Skip to main content
SpringerLink
Log in

Visualizing the Bacterial Cell Surface: An Overview

  • Protocol
  • First Online:
Bacterial Cell Surfaces

Part of the book series: Methods in Molecular Biology ((MIMB,volume 966))

Abstract

The ultrastructure of bacteria is only accessible by electron microscopy. Our insights into the architecture of cells and cellular compartments such as the envelope and appendages is thus dependent on the progress of preparative and imaging techniques in electron microscopy. Here, I give a short overview of the development and characteristics of methods applied for imaging (components of) the bacterial surface and refer to key investigations and exemplary results. In the beginning of electron microscopy, fixation of biological material and staining for contrast enhancement were the standard techniques. The results from freeze-etching, metal shadowing and from ultrathin-sections of plastic-embedded material shaped our view of the cellular organization of bacteria. The introduction of cryo-preparations, keeping samples in their natural environment, and three-dimensional (3D) electron microscopy of isolated protein complexes and intact cells opened the door to a new dimension and has provided insight into the native structure of macromolecules and the in situ organization of cells at molecular resolution. Cryo-electron microscopy of single particles, together with other methods of structure determination, and cellular cryo-electron tomography will provide us with a quasi-atomic model of the bacterial cell surface in the years to come.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. van Leeuwenhoek A (1684) Microscopical observations about animals in the scurf of the teeth, the substance called jvorms in the nose, and the cuticula consisting of scales. Phil Transact Royal Soc 159:308

    Google Scholar 

  2. Ehrlich P (1882) Deut Med Wochenschr 8:269–270

    Article  Google Scholar 

  3. Gram HC (1884) Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten. Fortschr Med 2:185–189

    Google Scholar 

  4. Salton MRJ (1964) The bacterial cell wall. American Elsevier Publ Co, New York

    Google Scholar 

  5. Beveridge TJ (1990) Mechanism of gram variability in selected bacteria. J Bacteriol 172:1609–1620

    PubMed  CAS  Google Scholar 

  6. Popescu A, Doyle RJ (1996) The gram stain after more than a century. Biotech Histochem 71:145–151

    Article  PubMed  CAS  Google Scholar 

  7. White PB (1926) Further studies of the Salmonella group. Great Britain Medical Research Council 103, p 3–160

    Google Scholar 

  8. Salmonella Subcommittee (1934) J Hyg 34:333–350

    Article  Google Scholar 

  9. Grimont PAD, Weill FX (2007) Antigenic formulae of the Salmonella servoars, 9th edn. World Health Organization Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur, Paris

    Google Scholar 

  10. Knoll M, Ruska E (1932) Das Elektronen­mikroskop. Z Phys 78:318–339

    Article  CAS  Google Scholar 

  11. Krause F (1937) Das magnetische Elektronen­mikroskop und seine Anwendung in der Biologie. Naturwissenschaften 25:817–825

    Article  CAS  Google Scholar 

  12. Marton L (1937) La microscopie électronique des objects biologiques. Bull Acad Roy Belg Cl Sci 23:672–678

    Google Scholar 

  13. Knaysi G (1949) Cytology of bacteria II. Bot Rev 15:106–151

    Article  CAS  Google Scholar 

  14. Chapman GB, Hillier J (1953) Electron microscopy of ultra-thin sections of bacteria I. Cellular division in Bacillus cereus. J Bacteriol 66:362–373

    PubMed  CAS  Google Scholar 

  15. Houwink AL (1953) A macromolecular monolayer in the cell wall of Spirillum spec. Biochim Biophys Acta 10:360–366

    Article  PubMed  CAS  Google Scholar 

  16. Müller HO (1942) Die Ausmessung der Tiefe übermikroskopischer Objekte. Kolloid- Zeitschrift 99:6–28

    Article  Google Scholar 

  17. Williams RC, Wyckoff RWG (1945) Electron shadow micrography of the tobacco mosaic virus protein. Science 101:594–596

    Article  PubMed  CAS  Google Scholar 

  18. Houwink AL (1956) Flagella, gas vacuoles and cell-wall structure in Halobacterium halobium; an electron microscope study. J Gen Microbiol 15:146–150

    PubMed  CAS  Google Scholar 

  19. Wildhaber I, Gross H, Engel A, Baumeister W (1985) The effects of air-drying and freeze- drying on the structure of a regular protein layer. Ultramicroscopy 16:411–422

    Article  Google Scholar 

  20. Guckenberger R (1985) Surface reliefs derived from heavy-metal-shadowed specimens—Fourier space technique applied to periodic objects. Ultramicroscopy 16:357–370

    Article  Google Scholar 

  21. Engelhardt H, Guckenberger R, Hegerl R, Baumeister W (1985) High resolution shadowing of freeze-dried bacterial photosynthetic membranes: multivariate statistical analysis and surface relief reconstruction. Ultramicroscopy 16:395–410

    Article  Google Scholar 

  22. Baumeister W, Guckenberger R, Engelhardt H, Woodcock CLF (1986) Metal shadowing and decoration in electron microscopy of biological macromolecules. Ann N Y Acad Sci 483:57–76

