DNA binding by the archaeal histone HMf results in positive supercoiling

HMf, a histone from the hyperthermophilic archaeon Methanothermus fervidus binds double-stranded DNA molecules in vitro, forming compact structures that visibly resemble eukaryal nucleosomes. We show here that HMf binding increases the helical periodicity of DNA molecules to approximately 11 base pairs (bp) per turn and that DNA molecules in these nucleosome-like structures are constrained in positive toroidal supercoils. Based on the mass of HMf needed to cause a change in linking number (delta Lk), the maximum delta Lk introduced into circular DNA molecules of known sizes, and electron microscopy, we estimate that each HMf-DNA structure contains between 90 and 150 bp of DNA wrapped in 1.5 positive toroidal supercoils around a core of four HMf molecules. A model and pathway for the formation of these structures in vitro are presented and the possible role of positive toroidal wrapping of the M. fervidus genome in vivo is discussed.