Abrusci P, Vergara-Irigaray M, Johnson S, Beeby MD, Hendrixson DR. 21.  et al. 2013. Architecture of the major component of the type III secretion system export apparatus. Nat. Struct. Mol. Biol. 20:99–104 [Google Scholar]
  22. Hu B, Morado DR, Margolin W, Rohde JR, Arizmendi O. 22.  et al. 2015. Visualization of the type III secretion sorting platform of Shigella flexneri. PNAS 112:1047–52 [Google Scholar]
  23. Beck M, Malmstrom JA, Lange V, Schmidt A, Deutsch EW, Aebersold R. 23.  2009. Visual proteomics of the human pathogen Leptospira interrogans. Nat. Methods 6:817–23 [Google Scholar]
  24. Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C. 24.  et al. 2009. Proteome organization in a genome-reduced bacterium. Science 326:1235–40 [Google Scholar]
  25. Komeili A, Li Z, Newman DK, Jensen GJ. 25.  2006. Magnetosomes are cell membrane invaginations organized by the actin-like protein MamK. Science 311:242–45 [Google Scholar]
  26. Scheffel A, Gruska M, Faivre D, Linaroudis A, Plitzko JM, Schuler D. 26.  2006. An acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria. Nature 440:110–14 [Google Scholar]
  27. Li Z, Trimble MJ, Brun YV, Jensen GJ. 27.  2007. The structure of FtsZ filaments in vivo suggests a force-generating role in cell division. EMBO J 26:4694–708 [Google Scholar]
  28. Salje J, Zuber B, Lowe J. 28.  2009. Electron cryomicroscopy of E. coli reveals filament bundles involved in plasmid DNA segregation. Science 323:509–12 [Google Scholar]
  29. Kuhn J, Briegel A, Morschel E, Kahnt J, Leser K. 29.  et al. 2010. Bactofilins, a ubiquitous class of cytoskeletal proteins mediating polar localization of a cell wall synthase in Caulobacter crescentus. EMBO J 29:327–39 [Google Scholar]
  30. Ingerson-Mahar M, Briegel A, Werner JN, Jensen GJ, Gitai Z. 30.  2010. The metabolic enzyme CTP synthase forms cytoskeletal filaments. Nat. Cell Biol. 12:739–46 [Google Scholar]
  31. Pilhofer M, Ladinsky MS, McDowall AW, Petroni G, Jensen GJ. 31.  2011. Microtubules in bacteria: Ancient tubulins build a five-protofilament homolog of the eukaryotic cytoskeleton. PLOS Biol 9:e1001213 [Google Scholar]
  32. Szwedziak P, Wang Q, Bharat TAM, Tsim M, Löwe J. 32.  2014. Architecture of the ring formed by the tubulin homologue FtsZ in bacterial cell division. eLife 3:e04601 [Google Scholar]
  33. Zhang P, Khursigara CM, Hartnell LM, Subramaniam S. 33.  2007. Direct visualization of Escherichia coli chemotaxis receptor arrays using cryo-electron microscopy. PNAS 104:3777–81 [Google Scholar]
  34. Briegel A, Ding HJ, Li Z, Werner J, Gitai Z. 34.  et al. 2008. Location and architecture of the Caulobacter crescentus chemoreceptor array. Mol. Microbiol. 69:30–41 [Google Scholar]
  35. Schlimpert S, Klein EA, Briegel A, Hughes V, Kahnt J. 35.  et al. 2012. General protein diffusion barriers create compartments within bacterial cells. Cell 151:1270–82 [Google Scholar]
  36. Schwartz CL, Sarbash VI, Ataullakhanov FI, McIntosh JR, Nicastro D. 36.  2007. Cryo-fluorescence microscopy facilitates correlations between light and cryo-electron microscopy and reduces the rate of photobleaching. J. Microsc. 227:98–109 [Google Scholar]
  37. Sartori A, Gatz R, Beck F, Rigort A, Baumeister W, Plitzko JM. 37.  2007. Correlative microscopy: bridging the gap between fluorescence light microscopy and cryo-electron tomography. J. Struct. Biol. 160:135–45 [Google Scholar]
  38. Bingle LE, Bailey CM, Pallen MJ. 38.  2008. Type VI secretion: a beginner's guide. Curr. Opin. Microbiol. 11:3–8 [Google Scholar]
  39. Mougous JD, Cuff ME, Raunser S, Shen A, Zhou M. 39.  et al. 2006. A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Science 312:1526–30 [Google Scholar]