    Article  PubMed  CAS  Google Scholar 

  23. Wildhaber I, Hegerl R, Barth M, Gross H, Baumeister W (1986) Three-dimensional reconstruction of a freeze-dried and metal-shadowed bacterial surface layer. Ultramicroscopy 19:57–68

    Article  Google Scholar 

  24. Bachmann L, Becker R, Leupold G, Barth M, Guckenberger R, Baumeister W (1985) Decoration and shadowing of freeze-etched catalase crystals. Ultramicroscopy 16:305–320

    Article  PubMed  CAS  Google Scholar 

  25. Rübenkamm E, Braun N, Bachmann L, Bacher A, Brandt J, Baumeister W, Weinkauf S (1995) Quantitative evaluation of heavy metal decoration on protein molecules: contrast, specificity and resolution. Ultramicroscopy 58:337–351

    Article  Google Scholar 

  26. Moor H, Mühlethaler K, Waldner H, Frey-Wyssling A (1961) A new freezing-ultramicrotome. J Biophys Biochem Cytol 10:1–13

    Article  PubMed  CAS  Google Scholar 

  27. Reimer L, Schulte C (1966) Elektronenmi-kroskopische Oberflächenabdrücke und ihr Auflösungsvermögen. Naturwissenschaften 53:489–497

    Article  PubMed  CAS  Google Scholar 

  28. Holt SC, Trüper HG, Takács BJ (1968) Fine structure of Ectothiorhodospira mobils strain 8113 thylakoids: chemical fixation and freeze-etching studies. Arch Mikrobiol 62:111–128

    Article  PubMed  CAS  Google Scholar 

  29. Engelhardt H (2007) Are S-layers exoskeletons? The basic function of surface protein layers revisited. J Struct Biol 160:115–124

    Article  PubMed  CAS  Google Scholar 

  30. Sleytr U, Adam H, Klaushofer H (1969) Die Feinstruktur der Zellwand und Cytoplas­mamembran von Clostridium nigrificans, dargestellt mit Hilfe der Gefrierätz- und Ultra­dünnschnittechnik. Arch Mikrobiol 66:40–58

    Article  PubMed  CAS  Google Scholar 

  31. Holt SC, Beveridge TJ (1982) Electron microscopy: its development and application to microbiology. Can J Microbiol 28:1–53

    Article  PubMed  CAS  Google Scholar 

  32. Schatten H (2011) Low voltage high-resolution SEM (LVHRSEM) for biological structural and molecular analysis. Micron 42:175–185

    Article  PubMed  CAS  Google Scholar 

  33. Binnig G, Rohrer H, Gerber C, Weibel E (1982) Surface studies by scanning tunneling microscopy. Phys Rev Lett 49:57–61

    Article  Google Scholar 

  34. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930–933

    Article  PubMed  Google Scholar 

  35. Wiegräbe W, Nonnenmacher M, Guckenberger R, Wolter O (1991) Atomic force microscopy of a hydrated bacterial surface protein. J Microsc 163:79–84

    Article  PubMed  Google Scholar 

  36. Müller DJ, Baumeister W, Engel A (1996) Conformational change of the hexagonally packed intermediate layer of Deinococcus radiodurans monitored by atomic force microscopy. J Bacteriol 178:3025–3030

    PubMed  Google Scholar 

  37. Schabert FA, Henn C, Engel A (1995) Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy. Science 268:92–94

    Article  PubMed  CAS  Google Scholar 

  38. Engel A, Schoenenberger C-A, Müller DJ (1997) High resolution imaging of native biological sample surfaces using scanning probe microscopy. Curr Opin Struct Biol 7:279–284

    Article  PubMed  CAS  Google Scholar 

  39. Scheuring S, Müller DJ, Stahlberg H, Engel H-A, Engel A (2002) Sampling the conformational space of membrane protein surfaces with the AFM. Eur Biophys J 31:172–178

    Article  PubMed  CAS  Google Scholar 

  40. Philippsen A, Im W, Engel A, Schirmer T, Roux B, Müller DJ (2002) Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophys J 82:1667–1676

    Article  PubMed  CAS  Google Scholar 

  41. Knapp HF, Wiegräbe W, Heim M, Eschrich R, Guckenberger R (1995) Atomic force microscope measurements and manipulation of Langmuir-Blodgett films with modified tips. Biophys J 69:708–715

    Article  PubMed  CAS  Google Scholar 

  42. Gonçalves RP, Scheuring S (2006) Manipulating and imaging individual membrane proteins by AFM. Surf Interface Anal 38:1413–1418

    Article  CAS  Google Scholar 

  43. Müller DJ (2008) AFM: a nanotool in membrane biology. Biochemistry 47:7986–7998

    Article  PubMed  CAS  Google Scholar 

  44. Anselmetti D, Hansmeier N, Kalinowski J, Martini J, Merkle T, Pamisano R, Ros R, Schmied K, Sischka A, Toensing K (2007) Analysis of subcellular surface structures, function and dynamics. Anal Bioanal Chem 387:83–89

