SHY1 encodes the yeast SURF1-family cytochrome c oxidase assembly factor. Shy1 is an intrinsic mitochondrial inner membrane protein required for efficient complex IV biogenesis, acting during early Cox1 maturation and coupling Cox1 translational regulation by the Mss51/Cox14 module to downstream complex IV assembly. Shy1 is not a mature cytochrome c oxidase subunit and is not a general unfolded-protein chaperone; its core role is assembly of mitochondrial respiratory chain complex IV.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0033617
mitochondrial respiratory chain complex IV assembly
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: The PANTHER/IBA annotation is consistent with direct yeast evidence and conserved SURF1-family biology. Shy1 is repeatedly shown to be required for efficient cytochrome c oxidase assembly and Cox1 maturation.
Reason: Core biological process for SHY1.
Supporting Evidence:
PMID:17882259
Shy1 is an assembly factor for complex IV in Saccharomyces cerevisiae
file:yeast/SHY1/SHY1-deep-research-falcon.md
Falcon deep research identifies SHY1 as a SURF1-family mitochondrial inner membrane complex IV assembly factor.
|
|
GO:0005739
mitochondrion
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Mitochondrial localization is correct for Shy1. The more specific mitochondrial inner membrane term is also present, but the broader mitochondrion annotation is supported by direct studies and family transfer.
Reason: Shy1 performs its assembly-factor function in mitochondria.
Supporting Evidence:
PMID:9162072
An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane.
|
|
GO:0005743
mitochondrial inner membrane
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: UniProt subcellular-location mapping to mitochondrial inner membrane is accurate and agrees with direct localization experiments.
Reason: Core localization for Shy1.
Supporting Evidence:
PMID:9162072
An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane.
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: InterPro transfer to the generic membrane term is directionally correct for a SURF1-family membrane protein but too broad for this curated review. Shy1 is specifically an inner mitochondrial membrane protein.
Reason: Replace generic membrane with the experimentally supported mitochondrial inner membrane location.
Proposed replacements:
mitochondrial inner membrane
Supporting Evidence:
PMID:9162072
An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane.
|
|
GO:0005515
protein binding
|
IPI
PMID:17882259 Shy1 couples Cox1 translational regulation to cytochrome c o... |
MARK AS OVER ANNOTATED |
Summary: Shy1 interactions with Cox14, Mss51, Coa1 and complex IV assembly intermediates are central to its biology, but the generic protein binding term is not informative. The functional consequence is complex IV assembly rather than protein binding as a standalone molecular function.
Reason: Use complex IV assembly and mitochondrial inner membrane annotations instead of generic protein binding.
Supporting Evidence:
PMID:17882259
Shy1 interacts with Mss51 and Cox14, translational regulators of Cox1.
|
|
GO:0005515
protein binding
|
IPI
PMID:17882260 Coa1 links the Mss51 post-translational function to Cox1 cof... |
MARK AS OVER ANNOTATED |
Summary: The Coa1/Shy1 interaction supports the assembly pathway model but does not justify retaining a generic protein binding MF annotation.
Reason: The interaction is better represented as part of complex IV assembly.
Supporting Evidence:
PMID:17882260
The interaction between Coa1 and Cox1, and the physical and genetic interactions between Coa1 and Mss51, Shy1 and Cox14 suggest that Coa1 coordinates the transition
|
|
GO:0016020
membrane
|
IDA
PMID:15306853 Mss51p and Cox14p jointly regulate mitochondrial Cox1p expre... |
MODIFY |
Summary: The direct membrane annotation is valid but less specific than the mitochondrial inner membrane annotations supported by SHY1 localization and function.
Reason: Use the specific inner mitochondrial membrane component term.
Proposed replacements:
mitochondrial inner membrane
Supporting Evidence:
PMID:9162072
An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane.
|
|
GO:0005777
peroxisome
|
HDA
PMID:35563734 Pls1 Is a Peroxisomal Matrix Protein with a Role in Regulati... |
KEEP AS NON CORE |
Summary: Retain as non-core only. The canonical and mechanistic Shy1 localization is the mitochondrial inner membrane. The peroxisome annotation comes from a high-throughput peroxisomal screen and has no demonstrated role in Shy1's complex IV assembly function.
Reason: Possible context-specific or high-throughput localization, not the core functional location.
Supporting Evidence:
PMID:35563734
we used a high-throughput screen to discover peroxisomal proteins in yeast.
|
|
GO:0005739
mitochondrion
|
HDA
PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... |
ACCEPT |
Summary: High-throughput mitochondrial proteomics detection is consistent with Shy1's established mitochondrial role.
Reason: Correct broad mitochondrial localization.
Supporting Evidence:
PMID:24769239
we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria extracted from yeast grown on fermentative (glucose or galactose) and respiratory (lactate) media
|
|
GO:0005739
mitochondrion
|
HDA
PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... |
ACCEPT |
Summary: Mitochondrial proteome detection is consistent with Shy1's canonical localization and function.
Reason: Correct broad mitochondrial localization.
Supporting Evidence:
PMID:16823961
A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS, 1D-SDS-PAGE combined with nano-LC-MS/MS and 2D-PAGE
|
|
GO:0005743
mitochondrial inner membrane
|
IDA
PMID:15306853 Mss51p and Cox14p jointly regulate mitochondrial Cox1p expre... |
ACCEPT |
Summary: Inner mitochondrial membrane localization is appropriate for Shy1's role in Cox1 maturation and complex IV assembly.
Reason: Core cellular component for Shy1 function.
Supporting Evidence:
PMID:15306853
The release of Mss51p from the complex occurs at a downstream step in the assembly pathway, probably catalyzed by Shy1p.
|
|
GO:0005743
mitochondrial inner membrane
|
IDA
PMID:9162072 SHY1, the yeast homolog of the mammalian SURF-1 gene, encode... |
ACCEPT |
Summary: The original SHY1 characterization directly localized Shy1 to the inner mitochondrial membrane.
