LYRM7 (LYR motif-containing protein 7; also MZM1L/C5orf31) is a small mitochondrial-matrix LYR-family assembly chaperone for respiratory Complex III (cytochrome bc1 / ubiquinol-cytochrome c reductase). It acts as a dedicated chaperone for the Rieske iron-sulfur protein UQCRFS1, binding and stabilising UQCRFS1 in the mitochondrial matrix prior to insertion of its [2Fe-2S] cluster and the subunit's translocation and incorporation into the late Complex III dimeric intermediate in the inner membrane. Its LYR motif recruits the Fe-S transfer cochaperone HSC20 (HSCB), coupling the UQCRFS1-LYRM7 intermediate to the ISCU-HSPA9-HSC20 cluster-delivery machinery. LYRM7 is non-catalytic and is the human ortholog of yeast Mzm1. Loss-of-function variants cause mitochondrial complex III deficiency, nuclear type 8 (a leukoencephalopathy).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005759
mitochondrial matrix
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) propagation placing LYRM7 in the mitochondrial matrix, where it acts as a chaperone. This is directly confirmed experimentally: LYRM7 binds and stabilises UQCRFS1 within the mitochondrial matrix.
Reason: The matrix location is the site of LYRM7's chaperone activity and is supported by direct experimental evidence (IDA, PMID:23168492) and the UniProt subcellular location, in addition to this phylogenetic inference. is_active_in is appropriate for the compartment where it chaperones UQCRFS1.
Supporting Evidence:
PMID:23168492
binding to this subunit within the
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
|
|
GO:0034551
mitochondrial respiratory chain complex III assembly
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) inference that LYRM7 is involved in Complex III assembly. This is the core biological process of the gene and is strongly supported experimentally.
Reason: LYRM7 is a bona fide Complex III assembly factor mediating the UQCRFS1/Rieske Fe-S protein incorporation step. This is the precise, well-evidenced core BP and is consistent across IBA, IDA (PMID:23168492), IEA and Reactome TAS annotations.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
|
|
GO:0044183
protein folding chaperone
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) assignment of a protein folding chaperone molecular function. LYRM7 is a non-catalytic chaperone that binds and stabilises (holds) its client UQCRFS1, so a chaperone MF is the correct, most informative non-catalytic molecular function.
Reason: The chaperone MF is directly supported: LYRM7 works as a UQCRFS1 chaperone, binding and stabilising the Rieske Fe-S protein prior to its incorporation into Complex III (PMID:23168492). This is the appropriate MF for this non-enzymatic assembly factor and is retained as the core molecular function; no catalytic activity should be assigned.
Supporting Evidence:
PMID:23168492
works as a human Rieske
file:human/LYRM7/LYRM7-uniprot.txt
Assembly factor required for Rieske Fe-S protein UQCRFS1
|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro2GO electronic annotation to the mitochondrion, based on the Complex1_LYR domain family. Correct but less specific than the matrix localisation.
Reason: Mitochondrial localisation is correct and well supported; this is simply a broader (parent) location than the experimentally established mitochondrial matrix. Retained as a valid, if general, CC annotation.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
|
|
GO:0005759
mitochondrial matrix
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: Electronic annotation to the mitochondrial matrix from the UniProt Swiss-Prot subcellular location vocabulary mapping. Matches the curated UniProt location and experimental evidence.
Reason: Consistent with the experimentally determined (IDA, PMID:23168492) and curated UniProt matrix location where LYRM7 chaperones UQCRFS1.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
|
|
GO:0006457
protein folding
|
IEA
GO_REF:0000108 |
ACCEPT |
Summary: Inter-ontology (logical) inference of a protein folding BP from the protein folding chaperone MF (GO:0044183). Consistent with LYRM7's role in stabilising/holding UQCRFS1.
Reason: This is a sound, if general, logical consequence of the chaperone MF. LYRM7 stabilises its unfolded/apo client UQCRFS1, which falls under protein folding. It is broader than the specific Complex III assembly BP but not incorrect. Kept as non-core context; the precise core BP is mitochondrial respiratory chain complex III assembly.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
stabilizing it prior to its translocation and insertion into the late
|
|
GO:0034551
mitochondrial respiratory chain complex III assembly
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro2GO electronic annotation to Complex III assembly, based on the LYRM7-specific InterPro family (IPR045298). Correct and matches experimental evidence.
Reason: The LYRM7/MZM1-LYRM7 family signature reliably predicts a Complex III assembly-factor role, which is experimentally confirmed. This is the core BP.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
|
|
GO:0005515
protein binding
|
IPI
PMID:24606901 Cochaperone binding to LYR motifs confers specificity of iro... |
MARK AS OVER ANNOTATED |
Summary: IPI (IntAct) capturing a physical interaction between LYRM7 and HSC20/HSCB (UniProt Q8IWL3), the Fe-S cluster transfer cochaperone. This is a real and functionally meaningful interaction (LYRM7's LYR motif is an HSC20 binding site), but the GO term "protein binding" is uninformative.
Reason: Bare protein binding (GO:0005515) conveys no specific molecular function. The underlying LYRM7-HSC20 interaction is genuine and biologically important (it couples the UQCRFS1-LYRM7 intermediate to the Fe-S transfer machinery), so this is not removed; but the term is retained only as an uninformative over-annotation. The informative MF is the chaperone activity (GO:0044183).
Supporting Evidence:
PMID:24606901
SDHAF1 and LYRM7, respectively, are HSC20 binding partners
|
|
GO:0005515
protein binding
|
IPI
PMID:27499296 Mitochondrial Protein Interaction Mapping Identifies Regulat... |
MARK AS OVER ANNOTATED |
Summary: IPI (IntAct) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) reported in a large-scale mitochondrial protein interaction map. UQCRFS1 is the physiological client of LYRM7, so the interaction is correct, but "protein binding" is uninformative.
Reason: The LYRM7-UQCRFS1 interaction is the core, well-established relationship of this gene, but bare GO:0005515 does not capture the chaperone function. Retained as an uninformative over-annotation rather than removed.
Supporting Evidence:
PMID:27499296
Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory
|
|
GO:0005515
protein binding
|
IPI
PMID:28380382 A Single Adaptable Cochaperone-Scaffold Complex Delivers Nas... |
MARK AS OVER ANNOTATED |
Summary: IPI (IntAct) capturing physical interactions of LYRM7 with UQCRFS1 (P47985) and with HSC20/HSCB (Q8IWL3). Both are physiologically central: the UQCRFS1-LYRM7 intermediate recruits HSC20 via LYRM7's LYR motif to deliver the [2Fe-2S] cluster to UQCRFS1.
Reason: The interactions are real and mechanistically important, but bare protein binding is uninformative and does not capture the chaperone/assembly-factor MF. Retained as an over-annotation rather than removed.
Supporting Evidence:
PMID:28380382
direct binding of the co-chaperone HSC20 to the LYR (Leucine, Tyrosine, Arginine) consensus sequence of LYRM7 was required for recruitment of the Fe-S transfer complex to the LYRM7-UQCRFS1 assembly intermediate
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: IPI from the HuRI binary (yeast two-hybrid) reference interactome mapping LYRM7 to SAT1 (P21673, spermidine/spermine N1-acetyltransferase). SAT1 has no known mitochondrial or Complex III role; this is most likely a non-physiological binary-screen hit.
Reason: Bare protein binding is uninformative, and this particular partner (SAT1) is not a plausible physiological interactor of a mitochondrial-matrix CIII assembly chaperone. Per curation policy, an experimental IPI is not removed on the basis of an incomplete assessment; it is marked as an uninformative (and here likely non-physiological) over-annotation.
Supporting Evidence:
PMID:32296183
A reference map of the human binary protein interactome
|
|
GO:0005515
protein binding
|
IPI
PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... |
MARK AS OVER ANNOTATED |
Summary: IPI (BioPlex) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a proteome-scale affinity-purification interactome. Consistent with the core LYRM7-UQCRFS1 client relationship.
Reason: Correct interaction with the physiological client UQCRFS1, but bare GO:0005515 is uninformative. Retained as an over-annotation rather than removed; the chaperone MF (GO:0044183) captures the function.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human
|
|
GO:0005515
protein binding
|
IPI
PMID:40205054 Multimodal cell maps as a foundation for structural and func... |
MARK AS OVER ANNOTATED |
Summary: IPI capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a large-scale cell-map / structural-functional genomics interactome. Consistent with the core client relationship.
