The environmentally-regulated interplay between three-dimensional chromatin organisation and transcription of the Escherichia coli proVWX operon

Nucleoid associated proteins maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-modelling. Here, we provide the first in vivo evidence supporting this hypothesis. Using RT-qPCR and 3C-qPCR, we show that activation of the H-NS-regulated, osmosensitive proVWX operon of Escherichia coli in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges in cells adapted to hyperosmolarity represses the operon. While the DRE—H-NS—URE bridge is disrupted by hyperosmolarity, the DRE—H-NS—ygaY bridge weakens and requires active transcription to be dismantled. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that structural regulation of expression may be a typical feature of transcriptional control in bacteria. Chromosome conformation capture experiments to test how various cell fixation techniques, and the enrichment of DNA-protein complexes impact the signal-to-noise ratio in chromosome contact maps.