title: Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF).
abstract: The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ 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 that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed 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.
authors.affiliation: Department of Physics, National University of Singapore, Singapore, Singapore.
authors.forename: Jie
authors.initials: J
authors.lastname: Lin
authors.forename: Hu
authors.initials: H
authors.lastname: Chen
authors.forename: Peter
authors.initials: P
authors.lastname: Dröge
authors.forename: Jie
authors.initials: J
authors.lastname: Yan
mesh_terms: D042002:Chromatin Assembly and Disassembly / Q000502:physiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D034982:Integration Host Factors / Q000378:metabolism*; D008274:Magnesium; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D034982:Integration Host Factors; D008274:Magnesium