Reason: Correct interaction with UQCRFS1 but bare protein binding is uninformative. Retained as an over-annotation; the informative MF is the chaperone activity.
Supporting Evidence:
PMID:40205054
Multimodal cell maps as a foundation for structural and functional genomics
|
|
GO:0034551
mitochondrial respiratory chain complex III assembly
|
TAS
Reactome:R-HSA-9865881 |
ACCEPT |
Summary: Reactome (TAS) annotation placing LYRM7 in the Complex III assembly pathway. Matches the core, experimentally supported BP.
Reason: Reactome curates LYRM7 as a Complex III assembly factor (the UQCRFS1/Rieske protein binds and is stabilised by LYRM7). This is the correct core BP.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
ACCEPT |
Summary: High-throughput annotation of LYRM7 to the mitochondrion from a quantitative high-confidence human mitochondrial proteome. Consistent with the curated matrix localisation.
Reason: Independent proteomic support for mitochondrial localisation; broader than the specific matrix location but correct.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
|
|
GO:0044183
protein folding chaperone
|
TAS
Reactome:R-HSA-9866253 |
ACCEPT |
Summary: Reactome (TAS) assignment of the protein folding chaperone MF, corresponding to the reaction in which apo-UQCRFS1 binds and is stabilised by LYRM7. Matches the core chaperone function.
Reason: Reactome curates LYRM7 as the chaperone that binds and stabilises apo-UQCRFS1 in the matrix, the correct non-catalytic MF for this assembly factor. Core molecular function.
Supporting Evidence:
PMID:23168492
works as a human Rieske
|
|
GO:0005759
mitochondrial matrix
|
TAS
Reactome:R-HSA-9866253 |
ACCEPT |
Summary: Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, the compartment where apo-UQCRFS1 binds LYRM7. Matches experimental and curated localisation.
Reason: Consistent with the experimentally established matrix location where LYRM7 chaperones UQCRFS1.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
|
|
GO:0005759
mitochondrial matrix
|
TAS
Reactome:R-HSA-9866272 |
ACCEPT |
Summary: Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, associated with the reaction inserting the [2Fe-2S] cluster into UQCRFS1 as part of the UQCRFS1:LYRM7 complex.
Reason: Consistent with the matrix location where the LYRM7-UQCRFS1 intermediate recruits the Fe-S transfer machinery for cluster insertion.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
|
|
GO:0005515
protein binding
|
IPI
PMID:23168492 LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step... |
MARK AS OVER ANNOTATED |
Summary: IPI (UniProt) capturing the physical interaction between LYRM7 and UQCRFS1 (P47985) from the primary characterisation paper, in which LYRM7 was shown to bind and stabilise the Rieske Fe-S protein. This is the defining, physiological interaction of LYRM7.
Reason: The LYRM7-UQCRFS1 interaction is the core relationship establishing LYRM7 as the UQCRFS1 chaperone, so it is not removed; however, bare protein binding (GO:0005515) is uninformative and does not capture the chaperone MF. The chaperone activity (GO:0044183) is the informative MF that should represent this function.
Supporting Evidence:
PMID:23168492
works as a human Rieske
|
|
GO:0005759
mitochondrial matrix
|
IDA
PMID:23168492 LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step... |
ACCEPT |
Summary: Direct experimental (IDA) localisation of LYRM7 to the mitochondrial matrix from the primary characterisation study. This is the strongest evidence for the core localisation.
Reason: LYRM7 was experimentally shown to reside in and act within the mitochondrial matrix, where it binds and stabilises UQCRFS1. Core CC annotation.
Supporting Evidence:
PMID:23168492
binding to this subunit within the
file:human/LYRM7/LYRM7-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix
|
|
GO:0031966
mitochondrial membrane
|
IDA
PMID:23168492 LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step... |
KEEP AS NON CORE |
Summary: Direct experimental (IDA) detection of a pool of LYRM7 associated with the mitochondrial membrane, consistent with its transient association with the membrane-embedded late Complex III dimeric intermediate during UQCRFS1 insertion.
