Cleavage kinetics of human mitochondrial RNase P and contribution of its non-nuclease subunits

RNase P is the endonuclease responsible for the 5-end processing of tRNA precursors (pre-tRNAs). Unlike the single-subunit protein-only RNase P (PRORP) found in plants or protists, human mitochondrial RNase P is a multi-enzyme assembly that in addition to the homologous PRORP subunit comprises a methyltransferase (TRMT10C) and a dehydrogenase (SDR5C1) subunit; these proteins, but not their enzymatic activities, are required for efficient pre-tRNA cleavage. Here we report a detailed kinetic analysis of the cleavage reaction by human PRORP and its interplay with TRMT10C-SDR5C1 using a comprehensive set of mitochondrial pre-tRNAs. Surprisingly, we found that PRORP alone binds pre-tRNAs with nanomolar affinity and can even cleave some of them at reduced efficiency without the other subunits. Thus, the ancient binding mode, involving the tRNA elbow and PRORPs PPR domain, seems retained by human PRORP, and its metallonuclease domain is in principle correctly folded and functional. Our findings support a model according to which the main function of TRMT10C-SDR5C1 is to direct PRORPs nuclease domain to the cleavage site, thereby increasing the rate and accuracy of cleavage. Human PRORPs dependence on the extra tRNA binder appears to have evolved to secure specificity in the cleavage of the structurally degenerating mitochondrial tRNAs.