Reason: Direct localization evidence for the core site of action.
Supporting Evidence:
PMID:9162072
An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane.
|
|
GO:0033617
mitochondrial respiratory chain complex IV assembly
|
IMP
PMID:17882259 Shy1 couples Cox1 translational regulation to cytochrome c o... |
ACCEPT |
Summary: Strong mutant and biochemical evidence supports Shy1 as a complex IV assembly factor that links Cox1 translational control with assembly intermediate progression.
Reason: Core biological process supported by direct experimental evidence.
Supporting Evidence:
PMID:17882259
We suggest that Shy1 links Cox1 translational regulation to complex IV assembly and supercomplex formation.
|
|
GO:0051082
unfolded protein binding
|
IMP
PMID:11389896 Shy1p occurs in a high molecular weight complex and is requi... |
MARK AS OVER ANNOTATED |
Summary: The evidence shows that Shy1 occurs in an assembly-associated complex and is required for efficient cytochrome c oxidase assembly. It does not show general unfolded-protein binding or a broad chaperone substrate range.
Reason: The annotation over-interprets an assembly-factor phenotype. Shy1 should be curated to complex IV assembly rather than generic unfolded protein binding.
Supporting Evidence:
PMID:11389896
Shy1p may either facilitate assembly of the enzyme, or increase its stability.
|
|
GO:0005743
mitochondrial inner membrane
|
IDA
PMID:9162072 SHY1, the yeast homolog of the mammalian SURF-1 gene, encode... |
ACCEPT |
Summary: Duplicate direct UniProt annotation for Shy1 inner mitochondrial membrane localization; retain because it accurately reflects the original experimental localization.
Reason: Direct localization evidence for the core site of action.
Supporting Evidence:
PMID:9162072
An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane.
|
Q: Is there enough direct evidence to annotate a specific Shy1 molecular function for Cox1 cofactor insertion or assembly-intermediate stabilization, rather than leaving SHY1 represented only by the biological-process term for complex IV assembly?
Suggested experts: Mick DU, Rehling P, Winge DR
Experiment: Reconstitute Shy1-containing Cox1 assembly intermediates with Cox14, Mss51, Coa1 and cofactor-insertion factors, then test Shy1 mutants for Cox1 cofactor incorporation, assembly-intermediate stability, and release of Mss51.
Hypothesis: Shy1 promotes Cox1 heme a3:CuB maturation or maintains Cox1 in an assembly-competent state rather than binding unfolded proteins generally.
Type: mitochondrial complex IV assembly intermediate assay
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T10:06:07.946367'
end_time: '2026-05-04T10:18:23.963932'
duration_seconds: 736.02
template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: SHY1
gene_symbol: SHY1
uniprot_accession: P53266
protein_description: 'RecName: Full=Cytochrome oxidase assembly protein SHY1; AltName:
Full=SURF1 homolog of Yeast; AltName: Full=SURF1-like protein;'
gene_info: Name=SHY1; OrderedLocusNames=YGR112W; ORFNames=G6150;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the SURF1 family. .
protein_domains: Surf1/Shy1. (IPR002994); Surf1/Surf4. (IPR045214); SURF1 (PF02104)
provider_config:
timeout: 600
max_retries: 3
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citation_count: 20
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'SHY1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene SHY1 (gene ID: SHY1, UniProt: P53266) in yeast.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'SHY1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene SHY1 (gene ID: SHY1, UniProt: P53266) in yeast.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
SHY1 (YGR112W) encodes Shy1, a conserved SURF1-family mitochondrial inner membrane protein required for efficient cytochrome c oxidase (Complex IV; COX) biogenesis and respiratory competence in budding yeast. Genetic, biochemical, and complex-isolation studies support a model in which Shy1 acts during early Cox1 maturation/assembly, coordinating cofactor-center maturation (notably heme a3:CuB formation) with assembly intermediates, and coupling assembly status to Cox1 translational regulation via interaction with the Mss51/Cox14 regulatory module. (mick2007shy1couplescox1 pages 1-3, bestwick2010analysisofleigh pages 3-4)
The literature explicitly identifies SHY1 as the yeast homolog of mammalian SURF1, and the gene cloned to complement respiration-deficient pet mutants is identical to ORF YGR112W; the gene was named SHY1 (Surf Homolog of Yeast). (mashkevich1997shy1theyeast pages 1-1)
The core primary literature establishing and characterizing Shy1 is in budding yeast (Saccharomyces cerevisiae), consistent with the UniProt organism context provided. (mashkevich1997shy1theyeast pages 1-1, mick2007shy1couplescox1 pages 1-1)
Shy1 is described as a conserved SURF1-family protein with two predicted transmembrane segments (near N- and C-termini) and mitochondrial targeting features, and it behaves as an intrinsic mitochondrial membrane protein in biochemical extraction assays. (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast pages 7-7)
Sub-mitochondrial topology is consistent with an inner mitochondrial membrane (IMM) localization, with much of the polypeptide exposed to the intermembrane space (IMS). (mick2007shy1couplescox1 pages 1-3)
Conclusion: The SHY1 gene/protein studied in the cited literature matches the user-supplied UniProt entry P53266 (cytochrome oxidase assembly protein Shy1; SURF1 family) from S. cerevisiae. (mashkevich1997shy1theyeast pages 1-1, mick2007shy1couplescox1 pages 1-1)
SHY1 encodes an assembly factor (not a catalytic enzyme subunit) required for efficient formation of functional cytochrome c oxidase (COX/Complex IV) in mitochondria. Loss of SHY1 decreases assembled complex IV abundance/activity and impairs respiratory growth. (nijtmans2001shy1poccursin pages 1-2, mick2007shy1couplescox1 pages 1-3)
