FMC1 (formerly C7orf55) is a small (113 aa) nuclear-encoded mitochondrial protein with a single LYR_2 (Complex1_LYR_2) motif domain and a disordered C-terminal tail. It localizes to mitochondria and is required for normal levels of the mitochondrial F1Fo ATP synthase (complex V). In human cells lacking FMC1 the F1 subunits ATP5F1A and ATP5F1B are reduced, less fully assembled complex V is present, and complex V ATPase activity falls, while the other respiratory complexes are unaffected; all of these defects are rescued by re-expressing FMC1. FMC1 binds ATPAF2, the chaperone for the F1 alpha subunit, which places it in the F1 assembly pathway as an assembly factor or cofactor for ATPAF2. It has no known enzymatic activity. Its exact molecular role is not known, and it is not known whether it acts during assembly or stabilizes the assembled F1 sector. FMC1 belongs to an animal-specific PANTHER family (PTHR31716). The yeast protein Fmc1p, which supports F1 assembly through Atp12p at high temperature, has the same LYR_2 domain but falls in a separate PANTHER family.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:28719601 CLIC, a tool for expanding biological pathways based on co-e... | REMOVE | Summary: IPI for the FMC1 (C7orf55) interaction with ATPAF2 (Q8N5M1), identified by FLAG-IP/mass spectrometry from a mitochondria-rich fraction and confirmed by reciprocal co-immunoprecipitation with ATPAF2-V5. Reason: The interaction is well supported and biologically meaningful (ATPAF2 is the F1 alpha-subunit assembly chaperone, so the interaction places FMC1 in the F1 assembly pathway). However, bare GO:0005515 protein binding carries no functional information, and per project policy it is removed; removal does not mean the interaction is false. No more informative MF term is justified, because the paper does not establish what FMC1 does to ATPAF2 (e.g. chaperone-binding, adaptor or stabilizing activity). The interaction is captured in the description and core function narrative. This matches the treatment of the reciprocal row in the ATPAF2 review. Supporting Evidence: PMID:28719601 To confirm this binding association, we also tagged ATPAF2 with a V5 tag and showed that immunoprecipitation of ATPAF2-V5 binds C7orf55-FLAG (Fig 6E). |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: High-throughput assignment from the MitoCoP high-confidence human mitochondrial proteome (subtractive/spatial proteomics plus importomics). Reason: Consistent with direct immunofluorescence of endogenous FMC1 co-localizing with a mitochondrial marker (PMID:28719601) and with the protein's established role in complex V biogenesis. FMC1 is not named in the cached text of the proteome paper (the assignment is in supplementary tables), so the IDA row is the primary support; the HTP row reinforces it. Supporting Evidence: PMID:34800366 We defined a human mitochondrial high-confidence proteome (MitoCoP) of 1,134 protein-coding genes, including 91 proteins previously not localized to mitochondria experimentally. PMID:28719601 First, we confirmed mitochondrial localization (Fig 6A) by immunostaining with antibodies to endogenous C7orf55 |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference from node PTN001271866 (PTHR31716:SF1); human FMC1 is itself the experimental donor. Reason: Human FMC1 is the donor for this node, and its own IDA (PMID:28719601) grounds the IBA. It is expected and correct that the target appears in its own WITH/FROM. Here the IBA adds the claim that mitochondrial localization is inherited across the animal FMC1 clade. Supporting Evidence: PMID:28719601 First, we confirmed mitochondrial localization (Fig 6A) by immunostaining with antibodies to endogenous C7orf55 |
| GO:0005739 mitochondrion | IDA PMID:28719601 CLIC, a tool for expanding biological pathways based on co-e... | ACCEPT | Summary: Confocal immunofluorescence of endogenous C7orf55/FMC1 in HeLa cells co-localizing with mito-dsRed. Reason: Direct experimental localization of the endogenous protein. No sub-mitochondrial compartment was determined. Matrix localization (as for yeast Fmc1p and for ATPAF2) is plausible but not shown for human FMC1, so the general term is as precise as the human evidence allows. Supporting Evidence: PMID:28719601 Confocal microscopy of HeLa cells expressing a mitochondria-targeted version of dsRed (mito-dsRed) immunolabeled with antibodies to endogenous C7orf55. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0173 Mitochondrion), itself based on PMID:28719601. Reason: Reflects the curated UniProt subcellular location, which rests on the experimental immunofluorescence. It is consistent with the IDA, HTP and IBA rows for the same term. Supporting Evidence: UniProtKB:Q96HJ9 SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:28719601} |
| GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at node PTN001271866 (PTHR31716:SF1). Human FMC1 is the sole experimental donor. Reason: The node is grounded in human FMC1's own IMP (knockout/rescue) and its physical association with ATPAF2 (PMID:28719601). FMC1 is in the clade (PTHR31716:SF1), and there is no evidence of loss or divergence in human. PAINT propagated only this BP and the mitochondrion CC from the donor, and no MF; this fits the absence of any measured molecular activity. The yeast Fmc1p data (PMID:11096112) are not part of this node's support, because yeast Fmc1 falls in a different PANTHER family (PTHR28015) and shows no BLASTP-detectable similarity to human FMC1. Supporting Evidence: PMID:28719601 All the defects in complex V were entirely rescued by the reintroduction of a CRISPR-resistant version of C7orf55 (Fig 6B and 6C, fourth column). |
| GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly | IMP PMID:28719601 CLIC, a tool for expanding biological pathways based on co-e... | ACCEPT | Summary: CRISPR knockout of C7orf55/FMC1 in K562 cells reduced the F1 subunits ATP5A/ATP5B and fully assembled complex V on BN-PAGE, and lowered in-gel ATPase activity. Re-expressing CRISPR-resistant FMC1 rescued all of these defects. Reason: This is the core process. Three independent sgRNAs were used, the defect was specific to complex V among the five OXPHOS complexes, and rescue was complete. Taken alone, knockout data show only necessity. Here they come with a physical interaction with ATPAF2, a dedicated F1 assembly chaperone, which supports FMC1 doing part of the assembly work as a cofactor of the assembly machinery rather than being needed indirectly. One caveat: steady-state BN-PAGE cannot fully separate a defect in assembly from instability of the assembled complex. The authors frame the result as "assembly or regulation", and UniProt describes the function as "assembly/stability". GO:0033615 remains the best-fitting term. Supporting Evidence: PMID:28719601 In agreement with our prediction, in the absence of C7orf55 we observed a specific destabilization of the mitochondrial complex V using three assays: (i) the steady-state levels of the F1 ATP synthase subunits ATP5A and ATP5B were reduced in a denaturing SDS-PAGE gel (Fig 6B); (ii) the abundance of the fully-assembled complex V was reduced in a blue-native PAGE (Fig 6C, top panel); and (iii) the activity of complex V was reduced in an in-gel ATPase activity assay (Fig 6C, bottom panel). PMID:28719601 These experiments confirm the validity of CLIC’s functional prediction that C7orf55 is required for mitochondrial ATP synthase function and specifically that C7orf55 binds a known assembly factor of this complex. |
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Download this section (compressed HTML)Q: Does human FMC1 act during F1 assembly (for example by modulating ATPAF2 binding to the F1 alpha subunit), or does it stabilize the assembled F1 sector? Is its requirement conditional on temperature, as for yeast Fmc1p?
Q: Is the functional parallel between yeast Fmc1p-Atp12p and human FMC1-ATPAF2 the result of true orthology that PANTHER does not resolve (PTHR28015 vs PTHR31716, linked only by the LYR_2 domain), or of convergent recruitment of an LYR-motif protein?
Q: Like other LYR-motif proteins, does FMC1 bind the acyl-carrier protein NDUFAB1 (ACPM), and is that binding needed for its role in complex V?
Experiment: Run pulse-chase or SILAC-based complex V assembly kinetics in FMC1-knockout versus rescued cells, with and without mild heat stress, to tell an assembly defect from instability of the assembled complex.
Type: complexome profiling / assembly kinetics
Experiment: Map the FMC1-ATPAF2 interface by mutating residues predicted by the coevolution/AlphaFold model, then test whether interface mutants still rescue complex V levels in knockout cells.
Type: structure-guided mutagenesis and rescue
Experiment: Determine the sub-mitochondrial localization of FMC1 (protease protection, carbonate extraction, APEX2 proximity labelling), and test whether its LYR motif binds NDUFAB1.
Type: sub-mitochondrial fractionation and interaction mapping
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