1887

Abstract

Replication and segregation of the genetic information is necessary for a cell to proliferate. In , the Par system (ParA/Soj, ParB/Spo0J and ) is required for segregation of the chromosome origin () region and for proper control of DNA replication initiation. ParB binds sites clustered near the origin of replication and assembles into sliding clamps that interact with ParA to drive origin segregation through a diffusion-ratchet mechanism. As part of this dynamic process, ParB stimulates ParA ATPase activity to trigger its switch from an ATP-bound dimer to an ADP-bound monomer. In addition to its conserved role in DNA segregation, ParA is also a regulator of the master DNA replication initiation protein DnaA. We hypothesized that in the location of the Par system proximal to would be necessary for ParA to properly regulate DnaA. To test this model, we constructed a range of genetically modified strains with altered numbers and locations of sites, many of which perturbed chromosome origin segregation as expected. Contrary to our hypothesis, the results show that regulation of DNA replication initiation by ParA is maintained when a site is separated from . Because a single site is sufficient for proper control of ParA, the results are consistent with a model where ParA is efficiently regulated by ParB sliding clamps following loading at .

Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award BB/S00257X/1)
    • Principle Award Recipient: HenrikStrahl
  • Wellcome Trust (Award 204985/Z/16/Z)
    • Principle Award Recipient: HeathMurray
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-10-27
2024-10-10
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References

