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

Taylor, James; Pastrana, César L.; Butterer, Annika; Pernstich, Christian; Gwynn, Emma J.; Sobott, Frank; Moreno‐Herrero, Fernando; Dillingham, Mark S.

doi:10.1093/nar/gku1295

Cited by 73 publications

(187 citation statements)

References 36 publications

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“…Recent experiments using magnetic tweezers support the idea that the complexes are not highly ordered (Taylor et al, 2015). ParB-ParB (dimer-dimer) interactions via the N-terminal domain must contribute to higher-order complex assembly and function.…”

Section: Flexibility and Order In Partition Complex Assemblymentioning

confidence: 94%

ParB Partition Proteins: Complex Formation and Spreading at Bacterial and Plasmid Centromeres

Funnell

2016

Front. Mol. Biosci.

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In bacteria, active partition systems contribute to the faithful segregation of both chromosomes and low-copy-number plasmids. Each system depends on a site-specific DNA binding protein to recognize and assemble a partition complex at a centromere-like site, commonly called parS. Many plasmid, and all chromosomal centromere-binding proteins are dimeric helix-turn-helix DNA binding proteins, which are commonly named ParB. Although the overall sequence conservation among ParBs is not high, the proteins share similar domain and functional organization, and they assemble into similar higher-order complexes. In vivo, ParBs “spread,” that is, DNA binding extends away from the parS site into the surrounding non-specific DNA, a feature that reflects higher-order complex assembly. ParBs bridge and pair DNA at parS and non-specific DNA sites. ParB dimers interact with each other via flexible conformations of an N-terminal region. This review will focus on the properties of the HTH centromere-binding protein, in light of recent experimental evidence and models that are adding to our understanding of how these proteins assemble into large and dynamic partition complexes at and around their specific DNA sites.

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Section: Flexibility and Order In Partition Complex Assemblymentioning

confidence: 94%

ParB Partition Proteins: Complex Formation and Spreading at Bacterial and Plasmid Centromeres

Funnell

2016

Front. Mol. Biosci.

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“…14), the minimal density of ParB is ∼1,000/μm 2 , consistent with estimates of ParB density on P1 plasmid of approximately one dimer per 30 bp (25). This points to the critical role of the "ParB-spreading" process in which ParB binding to parS on the plasmid nucleates higher-order complex assembly involving a large number of ParBs to promote plasmid segregation (26)(27)(28)(29)(30). Conversely, if the density of ParB was too high, too many ParA-ParB bonds formed resulting in the decrease of both the persistence and the speed (Fig.…”

Section: Directed and Persistent Movement Emerges From A Mechanochemicalmentioning

confidence: 99%

Directed and persistent movement arises from mechanochemistry of the ParA/ParB system

Vecchiarelli

Mizuuchi

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

105

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The segregation of DNA before cell division is essential for faithful genetic inheritance. In many bacteria, segregation of low-copy number plasmids involves an active partition system composed of a nonspecific DNA-binding ATPase, ParA, and its stimulator protein ParB. The ParA/ParB system drives directed and persistent movement of DNA cargo both in vivo and in vitro. Filament-based models akin to actin/microtubule-driven motility were proposed for plasmid segregation mediated by ParA. Recent experiments challenge this view and suggest that ParA/ParB system motility is driven by a diffusion ratchet mechanism in which ParB-coated plasmid both creates and follows a ParA gradient on the nucleoid surface. However, the detailed mechanism of ParA/ParB-mediated directed and persistent movement remains unknown. Here, we develop a theoretical model describing ParA/ParB-mediated motility. We show that the ParA/ParB system can work as a Brownian ratchet, which effectively couples the ATPase-dependent cycling of ParA-nucleoid affinity to the motion of the ParB-bound cargo. Paradoxically, this resulting processive motion relies on quenching diffusive plasmid motion through a large number of transient ParA/ParB-mediated tethers to the nucleoid surface. Our work thus sheds light on an emergent phenomenon in which nonmotor proteins work collectively via mechanochemical coupling to propel cargos-an ingenious solution shaped by evolution to cope with the lack of processive motor proteins in bacteria.ParA ATPase | Brownian ratchet | theoretical model | motility

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“…ParB proteins form large nucleoprotein complexes at parS sites that span 10-20 kb of flanking DNA (Murray et al 2006;Breier and Grossman 2007) mediated by nearest neighbor and bridging interactions (Graham et al 2014;Taylor et al 2015). To determine whether these nucleoprotein complexes are required for long-range interactions, we performed Hi-C on cells harboring a ParB point mutant (G77S) that binds parS sites with affinity similar to wild type but does not spread to neighboring sites (Breier and Grossman 2007;Graham et al 2014).…”

Section: Global Changes In Chromosome Conformation In Cells Lacking Pmentioning

confidence: 99%

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis

et al. 2015

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SMC condensin complexes play a central role in compacting and resolving replicated chromosomes in virtually all organisms, yet how they accomplish this remains elusive. In Bacillus subtilis, condensin is loaded at centromeric parS sites, where it encircles DNA and individualizes newly replicated origins. Using chromosome conformation capture and cytological assays, we show that condensin recruitment to origin-proximal parS sites is required for the juxtaposition of the two chromosome arms. Recruitment to ectopic parS sites promotes alignment of large tracks of DNA flanking these sites. Importantly, insertion of parS sites on opposing arms indicates that these "zip-up" interactions only occur between adjacent DNA segments. Collectively, our data suggest that condensin resolves replicated origins by promoting the juxtaposition of DNA flanking parS sites, drawing sister origins in on themselves and away from each other. These results are consistent with a model in which condensin encircles the DNA flanking its loading site and then slides down, tethering the two arms together. Lengthwise condensation via loop extrusion could provide a generalizable mechanism by which condensin complexes act dynamically to individualize origins in B. subtilis and, when loaded along eukaryotic chromosomes, resolve them during mitosis.

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

Cited by 73 publications

References 36 publications

ParB Partition Proteins: Complex Formation and Spreading at Bacterial and Plasmid Centromeres

ParB Partition Proteins: Complex Formation and Spreading at Bacterial and Plasmid Centromeres

Directed and persistent movement arises from mechanochemistry of the ParA/ParB system

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis

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