Abstract
Hfq is a bacterial pleiotropic regulator that mediates several aspects of nucleic acids metabolism. The protein notably influences translation and turnover of cellular RNAs. Although most previous contributions concentrated on Hfq's interaction with RNA, its association to DNA has also been observed in vitro and in vivo. Here, we focus on DNA-compacting properties of Hfq. Various experimental technologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy and small angle neutron scattering have been used to follow the assembly of Hfq on DNA. Our results show that Hfq forms a nucleoprotein complex, changes the mechanical properties of the double helix and compacts DNA into a condensed form. We propose a compaction mechanism based on protein-mediated bridging of DNA segments. The propensity for bridging is presumably related to multi-arm functionality of the Hfq hexamer, resulting from binding of the C-terminal domains to the duplex. Results are discussed in regard to previous results obtained for H-NS, with important implications for protein binding related gene regulation.
Highlights
Hfq is a widespread and phylogenetically conserved protein found at high concentration in bacteria
T4-DNA molecules with a concentration of 3 mg of DNA/l were incubated with the relevant buffer for at least 24 h
It was checked that the DNA molecules are in the coil state before they were brought into the channels of the nanofluidic device with an electric field
Summary
Hfq is a widespread and phylogenetically conserved protein found at high concentration in bacteria Consistent with this high level of expression, the protein is central to multiple regulatory processes. Pleiotropic functions of Hfq have been highlighted when the hfq gene was disrupted in Escherichia coli, yielding a decrease in growth rate, an increase in UV, oxidant and osmo sensitivity, as well as decreased negative supercoiling of plasmids [2] Most of these hfq-null phenotypes are due to the implication of Hfq in RNA regulation by small noncoding RNA (sRNA) [3]. Hfq is required to mediate sRNA stress-response This regulatory mechanism is based on the hybridization of sRNA to its target mRNA, altering mRNA expression. The hybridization of sRNA occurs in the vicinity of the ribosome binding site to prevent the initiation of translation, a process concomitant with a decrease in mRNA stability [4,5]
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