Reason: Membrane association is a real but secondary/transient aspect of LYRM7 function: its primary site of action is the matrix, where it chaperones UQCRFS1; the membrane pool reflects delivery of UQCRFS1 to the inner-membrane CIII intermediate. Kept but marked non-core relative to the matrix localisation.
Supporting Evidence:
file:human/LYRM7/LYRM7-uniprot.txt
stabilizing it prior to its translocation and insertion into the late
|
|
GO:0034551
mitochondrial respiratory chain complex III assembly
|
IDA
PMID:23168492 LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step... |
ACCEPT |
Summary: Direct experimental (IDA) evidence that LYRM7 is required for the UQCRFS1 insertion step of Complex III assembly. This is the definitive experimental support for the core BP.
Reason: The primary study established LYRM7 as a Complex III assembly factor acting at the UQCRFS1 incorporation step; this is the core, best-supported biological process.
Supporting Evidence:
PMID:23168492
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
|
|
GO:0045333
cellular respiration
|
IDA
PMID:23168492 LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last step... |
MARK AS OVER ANNOTATED |
Summary: IDA annotation to cellular respiration, based on the observation that loss of LYRM7 impairs Complex III activity and hence respiration. LYRM7 is an assembly factor, not itself a respiratory-chain component; its effect on respiration is indirect (via enabling functional Complex III).
Reason: LYRM7 does not itself carry out or directly participate in respiration; it enables assembly of Complex III, whose activity is required for respiration. The precise, mechanistically accurate BP is mitochondrial respiratory chain complex III assembly (GO:0034551). Cellular respiration is an over-annotation capturing a downstream consequence rather than LYRM7's direct role. Not removed (experimental annotation) but flagged as over-annotated.
Supporting Evidence:
PMID:23168492
which enables formation of the mature and functional CIII
|
Q: Does LYRM7 act purely as a holdase that stabilises apo-UQCRFS1, or does it also actively template/position UQCRFS1 for [2Fe-2S] cluster receipt and membrane insertion?
Experiment: Reconstitute the UQCRFS1-LYRM7 intermediate with the HSC20-HSPA9-ISCU Fe-S transfer complex in vitro to determine the minimal components and the order of cluster insertion versus membrane insertion of UQCRFS1.
id: Q5U5X0
gene_symbol: LYRM7
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
LYRM7 (LYR motif-containing protein 7; also MZM1L/C5orf31) is a small mitochondrial-matrix
LYR-family assembly chaperone for respiratory Complex III (cytochrome bc1 / ubiquinol-cytochrome
c reductase). It acts as a dedicated chaperone for the Rieske iron-sulfur protein UQCRFS1,
binding and stabilising UQCRFS1 in the mitochondrial matrix prior to insertion of its
[2Fe-2S] cluster and the subunit's translocation and incorporation into the late Complex III
dimeric intermediate in the inner membrane. Its LYR motif recruits the Fe-S transfer cochaperone
HSC20 (HSCB), coupling the UQCRFS1-LYRM7 intermediate to the ISCU-HSPA9-HSC20 cluster-delivery
machinery. LYRM7 is non-catalytic and is the human ortholog of yeast Mzm1. Loss-of-function
variants cause mitochondrial complex III deficiency, nuclear type 8 (a leukoencephalopathy).
existing_annotations:
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetic (IBA) propagation placing LYRM7 in the mitochondrial matrix, where it acts
as a chaperone. This is directly confirmed experimentally: LYRM7 binds and stabilises
UQCRFS1 within the mitochondrial matrix.
action: ACCEPT
reason: >-
The matrix location is the site of LYRM7's chaperone activity and is supported by direct
experimental evidence (IDA, PMID:23168492) and the UniProt subcellular location, in
addition to this phylogenetic inference. is_active_in is appropriate for the compartment
where it chaperones UQCRFS1.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
binding to this subunit within the
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
id: GO:0034551
label: mitochondrial respiratory chain complex III assembly
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: >-
Phylogenetic (IBA) inference that LYRM7 is involved in Complex III assembly. This is the
core biological process of the gene and is strongly supported experimentally.
