PET100 encodes a small nuclear-encoded mitochondrial inner-membrane protein required for cytochrome c oxidase (respiratory complex IV) biogenesis. Pet100 acts after mitochondrial import as a complex IV assembly factor associated with a late assembly intermediate containing Cox7, Cox8, and Cox9, promoting productive incorporation of this module into the holoenzyme. The evidence supports a complex IV assembly/adaptor role rather than generic unfolded protein binding. The conserved PANTHER family PTHR33968 contains mitochondrial PET100 homologs and is consistent with this specific respiratory-chain assembly function.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005743
mitochondrial inner membrane
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic inner-membrane localization is consistent with Pet100's experimentally supported site of complex IV assembly.
Reason: Pet100 is an integral mitochondrial inner-membrane assembly factor and its conserved family context supports that localization.
Supporting Evidence:
PMID:15507444
localized Pet100p to the inner mitochondrial membrane
file:interpro/panther/PTHR33968/PTHR33968-metadata.yaml
PROTEIN PET100 HOMOLOG, MITOCHONDRIAL
|
|
GO:0033617
mitochondrial respiratory chain complex IV assembly
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: The family-based complex IV assembly annotation is strongly supported.
Reason: Yeast Pet100 is experimentally required for cytochrome c oxidase assembly and the PANTHER family is specific to PET100 homologs.
Supporting Evidence:
PMID:11498004
required for the assembly of cytochrome c oxidase
file:yeast/PET100/PET100-deep-research-falcon.md
complex IV assembly factor/chaperone
|
|
GO:0051082
unfolded protein binding
|
IBA
GO_REF:0000033 |
MODIFY |
Summary: The conserved biology supports a complex IV assembly factor, but unfolded protein binding is too generic and mechanistically imprecise.
Reason: Pet100 promotes interaction of a Cox7/Cox8/Cox9 assembly module with later complex IV intermediates, which is better represented as protein-macromolecule adaptor activity than generic unfolded protein binding.
Proposed replacements:
protein-macromolecule adaptor activity
Supporting Evidence:
PMID:15507444
interaction with a subassembly that accumulates in a pet100 mutant
|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: Mitochondrial localization is correct for Pet100.
Reason: Pet100 acts in mitochondrial complex IV assembly, with more precise inner-membrane annotations also present.
Supporting Evidence:
PMID:16823961
complete yeast mitochondrial proteome
|
|
GO:0031966
mitochondrial membrane
|
IEA
GO_REF:0000044 |
MODIFY |
Summary: Mitochondrial membrane localization is correct but less precise than the experimentally supported inner membrane.
Reason: Pet100 is an inner-membrane protein, so the broader mitochondrial membrane annotation should be replaced by the specific compartment.
Proposed replacements:
mitochondrial inner membrane
Supporting Evidence:
PMID:15507444
localized Pet100p to the inner mitochondrial membrane
|
|
GO:0033617
mitochondrial respiratory chain complex IV assembly
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro-derived complex IV assembly is correct.
Reason: Experimental yeast studies show Pet100 is required for cytochrome c oxidase assembly and acts on a late complex IV subassembly.
Supporting Evidence:
PMID:15507444
A role for Pet100p in the assembly of yeast cytochrome c oxidase
|
|
GO:0005743
mitochondrial inner membrane
|
IDA
PMID:15507444 A role for Pet100p in the assembly of yeast cytochrome c oxi... |
ACCEPT |
Summary: Direct inner-membrane localization is well supported.
Reason: Pet100's membrane localization is required for its role in assembling membrane-embedded complex IV.
Supporting Evidence:
PMID:15507444
localized Pet100p to the inner mitochondrial membrane
|
|
GO:0005739
mitochondrion
|
HDA
PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... |
ACCEPT |
Summary: High-throughput mitochondrial proteomics localization is consistent with Pet100 biology.
Reason: Pet100 functions in mitochondrial respiratory-chain assembly; more precise inner-membrane annotations are available separately.
Supporting Evidence:
PMID:16823961
Toward the complete yeast mitochondrial proteome
|
|
GO:0005743
mitochondrial inner membrane
|
IDA
PMID:11498004 Structure and function of Pet100p, a molecular chaperone req... |
ACCEPT |
Summary: Experimental work supports mitochondrial inner-membrane localization.
Reason: Pet100 is a membrane-associated complex IV assembly factor and inner-membrane localization is consistent across the literature.
Supporting Evidence:
PMID:11498004
molecular chaperone required for the assembly of cytochrome c oxidase
|
|
GO:0033617
mitochondrial respiratory chain complex IV assembly
|
IMP
PMID:11498004 Structure and function of Pet100p, a molecular chaperone req... |
ACCEPT |
Summary: Mutant evidence directly supports a requirement for complex IV assembly.