    Article  PubMed  CAS  Google Scholar 

  45. Marton L (1976) Early application of electron microscopy to biology. Ultramicroscopy 1:281–296

    Article  PubMed  CAS  Google Scholar 

  46. Baker RF, Pease DC (1949) Sectioning of the bacterial cell for the electron microscope. Nature 163:282

    Article  PubMed  CAS  Google Scholar 

  47. Sjöstrand FS (1953) A new microtome for ultrathin sectioning for high resolution electron microscopy. Experientia 9:114–115

    Article  PubMed  Google Scholar 

  48. Kellenberger E, Ryter A (1958) Cell wall and cytoplasmic membrane of Escherichia coli. J Biophys Biochem Cytol 4:323–326

    Article  PubMed  CAS  Google Scholar 

  49. Murray RGE (1963) On the cell wall structure of Spirillum serpens. Can J Microbiol 9:381–392

    Article  CAS  Google Scholar 

  50. Claus GW, Roth LE (1964) Fine structure of the gram-negative bacterium Acetobacter suboxydans. J Cell Biol 20:217–233

    Article  PubMed  CAS  Google Scholar 

  51. Costerton JW (1979) The role of electron microscopy in the elucidation of bacterial structure and function. Annu Rev Microbiol 33:459–479

    Article  PubMed  CAS  Google Scholar 

  52. Sleytr UB (1978) Regular arrays of macromolecules on bacterial cell walls: structure, chemistry, assembly, and function. Int Rev Cytol 53:1–64

    Article  PubMed  CAS  Google Scholar 

  53. Remsen CC, Watson SW, Trüper HG (1970) Macromolecular subunits in the walls of marine photosynthetic bacteria. J Bacteriol 103:254–257

    PubMed  CAS  Google Scholar 

  54. Hageage GJ, Gherna RL (1971) Surface structure of Chromatium okenii and Chromatium weissei. J Bacteriol 106:687–690

    PubMed  Google Scholar 

  55. Jeffries P, Wilkinson JF (1978) Electron microscopy of the cell wall complex of Methylomonas albus. Arch Microbiol 119:227–229

    Article  Google Scholar 

  56. Murray RGE (1978) Form and function. In: Norris JR, Richmond MH (eds) Essays in microbiology. I Bacteria. Wiley, New York, pp 2/30–2/31

    Google Scholar 

  57. Emde B, Wehrli E, Baumeister W (1980) The topography of the cell wall of Micrococcus radiodurans. In: Brederoo P, de Priester W (ed) Proc 7th Europ Congr Electron Microscopy, vol. 2, Leiden, 1980, p 460–461

    Google Scholar 

  58. Graham LL, Beveridge TJ (1990) Evaluation of freeze-substitution and conventional embedding protocols for routine electron microscopic processing of eubacteria. J Bacteriol 172:2141–2149

    PubMed  CAS  Google Scholar 

  59. Tokunaga M, Kusamichi M, Koike H (1986) Ultrastructure of outermost layer of cell wall in Candida albicans observed by rapid-freezing technique. J Electron Microsc 35:237–246

    CAS  Google Scholar 

  60. Fernández-Morán H (1960) Low-temperature preparation techniques for electron microscopy of biological specimens based on rapid freezing with liquid Helium II. Ann N Y Acad Sci 85:689–713

    Article  PubMed  Google Scholar 

  61. Dubochet J, McDowall AW, Menge B, Schmid EN, Lickfeld KG (1983) Electron microscopy of frozen-hydrated bacteria. J Bacteriol 155:381–390

    PubMed  CAS  Google Scholar 

  62. Al-Amoudi A, Chang J-J, Leforestier A, McDowall A, Salamin LM, Norlén LPO, Richter K, Blanc NS, Studer D, Dubochet J (2004) Cryo-electron microscopy of vitreous sections. EMBO J 23:3583–3588

    Article  PubMed  CAS  Google Scholar 

  63. Dubochet J (2012) Cryo-EM—the first thirty years. J Microsc 245:221–224

    Article  PubMed  CAS  Google Scholar 

  64. Dubochet J, McDowall AW (1981) Vitrification of pure water for electron microscopy. J Microsc 124:RP3–RP4

    Article  Google Scholar 

  65. Plitzko JM, Baumeister W (2007) Cryoelectron tomography (CET). In: Hawkes PW, Spence JCH (eds) Science of microscopy, vol I. Springer, New York, pp 535–604

    Chapter  Google Scholar 

  66. Shimoni E, Müller M (1998) On optimizing high-pressure freezing: from heat transfer theory to a new microbiopsy device. J Microsc 192:236–247

    Article  PubMed  CAS  Google Scholar 

  67. Matias VRF, Beveridge TJ (2005) Cryo-electron microscopy reveals native polymeric cell wall structure in Bacillus subtilis 168 and the existence of a periplasmic space. Mol Microbiol 56:240–251

