Nucleoid-associated proteins HU and IHF: oligomerization in solution and hydrodynamic properties

Abstract

The structure and function of the bacterial nucleoid is controlled by nucleoid-associated NAP proteins. In any phase of growth, various NAPs, acting sequentially, condense the nucleoid and provide its transcriptionally active structure. However, in the late stationary phase, only one of the NAPs, the Dps protein, is strongly expressed, and DNA-protein crystals are formed that transform the nucleoid into a static, transcriptionally inactive structure, effectively protected from external influences. The discovery of crystal structures in living cells and the association of this phenomenon with bacterial resistance to antibiotics has aroused great interest in studying this phenomenon. The aim of this work is to obtain and compare the structures of two related NAPs (HU and IHF), since they are the ones that accumulate in the cell at the late stationary stage of growth, which precedes the formation of the protective DNA-Dps crystalline complex. For structural studies, two complementary methods were used in the work: small-angle X-ray scattering (SAXS) as the main method for studying the structure of proteins in solution and dynamic light scattering as an additional one. Various approaches and computer programs were used to interpret the SAXS data, which made it possible to determine the macromolecular characteristics and obtain reliable structural 3D models of various oligomeric forms of the HU and IHF proteins. It was shown that these proteins oligomerize in solution to varying degrees, and IHF is characterized by the presence of large oligomers consisting of initial dimers arranged in a chain. It was suggested that just before Dps expression, it is this protein that forms the toroidal structures previously observed in vivo and prepares the platform for the formation of DNA-Dps crystals. The results obtained are necessary for further study of the phenomenon of biocrystal formation in bacterial cells and finding ways to overcome the resistance of various pathogens to external conditions.