A physical approach to segregation and folding of the Caulobacter crescentus genome

Molecular Microbiology

Volumn 82, Issue 6, 2011, Pages 1311-1315

  Dame, Remus T ^a,b   Tark Dame, Mariliis ^c   Schiessel, Helmut ^d  

^a LEIDEN UNIVERSITY   (Netherlands)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d UNIVERSITEIT LEIDEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; HU 1 PROTEIN; HU 2 PROTEIN; PARB PROTEIN; POLYMER; UNCLASSIFIED DRUG;

BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BINDING SITE; CAULOBACTER CRESCENTUS; CHROMOSOME SEGREGATION; DNA FLANKING REGION; ESCHERICHIA COLI; GENE LOCUS; GENE REPLICATION; GENE SEGREGATION; GENETIC DISTANCE; GENOME ANALYSIS; GENOME FOLDING; NONHUMAN; NOTE; PARS GENE; PRIORITY JOURNAL;

BACTERIAL PROTEINS; CAULOBACTER CRESCENTUS; CHROMOSOME SEGREGATION; CHROMOSOMES, BACTERIAL; DNA REPLICATION; DNA-BINDING PROTEINS; GENOME, BACTERIAL; TIME-LAPSE IMAGING;

BACTERIA (MICROORGANISMS); CAULOBACTER VIBRIOIDES; EUKARYOTA;

EID: 83355177982     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2011.07898.x     Document Type: Note

References (47)

1. Banigan, E.J., Gelbart, M.A., Gitai, Z., Wingreen, N.S., and Liu, A.J. (2011) Filament depolymerization can explain chromosome pulling during bacterial mitosis. PLoS Comput Biol 7: e1002145.
2. Boccard, F., Esnault, E., and Valens, M. (2005) Spatial arrangement and macrodomain organization of bacterial chromosomes. Mol Microbiol 57: 9-16.
3. Bohn, M., Heermann, D.W., and van Driel, R. (2007) Random loop model for long polymers. Phys Rev E Stat Nonlin Soft Matter Phys 76: 051805.
4. Cho, H., McManus, H.R., Dove, S.L., and Bernhardt, T.G. (2011) Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist. Proc Natl Acad Sci USA 108: 3773-3778.
5. Cook, P.R. (2010) A model for all genomes: the role of transcription factories. J Mol Biol 395: 1-10.
6. Cunha, S., Woldringh, C.L., and Odijk, T. (2001) Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids. J Struct Biol 136: 53-66.
7. Dame, R.T. (2005) The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol 56: 858-870.
8. Dame, R.T., Wyman, C., and Goosen, N. (2000) H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 28: 3504-3510.
9. Dame, R.T., Noom, M.C., and Wuite, G.J. (2006) Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444: 387-390.
10. Dame, R.T., Kalmykowa, O.J., and Grainger, D.C. (2011) Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria. PLoS Genet 7: e1002123.
11. Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002) Capturing chromosome conformation. Science 295: 1306-1311.
12. Deng, S., Stein, R.A., and Higgins, N.P. (2005) Organization of supercoil domains and their reorganization by transcription. Mol Microbiol 57: 1511-1521.
13. Dillon, S.C., and Dorman, C.J. (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8: 185-195.
14. Dingwall, A., and Shapiro, L. (1989) Rate, origin, and bidirectionality of Caulobacter chromosome replication as determined by pulsed-field gel electrophoresis. Proc Natl Acad Sci USA 86: 119-123.
15. Emanuel, M., Radja, N.H., Henriksson, A., and Schiessel, H. (2009) The physics behind the larger scale organization of DNA in eukaryotes. Phys Biol 6: 025008.
16. Grosberg, A.Y., Nechaev, S.K., and Shakhnovich, E.I. (1988) The role of topological constraints in the kinetics of collapse of macromolecules. J Phys France 49: 2095-2100.
17. Grosberg, A.Y., Rabin, Y., Havlin, S., and Neer, A. (1993) Crumpled globule model of the three-dimensional structure of DNA. Europhys Lett 23: 373-378.
18. Halverson, J.D., Lee, W.B., Grest, G.S., Grosberg, A.Y., and Kremer, K. (2011) Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics. J Chem Phys 134: 204904.
19. Hong, S.H., and McAdams, H.H. (2011) Compaction and transport properties of newly replicated Caulobacter crescentus DNA. Mol Microbiol 82: 1349-1358.
20. Lee, S.F., Thompson, M.A., Schwartz, M.A., Shapiro, L., and Moerner, W.E. (2011) Super-resolution imaging of the nucleoid-associated protein HU in Caulobacter crescentus. Biophys J 100: L31-L33.
21. Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., etal. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
22. Lua, R.C., Borovinskiy, A.L., and Grosberg, A.Y. (2004) Fractal and statistical properties of large compact polymers: a computational study. Polymer 45: 717-731.
23. Luijsterburg, M.S., White, M.F., van Driel, R., and Dame, R.T. (2008) The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 43: 393-418.
24. Mercier, R., Petit, M.A., Schbath, S., Robin, S., El Karoui, M., Boccard, F., and Espeli, O. (2008) The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. Cell 135: 475-485.
25. Mirny, L.A. (2011) The fractal globule as a model of chromatin architecture in the cell. Chromosome Res 19: 37-51.
26. Niki, H., Yamaichi, Y., and Hiraga, S. (2000) Dynamic organization of chromosomal DNA in Escherichia coli. Genes Dev 14: 212-223.
27. Noom, M.C., Navarre, W.W., Oshima, T., Wuite, G.J., and Dame, R.T. (2007) H-NS promotes looped domain formation in the bacterial chromosome. Curr Biol 17: R913-R914.
28. van Noort, J., Verbrugge, S., Goosen, N., Dekker, C., and Dame, R.T. (2004) Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci USA 101: 6969-6974.
29. Petrushenko, Z.M., Cui, Y., She, W., and Rybenkov, V.V. (2010) Mechanics of DNA bridging by bacterial condensin MukBEF in vitro and in singulo. EMBO J 29: 1126-1135.
30. Pinson, V., Takahashi, M., and Rouviere-Yaniv, J. (1999) Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J Mol Biol 287: 485-497.
31. Postow, L., Hardy, C.D., Arsuaga, J., and Cozzarelli, N.R. (2004) Topological domain structure of the Escherichia coli chromosome. Genes Dev 18: 1766-1779.
32. Ptacin, J.L., Lee, S.F., Garner, E.C., Toro, E., Eckart, M., Comolli, L.R., etal. (2010) A spindle-like apparatus guides bacterial chromosome segregation. Nat Cell Biol 12: 791-798.
33. Rosa, A., and Everaers, R. (2008) Structure and dynamics of interphase chromosomes. PLoS Comput Biol 4: e1000153.
34. Rouviere-Yaniv, J., and Gros, F. (1975) Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli. Proc Natl Acad Sci USA 72: 3428-3432.
35. Sanchez-Romero, M.A., Busby, S.J., Dyer, N.P., Ott, S., Millard, A.D., and Grainger, D.C. (2010) Dynamic distribution of seqa protein across the chromosome of Escherichia coli K-12. MBio 1: 00012-10.
36. Schofield, W.B., Lim, H.C., and Jacobs-Wagner, C. (2010) Cell cycle coordination and regulation of bacterial chromosome segregation dynamics by polarly localized proteins. EMBO J 29: 3068-3081.
37. Schwartz, M.A., and Shapiro, L. (2011) An SMC ATPase mutant disrupts chromosome segregation in Caulobacter. Mol Microbiol 82: 1359-1374.
38. Shebelut, C.W., Guberman, J.M., van Teeffelen, S., Yakhnina, A.A., and Gitai, Z. (2010) Caulobacter chromosome segregation is an ordered multistep process. Proc Natl Acad Sci USA 107: 14194-14198.
39. Shellman, V.L., and Pettijohn, D.E. (1991) Introduction of proteins into living bacterial cells: distribution of labeled HU protein in Escherichia coli. J Bacteriol 173: 3047-3059.
40. Skoko, D., Wong, B., Johnson, R.C., and Marko, J.F. (2004) Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes. Biochemistry 43: 13867-13874.
41. Tark-Dame, M., van Driel, R., and Heermann, D.W. (2011) Chromatin folding - from biology to polymer models and back. J Cell Sci 124: 839-845.
42. Tonthat, N.K., Arold, S.T., Pickering, B.F., Van Dyke, M.W., Liang, S., Lu, Y., etal. (2011) Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check. EMBO J 30: 154-164.
43. Umbarger, M.A., Toro, E., Wright, M.A., Porreca, G.J., Bau, D., Hong, S.H., etal. (2011) The three-dimensional architecture of a bacterial genome. Mol Cell 44: 252-264.
44. Viollier, P.H., Thanbichler, M., McGrath, P.T., West, L., Meewan, M., McAdams, H.H., and 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.
45. Wang, W., Li, G.W., Chen, C., Xie, X.S., and Zhuang, X. (2011) Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333: 1445-1449.
46. Wery, M., Woldringh, C.L., and Rouviere-Yaniv, J. (2001) HU-GFP and DAPI co-localize on the Escherichia coli nucleoid. Biochimie 83: 193-200.
47. Wiggins, P.A., Cheveralls, K.C., Martin, J.S., Lintner, R., and Kondev, J. (2010) Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament. Proc Natl Acad Sci USA 107: 4991-4995.