Imaging the bacterial nucleoid

Bacterial Chromatin

Volumn 9789048134731, Issue , 2010, Pages 13-30

  Margolin, William ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

Actin; Bacteria; Cytokinesis; Cytoskeleton; Fluorescence; GFP; Localization; Nucleoid; Protein; Segregation; Tubulin

Indexed keywords

EID: 79952367666     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-90-481-3473-1_2     Document Type: Chapter

References (68)

1. Adler HI, Fisher W, Cohen A, Hardigree A (1967) Miniature E. coli cells deficient in DNA. Proc Natl Acad Sci USA 57:321-326
2. Aussel L, Barre FX, Aroyo M, Stasiak A, Stasiak AZ, Sherratt D (2002) FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell 108:195-205
3. Barry CE 3rd, Hayes SF, Hackstadt T (1992) Nucleoid condensation in Escherichia coli that express a chlamydial histone homolog. Science 256:377-379
4. Bath J, Wu LJ, Errington J, Wang JC (2000) Role of Bacillus subtilis SpoIIIE in DNA transport across the mother cell-prespore division septum. Science 290:995-997
5. Bendich AJ, Drlica K (2000) Prokaryotic and eukaryotic chromosomes: what's the difference? Bioessays 22:481-486
6. Ben-Yehuda S, Rudner DZ, Losick R (2003) RacA, a bacterial protein that anchors chromosomes to the cell poles. Science 299:532-536
7. Bernhardt TG, de Boer PA (2005) SlmA, a nucleoid-associated, FtsZ-binding protein required for blocking septal ring assembly over chromosomes in E. coli. Mol Cell 18:555-564
8. Bi E, Lutkenhaus J (1991) FtsZ ring structure associated with division in Escherichia coli. Nature 354:161-164
9. Bigot S, Sivanathan V, Possoz C, Barre FX, Cornet F (2007) FtsK, a literate chromosome segregation machine. Mol Microbiol 64:1434-1441
10. Bohrmann B, Villiger W, Johansen R, Kellenberger E (1991) Coralline shape of the bacterial nucleoid after cryofixation. J Bacteriol 173:3149-3158
11. Britton RA, Grossman AD (1999) Synthetic lethal phenotypes caused by mutations affecting chromosome partitioning in Bacillus subtilis. J Bacteriol 181:5860-5864
12. Bylund JE, Haines MA, Piggot PJ, Higgins ML (1993) Axial filament formation in Bacillus subtilis: induction of nucleoids of increasing length after addition of chloramphenicol to exponential-phase cultures approaching stationary phase. J Bacteriol 175:1886-1890
13. Costerton JW, Poffenroth L, Wilt JC, Kordova N (1976) Ultrastructural studies of the nucleoids of the pleomorphic forms of Chlamydia psittaci 6BC: a comparison with bacteria. Can J Microbiol 22:16-28
14. Danilova O, Reyes-Lamothe R, Pinskaya M, Sherratt D, Possoz C (2007) MukB colocalizes with the oriC region and is required for organization of the two Escherichia coli chromosome arms into separate cell halves. Mol Microbiol 65:1485-1492
15. Dworsky P, Schaechter M (1973) Effect of rifampin on the structure and membrane attachment of the nucleoid of Escherichia coli. J Bacteriol 116:1364-1374
16. Eltsov M, Dubochet J (2005) Fine structure of the Deinococcus radiodurans nucleoid revealed by cryoelectron microscopy of vitreous sections. J Bacteriol 187:8047-8054
17. Eltsov M, Zuber B (2006) Transmission electron microscopy of the bacterial nucleoid. J Struct Biol 156:246-254
18. Ferullo DJ, Lovett ST (2008) The stringent response and cell cycle arrest in Escherichia coli. PLoS Genet 4:e1000300
19. Frenkiel-Krispin D, Ben-Avraham I, Englander J, Shimoni E, Wolf SG, Minsky A (2004) Nucleoid restructuring in stationary-state bacteria. Mol Microbiol 51:395-405
20. Harry EJ, Rodwell J, Wake RG (1999) Co-ordinating DNA replication with cell division in bacteria: a link between the early stages of a round of replication and mid-cell Z ring assembly. Mol Microbiol 33:33-40
21. Heinzen RA, Howe D, Mallavia LP, Rockey DD, Hackstadt T (1996) Developmentally regulated synthesis of an unusually small, basic peptide by Coxiella burnetii. Mol Microbiol 22:9-19
