Characterization and comparison of nucleoid proteins in different bacterial species

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We developed a new method, GeF-seq, which enables to determine the binding regions of DNA binding proteins with 1bp resolution. We applied GeF-seq to determine the regions in which nucleoid proteins interact with genome DNA in Escherichia coli and Bacillus subtilis, which are evolutionally separated bacteria. The analysis revealed that, although HU protein, which are conserved across almost bacteria species, showed non-sequence-specific bindings with genome DNA in both Escherichia coli and Bacillus subtilis, Fis and IHF, which are unique nucleoid proteins in Escherichia coli, interacted with the specific sequences, resulting in formation of bend and hairpin structures in the genomic DNA. This suggested that there might be unique structures of nucleoid formed with Fis and IHF in E. coli.