The bacterial nucleoid: from electron microscopy to polymer physics

by Prof. Conrad Woldringh

Swammerdam Institute for Life Sciences (SILS), University of Amsterdam

at Biological and soft-matter physics

Thu, 08 Dec 2022, 12:10
Sacta-Rashi Building for Physics (54), room 207

Abstract

In the 1960’s, electron microscopy has not given us a clear answer regarding the compact or dispersed organization of the bacterial nucleoid. Differences between DNA in the eukaryotic nucleus and in the nucleoid are shortly discussed.
Phase contrast microscopy of bacterial cells immersed in a high protein concentration, shows the nucleoid as a cloudlike structure with lower density (refractive index, RI) than the cytoplasm. However, using fluorescence microscopy, many studies show that the nucleoid does not exclude particles up to a diameter of 25 nm. This raises the question whether the nucleoid can maintain its low density by mere exclusion of larger particles, like (poly)ribosomes, without excluding smaller, soluble proteins.
The question why the DNA does not spread throughout the cytoplasm, has been approached by considering macro-molecular interactions between DNA supercoil segments (causing expansion) and between DNA and proteins (causing compaction). This so-called “depletion theory” (Odijk, 1998), has given us a mechanistic insight in phase separation of DNA into regions of lower density than that of the cytoplasm. Microscopic techniques like spatial light interference (SLIM) and digital holographic (DHM) microscopy, seem to confirm the lower nucleoid RI in bacteria like Escherichia coli.
Two different organizations of the nucleoid in bacteria are discussed: the transversal arrangement in a minority of species (e.g. E. coli) and the llongitudinal arrangement in ~80% of sequenced species (e.g. Caulobacter crescentus). The latter contain the widely conserved proteins of the ParABS-system that direct the segregation of daughter strands. However, it is proposed that in both arrangements, the basis for the robust and opposing movement of replicated DNA strands must lie in their de-mixed state within the replication bubble that develops and expands within the parental DNA network.

Created on 01-12-2022 by Feingold, Mario (mario)
Updaded on 01-12-2022 by Feingold, Mario (mario)