Complex IV is the terminal oxidase of the respiratory chain, and its biogenesis requires stepwise assembly of mitochondria-encoded and nuclear-encoded subunits plus cofactor-center maturation (e.g., heme and copper centers). Shy1/SURF1-family proteins are implicated at the stage of Cox1 maturation, where formation of the heme a3:CuB catalytic center is a critical step. (bestwick2010analysisofleigh pages 3-4, stiburek2009theroleof pages 23-26)
In yeast, Cox1 synthesis is regulated by feedback mechanisms in which the translational activator Mss51 is sequestered in assembly intermediates when downstream assembly is blocked. Shy1 physically associates with Mss51 and Cox14, and thereby is positioned to link Cox1 synthesis regulation to Cox1 maturation/assembly progress. (mick2007shy1couplescox1 pages 1-3, reinhold2011mimickingasurf1 pages 2-3)
Multiple lines of evidence indicate Shy1 is required for efficient Complex IV assembly:
- Disruption of SHY1 strongly reduces steady-state assembled COX to ~30% of control, yet remaining assembled COX can appear enzymatically normal. (nijtmans2001shy1poccursin pages 1-2)
- Shy1 mediates formation of the heme a3:CuB center in Cox1 (a key catalytic cofactor center), and mutations in Shy1 can cause impaired Cox1 “hemylation” and changes in copper-related phenotypes. (bestwick2010analysisofleigh pages 3-4, bestwick2010analysisofleigh pages 1-2)
Mechanistic proposals (with experimental anchoring):
- Shy1/SURF1 has been proposed to function as a heme insertase or as a chaperone maintaining Cox1 competent for heme insertion; loss of SURF1 leads to accumulation of assembly intermediates. (reinhold2011mimickingasurf1 pages 2-3)
- Comparative evidence summarized in authoritative synthesis suggests bacterial Surf1 homologs can bind heme a in vivo and are implicated in heme insertion/stabilization for terminal oxidase biogenesis, supporting a conserved biochemical theme for the family (but direct heme-binding by yeast Shy1 is not demonstrated in the provided excerpts). (stiburek2009theroleof pages 23-26)
Shy1 is not merely a static assembly factor: it participates in regulatory complexes that couple Cox1 synthesis and assembly state.
- Shy1 associates with the Cox1 translational regulators Mss51 and Cox14, forming complexes that connect translational regulation to early assembly. (mick2007shy1couplescox1 pages 1-3)
- Patient-mutation–mimicking Shy1 alleles demonstrate that COX assembly can be uncoupled from translational feedback: e.g., a Shy1 mutant can accumulate in ~200 kDa intermediates and bypass feedback control on Cox1 expression but still block later assembly steps, revealing separable functional contributions. (reinhold2011mimickingasurf1 pages 1-2, reinhold2011mimickingasurf1 pages 10-11)
SHY1 functions in the mitochondrial oxidative phosphorylation (OXPHOS) biogenesis pathway, specifically in Complex IV assembly, acting at or near the Cox1 maturation stage and influencing formation of later supercomplexes containing Complex III and IV. (mick2007shy1couplescox1 pages 1-1, mick2007shy1couplescox1 pages 1-3)
Shy1-containing assembly intermediates can associate with other respiratory complexes:
- Purification and complex-association evidence supports Shy1 association with respiratory chain complexes III/IV and transitional supercomplex states. (mick2007shy1couplescox1 pages 1-3, mick2007shy1couplescox1 pages 1-1)
- In a 2024 fission yeast study (see §5), the SURF1 homolog also co-immunoprecipitates with a complex III subunit and BN-PAGE supports links to supercomplex biology, supporting conserved network positioning of SURF1-family proteins. (luo2024characterizationofshy1 pages 11-13, luo2024characterizationofshy1 pages 1-2)
Yeast SHY1 literature is foundational (1997–2011), but 2024 work updates the field with cross-yeast comparative and interaction-network evidence relevant to SURF1-family mechanistic questions.
A 2024 primary study characterized Shy1 in Schizosaccharomyces pombe as a SURF1-domain IMM protein with two transmembrane segments and reported:
- Physical interactions with complex IV subunits and assembly factors; co-immunoprecipitation of a complex III subunit (Rip1) suggested involvement in III–IV supercomplex associations. (luo2024characterizationofshy1 pages 1-2, luo2024characterizationofshy1 pages 11-13)
- BN-PAGE evidence that complex IV abundance is diminished in ∆shy1 strains. (luo2024characterizationofshy1 pages 1-2)
- An interaction network linking Shy1 to Cox1-related factors (including Mss51), copper chaperones, and heme-related factors such as Cox10/Cox11 homologs (interaction scores in their Table 1). (luo2024characterizationofshy1 pages 6-10)
Interpretation for S. cerevisiae SHY1 annotation: While organism-specific compensatory effects exist in S. pombe, these data reinforce that SURF1-family proteins sit at a conserved nexus connecting Cox1 expression/maturation, cofactor insertion pathways, and respiratory complex organization. (luo2024characterizationofshy1 pages 11-13, luo2024characterizationofshy1 pages 6-10)
Because SURF1 mutations are a frequent cause of Leigh syndrome, yeast SHY1 has been used as an experimentally tractable model to test pathogenic mechanisms of SURF1 alleles.
- Mimicking specific patient alleles in yeast revealed separable roles for SURF1/Shy1 in assembly progression vs translational coupling, and highlighted how variants can cause turnover defects or accumulation in specific assembly intermediates. (reinhold2011mimickingasurf1 pages 1-2, reinhold2011mimickingasurf1 pages 10-11)
SHY1 mutant phenotypes can be modified by nuclear genetic changes or transcriptional activators.