  40. Pukatzki S, Ma AT, Sturtevant D, Krastins B, Sarracino D. 40.  et al. 2006. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. PNAS 103:1528–33 [Google Scholar]
  41. Cascales E. 41.  2008. The type VI secretion toolkit. EMBO Rep 9:735–41 [Google Scholar]
  42. Boyer F, Fichant G, Berthod J, Vandenbrouck Y, Attree I. 42.  2009. Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: What can be learned from available microbial genomic resources?. BMC Genom 10:104 [Google Scholar]
  43. Shalom G, Shaw JG, Thomas MS. 43.  2007. In vivo expression technology identifies a type VI secretion system locus in Burkholderia pseudomallei that is induced upon invasion of macrophages. Microbiology 153:2689–99 [Google Scholar]
  44. Ma AT, Mekalanos JJ. 44.  2010. In vivo actin cross-linking induced by Vibrio cholerae type VI secretion system is associated with intestinal inflammation. PNAS 107:4365–70 [Google Scholar]
  45. MacIntyre DL, Miyata ST, Kitaoka M, Pukatzki S. 45.  2010. The Vibrio cholerae type VI secretion system displays antimicrobial properties. PNAS 107:19520–24 [Google Scholar]
  46. Schwarz S, Hood RD, Mougous JD. 46.  2010. What is type VI secretion doing in all those bugs?. Trends Microbiol 18:531–37 [Google Scholar]
  47. Pukatzki S, Ma AT, Revel AT, Sturtevant D, Mekalanos JJ. 47.  2007. Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. PNAS 104:15508–13 [Google Scholar]
  48. Leiman PG, Basler M, Ramagopal UA, Bonanno JB, Sauder JM. 48.  et al. 2009. Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin. PNAS 106:4154–59 [Google Scholar]
  49. Pell LG, Kanelis V, Donaldson LW, Howell PL, Davidson AR. 49.  2009. The phage λ major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system. PNAS 106:4160–65 [Google Scholar]
  50. Bonemann G, Pietrosiuk A, Diemand A, Zentgraf H, Mogk A. 50.  2009. Remodelling of VipA/VipB tubules by ClpV-mediated threading is crucial for type VI protein secretion. EMBO J 28:315–25 [Google Scholar]
  51. Bonemann G, Pietrosiuk A, Mogk A. 51.  2010. Tubules and donuts: a type VI secretion story. Mol. Microbiol. 76:815–21 [Google Scholar]
  52. Basler M, Pilhofer M, Henderson GP, Jensen GJ, Mekalanos JJ. 52.  2012. Type VI secretion requires a dynamic contractile phage tail-like structure. Nature 483:182–86This study revealed the contractile mechanism of the type VI secretion system by in situ imaging. [Google Scholar]
  53. Delk AS, Dekker CA. 53.  1972. Characterization of rhapidosomes of Saprospira grandis. J. Mol. Biol. 64:287–95 [Google Scholar]
  54. Shikuma NJ, Pilhofer M, Weiss GL, Hadfield MG, Jensen GJ, Newman DK. 54.  2014. Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 343:529–33 [Google Scholar]
  55. Kube S, Kapitein N, Zimniak T, Herzog F, Mogk A, Wendler P. 55.  2014. Structure of the VipA/B type VI secretion complex suggests a contraction-state-specific recycling mechanism. Cell Rep 8:20–30 [Google Scholar]
  56. Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T. 56.  et al. 2015. Structure of the type VI secretion system contractile sheath. Cell 160:952–62 [Google Scholar]
  57. Clemens DL, Ge P, Lee BY, Horwitz MA, Zhou ZH. 57.  2015. Atomic structure of T6SS reveals interlaced array essential to function. Cell 160:940–51 [Google Scholar]
  58. Ge P, Scholl D, Leiman PG, Yu X, Miller JF, Zhou ZH. 58.  2015. Atomic structures of a bactericidal contractile nanotube in its pre- and postcontraction states. Nat. Struct. Mol. Biol. 22:377–82 [Google Scholar]
  59. Shi W, Zusman DR. 59.  1993. The two motility systems of Myxococcus xanthus show different selective advantages on various surfaces. PNAS 90:3378–82 [Google Scholar]
