Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes.

Transcription generates local topological and mechanical constraints on the DNA fiber, leading to the generation of supercoiled chromosome domains in bacteria. However, the global impact of transcription on chromosome organization remains elusive, as the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~5-10 kb). Here we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units. We show that transcriptional units form discrete three-dimensional transcription-induced domains that impose mechanical and topological constraints on their neighboring sequences at larger scales, modifying their localization and dynamics. These results show that transcriptional domains constitute primary building blocks of bacterial chromosome folding and locally impose structural and dynamic constraints.

The Two-Component System ZraPSR Is a Novel ESR that Contributes to Intrinsic Antibiotic Tolerance in Escherichia coli.

During their lifecycle, bacteria are exposed to continuous changes in their environment, some of which are stressful and can be harmful. The cell envelope is the first line of defense against a hostile environment, but it is also the first target for damage. To deal with this problem, bacteria have evolved systems collectively called "envelope stress response," or ESR, dedicated to the detection and repair of damaged components. Here we decided to investigate whether the atypical two-component system ZraP-SR is a novel ESR. Based on the screening of more than 240 drugs using the Biolog technology, we show that the deletion of zraP or zraR confers increased susceptibility to five classes of antibiotics and to some environmental stress targeting the envelope. Using a microscopy approach, we also establish that ZraP and ZraR are required to maintain envelope integrity. So far, the ZraR regulator was only known to activate the transcription of zraP and zraSR. Using chromatin immunoprecipitation followed by sequencing and RT-qPCR, we have now identified 25 additional genes regulated by ZraR, the majority of which are involved in the response against stress. Taken together, our results demonstrate that ZraP-SR is a novel ESR.