22. Hinnebusch BJ, Bendich AJ (1997) The bacterial nucleoid visualized by fluorescence microscopy of cells lysed within agarose: comparison of Escherichia coli and spirochetes of the genus Borrelia. J Bacteriol 179:2228-2237
23. Hirano T (2006) At the heart of the chromosome: SMC proteins in action. Nat Rev Mol Cell Biol 7:311-322
24. Janakiraman A, Goldberg MB (2004) Evidence for polar positional information in E.coli independent of cell division and nucleoid occlusion. Proc Natl Acad Sci USA 101:835-840
25. Johnston D, Tavano C, Wickner S, Trun N (2006) Specificity of DNA binding and dimerization by CspE from Escherichia coli. J Biol Chem 281:40208-40215
26. Kar S, Edgar R, Adhya S (2005) Nucleoid remodeling by an altered HU protein: reorganization of the transcription program. Proc Natl Acad Sci USA 102:16397-16402
27. Kruse T, Blagoev B, Lobner-Olesen A, Wachi M, Sasaki K, Iwai N, Mann M, Gerdes K (2006) Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli. Genes Dev 20:113-124
28. Lee KS, Bumbaca D, Kosman J, Setlow P, Jedrzejas MJ (2008) Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species. Proc Natl Acad Sci USA 105(8):2806-2811
29. Lee KC, Webb RI, Fuerst JA (2009) The cell cycle of the planctomycete Gemmata obscuriglobus with respect to cell compartmentalization. BMC Cell Biol 10:4
30. Mason DJ, Powelson DM (1956) Nuclear division as observed in live bacteria by a new technique. J Bacteriol 71:474-479
31. Mendell JE, Clements KD, Choat JH, Angert ER (2008) Extreme polyploidy in a large bacterium. Proc Natl Acad Sci USA 105:6730-6734
32. Morikawa K, Ohniwa RL, Kim J, Maruyama A, Ohta T, Takeyasu K (2006) Bacterial nucleoid dynamics: oxidative stress response in Staphylococcus aureus. Genes Cells 11:409-423
33. Morlot C, Zapun A, Dideberg O, Vernet T (2003) Growth and division of Streptococcus pneumoniae: localization of the high molecular weight penicillin-binding proteins during the cell cycle. Mol Microbiol 50:845-855
34. Niki H, Hiraga S (1998) Polar localization of the replication origin and terminus in Escherichia coli nucleoids during chromosome partitioning. Genes Dev 12:1036-1045
35. Niki H, Imamura R, Kitaoka M, Yamanaka K, Ogura T, Hiraga S (1992) E. coli MukB protein involved in chromosome partition forms a homodimer with a rod-and-hinge structure having DNA binding and ATP/GTP binding activities. EMBO J 11:5101-5109
36. Niki H, Yamaichi Y, Hiraga S (2000) Dynamic organization of chromosomal DNA in Escherichia coli. Genes Dev 14:212-223
37. Ohniwa RL, Morikawa K, Kim J, Ohta T, Ishihama A, Wada C, Takeyasu K (2006) Dynamic state of DNA topology is essential for genome condensation in bacteria. EMBO J 25:5591-5602
38. Ohniwa RL, Morikawa K, Takeshita SL, Kim J, Ohta T, Wada C, Takeyasu K (2007) Transcriptioncoupled nucleoid architecture in bacteria. Genes Cells 12:1141-1152
39. Piekarski G (1937) Zytologische Untersuchungen an Paratyphus- und Coli bacterien. Arch Mikrobiol 8:428-429
40. Ragkousi K, Cowan AE, Ross MA, Setlow P (2000) Analysis of nucleoid morphology during germination and outgrowth of spores of Bacillus species. J Bacteriol 182:5556-5562
41. Ramos A, Letek M, Campelo AB, Vaquera J, Mateos LM, Gil JA (2005) Altered morphology produced by ftsZ expression in Corynebacterium glutamicum ATCC 13869. Microbiology 151:2563-2572
42. Robinow C, Kellenberger E (1994) The bacterial nucleoid revisited. Microbiol Rev 58:211-232
43. Rothfield L, Taghbalout A, Shih YL (2005) Spatial control of bacterial division-site placement. Nat Rev Microbiol 3:959-968
44. Sarkar T, Petrov AS, Vitko JR, Santai CT, Harvey SC, Mukerji I, Hud NV (2009) Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: implications for the role of IHF in the compaction of bacterial chromatin. Biochemistry 48:667-675
45. Sawitzke JA, Austin S (2000) Suppression of chromosome segregation defects of Escherichia coli muk mutants by mutations in topoisomerase I. Proc Natl Acad Sci USA 97:1671-1676
46. Spurio R, Durrenberger M, Falconi M, La Teana A., Pon CL, Gualerzi CO (1992) Lethal overproduction of the Escherichia coli nucleoid protein H-NS: ultramicroscopic and molecular autopsy. Mol Gen Genet 231:201-211
47. Stempen H (1950) Demonstration of the chromatinic bodies of Escherichia coli and Proteus vulgaris with the aid of the phase contrast microscope. J Bacteriol 60:81-87
48. Sun Q, Margolin W (2001) Influence of the nucleoid on placement of FtsZ and MinE rings in Escherichia coli. J Bacteriol 183:1413-1422
49. Sun Q, Margolin W (2004) Effects of perturbing nucleoid structure on nucleoid occlusion-mediated toporegulation of FtsZ ring assembly. J Bacteriol 186:3951-3959
50. Teleman AA, Graumann PL, Lin D C H, Grossman AD, Losick R (1998) Chromosome arrangement within a bacterium. Curr Biol 8:1102-1109
51. Thanbichler M, Shapiro L (2006) MipZ, a spatial regulator coordinating chromosome segregation with cell division in Caulobacter. Cell 126:147-162
52. Thiem S, Kentner D, Sourjik V (2007) Positioning of chemosensory clusters in E. coli and its relation to cell division. EMBO J 26:1615-1623
53. van Helvoort JM, Kool J, Woldringh CL (1996) Chloramphenicol causes fusion of separated nucleoids in Escherichia coli K-12 cells and filaments. J Bacteriol 178:4289-4293
54. Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L (2004) Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc Natl Acad Sci USA 101:9257-9262
55. Webb CD, Teleman A, Gordon S, Straight A, Belmont A, Lin DC, Grossman AD, Wright A, Losick R (1997) Bipolar localization of the replication origin regions of chromosomes in vegetative and sporulating cells of B. subtilis. Cell 88:667-674
56. Weitao T, Nordström K, Dasgupta S (1999) Mutual suppression of mukB and seqA phenotypes might arise from their opposing influences on the escherichia coli nucleoid structure. Mol Microbiol 34:157-168
57. Woldringh CL (1976) Morphological analysis of nuclear separation and cell division during the life cycle of Escherichia coli. J Bacteriol 125:248-257
58. Woldringh CL (2002) The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation. Mol Microbiol 45:17-29
59. Woldringh C, Mulder E, Valkenburg J, Wientjes F, Zaritsky A, Nanninga N (1990) Role of the nucleoid in the toporegulation of division. Res Microbiol 141:39-49
60. Wu LJ, Errington J (2004) Coordination of cell division and chromosome segregation by a nucleoid occlusion protein in Bacillus subtilis. Cell 117:915-925
61. Yamaichi Y, Niki H (2004) migS, a cis-acting site that affects bipolar positioning of oriC on the Escherichia coli chromosome. EMBO J 23:221-233
62. Yamanaka K, Mitani T, Ogura T, Niki H, Hiraga S (1994) Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli. Mol Microbiol 13:301-312
63. Yu X-C, Margolin W (1999) FtsZ ring clusters in min and partition mutants: role of both the Min system and the nucleoid in regulating FtsZ ring localization. Mol Microbiol 32:315-326
64. Yu X-C, Tran AH, Sun Q, Margolin W (1998a) Localization of cell division protein FtsK to the Escherichia coli septum and identification of a potential N-terminal targeting domain. J Bacteriol 180:1296-1304
65. Yu XC, Weihe EK, Margolin W (1998b) Role of the C terminus of FtsK in Escherichia coli chromosome segregation. J Bacteriol 180:6424-6428
66. Zimmerman SB (2003) Underlying regularity in the shapes of nucleoids of Escherichia coli: implications for nucleoid organization and partition. J Struct Biol 142:256-265
67. Zimmerman SB (2006) Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase. J Struct Biol 153:160-175
68. Zimmerman JM, Battista JR (2005) A ring-like nucleoid is not necessary for radioresistance in the Deinococcaceae. BMC Microbiol 5:17