- Nuclear revertants can increase assembled COX by ~4–5× and restore respiration to ~78% of wild type, supporting the concept that upstream expression/biogenesis capacity can buffer COX assembly defects. (barrientos2002shy1pisnecessary pages 1-2, barrientos2002shy1pisnecessary pages 2-3)
- Overexpression of transcriptional activators (HAP-related) can partially rescue respiration and strongly improve generation time on non-fermentable carbon sources (e.g., HAP4 high-copy suppression). (fontanesi2008transcriptionalactivatorshapnfy pages 2-4)
The following table consolidates key quantitative measures from primary studies (COX activities, respiration rates, inhibitor sensitivities, and growth rates).
| Study (author year, journal) | Strain/allele | Assay/metric | Result (include numeric values and units or %) | Interpretation |
|---|---|---|---|---|
| Mashkevich 1997, J Biol Chem | Wild type (W303-1A) | Cytochrome c oxidase activity | 1.72 (table units) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Reference wild-type COX activity |
| Mashkevich 1997, J Biol Chem | W125 | Cytochrome c oxidase activity | 1.32 (~77% of WT) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Partial COX deficiency |
| Mashkevich 1997, J Biol Chem | C173/U1 | Cytochrome c oxidase activity | 1.04 (~60% of WT) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Partial COX deficiency |
| Mashkevich 1997, J Biol Chem | W303ΔSHY1(H) | Cytochrome c oxidase activity | 1.29 (~75% of WT) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Partial reduction in COX activity |
| Mashkevich 1997, J Biol Chem | W303ΔSHY1(U) | Cytochrome c oxidase activity | 0.67 (~39% of WT) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Stronger COX defect |
| Mashkevich 1997, J Biol Chem | Wild type (W303-1A) | NADH oxidase | 1.11 (table units) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Reference wild-type respiratory activity |
| Mashkevich 1997, J Biol Chem | W125 | NADH oxidase | 0.33 (~30% of WT); text states 30% of wild-type NADH oxidase activity (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Severe respiratory impairment despite residual activity |
| Mashkevich 1997, J Biol Chem | C173/U1 | NADH oxidase | 0.18 (~16% of WT) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Severe respiratory impairment |
| Mashkevich 1997, J Biol Chem | W303ΔSHY1(H) | NADH oxidase | 1.09 (~98% of WT) (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Near-normal NADH oxidase despite COX reduction |
| Mashkevich 1997, J Biol Chem | W303ΔSHY1(U) | NADH oxidase | 0.21 (~19% of WT); text states 20% of wild-type NADH oxidase activity (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | Strong respiratory defect; no appreciable growth on glycerol or ethanol |
| Mashkevich 1997, J Biol Chem | Wild type and shy1-related strains | ATPase activity | ≈5.6–6.6 across strains (mashkevich1997shy1theyeast pages 3-4, mashkevich1997shy1theyeast media c0394742) | ATPase largely unaffected relative to respiratory defects |
| Nijtmans 2001, FEBS Lett | shy1 disruptant/null | Assembled cytochrome c oxidase | Approximately 30% of control (nijtmans2001shy1poccursin pages 1-2) | SHY1 is required for efficient COX assembly, but some holo-COX remains |
| Nijtmans 2001, FEBS Lett | Shy1p complex | Apparent complex size | About 250 kDa (nijtmans2001shy1poccursin pages 1-2) | Shy1p occurs in a higher-molecular-weight assembly-associated complex |
| Barrientos 2002, EMBO J | shy1 mutants | Fully assembled and functional COX | ~10±15% (barrientos2002shy1pisnecessary pages 1-2) | Severe COX deficiency in shy1 mutants |
| Barrientos 2002, EMBO J | DSHY1 (shy1 null) | Whole-cell respiration rate | ~20% of wild type (barrientos2002shy1pisnecessary pages 1-2, barrientos2002shy1pisnecessary pages 2-3) | Major respiratory defect |
| Barrientos 2002, EMBO J | DSHY1 (shy1 null) | Inhibitor sensitivity of residual respiration | 59% inhibition by antimycin A; 93% inhibition by KCN (barrientos2002shy1pisnecessary pages 1-2, barrientos2002shy1pisnecessary pages 2-3) | Residual respiration still largely mitochondrial/COX-linked |
| Barrientos 2002, EMBO J | Nuclear revertant of DSHY1 | Whole-cell respiration rate | 78% of wild type (barrientos2002shy1pisnecessary pages 1-2, barrientos2002shy1pisnecessary pages 2-3) | Suppression strongly restores respiratory function |
| Barrientos 2002, EMBO J | DSHY1 mitochondria | NADH oxidation | 14% of wild type (barrientos2002shy1pisnecessary pages 2-3) | Mitochondrial respiratory chain severely compromised |
| Barrientos 2002, EMBO J | Revertant mitochondria | NADH oxidation | ~60% of wild type (barrientos2002shy1pisnecessary pages 2-3) | Partial biochemical rescue |
| Barrientos 2002, EMBO J | Revertant mitochondria | COX specific activity | ~4-fold higher than mutant; 37–40% of wild type (barrientos2002shy1pisnecessary pages 2-3) | Suppression improves COX abundance/activity but not fully to WT |
| Barrientos 2002, EMBO J | Wild type vs mutant | P/O ratio | 1.31 (wild type) vs 1.17 (mutant) (barrientos2002shy1pisnecessary pages 2-3) | Oxidative phosphorylation efficiency only modestly reduced relative to respiration defect |
| Barrientos 2002, EMBO J | Wild type | Doubling time on glycerol | 2.4 h (barrientos2002shy1pisnecessary pages 2-3) | Baseline respiratory growth |
| Barrientos 2002, EMBO J | Revertant | Doubling time on glycerol | 3.3 h (barrientos2002shy1pisnecessary pages 2-3) | Near-wild-type respiratory growth restored |
| Barrientos 2002, EMBO J | Mutant | Doubling time on glycerol | 28 h (barrientos2002shy1pisnecessary pages 2-3) | Severe respiratory growth defect |
| Fontanesi 2008, Hum Mol Genet | shy1 mutant | Generation time in ethanol–glycerol | 28 h (fontanesi2008transcriptionalactivatorshapnfy pages 2-4) | Confirms severe non-fermentable growth defect |
| Fontanesi 2008, Hum Mol Genet | Wild type | Generation time in ethanol–glycerol | 2.4 h (fontanesi2008transcriptionalactivatorshapnfy pages 2-4) | Reference respiratory growth |
| Fontanesi 2008, Hum Mol Genet | shy1 mutant + HAP4 high-copy | Generation time in ethanol–glycerol | 4.2 h (fontanesi2008transcriptionalactivatorshapnfy pages 2-4) | HAP4 strongly suppresses shy1 respiratory growth defect |
| Fontanesi 2008, Hum Mol Genet | shy1 null | KCN-sensitive endogenous respiration | Increased from 15% to 20% of wild type with HAP2 overexpression (fontanesi2008transcriptionalactivatorshapnfy pages 2-4) | HAP2 partially suppresses respiratory defect |
| Fontanesi 2008, Hum Mol Genet | W125 point mutant | KCN-sensitive endogenous respiration | Increased from 18% to 25% of wild type with HAP2 overexpression (fontanesi2008transcriptionalactivatorshapnfy pages 2-4) | HAP2 partially suppresses point-mutant respiratory defect |
| Fontanesi 2008, Hum Mol Genet | HAP4 expression | HAP4 mRNA regulation | 4–5-fold higher mRNA on lactate vs glucose (fontanesi2008transcriptionalactivatorshapnfy pages 2-4) | Carbon-responsive transcription likely contributes to suppression context |
Table: This table compiles numeric phenotypes reported for Saccharomyces cerevisiae shy1 mutants and suppressors across key studies, including enzyme activities, respiration, COX assembly, inhibitor sensitivity, and growth rates. It is useful for quickly comparing the severity of SHY1 loss and the extent of genetic suppression.
