Single particle and molecular assembly analysis of polyribosomes by single- and double-tilt cryo electron tomography

Ultramicroscopy

Volumn 126, Issue , 2013, Pages 33-39

  Myasnikov, Alexander G ^a   Afonina, Zhanna A ^b   Klaholz, Bruno P ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

Author keywords

3D reconstruction; Classification; Cryo electron tomography; Double tilt; Dual axis; Electron microscopy; Image processing; Polysome; Ribosome; Single particle; Sub tomogram averaging

Indexed keywords

3D RECONSTRUCTION; CRYO-ELECTRON TOMOGRAPHY; DOUBLE TILT; DUAL AXIS; POLYSOME; RIBOSOME; SINGLE PARTICLE; SUB-TOMOGRAM AVERAGING;

CLASSIFICATION (OF INFORMATION); ELECTRIC IMPEDANCE TOMOGRAPHY; ELECTRON MICROSCOPY; IMAGE PROCESSING; MACROMOLECULES; THREE DIMENSIONAL; THREE DIMENSIONAL COMPUTER GRAPHICS;

QUALITY CONTROL;

ARTICLE; CELL STRUCTURE; CONTRAST ENHANCEMENT; CONTROLLED STUDY; CORRELATION ANALYSIS; CRYOELECTRON MICROSCOPY; DATA ANALYSIS; EUKARYOTIC CELL; IMAGE QUALITY; NONHUMAN; PLANT CELL; POLYSOME; QUANTITATIVE ANALYSIS; SINGLE CELL ANALYSIS; STATISTICAL ANALYSIS; THREE DIMENSIONAL IMAGING;

CRYOELECTRON MICROSCOPY; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MULTIVARIATE ANALYSIS; POLYRIBOSOMES; SIGNAL-TO-NOISE RATIO; TOMOGRAPHY;

EID: 84873142598     PISSN: 03043991     EISSN: 18792723     Source Type: Journal    
DOI: 10.1016/j.ultramic.2012.12.009     Document Type: Article

References (50)