  60. Kaiser D. 60.  1979. Social gliding is correlated with the presence of pili in Myxococcus xanthus. PNAS 76:5952–56 [Google Scholar]
  61. Wu SS, Kaiser D. 61.  1995. Genetic and functional evidence that Type IV pili are required for social gliding motility in Myxococcus xanthus. Mol. Microbiol. 18:547–58 [Google Scholar]
  62. Strom MS, Lory S. 62.  1993. Structure-function and biogenesis of the type IV pili. Annu. Rev. Microbiol. 47:565–96 [Google Scholar]
  63. Sun H, Zusman DR, Shi W. 63.  2000. Type IV pilus of Myxococcus xanthus is a motility apparatus controlled by the frz chemosensory system. Curr. Biol 10:1143–46 [Google Scholar]
  64. Li Y, Sun H, Ma X, Lu A, Lux R. 64.  et al. 2003. Extracellular polysaccharides mediate pilus retraction during social motility of Myxococcus xanthus. PNAS 100:5443–48 [Google Scholar]
  65. Clausen M, Jakovljevic V, Sogaard-Andersen L, Maier B. 65.  2009. High-force generation is a conserved property of type IV pilus systems. J. Bacteriol. 191:4633–38 [Google Scholar]
  66. Wu SS, Wu J, Kaiser D. 66.  1997. The Myxococcus xanthus pilT locus is required for social gliding motility although pili are still produced. Mol. Microbiol. 23:109–21 [Google Scholar]
  67. Wall D, Kolenbrander PE, Kaiser D. 67.  1999. The Myxococcus xanthus pilQ(sglA) gene encodes a secretin homolog required for type IV pilus biogenesis, social motility, and development. J. Bacteriol 181:24–33 [Google Scholar]
  68. Yang Z, Geng Y, Xu D, Kaplan HB, Shi W. 68.  1998. A new set of chemotaxis homologues is essential for Myxococcus xanthus social motility. Mol. Microbiol. 30:1123–30 [Google Scholar]
  69. Vlamakis HC, Kirby JR, Zusman DR. 69.  2004. The Che4 pathway of Myxococcus xanthus regulates type IV pilus-mediated motility. Mol. Microbiol. 52:1799–811 [Google Scholar]
  70. Mignot T, Merlie JP Jr., Zusman DR. 70.  2005. Regulated pole-to-pole oscillations of a bacterial gliding motility protein. Science 310:855–57 [Google Scholar]
  71. Tammam S, Sampaleanu LM, Koo J, Manoharan K, Daubaras M. 71.  et al. 2013. PilMNOPQ from the Pseudomonas aeruginosa type IV pilus system form a transenvelope protein interaction network that interacts with PilA. J. Bacteriol. 195:2126–35 [Google Scholar]
  72. Li C, Wallace RA, Black WP, Li YZ, Yang Z. 72.  2013. Type IV pilus proteins form an integrated structure extending from the cytoplasm to the outer membrane. PLOS ONE 8:e70144 [Google Scholar]
  73. Friedrich C, Bulyha I, Sogaard-Andersen L. 73.  2014. Outside-in assembly pathway of the type IV pilus system in Myxococcus xanthus. J. Bacteriol. 196:378–90 [Google Scholar]
  74. Jakovljevic V, Leonardy S, Hoppert M, Sogaard-Andersen L. 74.  2008. PilB and PilT are ATPases acting antagonistically in type IV pilus function in Myxococcus xanthus. J. Bacteriol. 190:2411–21 [Google Scholar]
  75. Wall D, Kaiser D. 75.  1999. Type IV pili and cell motility. Mol. Microbiol. 32:1–10 [Google Scholar]
  76. Chang YW, Rettberg L, Treuner-Lange A, Iwasa J, Sogaard-Andersen L, Jensen GJ. 76.  2016. Architecture of the type IVa pilus machine. Science 351:aad2001This work created a pseudoatomic map of a molecular machine in vivo in its entirety. [Google Scholar]
  77. Dobell C. 77.  1932. Antony van Leeuwenhoek and His “Little Animals.” New York: Harcourt, Brace, and Company [Google Scholar]
  78. Satir P. 78.  1974. How cilia move. Scientific American 231:Oct.44–52 [Google Scholar]
  79. Gibbons BH, Baccetti B, Gibbons IR. 79.  1985. Live and reactivated motility in the 9 + 0 flagellum of Anguilla sperm. Cell Motil. Cytoskelet. 5:333–50 [Google Scholar]
