Study of the Deinococcus radiodurans nucleoid by cryoelectron microscopy of vitreous sections: Supplementary comments

Journal of Bacteriology

Volumn 188, Issue 17, 2006, Pages 6053-6058

  Eltsov, Mikhail ^a   Dubochet, Jacques ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

CHROMATIN CONDENSATION; CRYOELECTRON MICROSCOPY; DEINOCOCCUS RADIODURANS; DNA DAMAGE; DNA PACKAGING; DNA REPAIR; DNA STRAND BREAKAGE; DNA STRUCTURE; NONHUMAN; PRIORITY JOURNAL; REVIEW; TRANSMISSION ELECTRON MICROSCOPY;

CELL NUCLEOLUS; CRYOELECTRON MICROSCOPY; DEINOCOCCUS; DNA, BACTERIAL;

DEINOCOCCUS RADIODURANS;

EID: 33748993717     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00230-06     Document Type: Review

References (34)

1. Al-Amoudi, A., J. J. Chang, A. Leforestier, A. McDowall, L. M. Salamin, L. P. Norlen, K. Richter, N. S. Blanc, D. Studer, and J. Dubochet. 2004. Cryoelectron microscopy of vitreous sections. EMBO J. 23:3583-3588.
2. Al-Amoudi, A., D. Studer, and J. Dubochet. 2005. Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy. J. Struct. Biol. 150:109-121.
3. Allen, G. S., A. Zavialov, R. Gursky, M. Ehrenberg, and J. Frank. 2005. The cryo-EM structure of a translation initiation complex from Escherichia coli. Cell 121:703-712.
4. Angell, C. A. 2004. Amorphous water. Annu. Rev. Phy. Chem. 55:559-583.
5. Baumeister, W., M. Barth, R. Hegerl, R. Guckenberger, M. Hahn, and W. O. Saxton. 1986. Three-dimensional structure of the regular surface layer (HPI layer) of Deinococcus radiodurans. J. Mol. Biol. 187:241-250.
6. Bednar, J., P. Furrer, A. Stasiak, J. Dubochet, E. H. Egelman, and A. D. Bates. 1994. The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. J. Mol. Biol. 235:825-847.
7. Bouchet-Marquis, C., J. Dubochet, and S. Fakan. 2006. Cryoelectron microscopy of vitrified sections: a new challenge for the analysis of functional nuclear architecture. Histochem. Cell Biol. 125:43-51.
8. Brooks, B. W., R. G. Murray, J. L. Johnson, E. Stackebrandt, C. R. Woese, and G. E. Fox. 1980. Red-pigmented micrococci: a basis for taxonomy. Int. J. Syst. Microbiol. 30:627-646.
9. Cox, M. M., and J. R. Battista. 2005. Deinococcus radiodurans - the consummate survivor. Nat. Rev. Microbiol. 3:882-892.
10. Daly, M. J., E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, A. Venkateswaran, M. Hess, M. V. Omelchenko, H. M. Kostandarithes, K. S. Makarova, L. P. Wackett, J. K. Fredrickson, and D. Ghosal. 2004. Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science 306:1025-1028.
11. Daly, M. J., O. Ling, and K. W. Minton. 1994. Interplasmidic recombination following irradiation of the radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 176:7506-7515.
12. Daly, M. J., and K. W. Minton. 1996. An alternative pathway of recombination of chromosomal fragments precedes recA-dependent recombination in the radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 178: 4461-4471.
13. Daly, M. J., and K. W. Minton. 1995. Interchromosomal recombination in the extremely radioresistant bacterium Deinococcus radiodurans. J. Bacteriol. 177:5495-5505.
14. Dubochet, J., J. Bednar, P. Furrer, A. Z. Stasiak, A. Stasiak, and A. A. Bolshoy. 1994. Determination of the DNA helical repeat by cryo-electron microscopy. Nat. Struct. Biol. 1:361-363.
15. Eltsov, M., and J. Dubochet. 2005. Fine structure of the Deinococcus radiodurans nucleoid revealed by cryoelectron microscopy of vitreous sections. J. Bacteriol. 187:8047-8054.