    Article  PubMed  CAS  Google Scholar 

  68. Matias VRF, Beveridge TJ (2006) Native cell wall organization shown by cryo-electron microscopy confirms the existence of a periplasmic space in Staphylococcus aureaus. J Bacteriol 188:1011–1021

    Article  PubMed  CAS  Google Scholar 

  69. Hoffmann C, Leis A, Niederweis M, Plitzko JM, Engelhardt H (2008) Disclosure of the mycobacterial outer membrane: cryo-electron tomography and vitreous sections reveal the lipid bilayer structure. Proc Natl Acad Sci U S A 105:3963–3967

    Article  PubMed  CAS  Google Scholar 

  70. Zuber B, Chami M, Houssin C, Dubochet J, Griffith G, Daffé M (2008) Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state. J Bacteriol 190:5672–5680

    Article  PubMed  CAS  Google Scholar 

  71. Paul TR, Beveridge TJ (1992) Reevaluation of envelope profiles and cytoplasmic ultrastructure of mycobacteria processed by conventional embedding and freeze- substitution protocols. J Bacteriol 174:6508–6517

    PubMed  CAS  Google Scholar 

  72. Bleck CKE, Merz A, Gutierrez MG, Walther P, Dubochet J, Zuber B, Griffith G (2009) Comparison of different methods for thin sections EM analysis of Mycobacterium smegmatis. J Microsc 237:23–38

    Article  CAS  Google Scholar 

  73. Al-Amoudi A, Studer D, Dubochet J (2005) Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy. J Struct Biol 150:109–121

    Article  PubMed  CAS  Google Scholar 

  74. Han H-M, Zuber B, Dubochet J (2008) Compression and crevasses in vitreous sections under different cutting conditions. J Microsc 230:167–171

    Article  PubMed  Google Scholar 

  75. Zuber B, Haenni M, Ribeiro T, Minnig K, Lopes F, Moreillon P, Dubochet J (2006) Granular layer in the periplasmic space of gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa revealed by cryo-electron microscopy of vitreous sections. J Bacteriol 188:6652–6660

    Article  PubMed  CAS  Google Scholar 

  76. Ballerini M, Milani M, Batani M, Squadrini F (2001) Focused ion beam techniques for the analysis of biological samples: a revolution in ultramicroscopy? Proc SPIE 4261:92–104

    Article  Google Scholar 

  77. Heymann JAW, Hayles M, Gestmann I, Giannuzzi LA, Lich B, Subramaniam S (2006) Site-specific 3D imaging of cells and tissues with a dual beam microscope. J Struct Biol 155:63–73

    Article  PubMed  Google Scholar 

  78. Marko M, Hsieh C, Moberlychan W, Mannella CA, Frank J (2006) Focused ion beam milling of vitreous water: prospects for an alternative to cryo-ultramicrotomy of frozen- hydrated biological samples. J Microsc 222:42–47

    Article  PubMed  CAS  Google Scholar 

  79. Marko M, Hsieh C, Schalek R, Frank J, Mannella C (2007) Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy. Nat Methods 4:2015–2017

    Article  CAS  Google Scholar 

  80. Rigort A, Bäuerlein FJB, Leis A, Gruska M, Hoffmann C, Laugks T, Böhm U, Eibauer M, Gnaegi H, Baumeister W, Plitzko JM (2010) Micromachining tools and correlative approaches for cellular cryo-electron tomography. J Struct Biol 172:169–179

    Article  PubMed  Google Scholar 

  81. Rigort A, Bäuerlein FJB, Villa E, Eibauer M, Laugks T, Baumeister W, Plitzko JM (2012) Focused ion beam micromachining of ­eukaryotic cells for cryoelectron tomography. Proc Natl Acad Sci U S A 109:4449–4454

    Article  PubMed  CAS  Google Scholar 

  82. Brenner S, Horne RW (1959) A negative staining method for high resolution electron microscopy of viruses. Biochim Biophys Acta 34:103–110

    Article  PubMed  CAS  Google Scholar 

  83. Bremer A, Henn C, Engel A, Baumeister W, Aebi U (1992) Has negative staining still a place in biomacromolecular electron microscopy? Ultramicroscopy 46:85–111

    Article  PubMed  CAS  Google Scholar 

  84. Anderson TF (1962) Negative staining and its use in the study of viruses and their serological reactions. In: Harris RJC (ed) Symposium of the international society for cell biology, vol 1. Academic, New York, pp 251–262

    Google Scholar 

  85. DeRosier DJ, Klug A (1968) Reconstruction of three-dimensional structures from electron micrographs. Nature 217:130–134

    Article  Google Scholar 

  86. Hoppe W, Langer R, Knesch G, Poppe C (1968) Proteinkristallstrukturanalyse mit Elektronenstrahlen. Naturwissenschaften 55:333–336

    Article  PubMed  CAS  Google Scholar 

  87. Hoppe W, Gassmann J, Hunsmann N, Schramm HJ, Sturm M (1974) Three-dimensional reconstruction of individual negatively stained yeast fatty-acid synthetase molecules from tilt series in the electron microscope. Hoppe Seylers Z Physiol Chem 355:1483–1487

