LYRM protein (Leucine-Tyrosine-Arginine motif) also known as LYRMs, are a superfamily of small (11–22 kDa), basic, predominantly mitochondrial proteins found exclusively in eukaryotes and named after their conserved LYR-like motif near the N-terminus. They function as accessory subunits or assembly factors of OXPHOS complexes I, II, III and V and play essential roles in iron–sulfur (Fe–S) cluster biogenesis, mitochondrial translation, electron transfer flavoprotein (ETF) function, and acetate metabolism. Most LYRM proteins depend on mitochondrial fatty acid synthesis (mtFAS) for their function, as they are allosterically activated by binding to acylated mitochondrial acyl carrier protein (acyl-mtACP). It has been proposed that this mechanism evolved to protect cells from the toxic interaction of iron and oxygen.
Species distribution LYRM proteins are found exclusively in eukaryotes, but they differ between species. While LYRM proteins have been lost in anaerobic eukaryotes or are retained only in the form of LYRM4, twelve LYRM proteins occur in humans.
Human paralogs At least 12 LYRM proteins have been identified in humans (2019):
+Human LYRM paralogsLYRM protein GeneLYR-like motifm (kDa)pITarget locationFunctionInteraction partnerLYRM1 LYRM1LYR1410Mitoribosome (predicted)Insulin signaling Acyl-mtACP, MTRF1L (predicted)LYRM2 LYRM2LYR1111 Complex IAssociates with Complex I activityAcyl-mtACPLYRM3 NDUFB9LYK229Complex IStructural subunit Acyl-mtACPLYRM4 LYRM4/ISD11LYR1111Cysteine desulfurase NFS1Iron-sulfur cluster biogenesisAcyl-mtACP, NFS1 LYRM5 ETFRF1LYK1110Electron transfer flavoprotein (ETF)Accessory factorAcyl-mtACPLYRM6 NDUFA6 LYR1810Complex IStructural subunit Acyl-mtACP, NDUFS3 LYRM7 LYRM7/MZM1LLFK1210Complex IIIAssembly factorAcyl-mtACP, UQCRFS1, HSC20LYRM8 SDHAF1LYR1311Complex IIAssembly factorAcyl-mtACP, SDHB, HSC20LYRM9LYRM9/C17orf108LYR109Mitoribosome (predicted)UnknownAcyl-mtACP, MRPL57 (predicted)LYRM10 LYRM10/ACN9/SDHAF3LYK159Complex IIAssembly factorAcyl-mtACP, SDHBFMC1 FMC1/C7orf55TFR1310Complex VAssembly factorUnacylated holo-mtACP, ATP12L0R8F8 MIEF1 / AltMiD51 / MIEF1-MPMitoribosomeAssembly factorUnacylated holo-mtACP
Subcellular distribution With the exception of LYRM3 and LYRM6, which are embedded within mitochondrial Complex I, LYRM proteins are soluble matrix-located proteins.
They are synthesized in the cytosol by ribosomes after being transcribed from nuclear DNA, and are then imported into the mitochondria. Some members have also been identified in the cytosol and nucleus.
