Two-step processing of human frataxin by mitochondrial processing peptidase: Precursor and intermediate forms are cleaved at different rates

We showed previously that maturation of the human frataxin precursor (p-fxn) involves two cleavages by the mitochondrial processing peptidase (MPP). This observation was not confirmed by another group, however, who reported only one cleavage. Here, we demonstrate conclusively that MPP cleaves p-fxn in two sequential steps, yielding a 18,826-Da intermediate (i-fxn) and a 17,255-Da mature (m-fxn) form, the latter corresponding to endogenous frataxin in human tissues. The two cleavages occur between residues 41-42 and 55-56, and both match the MPP consensus sequence RX ↓ (X/S). Recombinant rat and yeast MPP catalyze the p → i step 4 and 40 times faster, respectively, than the i → m step. In isolated rat mitochondria, p-fxn undergoes a sequence of cleavages, p → i → m → d₁ → d², with d₁ and d₂ representing two C-terminal fragments of m-fxn produced by an unknown protease. The i → m step is limiting, and the overall rate of p → i → m does not exceed the rate of m → d₁ → d₂, such that the levels of m-fxn do not change during incubations as long as 3 h. Inhibition of the i → m step by a disease-causing frataxin mutation (W173G) leads to nonspecific degradation of i-fxn. Thus, the second of the two processing steps catalyzed by MPP limits the levels of mature frataxin within mitochondria.