1. Lucic V., Forster F., Baumeister W. Structural studies by electron tomography: from cells to molecules. Annual Review of Biochemistry 2005, 74:833-865.
2. Hoenger A., McIntosh J.R. Probing the macromolecular organization of cells by electron tomography. Current Opinion in Cell Biology 2009, 21(1):89-96.
3. Kurner J., Frangakis A.S., Baumeister W. Cryo-electron tomography reveals the cytoskeletal structure of Spiroplasma melliferum. Science 2005, 307(5708):436-438.
4. Schmid M.F., et al. Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. Journal of Molecular Biology 2006, 364(3):526-535.
5. Seybert A., Herrmann R., Frangakis A.S. Structural analysis of Mycoplasma pneumoniae by cryo-electron tomography. Journal of Structural Biology 2006, 156(2):342-354.
6. Comolli L.R., Kundmann M., Downing K.H. Characterization of intact subcellular bodies in whole bacteria by cryo-electron tomography and spectroscopic imaging. Journal of Microscopy 2006, 223(Pt 1):40-52.
7. Grunewald K., et al. Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 2003, 302(5649):1396-1398.
8. Medalia O., et al. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 2002, 298(5596):1209-1213.
9. Mader A., Elad N., Medalia O. Cryoelectron tomography of eukaryotic cells. Methods in Enzymology 2010, 483:245-265.
10. Wang K., et al. In vivo virus structures: simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography. Journal of Structural Biology 2011, 174(3):425-433.
11. P. Guichard, et al., Three dimensional morphology of rabies virus studied by cryo-electron tomography. Journal of Structural Biology, 2011.
12. J. Liu, et al., Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli. Virology, 2011.
13. Trepout S., et al. Structure of reconstituted bacterial membrane efflux pump by cryo-electron tomography. Biochimica et Biophysica Acta 2010, 1798(10):1953-1960.
14. Cope J., et al. Cryo-electron tomography of microtubule-kinesin motor complexes. Journal of Structural Biology 2009, 170(2):257-265.
15. Beck M., et al. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 2004, 306(5700):1387-1390.
16. Brandt F., et al. The native 3D organization of bacterial polysomes. Cell 2009, 136(2):261-271.
17. Brandt F., et al. The three-dimensional organization of polyribosomes in intact human cells. Molecular Cell 2010, 39(4):560-569.
18. Ortiz J.O., et al. Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ. Journal of Cell Biology 2010, 190(4):613-621.
19. de Marco A., et al. Structural analysis of HIV-1 maturation using cryo-electron tomography. Plos Pathogens 2010, 6(11):e1001215.
20. Vanhecke D., et al. Cryo-electron tomography: methodology, developments and biological applications. Journal of Microscopy 2010, 242(3):221-227.
21. Hoppe W., Schramm H.J., Sturm M., Hunsmann N., GaΒmann J. Three-dimensional electron microscopy of individual biological objects. Z. Naturforsch 1976, 31A:645-655.
22. Oettl H., Hegerl R., Hoppe W. Three-dimensional reconstruction and averaging of 50S ribosomal subunits of Escherichia coli from electron micrographs. Journal of Molecular Biology 1983, 163(3):431-450.
23. Frangakis A.S., et al. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(22):14153-14158.
24. Ortiz J.O., et al. Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. Journal of Structural Biology 2006, 156(2):334-341.
25. Best C., Nickell S., Baumeister W. Localization of protein complexes by pattern recognition. Methods in Cell Biology 2007, 79:615-638.
26. Nicastro D., et al. The molecular architecture of axonemes revealed by cryoelectron tomography. Science 2006, 313(5789):944-948.
27. Scheres S.H., et al. Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 2009, 17(12):1563-1572.
28. Annie Cavalier D.S., Humbel M. Handook of Cryo-Preparation Methods for Electron Microscopy 2009, 682. CRC press. first ed. G. Morel. (Ed.).
29. Iancu C.V., et al. A flip-flop rotation stage for routine dual-axis electron cryotomography. Journal of Structural Biology 2005, 151(3):288-297.
30. Taylor C.R., Rosenfield A.T. Limitations of computed tomography in the recognition of delayed splenic rupture. Journal of Computer Assisted Tomography 1984, 8(6):1205-1207.
31. Penczek P., et al. Double-tilt electron tomography. Ultramicroscopy 1995, 60(3):393-410.
32. Radermacher M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. Journal of Electron Microscopy Technique 1988, 9(4):359-394.
33. Lanzavecchia S., et al. Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers. Journal of Structural Biology 2005, 149(1):87-98.
34. Cantele F., et al. Simultaneous alignment of dual-axis tilt series. Journal of Structural Biology 2009, 169(2):192-199.
35. Murata K., et al. Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. Structure 2010, 18(8):903-912.
36. N.V. Dudkina, et al., Imaging of organelles by electron microscopy reveals protein-protein interactions in mitochondria and chloroplasts. FEBS Letters 584(12): 2510-2515.
37. Dudkina N.V., et al. Row-like organization of ATP synthase in intact mitochondria determined by cryo-electron tomography. Biochimica et Biophysica Acta 1797, 2:272-277.
38. Shirokov V.A., et al. Continuous-exchange protein-synthesizing systems. Methods in Molecular Biology 2007, 375:19-55.
39. Kopeina G.S., et al. Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA. Nucleic Acids Research 2008, 36(8):2476-2488.
40. Klaholz B.P., Myasnikov A.G., van Heel M. Visualization of release factor 3 on the ribosome during termination of protein synthesis. Nature 2004, 427(6977):862-865.
41. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using IMOD. Journal of Structural Biology 1996, 116(1):71-76.
42. van Heel M., et al. A new generation of the IMAGIC image processing system. Journal of Structural Biology 1996, 116(1):17-24.
43. Bartesaghi A., et al. Classification and 3D averaging with missing wedge correction in biological electron tomography. Journal of Structural Biology 2008, 162(3):436-450.
44. Forster F., et al. Classification of cryo-electron sub-tomograms using constrained correlation. Journal of Structural Biology 2008, 161(3):276-286.
45. Yu, L., et al., Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data. Journal of Structural Biology 171(1): 18-30.
46. Pettersen E.F., et al. UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry 2004, 25(13):1605-1612.
47. Halic M., et al. Localization and dynamic behavior of ribosomal protein L30e. Nature Structural and Molecular Biology 2005, 12(5):467-468.
48. Simonetti A., et al. Structure of the 30S translation initiation complex. Nature 2008, 455(7211):416-420.
49. Elad N., et al. Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. Journal of Structural Biology 2008, 162(1):108-120.
50. Penczek P.A., et al. Estimation of variance in single-particle reconstruction using the bootstrap technique. Journal of Structural Biology 2006, 154(2):168-183.