Structure LYRM proteins constitute a conserved family of small mitochondrial proteins defined by sequence homology to the Complex1_LYR-like superfamily (Pfam clan CL0491, which was identified by bioinformatic analysis and curated by P. Coggill (EMBL-EBI). The family was originally defined based on LYRM4, which stabilizes the cysteine desulfurase NFS1 within the mitochondrial iron–sulfur cluster (ISC) assembly machinery. The presence of an LYR tripeptide alone is not sufficient to classify a protein as an LYRM, as additional conserved amino acid residues must also be present. Members of this family share the following characteristic features:
Sequence features: a conserved LYR-like motif near the N-terminus (e.g. LYR, LYK, LFK, TFR), additional conserved amino acid residues downstream of the motif: basic residues, particularly arginine (R) and lysine (K), a highly conserved phenylalanine (F) residue, in some subfamilies, additional residues including tyrosine (Y) and glycine (G) at the C-terminus, Structural features: structural homology characterized by a conserved three-α-helix bundle, a hydrophobic channel formed by the three-α-helix bundle, accommodating the fatty acyl chain of acylated mtACP (except FMC1), General properties: a small protein size (11–22 kDa), a basic isoelectric point (pI ≈ 9–11),
Function The family was originally defined based on LYRM4, which stabilizes the cysteine desulfurase NFS1 within the mitochondrial iron–sulfur cluster (ISC) assembly machinery. All LYRM proteins have in common that they are found in mitochondrial target complexes that contain iron–sulfur clusters, synthesize them, or are functionally linked to them, such as the electron transfer protein and the mitochondrial ribosome. The only exception is FMC1, which acts at a target complex lacking iron–sulfur clusters, complex V, although this complex has been linked to mitochondrial iron uptake.
These features distinguish LYRM proteins from the broader term "LYR proteins", which has been used by some authors in the past for proteins that contain an LYR tripeptide—a motif frequently found in mitochondrial proteins such as SDHB, NDUFAF3, or mitochondrial ribosomal proteins—but that lack the additional defining characteristics of the LYRM family.
Iron–sulfur cluster biogensis In eukaryotes, iron–sulfur (Fe–S) clusters serve as versatile cofactors in redox reactions, electron transport, enzyme catalysis, regulation of gene expression, and DNA repair. They are assembled on the ISCU scaffold protein, with iron donated by frataxin and sulfur provided by the NFS1–LYRM4 complex. This complex binds acyl-mtACP via LYRM4, and this interaction stabilizes the otherwise degradation-prone complex. Once formed, Fe–S clusters are transferred to target proteins by a Fe–S transfer complex composed of ISCU, the co-chaperone HSC20, and the chaperone HSPA9.
The incorporation of iron–sulfur clusters into OXPHOS complexes II and III with the help of other LYRM proteins is covered below under "OXPHOS complex assembly".
OXPHOS complex assembly The assembly of these complexes depends on a tightly regulated and coordinated process involving transcription and translation of both nuclear- and mitochondrial-encoded subunits, import and assembly of individual subunits, and maturation through the insertion of essential cofactors such as iron–sulfur clusters. OXPHOS complexes can further assemble into higher-order structures known as supercomplexes, whose formation and stability are influenced by interactions between acylated mtACP and LYRM proteins.
Complex I (NADH:ubiquinone oxidoreductase) Three LYRM proteins—LYRM3, LYRM6, and LYRM2—are known to be associated with Complex I. The first complex of the respiratory chain couples NADH oxidation and ubiquinone reduction to proton pumping across the inner mitochondrial membrane and constitutes the largest single contributor to the proton motive force driving ATP synthesis. Under certain conditions, the reaction can reverse, resulting in the reduction of NAD+.
LYRM3 is an integral accessory subunit of Complex I, positioned in the distal proton-translocating module PD of the membrane arm. It forms a stable heterodimer with the neighboring mtACP, contributing to the stability and assembly of Complex I.
LYRM6 is also an integral accessory subunit of Complex I. It binds near the critical interface between the matrix arm (Q module) and the membrane arm (P module) of Complex I, forming a heterodimer with mtACP. Two adjacent loops of LYRM6 interact directly with central subunits of Complex I, helping stabilize this interface. In particular, LYRM6 plays a key role in stabilizing the TMH1-2 loop of subunit ND3, a structural element essential for the proton pumping mechanism.
LYRM2 is located in mitochondria, directly interacts with Complex I and increases its activity.
Complex II (Succinate dehydrogenase) LYRM8 and ACN9 are required for the assembly of the Fe–S cluster–containing subunit SDHB in Complex II. As part of the citric acid cycle, Complex II couples the oxidation of succinate to fumarate to the reduction of ubiquinone. The functions of LYRM8 and ACN9 involve interactions with acyl-mtACP.
