Membrane protein degradation by AAA proteases in mitochondria: Extraction of substrates from either membrane surface

Two AAA proteases, each with its catalytic site at the opposite membrane su rface, mediate the ATP-dependent degradation of mitochondrial inner membran e proteins. We demonstrate here that a model substrate polypeptide containi ng hydrophilic domains at both sides of the membrane can be completely degr aded by either of the AAA proteases, if solvent-exposed domains are in an u nfolded state. A short protein tail protruding from the membrane surface is sufficient to allow the proteolytic attack of an AAA protease that facilit ates domain unfolding at the opposite side. Our results provide a rationale for the membrane arrangement of AAA proteases in mitochondria and demonstr ate that degradation of membrane proteins by AAA proteases involves an acti ve extraction of transmembrane segments and transport of solvent-exposed do mains across the membrane.