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

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.

SUBMITTER: Jindal L

PROVIDER: S-EPMC4699459 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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

Jindal Lavisha L Emberly Eldon E

PLoS computational biology 20151215 12

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 ...[more]

PMID: 26670738

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Project description:Representatives of two families of bacterial Par proteins, ParA and ParB, are encoded by the majority of bacterial chromosomes in the close vicinity of oriC. ParA(Soj) and ParB(Spo0J) proteins of Pseudomonas aeruginosa are both important for optimal growth, nucleoids segregation, cell division and different types of motility. Comparative transcriptome analysis of parAnull, parBnull mutants versus parental PAO1161 strain of P. aeruginosa demonstrated global changes in genes expression pattern in logarithmic phase of planktonic cultures grown on rich medium. The set of genes that were similarly regulated in both mutant strains as compared to the wild-type strain as well as two sets of genes uniquely affected in the particular mutant were defined suggesting that ParA and ParB may act in common and independently. In general, many genes involved in cell division, DNA and RNA processing and metabolic processes were down-regulated in mutant cells, in contrast genes which products play a role in adaptation, protection, motility, cell-to-cell signaling as well as signal transduction increased their expression in par mutant cells. Besides their role in chromosome segregation, ParA and ParB seem to have the potential to regulate genes transcription. The altered expression of a large number of genes encoding known or predicted transcriptional regulators and genes coding for products involved in c-di-GMP signalling, suggests that the part of observed global changes in genes expression pattern in parAnull and parBnull mutants might be the effect of indirect regulation mediated by regulatory genes under ParA and ParB control. The extended regulatory network provides the mechanism to modulate genes expression in response to the stage of the chromosome segregation process and cell cycle. Pseudomonas aeruginosa PAO1161 (leu, r-, RifR), derivative of PAO1, as a control (reference) strain, Pseudomonas aeruginosa PAO1161 parA1-40::smh (parAnull) and Pseudomonas aeruginosa PAO1161 parB1-18::TcR (parBnull) disruption mutant strains were used in the experiments. Three independent biological replicates of total RNA were isolated for each strain from logarithmic (Log) phase of planktonic culture grown on rich medium (L broth) at 37oC. In total, nine samples of RNA were prepared.

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

Publications

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

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