LYRM8 functions as an assembly factor for Complex II, acting as a bridge between HSC20, as part of the Fe–S cluster transfer complex, and the SDHB subunit. As one of four subunits of Complex II, SDHB plays a central role in transferring electrons from subunit SDHA to ubiquinone via its three iron–sulfur clusters. HSC20 recognizes and binds with high affinity to LYR motifs; however, SDHB itself contains only two L(I)YR motifs, an IYR motif near the N-terminus and a LYR motif closer to the C-terminus. However, SDHB is not one of the LYRM proteins. Additionally, several aromatic amino acid regions within SDHB enable the transient binding of a LYRM8 protein through its arginine-rich C-terminal domain, thereby providing a LYRM site for HSC20 and thus contributing to Fe–S cluster incorporation into SDHB. Notably, LYRM8 itself also contains two LYR motifs, located at the N-terminus and in the central region, but HSC20 binds exclusively to the N-terminal motif.
ACN9 functions as an assembly factor involved in the maturation of Complex II. Specifically, it contributes to the incorporation of iron–sulfur (Fe–S) clusters into the SDHB subunit, which is essential for Complex II activity. However, its exact molecular role remains to be fully defined. Yeast data indicate that ACN9 plays a role in gluconeogenesis and in converting ethanol or acetate into carbohydrates.
Complex III (Coenzyme Q : cytochrome c – oxidoreductase) LYRM7 functions as an assembly factor for Complex III, acting as a chaperone for the Rieske iron-sulfur protein. Complex III's task is to transfer electrons from the two-electron carrier ubiquinone to the one-electron carrier cytochrome c via the Q cycle, while pumping protons to build a gradient. It functions as a dimer (CIII2), with each monomer composed of 11 subunits. Among these, three are catalytic: cytochrome b, cytochrome c1, and the Rieske iron-sulfur protein, which contains a [2Fe–2S] cluster (Rieske center). During the assembly process, a stable but non-functional "late core" pre-Complex III forms, containing all subunits except the Rieske iron-sulfur protein and subunit Qcr10. To complete the assembly, LYRM7 binds to and stabilizes the Rieske iron-sulfur protein in the mitochondrial matrix before its translocation to the inner membrane and subsequent integration into the pre-complex. This prevents the Rieske iron-sulfur protein from proteolytic degradation or temperature‑induced aggregation. Final incorporation of both the Rieske iron-sulfur protein and Qcr10 into pre-Complex III is then driven by the AAA-ATPase BCS1L, completing the assembly of complex III.
Complex V (ATP synthase) FMC1 acts as an assembly factor for Complex V by stabilizing ATP12, a chaperone required for proper F1 assembly, particularly under elevated temperatures. Complex V synthesizes ATP from ADP and inorganic phosphate by harnessing the proton motive force generated by the electron transport chain through a rotary catalytic mechanism. It consists of an Fo domain embedded in the inner mitochondrial membrane that translocates protons, and a matrix-exposed F₁ domain where ATP synthesis occurs. Within the F₁ domain, the catalytic hexameric ring of alternating α- and β-subunits requires ATP12 for assembly, with FMC1 supporting ATP12 at elevated temperatures; without this, subunits are not incorporated properly and aggregate in the mitochondrial matrix. Although FMC1 belongs to the LYRM protein family, its function is independent of acylated mtACP, consistent with the absence of key residues of the LYR motif and a channel formed by its three α-helices that is not sufficiently hydrophobic. Nevertheless, FMC1interacts with unacylated mtACP, enabling F1 domain assembly even when acetyl-CoA is limited. This ensures that Complex V remains functional during metabolic stress, allowing it to operate in reverse and hydrolyze ATP to maintain the proton gradient required for protein import and other transport processes.
Electron transfer flavoprotein function