In vivo compaction dynamics of bacterial DNA: A fingerprint of DNA/RNA demixing ?

TL;DR

This paper reviews recent in vivo microscopy studies revealing that bacterial DNA compaction is dynamic and likely driven by DNA/RNA demixing and phase separation influenced by crowding and electrostatic interactions.

Contribution

It proposes a novel model where DNA/RNA demixing and phase separation, modulated by crowding and electrostatics, explain nucleoid compaction in bacteria.

Findings

Nucleoid compaction is highly dynamic and influenced by environmental factors.

Evidence supports DNA/RNA demixing as a key mechanism in nucleoid formation.

Crowding and electrostatic forces synergistically promote DNA/RNA segregation.

Abstract

The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the cell volume. There is still no general agreement on the mechanism leading to the compaction of the DNA and the formation of the nucleoid. However, advances in in vivo sub-wavelength resolution microscopy techniques have recently allowed the observation of the nucleoid at an unprecedented level of detail. In particular, these observations show that the compaction of the nucleoid is not static but is instead a highly dynamic feature, which depends on several factors, like the richness of the nutrient, the cell cycle stage, temperature, the action of an osmotic shock or antibiotics, etc. After a short description of the electrolyte content of the cytosol and a brief overview of the different mechanisms that may lead to the formation of the nucleoid, this paper reviews some of the most fascinating recent results of in vivo sub-wavelength resolution microscopy. It is furthermore argued that these observations provide converging indications in favor of a model that describes the cytosol as an aqueous electrolyte solution containing several macromolecular species, where demixing and segregative phase separation occur between DNA and RNA (essentially rRNA and mRNA involved in translation complexes, but also the large amounts of rRNA synthesized at the rrn operons of cells growing in rich media). It is also pointed out that crowding may play a crucial role through its synergy with electrostatic forces. By constraining macromolecules to remain at short distances from one another and feel electrostatic interactions in spite of the strong screening exerted by electrolyte species, crowding favors stronger DNA/RNA demixing and nucleoid compaction.