Molecular insights into the m-AAA protease–mediated dislocation of transmembrane helices in the mitochondrial inner membrane

Abstract

Protein complexes involved in respiration, ATP synthesis, and protein import reside in the mitochondrial inner membrane; thus, proper regulation of these proteins is essential for cell viability. The -AAA protease, a conserved hetero-hexameric AAA (ATPase associated with diverse cellular activities) protease, composed of the Yta10 and Yta12 proteins, regulates mitochondrial proteostasis by mediating protein maturation and degradation. It also recognizes and mediates the dislocation of membrane-embedded substrates, including foreign transmembrane (TM) segments, but the molecular mechanism involved in these processes remains elusive. This study investigated the role of the TM domains in the-AAA protease by systematic replacement of one TM domain at a time in yeast. Our data indicated that replacement of the Yta10 TM2 domain abolishes membrane dislocation for only a subset of substrates, whereas replacement of the Yta12 TM2 domain impairs membrane dislocation for all tested substrates, suggesting different roles of the TM domains in each -AAA protease subunit. Furthermore,-AAA protease-mediated membrane dislocation was impaired in the presence of a large downstream hydrophilic moiety in a membrane substrate. This finding suggested that the -AAA protease cannot dislocate large hydrophilic domains across the membrane, indicating that the membrane dislocation probably occurs in a lipid environment. In summary, this study highlights previously underappreciated biological roles of TM domains of the-AAA proteases in mediating the recognition and dislocation of membrane-embedded substrates.

Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift

“…4J) show the highest levels of these proteins during the diauxic shift, followed by constant or a slightly lower allocation in the subsequent respiratory phase. These proteins are required in the assembly of mitochondrial enzymes complexes (Yta12 and Afg3) and the insertion of mitochondrial and some nuclear-encoded proteins in the inner mitochondrial membrane (Oxa1) (32,33). This suggests changes in this part of the mitochondria that principally occur during the diauxic shift may perform a regulatory role in initiating structural changes necessary for respiratory metabolism.…”

Protein Complexes Form a Basis for Complex Hybrid Incompatibility

“…For example, the inner membrane of the mitochondria has one of the highest known protein:lipid ratios, which is proposed to make membrane integrity relatively fragile among biological membranes. It has been observed in yeast that almost all of the known cases of DM incompatibilities are mitochondrial-nuclear incompatibilities, and that there is a highly conserved AAA-ATPase homeostasis machinery essential for maintaining the integrity of the inner membrane ( Francis and Thorsness, 2011 ; Lee et al, 2017 ). This suggests that in yeast the complexes of the inner mitochondrial membrane, such as the F1-F0 ATPase, are a “molecular branch point” in the natural history of yeast.…”

A Lineage-Specific Paralog of Oma1 Evolved into a Gene Family from Which a Suppressor of Male Sterility-Inducing Mitochondria Emerged in Plants

“…Many of the positively selected codons in the RF-Oma1 alleles are confined to the transmembrane helices. Yeast YTA12 is an m -AAA protease that is also involved in the quality control of mitochondria, and one of its transmembrane helices plays an important role in substrate recognition for dislocating the substrate from the membrane ( Lee et al. 2017 ).…”