    PubMed  CAS  Google Scholar 

  88. Frank J (1989) Image analysis of single molecules. Electron Microsc Rev 2:53–74

    Article  PubMed  CAS  Google Scholar 

  89. Hegerl R (1996) The EM program package: a platform for image processing in biological electron microscopy. J Struct Biol 116:30–34

    Article  PubMed  Google Scholar 

  90. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the IMAGIC image processing system. J Struct Biol 116:17–24

    Article  PubMed  Google Scholar 

  91. Sorzano COS, Marabini R, Velázques-Muriel J, Bilbao-Acstro JR, Scheres SHW, Carazo JM, Pascual-Montano A (2004) XMIPP: a new generation of an open-source image processing package for electron microscopy. J Struct Biol 148:194–204

    Article  PubMed  CAS  Google Scholar 

  92. Shaik TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc 3:1941–1974

    Article  CAS  Google Scholar 

  93. Korinek A, Beck F, Baumeister W, Nickell S, Plitzko JM (2011) Computer controlled cryo-electron microscopy—TOM2 a software package for high-throughput applications. J Struct Biol 175:394–405

    Article  PubMed  Google Scholar 

  94. Engelhardt H (1991) Electron microscopy of microbial cell wall proteins. Surface topography, three-dimensional reconstruction, and strategies for two-dimensional crystallization. In: Latgé JP, Boucias D (eds) Fungal cell wall and immune response, NATO ASI Series H53. Springer, Berlin, pp 11–25

    Google Scholar 

  95. Saxton WO, Baumeister W, Hahn M (1984) Three-dimensional reconstruction of imperfect two-dimensional crystals. Ultramicroscopy 13:57–70

    Article  PubMed  CAS  Google Scholar 

  96. Bingle WH, Engelhardt H, Page WJ, Baumeister W (1987) Three-dimensional structure of the regular tetragonal surface layer of Azotobacter vinelandii. J Bacteriol 169:5008–5015

    PubMed  CAS  Google Scholar 

  97. Engelhardt H, Cejka Z, Baumeister W (1988) Three-dimensional structure of surface layers from various Bacillus and Clostridium species. In: Sleytr UB, Messner P, Pum D, Sára M (eds) Crystalline bacterial cell surface layers. Springer, Berlin, pp 87–91

    Chapter  Google Scholar 

  98. Tsuboi A, Engelhardt H, Santarius U, Tsukagoshi N, Udaka S, Baumeister W (1989) Three-dimensional structure of the surface protein layer (MW layer) of Bacillus brevis 47. J Ultrastruct Mol Struct Res 102:178–187

    Article  PubMed  CAS  Google Scholar 

  99. Beveridge TJ, Pouwels PH, Sára M et al (1997) Functions of S-layers. FEMS Microbiol Rev 20:99–149

    Article  PubMed  CAS  Google Scholar 

  100. Engelhardt H, Peters J (1998) Structural research on surface layers—a focus on stability, surface layer homology domains, and surface layer-cell wall interactions. J Struct Biol 124:276–302

    Article  PubMed  CAS  Google Scholar 

  101. Engel A, Massalski A, Schindler H, Dorset DL, Rosenbusch JP (1985) Porin channel triplets merge into single outlets in Escherichia coli outer membranes. Nature 317:643–645

    Article  PubMed  CAS  Google Scholar 

  102. Chalcroft JP, Engelhardt H, Baumeister W (1987) Structure of the porin from a bacterial stalk. FEBS Lett 211:53–58

    Article  PubMed  CAS  Google Scholar 

  103. Sass JJ, Massalski A, Beckmann E, Büldt G, Dorset D, van Heel M, Rosenbusch JP, Zeitler E, Zemlin F (1988) High-resolution cryomicroscopy of porin (OmpF). In: Bailey GW (ed) Proc 46th Ann Meet Electron Microscopy Soc Am. San Francisco Press, San Francisco, pp 146–147

    Google Scholar 

  104. Jap B, Downing KH, Walian PJ (1990) Structure of PhoE porin in projection at 3.5 Å resolution. J Struct Biol 103:57–63

    Article  PubMed  CAS  Google Scholar 

  105. Weiss MS, Abele U, Weckesser J, Welte W, Schiltz E, Schulz GE (1991) Molecular architecture and electrostatic properties of a bacterial porin. Science 254:1627–1630

    Article  PubMed  CAS  Google Scholar 

  106. Trachtenberg S, DeRosier DJ, Macnab RM (1987) Three-dimensional structure of the complex flagellar filament of Rhizobium lupini and its relation to the structure of the plain filament. J Mol Biol 195:603–620

    Article  PubMed  CAS  Google Scholar 

  107. Morgan DG, Machnab RM, Francis NR, DeRosier DJ (1993) Domain organization of the subunit of the Salmonella typhimurium flagellar hook. J Mol Biol 229:79–84