  80. Vogel S. 80.  2003. Comparative Biomechanics: Life's Physical World Princeton, NJ: Princeton Univ. Press [Google Scholar]
  81. Okada Y, Takeda S, Tanaka Y, Izpisua Belmonte JC, Hirokawa N. 81.  2005. Mechanism of nodal flow: a conserved symmetry breaking event in left-right axis determination. Cell 121:633–44 [Google Scholar]
  82. Afzelius BA. 82.  2004. Cilia-related diseases. J. Pathol. 204:470–77 [Google Scholar]
  83. Manton I. 83.  1953. Number of fibrils in the cilia of green algae. Nature 171:485–86 [Google Scholar]
  84. Porter KR. 84.  1955. The fine structure of cells. Fed. Proc 14:673–82 [Google Scholar]
  85. Satir P. 85.  1961. Cilia. Scientific American 204:Feb.108–16 [Google Scholar]
  86. Satir P. 86.  1968. Studies on cilia. 3. Further studies on the cilium tip and a “sliding filament” model of ciliary motility. J. Cell Biol. 39:77–94 [Google Scholar]
  87. Summers KE, Gibbons IR. 87.  1971. Adenosine triphosphate-induced sliding of tubules in trypsin-treated flagella of sea-urchin sperm. PNAS 68:3092–96 [Google Scholar]
  88. Brokaw CJ. 88.  2009. Thinking about flagellar oscillation. Cell Motil. Cytoskelet. 66:425–36 [Google Scholar]
  89. Pazour GJ, Agrin N, Leszyk J, Witman GB. 89.  2005. Proteomic analysis of a eukaryotic cilium. J. Cell Biol. 170:103–13 [Google Scholar]
  90. Bui KH, Sakakibara H, Movassagh T, Oiwa K, Ishikawa T. 90.  2008. Molecular architecture of inner dynein arms in situ in Chlamydomonas reinhardtii flagella. J. Cell Biol. 183:923–32 [Google Scholar]
  91. Ishikawa T. 91.  2015. Cryo-electron tomography of motile cilia and flagella. Cilia 4:3 [Google Scholar]
  92. Sanchez T, Welch D, Nicastro D, Dogic Z. 92.  2011. Cilia-like beating of active microtubule bundles. Science 333:456–59 [Google Scholar]
  93. McEwen BF, Marko M, Hsieh CE, Mannella C. 93.  2002. Use of frozen-hydrated axonemes to assess imaging parameters and resolution limits in cryoelectron tomography. J. Struct. Biol. 138:47–57 [Google Scholar]
  94. Nicastro D, Schwartz C, Pierson J, Gaudette R, Porter ME, McIntosh JR. 94.  2006. The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313:944–48This study produced a 3D structure of the axoneme that revealed coordination of dyneins, which could explain functional bending. [Google Scholar]
  95. Ishikawa T, Sakakibara H, Oiwa K. 95.  2007. The architecture of outer dynein arms in situ. J. Mol. Biol. 368:1249–58 [Google Scholar]
  96. Heuser T, Raytchev M, Krell J, Porter ME, Nicastro D. 96.  2009. The dynein regulatory complex is the nexin link and a major regulatory node in cilia and flagella. J. Cell Biol. 187:921–33 [Google Scholar]
  97. Pigino G, Bui KH, Maheshwari A, Lupetti P, Diener D, Ishikawa T. 97.  2011. Cryoelectron tomography of radial spokes in cilia and flagella. J. Cell Biol. 195:673–87 [Google Scholar]
  98. Barber CF, Heuser T, Carbajal-Gonzalez BI, Botchkarev VV Jr., Nicastro D. 98.  2012. Three-dimensional structure of the radial spokes reveals heterogeneity and interactions with dyneins in Chlamydomonas flagella. Mol. Biol. Cell 23:111–20 [Google Scholar]
  99. Heuser T, Dymek EE, Lin J, Smith EF, Nicastro D. 99.  2012. The CSC connects three major axonemal complexes involved in dynein regulation. Mol. Biol. Cell 23:3143–55 [Google Scholar]
  100. Hoog JL, Bouchet-Marquis C, McIntosh JR, Hoenger A, Gull K. 100.  2012. Cryo-electron tomography and 3-D analysis of the intact flagellum in Trypanosoma brucei. J. Struct. Biol. 178:189–98 [Google Scholar]
  101. Carbajal-Gonzalez BI, Heuser T, Fu X, Lin J, Smith BW. 101.  et al. 2013. Conserved structural motifs in the central pair complex of eukaryotic flagella. Cytoskeleton 70:101–20 [Google Scholar]
  102. Yamamoto R, Song K, Yanagisawa HA, Fox L, Yagi T. 102.  et al. 2013. The MIA complex is a conserved and novel dynein regulator essential for normal ciliary motility. J. Cell Biol. 201:263–78 [Google Scholar]
  103. Dymek EE, Heuser T, Nicastro D, Smith EF. 103.  2011. The CSC is required for complete radial spoke assembly and wild-type ciliary motility. Mol. Biol. Cell 22:2520–31 [Google Scholar]
  104. Bui KH, Yagi T, Yamamoto R, Kamiya R, Ishikawa T. 104.  2012. Polarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme. J. Cell Biol. 198:913–25 [Google Scholar]
  105. Heuser T, Barber CF, Lin J, Krell J, Rebesco M. 105.  et al. 2012. Cryoelectron tomography reveals doublet-specific structures and unique interactions in the I1 dynein. PNAS 109:E2067–76 [Google Scholar]
  106. Oda T, Yanagisawa H, Yagi T, Kikkawa M. 106.  2014. Mechanosignaling between central apparatus and radial spokes controls axonemal dynein activity. J. Cell Biol. 204:807–19 [Google Scholar]
  107. Oda T, Kikkawa M. 107.  2013. Novel structural labeling method using cryo-electron tomography and biotin-streptavidin system. J. Struct. Biol. 183:305–11 [Google Scholar]
  108. Oda T, Yanagisawa H, Kamiya R, Kikkawa M. 108.  2014. A molecular ruler determines the repeat length in eukaryotic cilia and flagella. Science 346:857–60 [Google Scholar]
  109. Lin J, Yin W, Smith MC, Song K, Leigh MW. 109.  et al. 2014. Cryo-electron tomography reveals ciliary defects underlying human RSPH1 primary ciliary dyskinesia. Nat. Commun. 5:5727 [Google Scholar]
  110. Kamiya R. 110.  2002. Functional diversity of axonemal dyneins as studied in Chlamydomonas mutants. Int. Rev. Cytol. 219:115–55 [Google Scholar]
  111. Bui KH, Sakakibara H, Movassagh T, Oiwa K, Ishikawa T. 111.  2009. Asymmetry of inner dynein arms and inter-doublet links in Chlamydomonas flagella. J. Cell Biol. 186:437–46 [Google Scholar]
  112. Lin J, Okada K, Raytchev M, Smith MC, Nicastro D. 112.  2014. Structural mechanism of the dynein power stroke. Nat. Cell Biol. 16:479–85This work produced in situ snapshots of dynein conformations that revealed the mechanism of the dynein power stroke. [Google Scholar]
  113. Kite GL. 113.  1913. Studies on the physical properties of protoplasm. Am. J. Physiol. 32:146–64 [Google Scholar]
  114. Watson ML. 114.  1955. The nuclear envelope; its structure and relation to cytoplasmic membranes. J. Biophys. Biochem. Cytol. 1:257–70 [Google Scholar]
  115. Callan HG, Tomlin SG. 115.  1950. Experimental studies on amphibian oocyte nuclei. I. Investigation of the structure of the nuclear membrane by means of the electron microscope. Proc. R. Soc. B 137:367–78 [Google Scholar]
  116. Afzelius BA. 116.  1955. The ultrastructure of the nuclear membrane of the sea urchin oocyte as studied with the electron microscope. Exp. Cell Res. 8:147–58 [Google Scholar]
  117. Watson ML. 117.  1959. Further observations on the nuclear envelope of the animal cell. J. Biophys. Biochem. Cytol. 6:147–56 [Google Scholar]
  118. Faberge AC. 118.  1973. Direct demonstration of eight-fold symmetry in nuclear pores. Z. Zellforsch. Mikrosk. Anat. 136:183–90 [Google Scholar]
  119. Unwin PN, Milligan RA. 119.  1982. A large particle associated with the perimeter of the nuclear pore complex. J. Cell Biol. 93:63–75 [Google Scholar]
  120. Akey CW, Goldfarb DS. 120.  1989. Protein import through the nuclear pore complex is a multistep process. J. Cell Biol. 109:971–82 [Google Scholar]
  121. Hinshaw JE, Carragher BO, Milligan RA. 121.  1992. Architecture and design of the nuclear pore complex. Cell 69:1133–41 [Google Scholar]