  1. Messer W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev 2002; 26:355–374 [View Article] [PubMed]
    [Google Scholar]
  2. Wang X, Montero Llopis P, Rudner DZ. Bacillus subtilis chromosome organization oscillates between two distinct patterns. Proc Natl Acad Sci 2014; 111:12877–12882 [View Article]
    [Google Scholar]
  3. Mierzejewska J, Jagura-Burdzy G. Prokaryotic ParA-ParB-parS system links bacterial chromosome segregation with the cell cycle. Plasmid 2012; 67:1–14 [View Article] [PubMed]
    [Google Scholar]
  4. Gerdes K, Howard M, Szardenings F. Pushing and pulling in prokaryotic DNA segregation. Cell 2010; 141:927–942 [View Article] [PubMed]
    [Google Scholar]
  5. Gerdes K, Møller-Jensen J, Bugge Jensen R. Plasmid and chromosome partitioning: surprises from phylogeny. Mol Microbiol 2000; 37:455–466 [View Article] [PubMed]
    [Google Scholar]
  6. Livny J, Yamaichi Y, Waldor MK. Distribution of centromere-like parS sites in bacteria: insights from comparative genomics. J Bacteriol 2007; 189:8693–8703 [View Article] [PubMed]
    [Google Scholar]
  7. Leonard TA, Butler PJG, Löwe J. Structural analysis of the chromosome segregation protein Spo0J from Thermus thermophilus. Mol Microbiol 2004; 53:419–432 [View Article] [PubMed]
    [Google Scholar]
  8. Ireton K, Gunther NW 4th, Grossman AD. spo0J is required for normal chromosome segregation as well as the initiation of sporulation in Bacillus subtilis. J Bacteriol 1994; 176:5320–5329 [View Article] [PubMed]
    [Google Scholar]
  9. Soh Y-M, Davidson IF, Zamuner S, Basquin J, Bock FP et al. Self-organization of parS centromeres by the ParB CTP hydrolase. Science 2019; 366:1129–1133 [View Article] [PubMed]
    [Google Scholar]
  10. Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G et al. The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol Cell 2021; 81:3992–4007 [View Article] [PubMed]
    [Google Scholar]
  11. Osorio-Valeriano M, Altegoer F, Steinchen W, Urban S, Liu Y et al. ParB-type DNA segregation proteins are CTP-dependent molecular switches. Cell 2019; 179:1512–1524 [View Article]
    [Google Scholar]
  12. Jalal AS, Tran NT, Le TB. ParB spreading on DNA requires cytidine triphosphate in vitro. Elife 2020; 9:e53515 [View Article]
    [Google Scholar]
  13. Jalal AS, Tran NT, Stevenson CE, Chimthanawala A, Badrinarayanan A et al. A CTP-dependent gating mechanism enables ParB spreading on DNA. Elife 2021; 10:e69676 [View Article]
    [Google Scholar]
  14. Antar H, Soh Y-M, Zamuner S, Bock FP, Anchimiuk A et al. Relief of ParB autoinhibition by parS DNA catalysis and recycling of ParB by CTP hydrolysis promote bacterial centromere assembly. Sci Adv 2021; 7:eabj2854 [View Article] [PubMed]
    [Google Scholar]
  15. Murray H, Ferreira H, Errington J. The bacterial chromosome segregation protein Spo0J spreads along DNA from parS nucleation sites. Mol Microbiol 2006; 61:1352–1361 [View Article] [PubMed]
    [Google Scholar]
  16. Scholefield G, Whiting R, Errington J, Murray H. Spo0J regulates the oligomeric state of Soj to trigger its switch from an activator to an inhibitor of DNA replication initiation. Mol Microbiol 2011; 79:1089–1100 [View Article] [PubMed]
    [Google Scholar]
  17. Murray H, Errington J. Dynamic control of the DNA replication initiation protein DnaA by Soj/ParA. Cell 2008; 135:74–84 [View Article] [PubMed]
    [Google Scholar]
  18. Ogura Y, Ogasawara N, Harry EJ, Moriya S. Increasing the ratio of Soj to Spo0J promotes replication initiation in Bacillus subtilis. J Bacteriol 2003; 185:6316–6324 [View Article] [PubMed]
    [Google Scholar]
  19. Lee PS, Lin DCH, Moriya S, Grossman AD. Effects of the chromosome partitioning protein Spo0J (ParB) on oriC positioning and replication initiation in Bacillus subtilis. J Bacteriol 2003; 185:1326–1337 [View Article] [PubMed]
    [Google Scholar]
  20. Leonard TA, Butler PJ, Löwe J. Bacterial chromosome segregation: structure and DNA binding of the Soj dimer--a conserved biological switch. EMBO J 2005; 24:270–282 [View Article] [PubMed]
    [Google Scholar]
  21. Quisel JD, Lin DCH, Grossman AD. Control of development by altered localization of a transcription factor in B. subtilis. Mol Cell 1999; 4:665–672 [View Article] [PubMed]
    [Google Scholar]
  22. Scholefield G, Errington J, Murray H. Soj/ParA stalls DNA replication by inhibiting helix formation of the initiator protein DnaA. EMBO J 2012; 31:1542–1555 [View Article] [PubMed]
    [Google Scholar]
  23. Vecchiarelli AG, Neuman KC, Mizuuchi K. A propagating ATPase gradient drives transport of surface-confined cellular cargo. Proc Natl Acad Sci 2014; 111:4880–4885 [View Article]
    [Google Scholar]
  24. Lim HC, Surovtsev IV, Beltran BG, Huang F, Bewersdorf J et al. Evidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation. Elife 2014; 3:e02758 [View Article]
    [Google Scholar]
  25. Hwang LC, Vecchiarelli AG, Han Y-W, Mizuuchi M, Harada Y et al. ParA-mediated plasmid partition driven by protein pattern self-organization. EMBO J 2013; 32:1238–1249 [View Article] [PubMed]
    [Google Scholar]
  26. Vecchiarelli AG, Hwang LC, Mizuuchi K. Cell-free study of F plasmid partition provides evidence for cargo transport by a diffusion-ratchet mechanism. Proc Natl Acad Sci 2013; 110:E1390–7 [View Article]
    [Google Scholar]
  27. Wang X, Tang OW, Riley EP, Rudner DZ. The SMC condensin complex is required for origin segregation in Bacillus subtilis. Curr Biol 2014; 24:287–292 [View Article] [PubMed]
    [Google Scholar]
  28. Gruber S, Veening J-W, Bach J, Blettinger M, Bramkamp M et al. Interlinked sister chromosomes arise in the absence of condensin during fast replication in B. subtilis. Curr Biol 2014; 24:293–298 [View Article] [PubMed]
    [Google Scholar]
  29. Sullivan NL, Marquis KA, Rudner DZ. Recruitment of SMC by ParB-parS organizes the origin region and promotes efficient chromosome segregation. Cell 2009; 137:697–707 [View Article] [PubMed]
    [Google Scholar]
  30. Gruber S, Errington J. Recruitment of condensin to replication origin regions by ParB/SpoOJ promotes chromosome segregation in B. subtilis. Cell 2009; 137:685–696 [View Article] [PubMed]
    [Google Scholar]
  31. Britton RA, Lin DC, Grossman AD. Characterization of a prokaryotic SMC protein involved in chromosome partitioning. Genes Dev 1998; 12:1254–1259 [View Article] [PubMed]
    [Google Scholar]
  32. Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A et al. Condensin- and replication-mediated bacterial chromosome folding and origin condensation revealed by Hi-C and super-resolution imaging. Mol Cell 2015; 59:588–602 [View Article]
    [Google Scholar]
  33. Teleman AA, Graumann PL, Lin DCH, Grossman AD, Losick R. Chromosome arrangement within a bacterium. Curr Biol 1998; 8:1102–1109 [View Article] [PubMed]
    [Google Scholar]
  34. Lin DCH, Levin PA, Grossman AD. Bipolar localization of a chromosome partition protein in Bacillus subtilis. Proc Natl Acad Sci 1997; 94:4721–4726 [View Article]
    [Google Scholar]
  35. Autret S, Nair R, Errington J. 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 2001; 41:743–755 [View Article] [PubMed]
    [Google Scholar]
  36. Marston AL, Errington J. Dynamic movement of the ParA-like soj protein of B. subtilis and its dual role in nucleoid organization and developmental regulation. Molecular Cell 1999; 4:673–682 [View Article]
    [Google Scholar]
  37. Burkholder WF, Kurtser I, Grossman AD. Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis. Cell 2001; 104:269–279 [View Article]
    [Google Scholar]
  38. Veening JW, Murray H, Errington J. A mechanism for cell cycle regulation of sporulation initiation in Bacillus subtilis. Genes Dev 2009; 23:1959–1970 [View Article]
    [Google Scholar]
  39. Anagnostopoulos C, Spizizen J. Requirements for transformation in Bacillus subtilis. J Bacteriol 1961; 81:741–746 [View Article]
    [Google Scholar]
  40. Hamoen LW, Smits WK, de Jong A, Holsappel S, Kuipers OP. Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Res 2002; 30:5517–5528 [View Article]
    [Google Scholar]
  41. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M et al. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012; 9:676–682 [View Article]
    [Google Scholar]
  42. Strahl H, Ronneau S, González BS, Klutsch D, Schaffner-Barbero C et al. Transmembrane protein sorting driven by membrane curvature. Nat Commun 2015; 6:8728 [View Article]
    [Google Scholar]
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