Cryo-EM reveals the mechanism of DNA compaction by Mycobacterium smegmatis Dps2

DNA-binding protein under starvation (Dps), is a miniature ferritin complex which plays a vital role in protecting bacterial DNA during starvation for maintaining the integrity of bacteria from hostile conditions. Mycobacterium smegmatis is one such bacteria that express MsDps2, which binds DNA to protect it under oxidative and nutritional stress conditions. Several approaches, including cryo-electron tomography (Cryo-ET), were implemented to identify the structure of the Dps protein that is bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to be able to identify the DNA binding residues. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps protein. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA and identify that the region close to N-terminal confers the DNA binding property. Based on cryo-EM data, we performed mutations of several arginine residues proximal to DNA binding region, which dramatically reduced the MsDps2-DNA interaction. In addition, we demonstrated the proposed model for DNA compaction during lattice formation. We also pinpointed arginine residues, which are responsible for DNA binding in lattice arrangement of MsDps2. We performed single-molecule imaging experiments of MsDps2-DNA interactions that corroborate well with our structural studies.