action: ACCEPT
reason: >-
LYRM7 is a bona fide Complex III assembly factor mediating the UQCRFS1/Rieske Fe-S protein
incorporation step. This is the precise, well-evidenced core BP and is consistent across
IBA, IDA (PMID:23168492), IEA and Reactome TAS annotations.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
id: GO:0044183
label: protein folding chaperone
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetic (IBA) assignment of a protein folding chaperone molecular function. LYRM7
is a non-catalytic chaperone that binds and stabilises (holds) its client UQCRFS1, so a
chaperone MF is the correct, most informative non-catalytic molecular function.
action: ACCEPT
reason: >-
The chaperone MF is directly supported: LYRM7 works as a UQCRFS1 chaperone, binding and
stabilising the Rieske Fe-S protein prior to its incorporation into Complex III
(PMID:23168492). This is the appropriate MF for this non-enzymatic assembly factor and is
retained as the core molecular function; no catalytic activity should be assigned.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
works as a human Rieske
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: >-
Assembly factor required for Rieske Fe-S protein UQCRFS1
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: located_in
review:
summary: >-
InterPro2GO electronic annotation to the mitochondrion, based on the Complex1_LYR domain
family. Correct but less specific than the matrix localisation.
action: ACCEPT
reason: >-
Mitochondrial localisation is correct and well supported; this is simply a broader (parent)
location than the experimentally established mitochondrial matrix. Retained as a valid,
if general, CC annotation.
supported_by:
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
Electronic annotation to the mitochondrial matrix from the UniProt Swiss-Prot subcellular
location vocabulary mapping. Matches the curated UniProt location and experimental evidence.
action: ACCEPT
reason: >-
Consistent with the experimentally determined (IDA, PMID:23168492) and curated UniProt
matrix location where LYRM7 chaperones UQCRFS1.
supported_by:
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
id: GO:0006457
label: protein folding
evidence_type: IEA
original_reference_id: GO_REF:0000108
qualifier: involved_in
review:
summary: >-
Inter-ontology (logical) inference of a protein folding BP from the protein folding
chaperone MF (GO:0044183). Consistent with LYRM7's role in stabilising/holding UQCRFS1.
action: ACCEPT
reason: >-
This is a sound, if general, logical consequence of the chaperone MF. LYRM7 stabilises its
unfolded/apo client UQCRFS1, which falls under protein folding. It is broader than the
specific Complex III assembly BP but not incorrect. Kept as non-core context; the precise
core BP is mitochondrial respiratory chain complex III assembly.
supported_by:
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: >-
stabilizing it prior to its translocation and insertion into the late
- term:
id: GO:0034551
label: mitochondrial respiratory chain complex III assembly
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
InterPro2GO electronic annotation to Complex III assembly, based on the LYRM7-specific
InterPro family (IPR045298). Correct and matches experimental evidence.
action: ACCEPT
reason: >-
The LYRM7/MZM1-LYRM7 family signature reliably predicts a Complex III assembly-factor role,
which is experimentally confirmed. This is the core BP.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:24606901
qualifier: enables
review:
summary: >-
IPI (IntAct) capturing a physical interaction between LYRM7 and HSC20/HSCB (UniProt Q8IWL3),
the Fe-S cluster transfer cochaperone. This is a real and functionally meaningful interaction
(LYRM7's LYR motif is an HSC20 binding site), but the GO term "protein binding" is
uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Bare protein binding (GO:0005515) conveys no specific molecular function. The underlying
LYRM7-HSC20 interaction is genuine and biologically important (it couples the UQCRFS1-LYRM7
intermediate to the Fe-S transfer machinery), so this is not removed; but the term is
retained only as an uninformative over-annotation. The informative MF is the chaperone
activity (GO:0044183).
supported_by:
- reference_id: PMID:24606901
supporting_text: >-
SDHAF1 and LYRM7, respectively, are HSC20 binding partners
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:27499296
qualifier: enables
review:
summary: >-
IPI (IntAct) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) reported in
a large-scale mitochondrial protein interaction map. UQCRFS1 is the physiological client of
LYRM7, so the interaction is correct, but "protein binding" is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The LYRM7-UQCRFS1 interaction is the core, well-established relationship of this gene, but
bare GO:0005515 does not capture the chaperone function. Retained as an uninformative
over-annotation rather than removed.