    Article  PubMed  CAS  Google Scholar 

  108. Engelhardt H, Schuster SC, Baeuerlein E (1993) An Archimedian spiral: the basal disk of the Wolinella flagellar hook. Science 262:1046–1048

    Article  PubMed  CAS  Google Scholar 

  109. Woodcock CL, Baumeister W (1990) Different representations of a protein structure obtained with different negative stains. Eur J Cell Biol 51:45–52

    CAS  Google Scholar 

  110. Rachel R, Jakubowski U, Tietz H, Hegerl R, Baumeister W (1986) Projected structure of the surface protein of Deinococcus radiodurans determined to 8 Å resolution by cryomicroscopy. Ultramicroscopy 20:305–316

    Article  CAS  Google Scholar 

  111. Jakubowski U, Hegerl R, Formanek H, Volker S, Santarius U, Baumeister W (1988) Three-dimensional reconstruction of the HPI-layer of Deinococcus radiodurans embedded in Cd-thioglycerol. Inst Phys Conf Ser 93(3):381–382

    Google Scholar 

  112. Henderson R, Unwin PNT (1975) Three-dimensional model of purple membrane obtained by electron microscopy. Nature 257:28–32

    Article  PubMed  CAS  Google Scholar 

  113. Glaeser RM, Hall RJ (2011) Reaching the information limit in cyro-EM of biological macromolecules: experimental aspects. Biophys J 100:2331–2337

    Article  PubMed  CAS  Google Scholar 

  114. Penczek P, Radermacher M, Frank J (1992) Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 40:33–52

    Article  PubMed  CAS  Google Scholar 

  115. Frank J, Radermacher M (1992) Three-dimensional reconstruction of single particles negatively stained or in vitreous ice. Ultramicroscopy 46:241–262

    Article  PubMed  CAS  Google Scholar 

  116. Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo- microscopy. J Mol Biol 213:899–929

    Article  PubMed  CAS  Google Scholar 

  117. DeRosier DJ, Moore PB (1970) Reconstruction of three-dimensional images from electron micrographs of structures with helical symmetry. J Mol Biol 52:355–369

    Article  PubMed  CAS  Google Scholar 

  118. Morgan DG, DeRosier D (1992) Processing images of helical structures: a new twist. Ultramicroscopy 46:263–285

    Article  PubMed  CAS  Google Scholar 

  119. Egelman EH (2000) A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 85:225–234

    Article  PubMed  CAS  Google Scholar 

  120. Mimori Y, Samashita I, Murata K, Fujiyoshi Y, Yonekura K, Toyoshima C, Namba K (1995) The structure of the R-type straight flagellar filament of Salmonella at 9 Å resolution by electron cryomicroscopy. J Mol Biol 249:69–87

    Article  PubMed  CAS  Google Scholar 

  121. Morgan DG, Owen C, Melanson LA, DeRosier DJ (1995) Structure of bacterial flagellar filaments at 11 Å resolution: packing of the α-helices. J Mol Biol 249:88–110

    Article  PubMed  CAS  Google Scholar 

  122. Yonekura K, Maki-Yonekura S, Namba K (2003) Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424:643–650

    Article  PubMed  CAS  Google Scholar 

  123. Galkin VE, Yu X, Bielnicki J, Heuser J, Ewing CP, Guerry P, Egelman EH (2008) Divergence of quaternary structures among bacterial flagellar filaments. Science 320:382–385

    Article  PubMed  CAS  Google Scholar 

  124. Maki-Yonekura S, Yonekura K, Namba K (2010) Conformational change of flagellin for polymorphic supercoiling of the flagellar filament. Nat Struct Mol Biol 17:417–422

    Article  PubMed  CAS  Google Scholar 

  125. Samatey FA, Natsunami H, Imada K, Gagashima S, Shaikh T, Thomas DR, Chen JZ, DeRosier DJ, Kitao A, Namba K (2004) Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature 431:1062–1068

    Article  PubMed  CAS  Google Scholar 

  126. Shaik TR, Thomas DR, Chen JZ, Samatey FA, Matsunami H, Imada K, Namba K, DeRosier DJ (2005) A partial atomic structure for the flagellar hook of Salmonella typhimurium. Proc Natl Acad Sci U S A 102:1023–1028

    Article  CAS  Google Scholar 

  127. Fujii T, Kato T, Namba K (2009) Specific arrangement of α-helical coiled coils in the core domain of the bacterial flagellar hook for the universal joint function. Structure 17:1485–1493

    Article  PubMed  CAS  Google Scholar 

  128. Steven AC, Baumeister W (2008) The future is hybrid. J Struct Biol 163:186–195

    Article  PubMed  CAS  Google Scholar 

  129. Wriggers W (2010) Using Situs for the integration of multi-resolution structures. Biophys Rev 2:21–27

    Article  PubMed  Google Scholar 

  130. Trabuco LG, Schreiner E, Gumbart J, Hsin J, Villa E, Schulten K (2011) Applications of the molecular dynamics flexible fitting method. J Struct Biol 173:420–427