A key visual source for the enzyme activity dataset is the original Table II from Mashkevich et al. (1997). (mashkevich1997shy1theyeast media c0394742)
Across independent studies, SHY1 is best annotated as a mitochondrial inner membrane Complex IV assembly factor acting during Cox1 maturation/early assembly, with strong evidence for participation in the formation of the heme a3:CuB catalytic center and in coordinating assembly with translation control. (bestwick2010analysisofleigh pages 3-4, mick2007shy1couplescox1 pages 1-3)
Even with strong genetic/biochemical evidence, the precise biochemical action of Shy1 remains incompletely resolved in the provided sources: whether Shy1 directly binds/transfers heme a/a3, acts as a scaffold/chaperone for Cox1 conformational maturation, or mainly regulates/co-localizes cofactor insertion machinery is still under investigation. This uncertainty is explicitly reflected in mechanistic framing and cross-species summaries. (reinhold2011mimickingasurf1 pages 2-3, stiburek2009theroleof pages 23-26)
References
(mick2007shy1couplescox1 pages 1-3): David U Mick, Karina Wagner, Martin van der Laan, Ann E Frazier, Inge Perschil, Magdalena Pawlas, Helmut E Meyer, Bettina Warscheid, and Peter Rehling. Shy1 couples cox1 translational regulation to cytochrome c oxidase assembly. The EMBO Journal, 26:4347-4358, Oct 2007. URL: https://doi.org/10.1038/sj.emboj.7601862, doi:10.1038/sj.emboj.7601862. This article has 173 citations.
(bestwick2010analysisofleigh pages 3-4): Megan Bestwick, Mi-Young Jeong, Oleh Khalimonchuk, Hyung Kim, and Dennis R. Winge. Analysis of leigh syndrome mutations in the yeast surf1 homolog reveals a new member of the cytochrome oxidase assembly factor family. Molecular and Cellular Biology, 30:4480-4491, Sep 2010. URL: https://doi.org/10.1128/mcb.00228-10, doi:10.1128/mcb.00228-10. This article has 48 citations and is from a domain leading peer-reviewed journal.
(mashkevich1997shy1theyeast pages 1-1): Grigoriy Mashkevich, Barbara Repetto, D. Moira Glerum, Can Jin, and Alexander Tzagoloff. Shy1, the yeast homolog of the mammaliansurf-1 gene, encodes a mitochondrial protein required for respiration*. The Journal of Biological Chemistry, 272:14356-14364, May 1997. URL: https://doi.org/10.1074/jbc.272.22.14356, doi:10.1074/jbc.272.22.14356. This article has 175 citations.
(mick2007shy1couplescox1 pages 1-1): David U Mick, Karina Wagner, Martin van der Laan, Ann E Frazier, Inge Perschil, Magdalena Pawlas, Helmut E Meyer, Bettina Warscheid, and Peter Rehling. Shy1 couples cox1 translational regulation to cytochrome c oxidase assembly. The EMBO Journal, 26:4347-4358, Oct 2007. URL: https://doi.org/10.1038/sj.emboj.7601862, doi:10.1038/sj.emboj.7601862. This article has 173 citations.
(mashkevich1997shy1theyeast pages 3-4): Grigoriy Mashkevich, Barbara Repetto, D. Moira Glerum, Can Jin, and Alexander Tzagoloff. Shy1, the yeast homolog of the mammaliansurf-1 gene, encodes a mitochondrial protein required for respiration*. The Journal of Biological Chemistry, 272:14356-14364, May 1997. URL: https://doi.org/10.1074/jbc.272.22.14356, doi:10.1074/jbc.272.22.14356. This article has 175 citations.
(mashkevich1997shy1theyeast pages 7-7): Grigoriy Mashkevich, Barbara Repetto, D. Moira Glerum, Can Jin, and Alexander Tzagoloff. Shy1, the yeast homolog of the mammaliansurf-1 gene, encodes a mitochondrial protein required for respiration*. The Journal of Biological Chemistry, 272:14356-14364, May 1997. URL: https://doi.org/10.1074/jbc.272.22.14356, doi:10.1074/jbc.272.22.14356. This article has 175 citations.
