Effects of the nucleoid protein HU on the structure flexibility and ring-closure properties of DNA deduced from Monte-Carlo simulations

摘要

The histone-like heat unstable HU protein plays a key role in the organization and regulation of the Escherichia coli genome. The non-specific nature of HU binding to DNA complicates analysis of the mechanism by which the protein contributes to the looping of DNA. Conventional models of the looping of HU-bound duplexes attribute the changes in biophysical properties of DNA brought about by the random binding of protein to changes in the effective parameters of an ideal helical wormlike chain. Here we introduce a novel Monte-Carlo approach to study the effects of non-specific HU binding on the configurational properties of DNA directly. We randomly decorate segments of an ideal double-helical DNA with HU molecules that induce the bends and other structural distortions of the double helix found in currently available X-ray structures. We find that the presence of HU at levels approximating those found in the cell reduces the persistence length by roughly threefold compared to that of naked DNA. The binding of protein has particularly striking effects on the cyclization properties of short duplexes, altering the dependence of ring closure on chain length in a way that cannot be mimicked by a simple wormlike model and accumulating at higher than expected levels on successfully closed chains. Moreover, the uptake of protein on small minicircles depends upon chain length, taking advantage of the HU-induced deformations of DNA structure to facilitate ligation. Circular duplexes with bound HU show a much greater propensity than protein-free DNA to exist as negatively supercoiled topoisomers, suggesting a potential role of HU in organizing the bacterial nucleoid. The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo.