Compaction and condensation of DNA mediated by the C-terminal domain of Hfq

TL;DR

This study investigates how the C-terminal domain of Hfq protein in E. coli facilitates DNA compaction and condensation, revealing its role in DNA binding and mechanical property alteration through various biophysical experiments.

Contribution

It demonstrates the specific role of Hfq's C-terminal domain in DNA binding and compaction, providing new insights into bacterial nucleoid organization.

Findings

Hfq C-terminal arms bind DNA and induce condensation.

Hfq alters the mechanical properties of DNA.

C-terminal domain promotes DNA bridging and aggregation.

Abstract

Hfq is a bacterial protein that is involved in several aspects of nucleic acids metabolism. It has been described as one of the nucleoid associated proteins shaping the bacterial chromosome, although it is better known to influence translation and turnover of cellular RNAs. Here, we explore the role of Escherichia coli Hfq C-terminal domain in the compaction of double stranded DNA. Various experimental methodologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy, isothermal titration microcalorimetry, and electrophoretic mobility assays have been used to follow the assembly of the C-terminal and N-terminal regions of Hfq on DNA. Results highlight the role of Hfq C-terminal arms in DNA binding, change in mechanical properties of the double helix and compaction of DNA into a condensed form. The propensity for bridging and compaction of DNA by the C-terminal domain might be related to aggregation of bound protein and may have implications for protein binding related gene regulation.