(nijtmans2001shy1poccursin pages 1-2): L.G.J. Nijtmans, M. Artal Sanz, M. Bucko, M.H. Farhoud, M. Feenstra, G.A.J. Hakkaart, M. Zeviani, and L.A. Grivell. Shy1p occurs in a high molecular weight complex and is required for efficient assembly of cytochrome c oxidase in yeast. FEBS Letters, 498:46-51, Jun 2001. URL: https://doi.org/10.1016/s0014-5793(01)02447-4, doi:10.1016/s0014-5793(01)02447-4. This article has 89 citations and is from a peer-reviewed journal.
(stiburek2009theroleof pages 23-26): L Stibůrek. The role of human sco1, sco2, surf1 and oxa1l in the biogenesis of the mitochondrial oxidative phosphorylation system. Unknown journal, 2009.
(reinhold2011mimickingasurf1 pages 2-3): Robert Reinhold, Bettina Bareth, Martina Balleininger, Mirjam Wissel, Peter Rehling, and David U. Mick. Mimicking a surf1 allele reveals uncoupling of cytochrome c oxidase assembly from translational regulation in yeast. Human molecular genetics, 20 12:2379-93, Jun 2011. URL: https://doi.org/10.1093/hmg/ddr145, doi:10.1093/hmg/ddr145. This article has 28 citations and is from a domain leading peer-reviewed journal.
(bestwick2010analysisofleigh pages 1-2): Megan Bestwick, Mi-Young Jeong, Oleh Khalimonchuk, Hyung Kim, and Dennis R. Winge. Analysis of leigh syndrome mutations in the yeast surf1 homolog reveals a new member of the cytochrome oxidase assembly factor family. Molecular and Cellular Biology, 30:4480-4491, Sep 2010. URL: https://doi.org/10.1128/mcb.00228-10, doi:10.1128/mcb.00228-10. This article has 48 citations and is from a domain leading peer-reviewed journal.
(reinhold2011mimickingasurf1 pages 1-2): Robert Reinhold, Bettina Bareth, Martina Balleininger, Mirjam Wissel, Peter Rehling, and David U. Mick. Mimicking a surf1 allele reveals uncoupling of cytochrome c oxidase assembly from translational regulation in yeast. Human molecular genetics, 20 12:2379-93, Jun 2011. URL: https://doi.org/10.1093/hmg/ddr145, doi:10.1093/hmg/ddr145. This article has 28 citations and is from a domain leading peer-reviewed journal.
(reinhold2011mimickingasurf1 pages 10-11): Robert Reinhold, Bettina Bareth, Martina Balleininger, Mirjam Wissel, Peter Rehling, and David U. Mick. Mimicking a surf1 allele reveals uncoupling of cytochrome c oxidase assembly from translational regulation in yeast. Human molecular genetics, 20 12:2379-93, Jun 2011. URL: https://doi.org/10.1093/hmg/ddr145, doi:10.1093/hmg/ddr145. This article has 28 citations and is from a domain leading peer-reviewed journal.
(luo2024characterizationofshy1 pages 11-13): Ying Luo, Yuanqi Xu, Fawad Ahmad, Gang Feng, and Ying Huang. Characterization of shy1, the schizosaccharomyces pombe homolog of human surf1. Scientific Reports, Sep 2024. URL: https://doi.org/10.1038/s41598-024-72681-9, doi:10.1038/s41598-024-72681-9. This article has 8 citations and is from a peer-reviewed journal.
(luo2024characterizationofshy1 pages 1-2): Ying Luo, Yuanqi Xu, Fawad Ahmad, Gang Feng, and Ying Huang. Characterization of shy1, the schizosaccharomyces pombe homolog of human surf1. Scientific Reports, Sep 2024. URL: https://doi.org/10.1038/s41598-024-72681-9, doi:10.1038/s41598-024-72681-9. This article has 8 citations and is from a peer-reviewed journal.
(luo2024characterizationofshy1 pages 6-10): Ying Luo, Yuanqi Xu, Fawad Ahmad, Gang Feng, and Ying Huang. Characterization of shy1, the schizosaccharomyces pombe homolog of human surf1. Scientific Reports, Sep 2024. URL: https://doi.org/10.1038/s41598-024-72681-9, doi:10.1038/s41598-024-72681-9. This article has 8 citations and is from a peer-reviewed journal.
(barrientos2002shy1pisnecessary pages 1-2): A. Barrientos, D. Korr, and A. Tzagoloff. Shy1p is necessary for full expression of mitochondrial cox1 in the yeast model of leigh's syndrome. The EMBO Journal, 21:43-52, Jan 2002. URL: https://doi.org/10.1093/emboj/21.1.43, doi:10.1093/emboj/21.1.43. This article has 210 citations.
(barrientos2002shy1pisnecessary pages 2-3): A. Barrientos, D. Korr, and A. Tzagoloff. Shy1p is necessary for full expression of mitochondrial cox1 in the yeast model of leigh's syndrome. The EMBO Journal, 21:43-52, Jan 2002. URL: https://doi.org/10.1093/emboj/21.1.43, doi:10.1093/emboj/21.1.43. This article has 210 citations.
(fontanesi2008transcriptionalactivatorshapnfy pages 2-4): Flavia Fontanesi, Can Jin, Alexander Tzagoloff, and Antoni Barrientos. Transcriptional activators hap/nf-y rescue a cytochrome c oxidase defect in yeast and human cells. Human molecular genetics, 17 6:775-88, Mar 2008. URL: https://doi.org/10.1093/hmg/ddm349, doi:10.1093/hmg/ddm349. This article has 67 citations and is from a domain leading peer-reviewed journal.
(mashkevich1997shy1theyeast media c0394742): Grigoriy Mashkevich, Barbara Repetto, D. Moira Glerum, Can Jin, and Alexander Tzagoloff. Shy1, the yeast homolog of the mammaliansurf-1 gene, encodes a mitochondrial protein required for respiration*. The Journal of Biological Chemistry, 272:14356-14364, May 1997. URL: https://doi.org/10.1074/jbc.272.22.14356, doi:10.1074/jbc.272.22.14356. This article has 175 citations.
id: P53266
gene_symbol: SHY1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:559292
label: Saccharomyces cerevisiae
description: >-
SHY1 encodes the yeast SURF1-family cytochrome c oxidase assembly factor.
