Comparative analysis of mitochondrial N-termini from mouse, human, and yeast [Research]

The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by a N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that while presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved including a length of ~20-60aa, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-termini of mature proteins that follows the N-end rule from bacteria. As in yeast, ~80% of mouse presequence cleavage sites match canonical motifs for three mitochondrial peptidases (MPP, Imp55, Oct1) while the remainder do not match any known peptidase motifs. We show that mature mitochondrial proteins often exist with a spectrum of N-termini, consistent with a model of multiple cleavage events by MPP and Imp55. In addition to analysis of canonical targeting presequences, our N-terminal dataset allows exploration of other cleavage events -- and provides support for polypeptide cleavage into two distinct enzymes (Hsd17b4), protein cleavages key for signaling (Oma1, Opa1, Htra2, Mavs, Bcs2l13), and in several cases suggests novel protein isoforms (Scp2, Acadm, Adck3, Hsdl2, Dlst, Ogdh). We present an integrated catalog of mammalian mitochondrial N-termini that can be used as a community resource to investigate individual proteins, to elucidate mechanisms of mammalian mitochondrial processing, and to allow researchers to engineer tags distal to presequence cleavage.

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