The vital interplay of acyl-carrier proteins and LYR proteins (ACPM-LYRM) in mitochondria

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Mitochondria host essential biochemical pathways such as the oxidative phosphorylation (OXPHOS) system, Fe-S cluster biogenesis and -oxidation. Furthermore, mitochondria contain all enzymes to synthesize fatty acids in the bacterial type II mode (FAS II). A central element of the highly conserved mitochondrial FAS II machinery is the mitochondrial acyl-carrier protein (ACPM). Eukaryotic LYR (leucine/tyrosine/arginine) motif proteins (LYRMs) of the Complex1-LYR-like superfamily, that are mostly novel subunits or assembly factors of mitochondrial OXPHOS complexes I, II, III and V, were suggested as interaction partners for ACPM. In complex I from the aerobic yeast Yarrowia lipolytica ACPM1 and LYRM6, and ACPM2 and LYRM3, form two well defined accessory domains that are essential for enzymatic activity or assembly, respectively. However, in the 3.6-3.9 A resolution X-ray structure of Y. lipolytica complex I and in a recent intermediate resolution X-ray structural analysis of the distal membrane arm module of Bos taurus complex I all four proteins were only modeled as poly-alanine. My preliminary work strongly suggests that a fraction of ACPM1 coexists associated with the LYRM4(ISD11)-NFS1 complex involved in Fe-S cluster biogenesis and as a free matrix protein (matrix-ACPM1), respectively. The isolation of the ACPM1-LYRM4/NFS1 complex is consistent with a here proposed novel multi-component lipoic acid synthesis complex. In contrast to complex I subunit ACPMs (CI-ACPM), matrix-ACPM1 is N-terminally acetylated suggesting an sub-mitochondrial sorting mechanism that distributes ACPM1 to the matrix or to complex I. Initial mass spectrometry data indicated that a fraction of matrix-ACPM1 carries a nascent fatty acid chain (C9-C16-acyl-ACPM1 intermediates). We detected higher mass acyl groups attached to CI-ACPM1 and CI-ACPM2 but their identities are still unclear. A major focus of this project will be to unravel the function of matrix-ACPM1 and to resolve the role of the ACPM1-LYRM4/NFS1 complex in lipoic acid synthesis. An important step towards my goal to understand the association of ACPM1 with mitochondrial complex I on one hand and with the NFS1 complex on the other hand will be to identify the bound acyl groups. Structure determination of ACPM1, LYRM6 and of the ACPM1-LYRM4/NFS1 complex will reveal the molecular basis for anchoring of ACPM1 to LYRMs and is expected to provide important clues why the presence of an ACPM-LYRM domain is critical for the function of complex I and the NFS1 protein.