Shy1 is an intrinsic mitochondrial inner membrane protein required for
efficient complex IV biogenesis, acting during early Cox1 maturation and
coupling Cox1 translational regulation by the Mss51/Cox14 module to
downstream complex IV assembly. Shy1 is not a mature cytochrome c oxidase
subunit and is not a general unfolded-protein chaperone; its core role is
assembly of mitochondrial respiratory chain complex IV.
existing_annotations:
- term:
id: GO:0033617
label: mitochondrial respiratory chain complex IV assembly
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
The PANTHER/IBA annotation is consistent with direct yeast evidence and
conserved SURF1-family biology. Shy1 is repeatedly shown to be required
for efficient cytochrome c oxidase assembly and Cox1 maturation.
action: ACCEPT
reason: Core biological process for SHY1.
supported_by:
- reference_id: PMID:17882259
supporting_text: "Shy1 is an assembly factor for complex IV in Saccharomyces cerevisiae"
- reference_id: file:yeast/SHY1/SHY1-deep-research-falcon.md
supporting_text: Falcon deep research identifies SHY1 as a SURF1-family mitochondrial inner membrane complex IV assembly factor.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Mitochondrial localization is correct for Shy1. The more specific
mitochondrial inner membrane term is also present, but the broader
mitochondrion annotation is supported by direct studies and family
transfer.
action: ACCEPT
reason: Shy1 performs its assembly-factor function in mitochondria.
supported_by:
- reference_id: PMID:9162072
supporting_text: "An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane."
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
UniProt subcellular-location mapping to mitochondrial inner membrane is
accurate and agrees with direct localization experiments.
action: ACCEPT
reason: Core localization for Shy1.
supported_by:
- reference_id: PMID:9162072
supporting_text: "An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane."
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
InterPro transfer to the generic membrane term is directionally correct
for a SURF1-family membrane protein but too broad for this curated review.
Shy1 is specifically an inner mitochondrial membrane protein.
action: MODIFY
reason: Replace generic membrane with the experimentally supported mitochondrial inner membrane location.
proposed_replacement_terms:
- id: GO:0005743
label: mitochondrial inner membrane
supported_by:
- reference_id: PMID:9162072
supporting_text: "An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane."
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:17882259
review:
summary: >-
Shy1 interactions with Cox14, Mss51, Coa1 and complex IV assembly
intermediates are central to its biology, but the generic protein binding
term is not informative. The functional consequence is complex IV assembly
rather than protein binding as a standalone molecular function.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Use complex IV assembly and mitochondrial inner membrane annotations
instead of generic protein binding.
supported_by:
- reference_id: PMID:17882259
supporting_text: "Shy1 interacts with Mss51 and Cox14, translational regulators of Cox1."
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:17882260
review:
summary: >-
The Coa1/Shy1 interaction supports the assembly pathway model but does not
justify retaining a generic protein binding MF annotation.
action: MARK_AS_OVER_ANNOTATED
reason: The interaction is better represented as part of complex IV assembly.
supported_by:
- reference_id: PMID:17882260
supporting_text: "The interaction between Coa1 and Cox1, and the physical and genetic interactions between Coa1 and Mss51, Shy1 and Cox14 suggest that Coa1 coordinates the transition"
- term:
id: GO:0016020
label: membrane
evidence_type: IDA
original_reference_id: PMID:15306853
review:
summary: >-
The direct membrane annotation is valid but less specific than the
mitochondrial inner membrane annotations supported by SHY1 localization and
function.
action: MODIFY
reason: Use the specific inner mitochondrial membrane component term.
proposed_replacement_terms:
- id: GO:0005743
label: mitochondrial inner membrane
supported_by:
- reference_id: PMID:9162072
supporting_text: "An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane."
- term:
id: GO:0005777
label: peroxisome
evidence_type: HDA
original_reference_id: PMID:35563734
review:
summary: >-
Retain as non-core only. The canonical and mechanistic Shy1 localization is
the mitochondrial inner membrane. The peroxisome annotation comes from a
high-throughput peroxisomal screen and has no demonstrated role in Shy1's
complex IV assembly function.
action: KEEP_AS_NON_CORE
reason: Possible context-specific or high-throughput localization, not the core functional location.
supported_by:
- reference_id: PMID:35563734
supporting_text: "we used a high-throughput screen to discover peroxisomal proteins in yeast."
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HDA
original_reference_id: PMID:24769239
review:
summary: >-
High-throughput mitochondrial proteomics detection is consistent with
Shy1's established mitochondrial role.
action: ACCEPT
reason: Correct broad mitochondrial localization.
supported_by:
- reference_id: PMID:24769239
supporting_text: "we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria extracted from yeast grown on fermentative (glucose or galactose) and respiratory (lactate) media"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HDA
original_reference_id: PMID:16823961
review:
summary: >-
Mitochondrial proteome detection is consistent with Shy1's canonical
localization and function.
action: ACCEPT
reason: Correct broad mitochondrial localization.
supported_by:
- reference_id: PMID:16823961
supporting_text: "A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS, 1D-SDS-PAGE combined with nano-LC-MS/MS and 2D-PAGE"
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IDA
original_reference_id: PMID:15306853
review:
summary: >-
Inner mitochondrial membrane localization is appropriate for Shy1's role in
Cox1 maturation and complex IV assembly.
action: ACCEPT
reason: Core cellular component for Shy1 function.
supported_by:
- reference_id: PMID:15306853
supporting_text: "The release of Mss51p from the complex occurs at a downstream step in the assembly pathway, probably catalyzed by Shy1p."