supported_by:
- reference_id: PMID:27499296
supporting_text: Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:28380382
qualifier: enables
review:
summary: >-
IPI (IntAct) capturing physical interactions of LYRM7 with UQCRFS1 (P47985) and with
HSC20/HSCB (Q8IWL3). Both are physiologically central: the UQCRFS1-LYRM7 intermediate
recruits HSC20 via LYRM7's LYR motif to deliver the [2Fe-2S] cluster to UQCRFS1.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The interactions are real and mechanistically important, but bare protein binding is
uninformative and does not capture the chaperone/assembly-factor MF. Retained as an
over-annotation rather than removed.
supported_by:
- reference_id: PMID:28380382
supporting_text: >-
direct binding of the co-chaperone HSC20 to the LYR (Leucine, Tyrosine, Arginine)
consensus sequence of LYRM7 was required for recruitment of the Fe-S transfer complex to
the LYRM7-UQCRFS1 assembly intermediate
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
qualifier: enables
review:
summary: >-
IPI from the HuRI binary (yeast two-hybrid) reference interactome mapping LYRM7 to SAT1
(P21673, spermidine/spermine N1-acetyltransferase). SAT1 has no known mitochondrial or
Complex III role; this is most likely a non-physiological binary-screen hit.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Bare protein binding is uninformative, and this particular partner (SAT1) is not a plausible
physiological interactor of a mitochondrial-matrix CIII assembly chaperone. Per curation
policy, an experimental IPI is not removed on the basis of an incomplete assessment; it is
marked as an uninformative (and here likely non-physiological) over-annotation.
supported_by:
- reference_id: PMID:32296183
supporting_text: A reference map of the human binary protein interactome
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:33961781
qualifier: enables
review:
summary: >-
IPI (BioPlex) capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a
proteome-scale affinity-purification interactome. Consistent with the core LYRM7-UQCRFS1
client relationship.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Correct interaction with the physiological client UQCRFS1, but bare GO:0005515 is
uninformative. Retained as an over-annotation rather than removed; the chaperone MF
(GO:0044183) captures the function.
supported_by:
- reference_id: PMID:33961781
supporting_text: Dual proteome-scale networks reveal cell-specific remodeling of the human
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:40205054
qualifier: enables
review:
summary: >-
IPI capturing a physical interaction between LYRM7 and UQCRFS1 (P47985) in a large-scale
cell-map / structural-functional genomics interactome. Consistent with the core client
relationship.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Correct interaction with UQCRFS1 but bare protein binding is uninformative. Retained as an
over-annotation; the informative MF is the chaperone activity.
supported_by:
- reference_id: PMID:40205054
supporting_text: Multimodal cell maps as a foundation for structural and functional genomics
- term:
id: GO:0034551
label: mitochondrial respiratory chain complex III assembly
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9865881
qualifier: involved_in
review:
summary: >-
Reactome (TAS) annotation placing LYRM7 in the Complex III assembly pathway. Matches the
core, experimentally supported BP.
action: ACCEPT
reason: >-
Reactome curates LYRM7 as a Complex III assembly factor (the UQCRFS1/Rieske protein binds
and is stabilised by LYRM7). This is the correct core BP.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
qualifier: located_in
review:
summary: >-
High-throughput annotation of LYRM7 to the mitochondrion from a quantitative high-confidence
human mitochondrial proteome. Consistent with the curated matrix localisation.
action: ACCEPT
reason: >-
Independent proteomic support for mitochondrial localisation; broader than the specific
matrix location but correct.
supported_by:
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
id: GO:0044183
label: protein folding chaperone
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9866253
qualifier: enables
review:
summary: >-
Reactome (TAS) assignment of the protein folding chaperone MF, corresponding to the reaction
in which apo-UQCRFS1 binds and is stabilised by LYRM7. Matches the core chaperone function.
action: ACCEPT
reason: >-
Reactome curates LYRM7 as the chaperone that binds and stabilises apo-UQCRFS1 in the matrix,
the correct non-catalytic MF for this assembly factor. Core molecular function.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
works as a human Rieske
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9866253
qualifier: located_in
review:
summary: >-
Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, the compartment where
apo-UQCRFS1 binds LYRM7. Matches experimental and curated localisation.
action: ACCEPT
reason: >-
Consistent with the experimentally established matrix location where LYRM7 chaperones
UQCRFS1.
