Operational Principles for the Dynamics of the In Vitro ParA-ParB System

Lavisha Jindal and Eldon Emberly

PLOS Computational Biology, 2015, vol. 11, issue 12, 1-17

Abstract: In many bacteria the ParA-ParB protein system is responsible for actively segregating DNA during replication. ParB proteins move by interacting with DNA bound ParA-ATP, stimulating their unbinding by catalyzing hydrolysis, that leads to rectified motion due to the creation of a wake of depleted ParA. Recent in vitro experiments have shown that a ParB covered magnetic bead can move with constant speed over a DNA covered substrate that is bound by ParA. It has been suggested that the formation of a gradient in ParA leads to diffusion-ratchet like motion of the ParB bead but how it forms and generates a force is still a matter of exploration. Here we develop a deterministic model for the in vitro ParA-ParB system and show that a ParA gradient can spontaneously form due to any amount of initial spatial noise in bound ParA. The speed of the bead is independent of this noise but depends on the ratio of the range of ParA-ParB force on the bead to that of removal of surface bound ParA by ParB. We find that at a particular ratio the speed attains a maximal value. We also consider ParA rebinding (including cooperativity) and ParA surface diffusion independently as mechanisms for ParA recovery on the surface. Depending on whether the DNA covered surface is undersaturated or saturated with ParA, we find that the bead can accelerate persistently or potentially stall. Our model highlights key requirements of the ParA-ParB driving force that are necessary for directed motion in the in vitro system that may provide insight into the in vivo dynamics of the ParA-ParB system.Author Summary: Segregating genetic material is essential for cell survival over multiple generations. The process underlying the required spatio-temporal organization of DNA is mediated by the ParA-ParB-parS system. Recently, experiments have shown that directed motion can be reconstituted in vitro. In these experiments, a magnetic bead was covered with the protein ParB and was able to move ballistically over a surface of DNA that was bound by the protein ParA. How does this active transport spontaneously emerge? In this paper we present a deterministic model for the dynamics of ParA-ParB proteins. We show how spatial noise in surface bound ParA is sufficient for the creation of a gradient in ParA that can drive motion of ParB in vitro. The model explains certain key aspects of the in vitro ParA-ParB system and leads to testable predictions.

Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1004651

DOI: 10.1371/journal.pcbi.1004651

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