Charged residues in the H-NS linker drive DNA binding and gene silencing in single cells

H-NS is a nucleoid-associated protein that plays a major role in silencing pathogen genes. We discovered that the unstructured linker region connecting the N-terminal oligomerization and C-terminal DNA binding domains plays an important and surprising role in promoting DNA binding. Superresolution imaging identified H-NS foci that required DNA binding for their formation and were associated with the nucleoid. Removing the linker led to the disappearance of foci and a substantially lower affinity for DNA. It was proposed that H-NS compacts DNA, but decreasing DNA binding in cells did not lead to a relaxation of the nucleoid, suggesting H-NS does not play a major role in nucleoid compaction. Molecular dynamic simulations suggested that target acquisition by H-NS may involve sliding along the DNA.