SINGLE-MOLECULE STUDIES OF DNA ORGANIZATION BY BACTERIAL ARCHITECTURAL PROTEINS

Abstract

The integration host factor is an abundant nucleoid-associated protein and an essential co-factor for the site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting biological importance of non-specific binding of IHF. However, it is unclear how non-specific DNA association contributes to DNA organization. Using single DNA manipulation and AFM imaging methods, we show distinct modes of non-specific DNA binding of IHF. Changes in KCl and IHF concentrations, as well as force dramatically influence the degree of DNA-bending. Moreover, IHF crosslinks DNA into highly compact DNA meshworks in the presence of magnesium at low concentration of monovalent-ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation.