Structural characterization of the H-NS protein from Xylella fastidiosa and its interaction with DNA

► Xylella fastidiosa H-NS C-terminal domain structure differs from other H-NS proteins. ► Upon DNA binding small oligomers are formed. ► The DNA binding site includes helix 1, which is not seen in other H-NS proteins. The nucleoid-associated protein H-NS is a major component of the bacterial nucleoid involved in DNA compaction and transcription regulation. The NMR solution structure of the Xylella fastidiosa H-NS C-terminal domain (residues 56–134) is presented here and consists of two beta-strands and two alpha helices, with one loop connecting the two beta-strands and a second loop connecting the second beta strand and the first helix. The amide 1H and 15N chemical shift signals for a sample of XfH-NS56–134 were monitored in the course of a titration series with a 14-bp DNA duplex. Most of the residues involved in contacts to DNA are located around the first and second loops and in the first helix at a positively charged side of the protein surface. The overall structure of the Xylella H-NS C-terminal domain differ significantly from Escherichia coli and Salmonella enterica H-NS proteins, even though the DNA binding motif in loop 2 adopt similar conformation, as well as β-strand 2 and loop 1. Interestingly, we have also found that the DNA binding site is expanded to include helix 1, which is not seen in the other structures.