Four-dimensional imaging of E. coli nucleoid organization and dynamics in living cells

Cell

Volumn 153, Issue 4, 2013, Pages 882-895

  Fisher, Jay K ^a   Bourniquel, Aude ^a   Witz, Guillaume ^a   Weiner, Beth ^a   Prentiss, Mara ^b   Kleckner, Nancy ^a  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CELL; CELL CYCLE PHASE; CELL KINETICS; CELL ORGANELLE; CHROMOSOME; DNA REPLICATION; ESCHERICHIA COLI; IMAGING; MORPHOGENESIS; NONHUMAN; NUCLEOID; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BACTERIA (MICROORGANISMS);

EID: 84877694848     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.04.006     Document Type: Article

References (34)

1. M. Adams, and S. Fraden Phase behavior of mixtures of rods (tobacco mosaic virus) and spheres (polyethylene oxide, bovine serum albumin) Biophys. J. 74 1998 669 677
2. E.J. Banigan, M.A. Gelbart, Z. Gitai, N.S. Wingreen, and A.J. Liu Filament depolymerization can explain chromosome pulling during bacterial mitosis PLoS Comput. Biol. 7 2011 e1002145
3. D. Bates The bacterial replisome: back on track? Mol. Microbiol. 69 2008 1341 1348
4. D. Bates, and N. Kleckner Chromosome and replisome dynamics in E. coli: Loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation Cell 121 2005 1 13
5. D. Bates, J. Epstein, E. Boye, K. Fahrner, H. Berg, and N. Kleckner The Escherichia coli baby cell column: a novel cell synchronization method provides new insight into the bacterial cell cycle Mol. Microbiol. 57 2005 380 391
6. I.A. Berlatzky, A. Rouvinski, and S. Ben-Yehuda Spatial organization of a replicating bacterial chromosome Proc. Natl. Acad. Sci. USA 105 2008 14136 14140
7. D. Chaudhuri, and B.M. Mulder Spontaneous helicity of a polymer with side loops confined to a cylinder Phys. Rev. Lett. 108 2012 268305
8. S. Cunha, C.L. Woldringh, and T. Odijk Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids J. Struct. Biol. 136 2001 53 66
9. O. Espéli, R. Borne, P. Dupaigne, A. Thiel, E. Gigant, R. Mercier, and F. Boccard A MatP-divisome interaction coordinates chromosome segregation with cell division in E. coli EMBO J. 31 2012 3198 3211
10. N. Hadizadeh Yazdi, C.C. Guet, R.C. Johnson, and J.F. Marko Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions Mol. Microbiol. 86 2012 1318 1333
11. M.C. Joshi, A. Bourniquel, J. Fisher, B.T. Ho, D. Magnan, N. Kleckner, and D. Bates Escherichia coli sister chromosome separation includes an abrupt global transition with concomitant release of late-splitting intersister snaps Proc. Natl. Acad. Sci. USA 108 2011 2765 2770
12. S. Jun, and B. Mulder Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome Proc. Natl. Acad. Sci. USA 103 2006 12388 12393
13. N. Kleckner, D. Zickler, G.H. Jones, J. Dekker, R. Padmore, J. Henle, and J. Hutchinson A mechanical basis for chromosome function Proc. Natl. Acad. Sci. USA 101 2004 12592 12597
14. T.E. Kuhlman, and E.C. Cox Gene location and DNA density determine transcription factor distributions in Escherichia coli Mol. Syst. Biol. 8 2012 610
15. I.F. Lau, S.R. Filipe, B. Søballe, O.A. ∅kstad, F.X. Barre, and D.J. Sherratt Spatial and temporal organization of replicating Escherichia coli chromosomes Mol. Microbiol. 49 2003 731 743
16. K.P. Lemon, and A.D. Grossman The extrusion-capture model for chromosome partitioning in bacteria Genes Dev. 15 2001 2031 2041
17. A.H. Marceau, S. Bahng, S.C. Massoni, N.P. George, S.J. Sandler, K.J. Marians, and J.L. Keck Structure of the SSB-DNA polymerase III interface and its role in DNA replication EMBO J. 30 2011 4236 4247
18. V. Norris Hypothesis: chromosome separation in Escherichia coli involves autocatalytic gene expression, transertion and membrane-domain formation Mol. Microbiol. 16 1995 1051 1057
19. T. Odijk Osmotic compaction of supercoiled DNA into a bacterial nucleoid Biophys. Chem. 73 1998 23 29
20. R. Reyes-Lamothe, X. Wang, and D.J. Sherratt Escherichia coli and its chromosome Trends Microbiol. 16 2008 238 245
21. N. Rovinskiy, A.A. Agbleke, O. Chesnokova, Z. Pang, and N.P. Higgins Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome PLoS Genet. 8 2012 e1002845
22. M.T. Swulius, and G.J. Jensen The helical MreB cytoskeleton in E. coli MC1000/pLE7 is an artifact of the N-terminal YFP tag J. Bacteriol. 194 2012 6382 6386
23. E. Toro, and L. Shapiro Bacterial chromosome organization and segregation Cold Spring Harb. Perspect. Biol. 2 2010 a000349
24. E. Toro, S.H. Hong, H.H. McAdams, and L. Shapiro Caulobacter requires a dedicated mechanism to initiate chromosome segregation Proc. Natl. Acad. Sci. USA 105 2008 15435 15440
25. M.A. Umbarger, E. Toro, M.A. Wright, G.J. Porreca, D. Baù, S.H. Hong, M.J. Fero, L.J. Zhu, M.A. Marti-Renom, and H.H. McAdams The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation Mol. Cell 44 2011 252 264
26. A.G. Vecchiarelli, Y.W. Han, X. Tan, M. Mizuuchi, R. Ghirlando, C. Biertümpfel, B.E. Funnell, and K. Mizuuchi ATP control of dynamic P1 ParA-DNA interactions: a key role for the nucleoid in plasmid partition Mol. Microbiol. 78 2010 78 91
27. X. Wang, C. Possoz, and D.J. Sherratt Dancing around the divisome: asymmetric chromosome segregation in Escherichia coli Genes Dev. 19 2005 2367 2377
28. X. Wang, X. Liu, C. Possoz, and D.J. Sherratt The two Escherichia coli chromosome arms locate to separate cell halves Genes Dev. 20 2006 1727 1731
29. W. Wang, G.W. Li, C. Chen, X.S. Xie, and X. Zhuang Chromosome organization by a nucleoid-associated protein in live bacteria Science 333 2011 1445 1449
30. S.C. Weber, A.J. Spakowitz, and J.A. Theriot Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci Proc. Natl. Acad. Sci. USA 109 2012 7338 7343
31. G.M. Whitesides The origins and the future of microfluidics Nature 442 2006 368 373
32. P.A. Wiggins, K.C. Cheveralls, J.S. Martin, R. Lintner, and J. Kondev Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament Proc. Natl. Acad. Sci. USA 107 2010 4991 4995
33. J.S. Graham, R.C. Johnson, and J.F. Marko Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA Nucleic Acids Res. 39 2011 2249 2259
34. A. Yildiz, and P.R. Selvin Fluorescence imaging with one nanometer accuracy: application to molecular motors Acc Chem Res. 38 2005 574 582