Bacterial stress response

Dps, a nucleoid-associated protein found in bacteria, protects E. coli from a broad range of environmental stresses. The search to identify the mechanism of this protection has given us unique insights into how bacteria organize their cytoplasm.

In stationary phase, Dps becomes the most abundant protein in the entire cell.

Using fluorescence microscopy, we showed that Dps significantly condenses the nucleoid in starved cells.

EM images of starved bacteria cells have shown that Dps can pack the chromosome into very dense structures – on the left you can see a crystalline array observed in starved E. coli cells (Image from Loiko et al., arXiv:1901.11322).

Such a dense structure would seem to be incompatible with transcription or other processes.

However, using RNA-seq we observed that transcription is completely orthogonal to the condensation of DNA by Dps in the cell.

Somehow, Dps and RNA polymerase can access the same DNA without interfering with each other.

This phenomenon was also recreated in carefully controlled conditions in vitro.

Dps did not interfere with initiation or elongation of RNA transcripts, as demonstrated with a single-molecule magnetic tweezers assay.

However, other enzymes were completely blocked from accessing DNA bound to Dps.

Our working hypothesis is that Dps forms a phase-separated organelle, a structure identified in eukaryotes that had not previously been observed in bacteria. The liquid crystal phase of Dps and DNA creates small droplets in the cytoplasm that only some enzymes are able to penetrate. Other recent evidence suggests that phase-separated organelles might enclose other nucleic acids in the cell. We are gearing up to further explore the properties of Dps-DNA complexes using advanced microscopy to test our hypothesis.

•Abbondanzieri EA, Meyer AS. More than just a phase: The search for membraneless organelles in the bacterial cytoplasm. Current Genetics (2019)

•Janissen R, Arens MMA, Vtyurina NN, Rivai Z, Sunday ND, Eslami-Mossallam B, Gritsenko AA, Laan L, de Ridder D, Artsimovitch I, Dekker NH, Abbondanzieri EA, Meyer AS. Global DNA compaction in stationary-phase bacteria does not affect transcription. Cell (2018).

•Vtyurina NN, Dulin D, Docter MW, Meyer AS, Dekker NH, Abbondanzieri EA. An Ising model describes hysteresis in the process of DNA compaction by Dps. Proceedings of the National Academy of Sciences (2016).

•Karas VO, Westerlaken I, Meyer AS. The DNA-binding protein from starved cells (Dps) utilizes dual functions to defend cells against multiple stresses. Journal of Bacteriology (2015).