The biogenesis of mitochondria and the maintenance of mitochondrial functio
ns depends on an autonomous proteolytic system in the organelle which is hi
ghly conserved throughout evolution. Components of this system include proc
essing peptidases and ATP-dependent proteases, as well as molecular chapero
ne proteins and protein complexes with apparently regulatory functions. Whi
le processing peptidases mediate maturation of nuclear-encoded mitochondria
l preproteins, quality control within various subcompartments of mitochondr
ia is ensured by ATP-dependent pretenses which selectively remove non-assem
bled or misfolded polypeptides. Moreover; these proteases appear to control
the activity- or steady-state levels of specific regulatory proteins and t
hereby ensure mitochondrial genome integrity, gene expression and protein a
ssembly.