Revised role for Hfq bacterial regulator on DNA topology

Antoine Malabirade,Véronique Arluison,Frédéric Geinguenaud,David Partouche,Florent Busi,Thomas Bizien,Florian Turbant,Frank Wien,Pierre Recouvreux,Omar El Hamoui

doi:10.1038/s41598-018-35060-9

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.

Highlights

The hexameric Hfq is an abundant and phylogenetically conserved protein present in about half of bacteria and in some archaeal species
The mechanism by which Hfq binds nucleic acids is not fully understood, it is well-established that the inner pore on the proximal face of the torus binds U-rich RNA, that A-rich sequences bind to the distal face, and that the lateral rim
The distal face and the rim of the protein are involved in both DNA and RNA binding, while the proximal face seems to be involved in RNA fixation only[11,20]

Summary

Introduction

The hexameric Hfq is an abundant and phylogenetically conserved protein present in about half of bacteria and in some archaeal species. While the same region of Hfq is responsible of its propensity for self-assembly, DNA bridging and compaction[12,24], the relation between these properties remains unclear Both the architectural bridging properties of nucleoid associated proteins (NAPs) and their ability to self-associate may have a role on bacterial DNA condensation[25]. Some of the phenotypic effects due to the lack of Hfq may be attributed to defects in DNA-related processes; filamentation or slowed-down bacterial growth are for instance a sign of replication deregulation, sensitivity to mutagens could indicate unreliable DNA repair Motivated by this unsolved role of Hfq in DNA-related processes, we have investigated how Hfq interaction with DNA affects the nucleic acid structure[24]. Our results enable us to propose a mechanism underlying the function of Hfq in DNA packaging and its precise influence on plasmid supercoiling

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Results

Conclusion