    Article  PubMed  CAS  Google Scholar 

  131. Fujii T, Cheung M, Blanco A, Kato T, Blocker AJ, Namba K (2012) Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms. Proc Natl Acad Sci U S A 109:4461–4466

    Article  PubMed  CAS  Google Scholar 

  132. Young HS, Dang H, Lai Y, DeRosier DJ, Khan S (2003) Variable symmetry in Salmonella typhimurium flagellar motors. Biophys J 84:571–577

    Article  PubMed  CAS  Google Scholar 

  133. Thomas DR, Francis NR, Xu C, DeRosier DJ (2006) The three-dimensional structure of the flagellar rotor from a clockwise-locked mutant of Salmonella enterica serovar typhimurium. J Bacteriol 188:7039–7048

    Article  PubMed  CAS  Google Scholar 

  134. Minamino T, Imada K, Namba K (2008) Molecular motors of the bacterial flagella. Curr Opin Struct Biol 18:693–701

    Article  PubMed  CAS  Google Scholar 

  135. Schraidt O, Lefebre MD, Brunner MJ, Schmied WH, Schmidt A, Radics J, Mechtler K, Galán JE, Marlovits TC (2010) Topology and organization of the Salmonella typhimurium type III secretion needle complex components. PLoS Pathog 6:e1000824

    Article  PubMed  CAS  Google Scholar 

  136. Schraidt O, Marlovits TC (2011) Three-dimensional model of Salmonella´s needle complex at subnanometer resolution. Science 331:1192–1195

    Article  PubMed  CAS  Google Scholar 

  137. Fronzes R, Schäfer E, Wang L, Saibil HR, Orlova EV, Waksman G (2009) Structure of a type IV secretion system core complex. Science 323:266–268

    Article  PubMed  CAS  Google Scholar 

  138. Chandran V, Fronzes R, Duquerroy S, Cronin N, Navaza J, Waksman G (2009) Structure of the outer membrane complex of a type IV secretion system. Nature 462:1011–1015

    Article  PubMed  CAS  Google Scholar 

  139. Hart RG (1968) Electron microscopy of unstained biological material: the polytropic montage. Science 159:1464–1467

    Article  PubMed  CAS  Google Scholar 

  140. Dierksen K, Typke D, Hegerl R, Koster AJ, Baumeister W (1992) Towards automatic electron tomography. Ultramicroscopy 40:71–87

    Article  Google Scholar 

  141. Dierksen K, Typke D, Hegerl R, Baumeister W (1993) Towards automatic electron tomography II. Implementation of autofocus and low-dose procedures. Ultramicroscopy 49:109–120

    Article  Google Scholar 

  142. Grimm R, Koster J, Ziese U, Typke D, Baumeister W (1996) Zero-loss energy filtering under low-down conditions using a post-column energy filter. J Microsc 183:60–68

    Article  CAS  Google Scholar 

  143. Grimm R, Typke D, Baumeister W (1998) Improving image quality by zero-loss energy filtering: quantitative assessment by means of image cross-correlation. J Microsc 190:339–349

    Article  Google Scholar 

  144. Medalia O, Weber I, Frangaiks AS, Nicastro D, Gerisch G, Baumeister W (2002) Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298:1209–1213

    Article  PubMed  CAS  Google Scholar 

  145. Baumeister W (2002) Electron tomography: towards visualizing the molecular organization of the cytoskeleton. Curr Opin Struct Biol 12:679–684

    Article  PubMed  CAS  Google Scholar 

  146. Lucic V, Förster F, Baumeister W (2005) Structural studies by electron tomography: from cells to molecules. Annu Rev Biochem 74:833–865

    Article  PubMed  CAS  Google Scholar 

  147. Leis A, Rockel B, Andrees L, Baumeister W (2009) Visualizing cells at the nanoscale. Trends Biochem Sci 34:60–70

    Article  PubMed  CAS  Google Scholar 

  148. Nickell S, Hegerl R, Baumeister W, Rachel R (2003) Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J Struct Biol 141:34–42

    Article  PubMed  Google Scholar 

  149. Schrempf H, Koebsch I, Walter S, Engelhardt H, Meschke H (2011) Extracellular Streptomyces veiscles: amphorae for survival and defence. Microb Biotechnol 4:286–299

    Article  PubMed  CAS  Google Scholar 

  150. Gan L, Chen S, Jensen GJ (2008) Molecular organization of Gram-negative peptidoglycan. Proc Natl Acad Sci U S A 105:18953–18957

    Article  PubMed  CAS  Google Scholar 

  151. Murphy GE, Leadbetter JR, Jensen GJ (2006) In situ structure of the complete Treponema primitia flagellar motor. Nature 442:1062–1064

    Article  PubMed  CAS  Google Scholar 

  152. Izard J, Hsieh C-E, Limberger R, Mannella CA, Marko M (2008) Native cellular architecture of Treponema denticola revealed by cryo-electron tomography. J Struct Biol 163:10–17