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IDA
original_reference_id: PMID:9162072
review:
summary: >-
The original SHY1 characterization directly localized Shy1 to the inner
mitochondrial membrane.
action: ACCEPT
reason: Direct localization evidence for the core site of action.
supported_by:
- reference_id: PMID:9162072
supporting_text: "An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane."
- term:
id: GO:0033617
label: mitochondrial respiratory chain complex IV assembly
evidence_type: IMP
original_reference_id: PMID:17882259
review:
summary: >-
Strong mutant and biochemical evidence supports Shy1 as a complex IV
assembly factor that links Cox1 translational control with assembly
intermediate progression.
action: ACCEPT
reason: Core biological process supported by direct experimental evidence.
supported_by:
- reference_id: PMID:17882259
supporting_text: "We suggest that Shy1 links Cox1 translational regulation to complex IV assembly and supercomplex formation."
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IMP
original_reference_id: PMID:11389896
review:
summary: >-
The evidence shows that Shy1 occurs in an assembly-associated complex and
is required for efficient cytochrome c oxidase assembly. It does not show
general unfolded-protein binding or a broad chaperone substrate range.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The annotation over-interprets an assembly-factor phenotype. Shy1 should be
curated to complex IV assembly rather than generic unfolded protein binding.
supported_by:
- reference_id: PMID:11389896
supporting_text: "Shy1p may either facilitate assembly of the enzyme, or increase its stability."
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IDA
original_reference_id: PMID:9162072
review:
summary: >-
Duplicate direct UniProt annotation for Shy1 inner mitochondrial membrane
localization; retain because it accurately reflects the original
experimental localization.
action: ACCEPT
reason: Direct localization evidence for the core site of action.
supported_by:
- reference_id: PMID:9162072
supporting_text: "An antibody against the carboxyl-terminal half of Shy1p has been used to localize the protein in the inner mitochondrial membrane."
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: PMID:11389896
title: Shy1p occurs in a high molecular weight complex and is required for efficient assembly of cytochrome c oxidase in yeast.
findings:
- statement: Shy1 is required for efficient complex IV assembly but residual normal enzyme can still form.
supporting_text: "Steady-state levels of the enzyme were found to be strongly reduced, the total amount of assembled complex being approximately 30% of control."
- id: PMID:15306853
title: Mss51p and Cox14p jointly regulate mitochondrial Cox1p expression in Saccharomyces cerevisiae.
findings:
- statement: Shy1 likely acts downstream of the Cox14-Cox1-Mss51 regulatory complex.
supporting_text: "The release of Mss51p from the complex occurs at a downstream step in the assembly pathway, probably catalyzed by Shy1p."
- id: PMID:16823961
title: 'Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.'
findings: []
- id: PMID:17882259
title: Shy1 couples Cox1 translational regulation to cytochrome c oxidase assembly.
findings:
- statement: Shy1 is a complex IV assembly factor that interacts with Cox1 translational regulators and assembly intermediates.
supporting_text: "Shy1 interacts with Mss51 and Cox14, translational regulators of Cox1."
- id: PMID:17882260
title: Coa1 links the Mss51 post-translational function to Cox1 cofactor insertion in cytochrome c oxidase assembly.
findings:
- statement: Coa1 and Shy1 participate in the Cox1 maturation/cofactor insertion step of complex IV assembly.
supporting_text: "Shy1 has been implicated in formation of the heme a3-Cu(B) site in Cox1."
- id: PMID:24769239
title: Quantitative variations of the mitochondrial proteome and phosphoproteome during fermentative and respiratory growth in Saccharomyces cerevisiae.
findings: []
- id: PMID:35563734
title: Pls1 Is a Peroxisomal Matrix Protein with a Role in Regulating Lysine Biosynthesis.
findings: []
- id: PMID:9162072
title: SHY1, the yeast homolog of the mammalian SURF-1 gene, encodes a mitochondrial protein required for respiration.
findings:
- statement: SHY1 encodes the yeast SURF1 homolog and localizes to the inner mitochondrial membrane.
supporting_text: "The encoded protein is homologous to the product of the mammalian SURF-1 gene."
- id: file:yeast/SHY1/SHY1-deep-research-falcon.md
title: Falcon deep research report on SHY1
findings:
- statement: Falcon synthesis identifies SHY1 as a SURF1-family inner mitochondrial membrane complex IV assembly factor.
core_functions:
- description: >-
Shy1 is a SURF1-family mitochondrial inner membrane assembly factor for
cytochrome c oxidase. It acts during Cox1 maturation and assembly
intermediate progression, linking Mss51/Cox14-dependent Cox1 translational
regulation to complex IV assembly and supercomplex formation.
directly_involved_in:
- id: GO:0033617
label: mitochondrial respiratory chain complex IV assembly
locations:
- id: GO:0005743
label: mitochondrial inner membrane
supported_by:
- reference_id: PMID:17882259
supporting_text: "We suggest that Shy1 links Cox1 translational regulation to complex IV assembly and supercomplex formation."
- reference_id: file:yeast/SHY1/SHY1-deep-research-falcon.md
supporting_text: Falcon deep research emphasizes Cox1 maturation and complex IV assembly as the core SHY1 function.
proposed_new_terms: []
suggested_questions:
- question: >-
Is there enough direct evidence to annotate a specific Shy1 molecular
function for Cox1 cofactor insertion or assembly-intermediate stabilization,
rather than leaving SHY1 represented only by the biological-process term for
complex IV assembly?
experts:
- Mick DU
- Rehling P
- Winge DR
suggested_experiments:
- hypothesis: >-
Shy1 promotes Cox1 heme a3:CuB maturation or maintains Cox1 in an
assembly-competent state rather than binding unfolded proteins generally.
description: >-
Reconstitute Shy1-containing Cox1 assembly intermediates with Cox14, Mss51,
Coa1 and cofactor-insertion factors, then test Shy1 mutants for Cox1
cofactor incorporation, assembly-intermediate stability, and release of Mss51.
experiment_type: mitochondrial complex IV assembly intermediate assay