Structural Studies on the M. tuberculosis Nucleoid-associated-Protein, NapA, Indicates DNA Bridging Mechanism

Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. Interestingly, Mycobacterium tuberculosis (Mtb) lacks most common NAPs and only recently have NAPs been uncovered in this bacterium. One such protein, NapA, was revealed to be an essential Mtb NAP that can bridge DNA. NapA shows no sequence homology to any protein and hence its DNA-binding functions remain unclear. Here we describe structures of apo NapA and a DNA-bound complex of NapA. The NapA structures reveal a dimeric fold for the protein, which is supported by mass photometry analyses, with each subunit comprised of an extended α1 helix and C-terminal three-helix module. The α1 helices combine to form a helical-bundle dimer scaffold that forms dimer-of-dimers at elevated protein concentrations. Each NapA dimer projects two DNA interacting elements, that bind and link between DNA sites. Combined these studies provide mechanistic insight into the DNA binding and bridging capabilities of a unique NAP that appears broadly conserved among most Actinobacteria.