  122. Akey CW, Radermacher M. 122.  1993. Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy. J. Cell Biol. 122:1–19 [Google Scholar]
  123. Akey CW. 123.  1995. Structural plasticity of the nuclear pore complex. J. Mol. Biol. 248:273–93 [Google Scholar]
  124. Yang Q, Rout MP, Akey CW. 124.  1998. Three-dimensional architecture of the isolated yeast nuclear pore complex: functional and evolutionary implications. Mol. Cell 1:223–34 [Google Scholar]
  125. Pante N, Kann M. 125.  2002. Nuclear pore complex is able to transport macromolecules with diameters of about 39 nm. Mol. Biol. Cell 13:425–34 [Google Scholar]
  126. DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A. 126.  et al. 2009. Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol. Cell. Proteom. 8:2119–30 [Google Scholar]
  127. Doolittle RF, Feng DF, Tsang S, Cho G, Little E. 127.  1996. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470–47 [Google Scholar]
  128. Guttinger S, Laurell E, Kutay U. 128.  2009. Orchestrating nuclear envelope disassembly and reassembly during mitosis. Nat. Rev. Mol. Cell Biol. 10:178–91 [Google Scholar]
  129. Strambio-De-Castillia C, Niepel M, Rout MP. 129.  2010. The nuclear pore complex: bridging nuclear transport and gene regulation. Nat. Rev. Mol. Cell Biol. 11:490–501 [Google Scholar]
  130. Ribbeck K, Gorlich D. 130.  2001. Kinetic analysis of translocation through nuclear pore complexes. EMBO J 20:1320–30 [Google Scholar]
  131. Reichelt R, Holzenburg A, Buhle EL Jr., Jarnik M, Engel A, Aebi U. 131.  1990. Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components. J. Cell Biol. 110:883–94 [Google Scholar]
  132. Akey CW. 132.  1989. Interactions and structure of the nuclear pore complex revealed by cryo-electron microscopy. J. Cell Biol. 109:955–70 [Google Scholar]
  133. Hoelz A, Debler EW, Blobel G. 133.  2011. The structure of the nuclear pore complex. Annu. Rev. Biochem. 80:613–43 [Google Scholar]
  134. Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S. 134.  et al. 2015. Architecture of the fungal nuclear pore inner ring complex. Science 350:56–64 [Google Scholar]
  135. Hoelz A, Glavy JS, Beck M. 135.  2016. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up. Nat. Struct. Mol. Biol. 23:624–30 [Google Scholar]
  136. Schwartz TU. 136.  2016. The structure inventory of the nuclear pore complex. J. Mol. Biol. 428:1986–2000 [Google Scholar]
  137. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J. 137.  et al. 2007. The molecular architecture of the nuclear pore complex. Nature 450:695–701 [Google Scholar]
  138. Hurt E, Beck M. 138.  2015. Towards understanding nuclear pore complex architecture and dynamics in the age of integrative structural analysis. Curr. Opin. Cell Biol. 34:31–38 [Google Scholar]
  139. Stoffler D, Feja B, Fahrenkrog B, Walz J, Typke D, Aebi U. 139.  2003. Cryo-electron tomography provides novel insights into nuclear pore architecture: implications for nucleocytoplasmic transport. J. Mol. Biol. 328:119–30 [Google Scholar]
  140. Frenkiel-Krispin D, Maco B, Aebi U, Medalia O. 140.  2010. Structural analysis of a metazoan nuclear pore complex reveals a fused concentric ring architecture. J. Mol. Biol. 395:578–86 [Google Scholar]
  141. Beck M, Förster F, Ecke M, Plitzko JM, Melchior F. 141.  et al. 2004. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306:1387–90 [Google Scholar]
  142. Beck M, Lučić V, Förster F, Baumeister W, Medalia O. 142.  2007. Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449:611–15 [Google Scholar]
  143. Maimon T, Elad N, Dahan I, Medalia O. 143.  2012. The human nuclear pore complex as revealed by cryo-electron tomography. Structure 20:998–1006 [Google Scholar]
  144. McMullan G, Clark AT, Turchetta R, Faruqi AR. 144.  2009. Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 109:1411–16 [Google Scholar]
  145. Lin DH, Stuwe T, Schilbach S, Rundlet EJ, Perriches T. 145.  et al. 2016. Architecture of the symmetric core of the nuclear pore. Science 352:aaf1015Building on previous work, these studies have produced the most complete architectural models to date of the NPC. [Google Scholar]
  146. Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL. 146.  et al. 2016. Molecular architecture of the inner ring scaffold of the human nuclear pore complex. Science 352:363–65Building on previous work, these studies have produced the most complete architectural models to date of the NPC. [Google Scholar]
  147. Bui KH, von Appen A, DiGuilio AL, Ori A, Sparks L. 147.  et al. 2013. Integrated structural analysis of the human nuclear pore complex scaffold. Cell 155:1233–43This study pioneered an integrative approach to NPC structure solving with the first map of sufficient resolution to dock components. [Google Scholar]
  148. Eibauer M, Pellanda M, Turgay Y, Dubrovsky A, Wild A, Medalia O. 148.  2015. Structure and gating of the nuclear pore complex. Nat. Commun. 6:7532 [Google Scholar]
  149. Stuwe T, Correia AR, Lin DH, Paduch M, Lu VT. 149.  et al. 2015. Nuclear pores. Architecture of the nuclear pore complex coat. Science 347:1148–52 [Google Scholar]
  150. von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL. 150.  et al. 2015. In situ structural analysis of the human nuclear pore complex. Nature 526:140–43 [Google Scholar]
  151. Al-Amoudi A, Chang JJ, Leforestier A, McDowall A, Salamin LM. 151.  et al. 2004. Cryo-electron microscopy of vitreous sections. EMBO J 23:3583–88 [Google Scholar]
  152. Hsieh CE, Leith A, Mannella CA, Frank J, Marko M. 152.  2006. Towards high-resolution three-dimensional imaging of native mammalian tissue: electron tomography of frozen-hydrated rat liver sections. J. Struct. Biol. 153:1–13 [Google Scholar]
  153. Al-Amoudi A, Diez DC, Betts MJ, Frangakis AS. 153.  2007. The molecular architecture of cadherins in native epidermal desmosomes. Nature 450:832–37 [Google Scholar]
  154. Gan L, Ladinsky MS, Jensen GJ. 154.  2011. Organization of the smallest eukaryotic spindle. Curr. Biol. 21:1578–83 [Google Scholar]
  155. Dubochet J, Zuber B, Eltsov M, Bouchet-Marquis C, Al-Amoudi A, Livolant F. 155.  2007. How to “read” a vitreous section. Methods Cell Biol 79:385–406 [Google Scholar]
  156. Marko M, Hsieh C, Schalek R, Frank J, Mannella C. 156.  2007. Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy. Nat. Methods 4:215–17 [Google Scholar]
  157. Strunk KM, Wang K, Ke D, Gray JL, Zhang P. 157.  2012. Thinning of large mammalian cells for cryo-TEM characterization by cryo-FIB milling. J. Microsc. 247:220–27 [Google Scholar]
  158. Rigort A, Bauerlein FJ, Villa E, Eibauer M, Laugks T. 158.  et al. 2012. Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. PNAS 109:4449–54 [Google Scholar]
  159. Wagenknecht T, Hsieh C, Marko M. 159.  2015. Skeletal muscle triad junction ultrastructure by focused-ion-beam milling of muscle and cryo-electron tomography. Eur. J. Transl. Myol. 25:49–56 [Google Scholar]
  160. Mercogliano CP, DeRosier DJ. 160.  2007. Concatenated metallothionein as a clonable gold label for electron microscopy. J. Struct. Biol. 160:70–82 [Google Scholar]
  161. Wang Q, Mercogliano CP, Lowe J. 161.  2011. A ferritin-based label for cellular electron cryotomography. Structure 19:147–54 [Google Scholar]
  162. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S. 162.  et al. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–45 [Google Scholar]