16. Englander, J., E. Klein, V. Brumfeld, A. K. Sharma, A. J. Doherty, and A. Minsky. 2004. DNA toroids: framework for DNA repair in Deinococcus radiodurans and in germinating bacterial spores. J. Bacteriol. 186:5973-5977.
17. Ghosal, D., M. V. Omelchenko, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, A. Venkateswaran, M. Zhai, H. M. Kostandarithes, H. Brim, and K. S. Makarova. 2005. How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress. FEMS Microbiol. Rev. 29:361-375.
18. Harris, D. R., M. Tanaka, S. V. Saveliev, E. Jolivet, A. M. Earl, M. M. Cox, and J. R. Battista. 2004. Preserving genome integrity: the DdrA protein of Deinococcus radiodurans R1. PLoS Biol. 2:1629-1639.
19. Hobot, J. A., W. Villiger, J. Escaig, M. Maeder, A. Ryter, and E. Kellenberger. 1985. Shape and fine structure of nucleoids observed on sections of ultrarapidly frozen and cryosubstituted bacteria. J. Bacteriol. 162:960-971.
20. Hud, N. V., and K. H. Downing. 2001. Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: the fine structure of DNA toroids. Proc. Natl. Acad. Sci. USA 98:14925-14930.
21. Hud, N. V., and I. D. Vilfan. 2005. Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size. Annu. Rev. Biophys. Biomol. Struct. 34:295-318.
22. Karrasch, S., R. Hegerl, J. H. Hoh, W. Baumeister, and A. Engel. 1994. Atomic force microscopy produces faithful high-resolution images of protein surfaces in an aqueous environment. Proc. Natl. Acad. Sci. USA 91:836-838.
23. Leforestier, A, H. U. Nissen, and J. Dubochet. 1995. DNA-DNA interaction in thin layer analysed by cryo-electron microscopy. C. R. Acad. Sci. Ser. III 318:1015-1020.
24. Levin-Zaidman. S., J. Englander, E. Shimoni, A. K. Sharma, K. W. Minton, and A. Minsky. 2003. Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance? Science 299:254-256.
25. Livolant, F., and A. Leforestier. 1996. Condensed phases of DNA: structures and phase transitions. Prog. Polym. Sci. 21:1115-1164.
26. Lucic, V., F. Forster, and W. Baumeister. 2005. Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biochem. 74:833-865.
27. Matias, V. R., A. Al-Amoudi, J. Dubochet, and T. J. Beveridge. 2003. Cryotransmission electron microscopy of frozen-hydrated sections of Escherichia coli and Pseudomonas aeruginosa. J. Bacteriol. 185:6112-6118.
28. Minsky, A. 2003. Structural aspects of DNA repair: the role of restricted diffusion. Mol. Microbiol. 50:367-376.
29. Peters, J., and W. Baumeister. 1986. Molecular cloning, expression, and characterization of the gene for the surface (HPI) layer protein of Deinococcus radiodurans in Escherichia coli. J. Bacteriol. 167:1048-1054.
30. Sartori Blanc, N., A. Senn, A. Leforestier, F. Livolant, and J. Dubochet. 2001. DNA in human and stallion spermatozoa forms local hexagonal packing with twist and many defects. J. Struct. Biol. 134:76-81.
31. Studer, D., M. Michel, M. Wohlwend, E. B. Hunziker, and M. D. Buschmann. 1995. Vitrification of articular cartilage by high-pressure freezing. J. Microsc. 179:321-332.
32. Thornley, M. J., R. W. Horne, and A. M. Glauert. 1965. The fine structure of Micrococcus radiodurans. Arch. Mikrobiol. 51:267-289.
33. Valkenburg, J. A. C., and C. L. Woldringh. 1984. Phase separation between nucleoid and cytoplasm in Escherichia coli as defined by immersive refractometry. J. Bacteriol. 160:1151-1157.
34. Zimmerman, J. M., and J. R. Battista. 2005. A ring-like nucleoid is not necessary for radioresistance in the Deinococcaceae. BMC Microbiol. 5:17.