SUMMARY Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal new functions for these proteins (termed MXPs) we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend new mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function.

Coenzyme Q (CoQ) is an isoprenylated quinone that is essential for cellular respiration and is synthesized in mitochondria by the combined action of at least nine proteins (COQ1-9). Although most COQ proteins are known to catalyze modifications to CoQ precursors, the biochemical role of COQ9 remains unclear. Here, we report that a disease-related COQ9 mutation leads to extensive disruption of the CoQ protein biosynthetic complex in a mouse model, and that COQ9 specifically interacts with COQ7 through a series of conserved residues. Toward understanding how COQ9 can perform these functions, we solved the crystal structure of Homo sapiens COQ9 at 2.4 Å. Unexpectedly, our structure reveals that COQ9 has structural homology to the TFR family of bacterial transcriptional regulators, but that it adopts an atypical TFR dimer orientation and is not predicted to bind DNA. Our structure also reveals a lipid-binding site, and mass spectrometry-based analyses of purified COQ9 demonstrate that it associates with multiple lipid species, including CoQ itself. The conserved COQ9 residues necessary for its interaction with COQ7 comprise a surface patch around the lipid-binding site, suggesting that COQ9 might serve to present its bound lipid to COQ7. Collectively, our data define COQ9 as the first, to our knowledge, mammalian TFR structural homolog and suggest that its lipid-binding capacity and association with COQ7 are key features for enabling CoQ biosynthesis.biquinone, also known as coenzyme Q (CoQ), is a lipophilic, redox-active small molecule that is present in nearly every cellular membrane. CoQ is a critical component of the mitochondrial electron transport chain where it shuttles electrons from complexes I and II to complex III. In addition to its vital role in cellular respiration, CoQ is instrumental in cellular antioxidation, extracellular electron transport, and membrane rigidity (1).The de novo biosynthesis of CoQ in eukaryotes takes place in the mitochondrial matrix via the collective action of at least 10 proteins (COQ1-10; Fig. S1) (2). Mutations in these proteins can cause primary CoQ deficiency-a condition associated with cerebellar ataxia, kidney disease, isolated myopathy, and severe childhood-onset multisystemic disorders (3, 4). Alteration in CoQ levels has also been associated with significant life span extensions in organisms ranging from Saccharomyces cerevisiae to mice (5-7). In S. cerevisiae (2, 8, 9), and potentially in higher eukaryotes (10, 11), most of the COQ proteins form a biosynthetic complex on the matrix face of the inner mitochondrial membrane. Although the majority of these proteins catalyze chemical modifications to CoQ precursors, the biochemical functions for COQ4, 8, and 9 have yet to be elucidated (8, 12, 13). Recently, García-Corzo et al. developed a mouse harboring a truncated version of Coq9 (Coq9 R239X)-modeled after a similar mutation observed in a human patient-that causes an encephalomyopathy associated with CoQ deficiency (11,14). A hallmark feature of these mice is a decreas...

Lignin is a heterogeneous polymer of aromatic subunits that is a major component of lignocellulosic plant biomass. Understanding how microorganisms deconstruct lignin is important for understanding the global carbon cycle and could aid in developing systems for processing plant biomass into valuable commodities. Sphingomonad bacteria use stereospecific glutathione S-transferases (GSTs) called β-etherases to cleave the β-aryl ether (β-O-4) bond, the most common bond between aromatic subunits in lignin. Previously characterized bacterial β-etherases are homodimers that fall into two distinct GST subclasses: LigE homologues, which cleave the β(R) stereoisomer of the bond, and LigF homologues, which cleave the β(S) stereoisomer. Here, we report on a heterodimeric β-etherase (BaeAB) from the sphingomonad Novosphingobium aromaticivorans that stereospecifically cleaves the β(R)-aryl ether bond of the di-aromatic compound β-(2-methoxyphenoxy)-γ-hydroxypropiovanillone (MPHPV). BaeAB's subunits are phylogenetically distinct from each other and from other β-etherases, although they are evolutionarily related to LigF, despite the fact that BaeAB and LigF cleave different β-aryl ether bond stereoisomers. We identify amino acid residues in BaeAB's BaeA subunit important for substrate binding and catalysis, including an asparagine that is proposed to activate the GSH cofactor. We also show that BaeAB homologues from other sphingomonads can cleave β(R)-MPHPV and that they may be as common in bacteria as LigE homologues. Our results suggest that the ability to cleave the β-aryl ether bond arose independently at least twice in GSTs and that BaeAB homologues may be important for cleaving the β(R)-aryl ether bonds of lignin-derived oligomers in nature.

Highlights d COQ9 specifically accesses and binds membraneembedded aromatic isoprenes d An exposed tryptophan and an amphipathic helix control lipid and membrane binding d Interactions with the peripheral membrane enzyme COQ7 suggest lipid presentation d In vivo CoQ production relies on COQ9's membrane, lipid, and protein interactions