Mycobacterial protein compacts RNA differently with modifications

Mycobacterial DNA-binding protein 1 (MDP1) is a histone-like protein in Mycobacterium tuberculosis (Mtb) known to help organize the genome and support bacterial dormancy. Researchers have long understood that MDP1 can condense DNA, but its relationship with RNA has been unclear even as RNA-based control of gene activity becomes more appreciated during dormancy. To explore that gap, a team led by Noriyuki Kodera set out to see whether MDP1 can also induce RNA condensation. They used total RNA from E. coli as a model substrate and compared different forms of MDP1 to test how structure and chemical modifications affect its behavior. MDP1 is built from a structured HU-like region (HUR) and an intrinsically disordered region (IDR) that carries many post-translational modifications (PTMs). Those two parts and the PTMs are known to influence how MDP1 works on DNA, so the research asked whether the same features govern interactions with RNA. By directly imaging MDP1 with RNA, the team aimed to reveal whether and how the protein organizes RNA in ways that could matter for dormancy.

To visualize how MDP1 interacts with RNA, the study combined high-speed AFM and optical microscopy. Using total RNA from E. coli as a model substrate, the investigators compared "native" MDP1 isolated from Mtb, which is rich in PTMs, with MDP1 produced in E. coli that lacks those PTMs. The imaging showed a clear difference: native MDP1 from Mtb formed globular RNA condensates, compact, rounded assemblies visible by both high-speed AFM and optical microscopy. In contrast, MDP1 expressed in E. coli and therefore missing PTMs induced chain-like RNA condensates, producing extended, linked structures rather than compact blobs. The team also performed domain-specific analysis to dissect the roles of the parts of MDP1. That work revealed that the intrinsically disordered region (IDR), the cooperation between the IDR and the HU-like region (HUR), and the presence of PTMs are all essential for MDP1-induced RNA condensation. In short, both structure and chemical modification control whether MDP1 makes globular or chain-like RNA assemblies.

These findings point to a previously underappreciated ability of MDP1 to organize RNA, not just DNA, and suggest a mechanism by which Mycobacterium tuberculosis might rearrange its RNA when entering or maintaining dormancy. If MDP1 can drive RNA into distinct condensate forms depending on its PTMs and the balance between HUR and IDR, then the protein could play a direct role in shaping the physical organization of transcripts and potentially influencing which RNAs are available for translation or regulation during dormancy. The results therefore extend understanding of MDP1 beyond genome packaging to include RNA organization, highlighting the importance of post-translational modifications and disordered protein regions in bacterial molecular remodeling. While this study used total RNA from E. coli as a model substrate, the observed principles—IDR-driven condensation, synergy with a structured domain, and modulation by PTMs—suggest a versatile strategy MDP1 might use in Mtb. That perspective opens new directions for research into how bacterial proteins shape nucleic acid behavior under changing physiological states such as dormancy.