Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodelling by Hfq master regulator

Abstract

Bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, thanks to proteins called Nucleoid Associated Proteins (NAPs). The NAP composition of the nucleoid varies during the bacterial life cycle and is growth phase-dependent. Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq belongs to the bridging family of NAPs. Its bridging mechanism relies on the formation of the amyloid-like structure of Hfq C-terminal region. Here, using cryo soft X-ray tomography imaging of native unlabelled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid, especially during the stationary growth phase. Hfq influences both nucleoid volume and absorbance. Hfq cumulates direct effects and indirect effects due to sRNA-based regulation of other NAPs. Taken together, our findings reveal a new role for this protein in nucleoid remodelling that may serve in response to stress conditions and in adapting to changing environments. This implies that Hfq regulates nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNA.