Structural basis for impaired 5′ processing of a mutant tRNA associated with defects in neuronal homeostasis

n-Tr20 is a neuron-specific, cytoplasmic transfer RNA(Arg)(UCU) (tRNA(Arg)(UCU)) isodecoder that affects seizure susceptibility, neuronal excitability, and translation signaling in mice. In addition, the C50U substitution in n-Tr20 (n-Tr20(C50U)), which is found in the widely used C57BL/6J (B6J) inbred mouse line, contributes to neurodegeneration by epistatic interactions with mutations in Gtpbp1 or Gtpbp2, two factors that rescue ribosomal stalling. The brains of B6J mice have high levels of immature and low levels of mature n-Tr20(C50U), implicating defective tRNA biogenesis as the basis for neuronal dysfunction, a hypothesis tested in this study. We demonstrate that partially purified mouse brain ribonuclease P, the endonuclease responsible for 5′ maturation of tRNAs, exhibits at 1 mM magnesium a 20-fold lower apparent cleavage rate for processing the n-Tr20(C50U) precursor than the wild-type precursor. Thermal denaturation studies unexpectedly revealed that substituting the native C(50)-G(64) base pair with the U(50)-G(64) wobble pair in n-Tr20(C50U) increased the T(m) by as much as 8 °C, with the magnitude of the change dependent on [Mg(2+)]. Moreover, results from thermal denaturation, native gel electrophoresis, (1)H nuclear magnetic resonance spectroscopy, and kinetic studies collectively support the presence of stable alternative folds for n-Tr20(C50U) that may also be sampled transiently and in low abundance by the wild-type tRNA. These findings suggest that mutation-driven restructuring could foster nonnative folds and that conformational toggling of tRNAs poses an intrinsic risk for dysfunction when point mutations selectively stabilize nonnative states. This model may be applicable for understanding the molecular basis of other diseases that are associated with tRNA mutations.