Interplay of Polydisperse Set of Crowders in Compacting Escherichia coli Nucleoid

by Prof. Jaan Männik

University Of Tennessee

at Condensed Matter Theory Seminar

Wed, 22 May 2019, 13:30
Sacta-Rashi Building for Physics (54), room 207

Abstract

DNA-protein interactions, supercoiling, compaction by molecular crowders, and transient DNA attachments to cell membrane have all been implicated in organizing and compacting bacterial nucleoid. However, what contribution different factors have in compacting chromosomal DNA is not clear yet. Here we report on two sets of microfluidic experiments where we quantitatively study the role of molecular crowders in determining the size of Escherichia coli nucleoid in live cells. In the first set we used mother machine platform and rapidly change the osmolality of the growth medium. In the second set of measurements we squeeze individual cells in a device, referred to as the microanvil, which we designed for such measurements. In both sets of measurements water leaves the cell resulting in increased level of crowding. Both types of measurements show that for small increases in the crowder concentration the nucleoid behaves as a linear anisotropic spring. However, as the crowder concentration increases above 30% from the physiological level, the compressibility of the nucleoid decreases significantly akin to compression spring. These mechanical properties of the nucleoid hold in two significantly different growth rates where a different ratio of protein to ribosome based cytosolic crowders is present; thus indicating that compaction is not sensitive to the composition of crowders. The latter conclusion is further supported by coarse-grained Brownian dynamics simulations and by free energy arguments. Altogether, our results lend further support to the idea that a diverse array of cytosolic proteins and stable RNA molecules are the main factor compacting the bacterial DNA within the nucleoid.

Created on 07-05-2019 by Schechter, Moshe (smoshe)
Updaded on 07-05-2019 by Schechter, Moshe (smoshe)