supported_by:
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9866272
qualifier: located_in
review:
summary: >-
Reactome (TAS) localisation of LYRM7 to the mitochondrial matrix, associated with the
reaction inserting the [2Fe-2S] cluster into UQCRFS1 as part of the UQCRFS1:LYRM7 complex.
action: ACCEPT
reason: >-
Consistent with the matrix location where the LYRM7-UQCRFS1 intermediate recruits the Fe-S
transfer machinery for cluster insertion.
supported_by:
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:23168492
qualifier: enables
review:
summary: >-
IPI (UniProt) capturing the physical interaction between LYRM7 and UQCRFS1 (P47985) from the
primary characterisation paper, in which LYRM7 was shown to bind and stabilise the Rieske
Fe-S protein. This is the defining, physiological interaction of LYRM7.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The LYRM7-UQCRFS1 interaction is the core relationship establishing LYRM7 as the UQCRFS1
chaperone, so it is not removed; however, bare protein binding (GO:0005515) is uninformative
and does not capture the chaperone MF. The chaperone activity (GO:0044183) is the informative
MF that should represent this function.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
works as a human Rieske
- term:
id: GO:0005759
label: mitochondrial matrix
evidence_type: IDA
original_reference_id: PMID:23168492
qualifier: located_in
review:
summary: >-
Direct experimental (IDA) localisation of LYRM7 to the mitochondrial matrix from the primary
characterisation study. This is the strongest evidence for the core localisation.
action: ACCEPT
reason: >-
LYRM7 was experimentally shown to reside in and act within the mitochondrial matrix, where it
binds and stabilises UQCRFS1. Core CC annotation.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
binding to this subunit within the
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: "SUBCELLULAR LOCATION: Mitochondrion matrix"
- term:
id: GO:0031966
label: mitochondrial membrane
evidence_type: IDA
original_reference_id: PMID:23168492
qualifier: located_in
review:
summary: >-
Direct experimental (IDA) detection of a pool of LYRM7 associated with the mitochondrial
membrane, consistent with its transient association with the membrane-embedded late Complex
III dimeric intermediate during UQCRFS1 insertion.
action: KEEP_AS_NON_CORE
reason: >-
Membrane association is a real but secondary/transient aspect of LYRM7 function: its primary
site of action is the matrix, where it chaperones UQCRFS1; the membrane pool reflects delivery
of UQCRFS1 to the inner-membrane CIII intermediate. Kept but marked non-core relative to the
matrix localisation.
supported_by:
- reference_id: file:human/LYRM7/LYRM7-uniprot.txt
supporting_text: >-
stabilizing it prior to its translocation and insertion into the late
- term:
id: GO:0034551
label: mitochondrial respiratory chain complex III assembly
evidence_type: IDA
original_reference_id: PMID:23168492
qualifier: involved_in
review:
summary: >-
Direct experimental (IDA) evidence that LYRM7 is required for the UQCRFS1 insertion step of
Complex III assembly. This is the definitive experimental support for the core BP.
action: ACCEPT
reason: >-
The primary study established LYRM7 as a Complex III assembly factor acting at the UQCRFS1
incorporation step; this is the core, best-supported biological process.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- term:
id: GO:0045333
label: cellular respiration
evidence_type: IDA
original_reference_id: PMID:23168492
qualifier: involved_in
review:
summary: >-
IDA annotation to cellular respiration, based on the observation that loss of LYRM7 impairs
Complex III activity and hence respiration. LYRM7 is an assembly factor, not itself a
respiratory-chain component; its effect on respiration is indirect (via enabling functional
Complex III).
action: MARK_AS_OVER_ANNOTATED
reason: >-
LYRM7 does not itself carry out or directly participate in respiration; it enables assembly
of Complex III, whose activity is required for respiration. The precise, mechanistically
accurate BP is mitochondrial respiratory chain complex III assembly (GO:0034551). Cellular
respiration is an over-annotation capturing a downstream consequence rather than LYRM7's
direct role. Not removed (experimental annotation) but flagged as over-annotated.
