Mycobacterial DNA-binding protein 1 (MDP1) induces RNA condensation as revealed by high-speed AFM

ABSTRACT Mycobacterial DNA-binding protein 1 (MDP1) is a histone-like protein in Mycobacterium tuberculosis (Mtb) that contributes to genome organization and dormancy adaptation. MDP1 consists of a structured HU-like region (HUR), and a post-translational modifications (PTMs)-enriched intrinsically disordered region (IDR), that regulate its function. While its role in DNA condensation is well established, how MDP1 interacts with RNA remains unclear, despite growing recognition of transcriptional regulation during dormancy. Here, by using total RNA from E. coli as a model substrate, we investigated whether MDP1 induces RNA condensation. Our high-speed AFM and optical microscopy analysis shows that native MDP1 from Mtb, rich in PTMs, forms globular RNA condensates. In contrast, MDP1 expressed in E. coli , which lacks PTMs, induces chain-like RNA condensates. Domain-specific analysis revealed that the IDR, the synergy between the IDR and HUR, and PTMs are essential for MDP1-induced RNA condensation. These findings suggest that MDP1 mediates RNA organization during dormancy.