  163. Hess ST, Girirajan TP, Mason MD. 163.  2006. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91:4258–72 [Google Scholar]
  164. Rust MJ, Bates M, Zhuang X. 164.  2006. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3:793–95 [Google Scholar]
  165. Kaufmann R, Schellenberger P, Seiradake E, Dobbie IM, Jones EY. 165.  et al. 2014. Super-resolution microscopy using standard fluorescent proteins in intact cells under cryo-conditions. Nano Lett 14:4171–75 [Google Scholar]
  166. Chang YW, Chen S, Tocheva EI, Treuner-Lange A, Lobach S. 166.  et al. 2014. Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography. Nat. Methods 11:737–39 [Google Scholar]
  167. Liu B, Xue Y, Zhao W, Chen Y, Fan C. 167.  et al. 2015. Three-dimensional super-resolution protein localization correlated with vitrified cellular context. Sci. Rep. 5:13017 [Google Scholar]
  168. Arnold J, Mahamid J, Lucic V, de Marco A, Fernandez JJ. 168.  et al. 2016. Site-specific cryo-focused ion beam sample preparation guided by 3D correlative microscopy. Biophys. J. 110:860–69This study demonstrated that CLEM-guided cryo-FIB milling could render a target within a thick cell accessible to ECT. [Google Scholar]
  169. Beck M, Topf M, Frazier Z, Tjong H, Xu M. 169.  et al. 2011. Exploring the spatial and temporal organization of a cell's proteome. J. Struct. Biol. 173:483–96 [Google Scholar]
  170. Danev R, Buijsse B, Khoshouei M, Plitzko JM, Baumeister W. 170.  2014. Volta potential phase plate for in-focus phase contrast transmission electron microscopy. PNAS 111:15635–40 [Google Scholar]
  171. Asano S, Fukuda Y, Beck F, Aufderheide A, Förster F. 171.  et al. 2015. A molecular census of 26S proteasomes in intact neurons. Science 347:439–42 [Google Scholar]
  172. Brunet YR, Espinosa L, Harchouni S, Mignot T, Cascales E. 172.  2013. Imaging type VI secretion-mediated bacterial killing. Cell Rep 3:36–41 [Google Scholar]
  173. Basler M, Ho BT, Mekalanos JJ. 173.  2013. Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions. Cell 152:884–94 [Google Scholar]
  174. Velicer GJ, Yu YT. 174.  2003. Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus. Nature 425:75–78 [Google Scholar]
  175. Perez J, Jimenez-Zurdo JI, Martinez-Abarca F, Millan V, Shimkets LJ, Munoz-Dorado J. 175.  2014. Rhizobial galactoglucan determines the predatory pattern of Myxococcus xanthus and protects Sinorhizobium meliloti from predation. Environ. Microbiol 16:2341–50 [Google Scholar]
  176. Keane R, Berleman J. 176.  2016. The predatory life cycle of Myxococcus xanthus. Microbiology 162:1–11 [Google Scholar]
  177. Pan H, He X, Lux R, Luan J, Shi W. 177.  2013. Killing of Escherichia coli by Myxococcus xanthus in aqueous environments requires exopolysaccharide-dependent physical contact. Microb. Ecol 66:630–38 [Google Scholar]
  178. Berleman JE, Allen S, Danielewicz MA, Remis JP, Gorur A. 178.  et al. 2014. The lethal cargo of Myxococcus xanthus outer membrane vesicles. Front. Microbiol. 5:474 [Google Scholar]
  179. Briegel A, Li X, Bilwes AM, Hughes KT, Jensen GJ, Crane BR. 179.  2012. Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins. PNAS 109:3766–71 [Google Scholar]
  180. Oikonomou CM, Chang YW, Jensen GJ. 180.  2016. A new view into prokaryotic cell biology from electron cryotomography. Nat. Rev. Microbiol. 14:205–20 [Google Scholar]
  181. Satir P. 181.  1965. Studies on cilia: II. Examination of the distal region of the ciliary shaft and the role of the filaments in motility. J. Cell Biol. 26:805–34 [Google Scholar]
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