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
which enables formation of the mature and functional CIII
core_functions:
- description: >-
Non-catalytic protein-folding chaperone that binds and stabilises the Rieske iron-sulfur
protein UQCRFS1 in the mitochondrial matrix, holding it prior to [2Fe-2S] cluster insertion
and its incorporation into respiratory Complex III (cytochrome bc1). LYRM7's LYR motif also
recruits the Fe-S transfer cochaperone HSC20, coupling the UQCRFS1-LYRM7 intermediate to the
cluster-delivery machinery.
molecular_function:
id: GO:0044183
label: protein folding chaperone
directly_involved_in:
- id: GO:0034551
label: mitochondrial respiratory chain complex III assembly
locations:
- id: GO:0005759
label: mitochondrial matrix
supported_by:
- reference_id: PMID:23168492
supporting_text: >-
works as a human Rieske
- reference_id: PMID:23168492
supporting_text: >-
LYRM7/MZM1L is a novel human CIII assembly factor involved in the UQCRFS1
- reference_id: PMID:28380382
supporting_text: >-
direct binding of the co-chaperone HSC20 to the LYR (Leucine, Tyrosine, Arginine)
consensus sequence of LYRM7 was required for recruitment of the Fe-S transfer complex to
the LYRM7-UQCRFS1 assembly intermediate
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: GO_REF:0000108
title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
links
findings: []
- id: PMID:23168492
title: LYRM7/MZM1L is a UQCRFS1 chaperone involved in the last steps of mitochondrial
Complex III assembly in human cells.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Primary characterisation of human LYRM7/MZM1L. Establishes it as a mitochondrial-matrix
UQCRFS1 (Rieske Fe-S) chaperone and Complex III assembly factor. Supports the core MF, BP,
and matrix localisation.
- id: PMID:24606901
title: Cochaperone binding to LYR motifs confers specificity of iron sulfur cluster
delivery.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text explicitly names LYRM7 as an HSC20 (HSC20/HSCB) binding partner among the LYR-motif
family that assist Complex II/III assembly, supporting the LYRM7-HSC20 interaction.
- id: PMID:27499296
title: Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory
Chain Function.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Large-scale mitochondrial interaction map; source of an IntAct LYRM7-UQCRFS1 interaction.
Supports the physiological client relationship but not gene-specific mechanism.
- id: PMID:28380382
title: A Single Adaptable Cochaperone-Scaffold Complex Delivers Nascent Iron-Sulfur
Clusters to Mammalian Respiratory Chain Complexes I-III.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text details the UQCRFS1-LYRM7 intermediate recruiting HSC20 via LYRM7's LYR motif to
deliver the [2Fe-2S] cluster to UQCRFS1. Strong mechanistic support for the core function.
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
HuRI binary (Y2H) interactome; source of an IntAct LYRM7-SAT1 hit. SAT1 has no known
mitochondrial/CIII role, so this is likely a non-physiological binary-screen interaction.
- id: PMID:33961781
title: Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
BioPlex proteome-scale interactome; source of an IntAct LYRM7-UQCRFS1 interaction consistent
with the core client relationship.
- id: PMID:34800366
title: Quantitative high-confidence human mitochondrial proteome and its dynamics
in cellular context.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
High-confidence mitochondrial proteome; supports mitochondrial localisation of LYRM7 (HTP).
- id: PMID:40205054
title: Multimodal cell maps as a foundation for structural and functional genomics.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Large-scale cell-map interactome; source of an IntAct LYRM7-UQCRFS1 interaction consistent
with the core client relationship.
- id: Reactome:R-HSA-9865881
title: Complex III assembly
findings: []
- id: Reactome:R-HSA-9866253
title: apo-UQCRFS1 binds LYRM7
findings: []
- id: Reactome:R-HSA-9866272
title: 2Fe-2S is inserted in UQCRFS1
findings: []
- id: file:human/LYRM7/LYRM7-uniprot.txt
title: UniProtKB entry Q5U5X0 (LYRM7_HUMAN)
findings: []
suggested_questions:
- question: >-
Does LYRM7 act purely as a holdase that stabilises apo-UQCRFS1, or does it also
actively template/position UQCRFS1 for [2Fe-2S] cluster receipt and membrane insertion?
suggested_experiments:
- description: >-
Reconstitute the UQCRFS1-LYRM7 intermediate with the HSC20-HSPA9-ISCU Fe-S transfer complex
in vitro to determine the minimal components and the order of cluster insertion versus
membrane insertion of UQCRFS1.