Folding, Bridging, and Compaction of DNA by Nucleoid Associated Protein Hfq

Abstract

Nucleoid Associated Proteins (NAPs) play a key role in the folding, compaction and expression of the prokaryotic genome. We have investigated an exemplary NAP, that is Escherichia coli Hfq. Hfq takes the form of a hexameric, N-terminal torus with six protruding C-terminal arms. It is a bacterial pleiotropic regulator that mediates several aspects of nucleic acids metabolism. It notably influences translation and turnover of RNAs, but it also known to associate with double stranded DNA in vivo and in vitro. Here, we explore the role of Hfq 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, small angle neutron scattering, and electrophoretic mobility assays have been used to follow the assembly of full length Hfq as well as its C- and N-terminal regions on DNA. Results highlight the role of Hfq's 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.