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.
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