Human lncRNA RMRP interacts with DEAD-box helicases and modulates mitochondrial function

Abstract

The human long noncoding RNA (lncRNA) RMRP, initially identified as part of the RNase MRP complex, is linked to various human diseases. However, its structural flexibility and broader cellular roles are not well understood. Here, we offer a comprehensive analysis of RMRP’s structure in solution, its interactions with human proteins, and its mitochondrial functions. Using small-angle X-ray scattering (SAXS), we show that RMRP adopts different Mg2+-dependent shapes, shifting from an extended Y-shaped form to a more compact one as Mg2+ levels increase. We identified and characterized interactions between RMRP and the DEAD-box RNA helicases DDX5 and DDX3X, with DDX5 binding strongly and exhibiting ATP-dependent helicase activity on RMRP, while DDX3X mainly acts as an expression regulator. Both helicases are crucial for the proper mitochondrial localization of RMRP, working within a complex regulatory network. Functionally, reducing RMRP levels disrupts mitochondrial stability, leading to membrane depolarization and an increase in reactive oxygen species, without affecting cell growth. Mechanistically, RMRP specifically controls nuclear-encoded mitochondrial proteins involved in cristae structure (DNAJC11) and respiratory chain function (NDUFS8). Our results position RMRP as a structurally adaptable lncRNA that collaborates with RNA helicases to preserve mitochondrial health through specific gene regulation. These insights provide perspectives on RMRP’s biology and the molecular mechanisms underlying RMRP-related disorders, which could inform future therapies for conditions resulting from RMRP dysfunction.