Surfing biological surfaces: exploiting the nucleoid for partition and transport in bacteria

Abstract

The ParA family of ATPases is responsible for transporting bacterial chromosomes, plasmids and large protein machineries. ParAs pattern the nucleoid in vivo, but how patterning functions or is exploited in transport is of considerable debate. Here we discuss the process of self-organization into patterns on the bacterial nucleoid and explore how it relates to the molecular mechanism of ParA action. We review ParA-mediated DNA partition as a general mechanism of how ATP-driven protein gradients on biological surfaces can result in spatial organization on a mesoscale. We also discuss how the nucleoid acts as a formidable diffusion barrier for large bodies in the cell, and make the case that the ParA family evolved to overcome the barrier by exploiting the nucleoid as a matrix for movement.

Figure 1. Diffusion-ratchet models for the Par and Min systems

(A) ParA-mediated nucleoid patterning and plasmid transport. ParA-ATP* binds the nucleoid and ParB dimers load onto the plasmid (black squiggle). Interactions between ParB and nucleoid-bound ParA (ParA-ATP^c) bridge the plasmid to the nucleoid. ParA ATPase activity is stimulated by ParB, clearing ParA-ADP from the nucleoid in the vicinity of the plasmid. ParA exchanges ADP for ATP (ParA-ATP) and there is a delay time during the conformational change that creates ParA-ATP*. The delay allows ParA to randomly diffuse before re-associating with the nucleoid. The continual redistribution of nucleoid-bound ParA drives plasmid movement. After replication, the plasmids segregate bi-directionally as they chase high concentrations of nucleoid-bound ParA in opposite directions. (B) Min-mediated membrane patterning. MinD-ATP* binds the membrane. MinE binds MinD on the membrane (MinD-ATP^c), which licenses MinE to also bind the membrane (MinE*). MinD ATPase activity is stimulated by MinE*, clearing MinD-ADP from the membrane. MinE* immediately re-associates with a neighboring MinD dimer. MinD exchanges ADP for ATP, dimerizes and potentially undergoes further conformational changes that allow MinD to diffuse before re-associating with the membrane. At the wave front, the MinE:MinD ratio is low. While MinD is being released, MinE persistently re-associates with adjacent MinD dimers; thus increasing the MinE:MinD ratio towards the wave rear. At the wave rear, there is no available MinD for MinE to re-bind so both proteins release. (C) Persistent binding model for ParB. The ParA-ParB association produces ParA-ADP, which cannot bind the partition complex or nucleoid, and is consequently released into the cytoplasm. ParB on the other hand remains competent for immediate rebinding to another nucleoid-bound ParA dimer.

Figure 2. Positioning large bodies in bacteria

(A) Without a tether, multiple substrates are separated and positioned longitudinally equidistant to each other. (B) With a polar tether (X), the substrate segregates and one copy is transported across the nucleoid and tethered to the opposing pole. (C) Without active transport, nucleoid exclusion passively maintains the substrate at one pole.