Partition complex structure can arise from sliding and bridging of ParB dimers

Abstract

Chromosome segregation is vital for cell replication and in many bacteria is controlled by the ParABS system. A key part of this machinery is the association of ParB proteins to the parS-containing centromeric region to form the partition complex. Despite much work, the formation and structure of this nucleoprotein complex has remained unclear. However, it was recently discovered that CTP binding allows ParB dimers to entrap and slide along the DNA, as well as leading to more efficient condensation through ParB-mediated DNA bridging. Here, we use semi-flexible polymer simulations to show how these properties of sliding and bridging can explain partition complex formation. We find that transient ParB bridges can organise the DNA into either a globular state or into hairpins and helical structures, depending on the bridge lifetime. In separate stochastic simulations, we show that ParB sliding reproduces the experimentally measured multi-peaked binding profile of Caulobacter crescentus, indicating that bridging and other potential roadblocks are sufficiently short-lived that they do not hinder ParB spreading. Indeed, upon coupling the two simulation frameworks into a unified sliding and bridging model, we find that short-lived ParB bridges do not hinder ParB sliding and the model can reproduce both the ParB binding profile and the condensation of the nucleoprotein complex. Overall, our model clarifies the mechanism of partition complex formation and predicts its fine structure. We speculate that the DNA hairpins produced by ParB bridging underlie the secondary function of ParB to load the Structural Maintenance of Chromosome (SMC) complex onto the DNA.

DNA supercoiling enhances DNA condensation by ParB proteins

“…5D). Similar observations were made in previous modelling studies that indicated that the introduction of DNA supercoiling promoted the formation of partition complexes 35,36 . A recent study by Sekkouri Alaoui et al 58 however suggested no significant influence of supercoiling on the formation of partition complex in plasmids.…”

“…In previous in vivo and in vitro studies, ParB proteins were shown to be proficient at forming DNA condensates around the parS site 15,16,18,45,56,57 , and various current models suggest a strong dependence on ParB diffusion and self-self interaction. Notably, distant-site binding due to supercoiling-related proximity could severely alter the formation of ParB-DNA condensates, such as was proposed recently by Connolley et al 35 .…”

“…While our data clearly show a pronounced DNA condensation of supercoiled DNA by ParB, the above experiments did not resolve much of the internal structure of the condensate, i.e., whether it is a globular condensed cluster or a linear extended object such as plectoneme. Current models for DNA condensation by ParB proteins propose stochastic bridging interactions of distant segments 12,15 and possible DNA hairpins formed by laddering DNA segments 35 .…”

“…Vice versa, supercoiling is known to affect many processes in bacterial cells by changing the protein binding affinities and spatial organization of the DNA 26,34 . Recent in silico studies 35,36 suggested that supercoiling may, for example, strongly change the dynamics of the ParB-DNA partition complex by modulating the interactions between distal segments of the DNA.…”

Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation

“…Thus, for all other parameters being equal, the DoD-mode remained in fully extended conformation while MoD-mode dynamically collapsed the DNA into a condensed state. Notably, a recent model on the ParB:DNA condensation in Caulobacter crescentus suggests that DoD-mode could bring DNA into a condensed cluster ( 54 ). In this model, this is facilitated by the rapid re-formation of the ParB-ParB bridge after the proteinprotein connection is broken, whereby both proteins remain bound to the DNA.…”