Mobility of bacterial protein Hfq on dsDNA; Role of C-terminus mediated transient binding

TL;DR

This study investigates how the internal motion of DNA influences the mobility of bacterial Hfq protein lacking its C-terminus, revealing that DNA dynamics and transient binding significantly affect protein diffusion.

Contribution

It demonstrates the role of DNA internal motion and transient binding in regulating Hfq protein mobility, highlighting the importance of the C-terminus domain.

Findings

Mutant Hfq diffuses faster than wild type.

Slower DNA motion correlates with slower protein diffusion.

DNA internal motion modulates nucleoid-associated protein mobility.

Abstract

The mobility of protein is fundamental in the machinery of life. Here, we have investigated the effect of DNA binding in conjunction with DNA internal motion of the bacterial Hfq master regulator devoid of its amyloid C-terminus domain. Hfq is one of the most abundant nucleoid associated proteins that shape the bacterial chromosome and is involved in several aspects of nucleic acid metabolism. Fluorescence microscopy has been used to track a C-terminus domain lacking mutant form of Hfq on double stranded DNA, which is stretched by confinement to a rectangular nanofluidic channel. The mobility of the mutant is strongly accelerated with respect to the wild type variant. Furthermore, it shows a reverse dependence on the internal motion of DNA, in that slower motion results in slower protein diffusion. Results demonstrate the subtle role of DNA internal motion in controlling the mobility of a nucleoid associated protein, and, in particular, the importance of transient binding and moving DNA strands out of the way.