    Article  PubMed  CAS  Google Scholar 

  153. Chen S, Beeby M, Murphy GE, Leadbetter JR, Hendrixon DR, Briegel A, Li Z, Shi J, Tocheva EI, Müller A, Dobro MM, Jensen GJ (2011) Structural diversity of bacterial flagellar motors. EMBO J 30:2972–2981

    Article  PubMed  CAS  Google Scholar 

  154. Kürner J, Frangakis AS, Baumeister W (2005) Cryo-electron tomography reveals the cytoskeletal structure of Spiroplasma melliferum. Science 307:436–438

    Article  PubMed  CAS  Google Scholar 

  155. Jensen GJ, Briegel A (2007) How electron cryotomography is opening a new window onto prokaryotic ultrastructure. Curr Opin Struct Biol 17:260–267

    Article  PubMed  CAS  Google Scholar 

  156. Morris DM, Jensen GJ (2008) Toward a biomechanical understanding of whole bacterial cells. Annu Rev Biochem 77:583–613

    Article  PubMed  CAS  Google Scholar 

  157. Ting CS, Hsieh C, Sundararaman S, Mannella C, Marko M (2007) Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus, a globally important marine cyanobacterium. J Bacteriol 289:4485–4493

    Article  CAS  Google Scholar 

  158. Beck M, Malmström JA, Lange V, Schmidt A, Deutsch EW, Aebersold R (2009) Visual proteomics of the human pathogen Leptospira interrogans. Nat Methods 6:817–823

    Article  PubMed  CAS  Google Scholar 

  159. Ortiz JO, Brandt F, Matias VRF, Sennels L, Rappsilber J, Scheres SHW, Eibauer M, Hartl FU, Baumeister W (2010) Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ. J Cell Biol 190:613–621

    Article  PubMed  CAS  Google Scholar 

  160. Fernández JJ, Li S, Crowther RA (2006) CTF determination and correction in electron cryotomography. Ultramicroscopy 106:587–596

    Article  PubMed  CAS  Google Scholar 

  161. Xiong Q, Morphew MK, Schwartz CL, Hoenger AH, Mastronarde DN (2009) CTF determination and correction for low dose tomographic tilt series. J Struct Biol 168:378–387

    Article  PubMed  Google Scholar 

  162. Danev R, Nagayama K (2001) Transmission electron microscopy with zernike phase plate. Ultramicroscopy 88:243–252

    Article  PubMed  CAS  Google Scholar 

  163. Danev R, Kanamaru S, Marko M, Nagayama K (2010) Zernike phase contrast cryo- electron tomography. J Struct Biol 171:174–181

    Article  PubMed  Google Scholar 

  164. Rigort A, Günther D, Hegerl R, Baum D, Weber B, Prohaska S, Medalia O, Baumeister W, Hege H-C (2012) Automated segmentation of electron tomograms for a quantitative description of actin filament networks. J Struct Biol 177:135–144

    Article  PubMed  CAS  Google Scholar 

  165. Sartori A, Gatz R, Beck F, Rigort A, Baumeister W, Plitzko JM (2007) Correlative microscopy: bridging the gap between fluorescence light microscopy and cryo-electron tomography. J Struct Biol 160:135–145

    Article  PubMed  Google Scholar 

  166. Wang Q, Mercogliano CP, Löwe J (2011) A ferritin-based label for cellular electron cryotomography. Structure 19:147–154

    Article  PubMed  CAS  Google Scholar 

  167. Frangakis AS, Böhm J, Förster F, Nickell S, Nicastro D, Typke D, Hegerl R, Baumeister W (2002) Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc Natl Acad Sci U S A 99:14153–14158

    Article  PubMed  CAS  Google Scholar 

  168. Frangakis AS, Förster F (2004) Computational exploration of structural information from cryo-electron tomograms. Curr Opin Struct Biol 14:325–331

    Article  PubMed  CAS  Google Scholar 

  169. Nickell S, Kofler C, Leis AP, Baumeister W (2006) A visual approach to proteomics. Nat Rev Mol Cell Biol 7:225–230

    Article  PubMed  CAS  Google Scholar 

  170. Ortiz JO, Förster F, Kürner J, Linaroudis AA, Baumeister W (2006) Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. J Struct Biol 156:334–341

    Article  PubMed  CAS  Google Scholar 

  171. Eibauer M (2011) Korrektur der transferfunktionen CTF und MTF in der Kryoelektronentomographie. Thesis, Technical University of Munich

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Max-Planck-Institut für Biochemie, Martinsried, Germany

    Harald Engelhardt

Authors
  1. Harald Engelhardt
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Harald Engelhardt .

Editor information

Editors and Affiliations

  1. , Dept. of Biology and Biochemistry, University of Houston, Calhoun Road 4800, Houston, 77004, Texas, USA

    Anne H. Delcour

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this protocol

Cite this protocol

Engelhardt, H. (2013). Visualizing the Bacterial Cell Surface: An Overview. In: Delcour, A. (eds) Bacterial Cell Surfaces. Methods in Molecular Biology, vol 966. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-245-2_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-245-2_2

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-244-5

  • Online ISBN: 978-1-62703-245-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation