Specific and non-specific interactions of ParB with DNA: Implications for chromosome segregation

Nucleic Acids Research

Volumn 43, Issue 2, 2015, Pages 719-731

  Taylor, James A ^a   Pastrana, Cesar L ^b   Butterer, Annika ^c   Pernstich, Christian ^a   Gwynn, Emma J ^a   Sobott, Frank ^c   Moreno Herrero, Fernando ^b   Dillingham, Mark S ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^c UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DNA; DNA BINDING PROTEIN; PROTEIN BINDING;

BACILLUS SUBTILIS; CHEMISTRY; CHROMOSOME SEGREGATION; METABOLISM;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; CHROMOSOME SEGREGATION; DNA; DNA-BINDING PROTEINS; PROTEIN BINDING;

EID: 84941094741     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1295     Document Type: Article

References (36)

1. Gerdes, K., Howard, M., Szardenings, F. (2010) Pushing and pulling in prokaryotic DNA segregation. Cell, 141, 927-942.
2. Mierzejewska, J., Jagura-Burdzy, G. (2012) Prokaryotic ParA-ParB-parS system links bacterial chromosome segregation with the cell cycle. Plasmid, 67, 1-14.
3. Yamaichi, Y., Niki, H. (2000) Active segregation by the Bacillus subtilis partitioning system in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A., 97, 14656-14661.
4. Ireton, K., Gunther, N.W.t., Grossman, A.D. (1994) spo0J is required for normal chromosome segregation as well as the initiation of sporulation in Bacillus subtilis. J. Bacteriol., 176, 5320-5329.
5. Sharpe, M.E., Errington, J. (1996) The Bacillus subtilis soj-spo0J locus is required for a centromere-like function involved in prespore chromosome partitioning. Mol. Microbiol., 21, 501-509.
6. Lin, D.C., Grossman, A.D. (1998) Identification and characterization of a bacterial chromosome partitioning site. Cell, 92, 675-685.
7. Lee, P.S., Grossman, A.D. (2006) The chromosome partitioning proteins Soj (ParA) and Spo0J (ParB) contribute to accurate chromosome partitioning, separation of replicated sister origins, and regulation of replication initiation in Bacillus subtilis. Mol. Microbiol., 60, 853-869.
8. Lee, P.S., Lin, D.C., Moriya, S., Grossman, A.D. (2003) Effects of the chromosome partitioning protein Spo0J (ParB) on oriC positioning and replication initiation in Bacillus subtilis. J. Bacteriol., 185, 1326-1337.
9. Gruber, S., Errington, J. (2009) Recruitment of condensin to replication origin regions by ParB/SpoOJ promotes chromosome segregation in B. subtilis. Cell, 137, 685-696.
10. Sullivan, N.L., Marquis, K.A., Rudner, D.Z. (2009) Recruitment of SMC by ParB-parS organizes the origin region and promotes efficient chromosome segregation. Cell, 137, 697-707.
11. Breier, A.M., Grossman, A.D. (2007) Whole-genome analysis of the chromosome partitioning and sporulation protein Spo0J (ParB) reveals spreading and origin-distal sites on the Bacillus subtilis chromosome. Mol. Microbiol., 64, 703-718.
12. Murray, H., Ferreira, H., Errington, J. (2006) The bacterial chromosome segregation protein Spo0J spreads along DNA from parS nucleation sites. Mol. Microbiol., 61, 1352-1361.
13. Rodionov, O., Yarmolinsky, M. (2004) Plasmid partitioning and the spreading of P1 partition protein ParB. Mol. Microbiol., 52, 1215-1223.
14. Schumacher, M.A. (2008) Structural biology of plasmid partition: uncovering the molecular mechanisms of DNA segregation. Biochem. J., 412, 1-18.
15. Leonard, T.A., Butler, P.J., Lowe, J. (2004) Structural analysis of the chromosome segregation protein Spo0J from Thermus thermophilus. Mol. Microbiol., 53, 419-432.
16. Delbruck, H., Ziegelin, G., Lanka, E., Heinemann, U. (2002) An Src homology 3-like domain is responsible for dimerization of the repressor protein KorB encoded by the promiscuous IncP plasmid RP4. J. Biol. Chem., 277, 4191-4198.
17. Khare, D., Ziegelin, G., Lanka, E., Heinemann, U. (2004) Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB. Nat. Struct. Mol. Biol., 11, 656-663.
18. Schumacher, M.A., Funnell, B.E. (2005) Structures of ParB bound to DNA reveal mechanism of partition complex formation. Nature, 438, 516-519.
19. Schumacher, M.A., Mansoor, A., Funnell, B.E. (2007) Structure of a four-way bridged ParB-DNA complex provides insight into P1 segrosome assembly. J. Biol. Chem., 282, 10456-10464.
20. Schumacher, M.A., Piro, K.M., Xu, W. (2010) Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes. Nucleic Acids Res., 38, 4514-4526.
21. Autret, S., Nair, R., Errington, J. (2001) Genetic analysis of the chromosome segregation protein Spo0J of Bacillus subtilis: evidence for separate domains involved in DNA binding and interactions with Soj protein. Mol. Microbiol., 41, 743-755.
22. Scholefield, G., Whiting, R., Errington, J., Murray, H. (2011) Spo0J regulates the oligomeric state of Soj to trigger its switch from an activator to an inhibitor of DNA replication initiation. Mol. Microbiol., 79, 1089-1100.
23. Graham, T.G., Wang, X., Song, D., Etson, C.M., van Oijen, A.M., Rudner, D.Z., Loparo, J.J. (2014) ParB spreading requires DNA bridging. Genes Dev., 28, 1228-1238.
24. Broedersz, C.P., Wang, X., Meir, Y., Loparo, J.J., Rudner, D.Z., Wingreen, N.S. (2014) Condensation and localization of the partitioning protein ParB on the bacterial chromosome. Proc. Natl. Acad. Sci. U.S.A., 111, 8809-8814.
25. Fili, N., Mashanov, G.I., Toseland, C.P., Batters, C., Wallace, M.I., Yeeles, J.T., Dillingham, M.S., Webb, M.R., Molloy, J.E. (2010) Visualizing helicases unwinding DNA at the single molecule level. Nucleic Acids Res., 38, 4448-4457.
26. Fili, N., Toseland, C.P., Dillingham, M.S., Webb, M.R., Molloy, J.E. (2011) A single-molecule approach to visualize the unwinding activity of DNA helicases. Methods Mol. Biol., 778, 193-214.
27. Konijnenberg, A., Butterer, A., Sobott, F. (2013) Native ion mobility-mass spectrometry and related methods in structural biology. Biochim. Biophys. Acta, 1834, 1239-1256.
28. Strick, T.R., Allemand, J.F., Bensimon, D., Croquette, V. (1998) Behavior of supercoiled DNA. Biophys. J., 74, 2016-2028.
29. Seidel, R., van Noort, J., van der Scheer, C., Bloom, J.G., Dekker, N.H., Dutta, C.F., Blundell, A., Robinson, T., Firman, K., Dekker, C. (2004) Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat. Struct. Mol. Biol., 11, 838-843.
30. Carrasco, C., Gilhooly, N.S., Dillingham, M.S., Moreno-Herrero, F. (2013) On the mechanism of recombination hotspot scanning during double-stranded DNA break resection. Proc. Natl. Acad. Sci. U.S.A., 110, E2562-E2571.
31. Soberon, N.E., Lioy, V.S., Pratto, F., Volante, A., Alonso, J.C. (2011) Molecular anatomy of the Streptococcus pyogenes pSM19035 partition and segrosome complexes. Nucleic Acids Res., 39, 2624-2637.
32. Anderson, B.J., Larkin, C., Guja, K., Schildbach, J.F. (2008) Using fluorophore-labeled oligonucleotides to measure affinities of protein-DNA interactions. Methods Enzymol., 450, 253-272.
33. Skoko, D., Yan, J., Johnson, R.C., Marko, J.F. (2005) Low-force DNA condensation and discontinuous high-force decondensation reveal a loop-stabilizing function of the protein Fis. Phys. Rev. Lett., 95, 208101.
34. Camerini-Otero, R.D., Felsenfeld, G. (1977) Supercoiling energy and nucleosome formation: the role of the arginine-rich histone kernel. Nucleic Acids Res., 4, 1159-1181.
35. Huang, L., Yin, P., Zhu, X., Zhang, Y., Ye, K. (2011) Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100. Nucleic Acids Res., 39, 2954-2968.
36. Schumacher, M.A., Glover, T.C., Brzoska, A.J., Jensen, S.O., Dunham, T.D., Skurray, R.A., Firth, N. (2007) Segrosome structure revealed by a complex of ParR with centromere DNA. Nature, 450, 1268-1271.