The mitochondrial outer membrane contains two distinct machineries for protein import and protein sorting that function in a sequential manner: the general translocase of the outer membrane (TOM complex) and the sorting and assembly machinery (SAM complex), which is dedicated to -barrel proteins. The SAM core complex consists of three subunits, Sam35, Sam37, and Sam50, that can associate with a fourth subunit, the morphology component Mdm10, to form the SAM holo complex. Whereas the SAM core complex is required for the biogenesis of all -barrel proteins, Mdm10 and the SAM holo complex play a selective role in -barrel biogenesis by promoting assembly of Tom40 but not of porin. We report that Tom7, a conserved subunit of the TOM complex, functions in an antagonistic manner to Mdm10 in biogenesis of Tom40 and porin. We show that Tom7 promotes segregation of Mdm10 from the SAM holo complex into a low molecular mass form. Upon deletion of Tom7, the fraction of Mdm10 in the SAM holo complex is significantly increased, explaining the opposing functions of Tom7 and Mdm10 in -barrel sorting. Thus the role of Tom7 is not limited to the TOM complex. Tom7 functions in mitochondrial protein biogenesis by a new mechanism, segregation of a sorting component, leading to a differentiation of -barrel assembly.Mitochondria import the vast majority of their ϳ1,000 different proteins from the cytosol (1-3). Upon initial recognition and translocation by the general translocase of the outer mitochondrial membrane (TOM 5 complex), different classes of precursor proteins are distributed to the four mitochondrial subcompartments, outer membrane, intermembrane space, inner membrane, and matrix (4 -11). Preproteins carrying cleavable amino-terminal targeting signals (presequences) are transferred from the TOM complex to the presequence translocase of the inner membrane (TIM23 complex) and then sorted to matrix and inner membrane. Many mitochondrial proteins, however, are synthesized without cleavable presequences, including all outer membrane proteins and the majority of intermembrane space and inner membrane proteins. These proteins use distinct import and sorting machineries. Thus, in addition to the presequence pathway, three sorting pathways for non-cleavable mitochondrial precursor proteins have been identified, each of them starting at the TOM complex. Many hydrophobic inner membrane proteins, including the abundant metabolite carriers, are imported via small Tim proteins of the intermembrane space and the twin pore translocase of the inner membrane (TIM22 complex) (8, 12). Small proteins of the intermembrane space use a special import and assembly machinery that includes Mia40 and the sulfhydryl oxidase Erv1 (13-17). Outer membrane proteins are also initially transported via the TOM complex; however, the TOM complex is not able to integrate -barrel proteins into the membrane. Therefore, the outer membrane contains a separate sorting and assembly machinery (SAM complex) that directs membrane integration and assembly of -barrel...