Revised role for Hfq bacterial regulator on DNA topology

Abstract

Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNA. Besides these RNA-related functions, Hfq has also been described as one of the nucleoid associated proteins shaping the bacterial chromosome. Therefore, Hfq appears as a versatile nucleic acid-binding protein, which functions are probably even more numerous than those initially suggested. For instance, E. coli Hfq, and more precisely its C-terminal region (CTR), has been shown to induce DNA compaction into a condensed form. In this paper, we establish that DNA induces Hfq-CTR amyloidogenesis, resulting in a change of DNA local conformation. Furthermore, we clarify the effect of Hfq on DNA topology. Our results evidence that, even if the protein has a strong propensity to compact DNA thanks to its amyloid region, it does not affect overall DNA topology. We confirm however that hfq gene disruption influences plasmid supercoiling in vivo, indicating that the effect on DNA topology in former reports was indirect. Most likely, this effect is related to small regulatory sRNA-Hfq-based regulation of another protein that influences DNA supercoiling, possibly a nucleoid associated protein such as H-NS or Dps. Finally, we hypothesise that this indirect effect on DNA topology explains, at least partially, the previously reported effect of Hfq on plasmid replication efficiency.

Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli

“…While Hfq binds to DNA and RNA [41,66], its binding to G-quadruplex structures has not been investigated. Hfq:dG7 quadruplex complex formation was confirmed by EMSA and the equilibrium dissociation constant (Kd) of the complex was 1150 ± 110 nM as measured by fluorescence anisotropy ( Figure S4).…”

“…Mutations in Hfq can alter DNA topology and have pleiotropic effects in cells [35,39,41,43,78]. Hfq binds to sRNA and can alter mRNA translation or message stability [79] that can alter expression levels of many genes.…”

“…Hfq notably mediates translation efficiency by using stress-related small regulatory RNA (sRNA) and modulates the cellular levels of RNAs, either by changing their stability or through an unsolved transcriptional mechanism [37]. More recent analyses focused attention on the action of Hfq on nucleoid structure [35,[38][39][40][41][42]. These analyses evidenced that Hfq cooperatively binds to DNA through a DNA:protein:DNA bridging mechanism, that it can form filaments on DNA, changing the mechanical properties of the double helix, with important implications for bacterial transcription and replication [35,36].…”

The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment

“…Even though few studies have shed light on the role of Hfq in DNA metabolism, its direct or indirect role in DNA related processes is now firmly established [15]. Hfq has been shown to influence DNA supercoiling and compaction [4,18,19]. Some studies have also suggested a role for the protein in replication, transcription, and transposition efficiency [20][21][22][23][24].…”

Correlative infrared nanospectroscopy and transmission electron microscopy to investigate nanometric amyloid fibrils: prospects and challenges

“…Only a patch of 11 amino acids over 38 are necessary for Hfq to self‐assemble, but not to interact with nucleic acid (NA). As this analysis could open perspectives in the future to correlatively image nucleoprotein complexes (Malabirade et al ., ; Malabirade et al ., ), the synthetic 38 amino acid long sequence (referred as CTR 38 through the manuscript) rather than the shorter peptide with 11 amino acids was chosen for this work. With this sequence, in the absence of NA, about 20% of the peptide may show an intermolecular β‐sheet secondary structure characteristic of the amyloid moiety.…”