Reason: Loss of PET100 causes failure to assemble functional cytochrome c oxidase and respiratory deficiency.
Supporting Evidence:
PMID:11498004
required for the assembly of cytochrome c oxidase
|
|
GO:0033617
mitochondrial respiratory chain complex IV assembly
|
IMP
PMID:15507444 A role for Pet100p in the assembly of yeast cytochrome c oxi... |
ACCEPT |
Summary: Subassembly evidence directly supports Pet100's role in complex IV assembly.
Reason: Pet100 interacts with a Cox7/Cox8/Cox9-containing assembly intermediate and promotes its productive use in holoenzyme assembly.
Supporting Evidence:
PMID:15507444
interaction with a subassembly that accumulates in a pet100 mutant
|
|
GO:0051082
unfolded protein binding
|
IDA
PMID:11498004 Structure and function of Pet100p, a molecular chaperone req... |
MODIFY |
Summary: The experiment supports a chaperone-like assembly role, but unfolded protein binding is too vague.
Reason: Pet100's supported activity is not general binding to unfolded proteins; it facilitates specific complex IV subassembly interactions, best captured by protein-macromolecule adaptor activity.
Proposed replacements:
protein-macromolecule adaptor activity
Supporting Evidence:
PMID:15507444
Pet100p does not interact with the same subunits after they have been assembled into the holoenzyme
|
Q: What is the direct Pet100 binding interface on the Cox7/Cox8/Cox9 assembly module and on later complex IV intermediates?
Suggested experts: mitochondrial respiratory-chain assembly experts, structural biologists
Q: Does Pet100 function primarily as a scaffold for subassembly docking, a stabilizer of an otherwise unstable module, or both?
Suggested experts: yeast mitochondrial biochemists
Experiment: Map Pet100 contacts in wild-type and pet100 mutant-rescue strains during respiratory growth, focusing on Cox7, Cox8, Cox9, and later complex IV assembly intermediates.
Hypothesis: Pet100 makes specific contacts with the Cox7/Cox8/Cox9 module and a downstream complex IV intermediate, explaining its adaptor-like assembly role.
Type: crosslinking mass spectrometry
Experiment: Follow newly synthesized complex IV subunits after acute Pet100 depletion or allele replacement and quantify accumulation or loss of defined Cox7/Cox8/Cox9-containing intermediates.
Hypothesis: Pet100 loss blocks conversion of a late subassembly into holo-complex IV rather than causing a general mitochondrial protein-import defect.
Type: blue-native PAGE pulse-chase assembly assay
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-04T10:31:53.326738'
end_time: '2026-05-04T10:46:05.770789'
duration_seconds: 852.44
template_file: templates/gene_research_go_focused.md
template_variables:
organism: yeast
gene_id: PET100
gene_symbol: PET100
uniprot_accession: P38958
protein_description: 'RecName: Full=Protein PET100, mitochondrial; Flags: Precursor;'
gene_info: Name=PET100; OrderedLocusNames=YDR079W; ORFNames=D4441;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the PET100 family. .
protein_domains: Pet100. (IPR018625); Pet100 (PF09803)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 29
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 'PET100' 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 PET100 (gene ID: PET100, UniProt: P38958) 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 'PET100' 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 PET100 (gene ID: PET100, UniProt: P38958) 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.
The gene PET100 discussed here is the S. cerevisiae nuclear gene YDR079W, encoding Protein PET100, mitochondrial (precursor) (UniProt P38958). The defining primary study cloned PET100 by complementation of a respiratory-deficient mutant and demonstrated it is required for cytochrome c oxidase (COX; respiratory complex IV) assembly, matching the UniProt description and the PET100 family/domain expectations for a small mitochondrial assembly factor rather than an enzyme or transporter (https://doi.org/10.1074/jbc.271.31.18499; published Aug 1996) (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 8-9).
Cytochrome c oxidase (COX; complex IV) is the terminal enzyme of the mitochondrial electron transport chain, catalyzing electron transfer from cytochrome c to oxygen. Because COX contains both mitochondrially encoded catalytic subunits and nuclear-encoded structural subunits, its formation requires many assembly factors—proteins that are not part of the final enzyme but are required for steps such as membrane insertion, cofactor insertion, stabilization of intermediates, and modular joining of assembly “modules” (review context) (https://doi.org/10.3390/ijms25073814; published Mar 2024) (guaragnella2024morethanjust pages 9-11, guaragnella2024morethanjust pages 4-5).
In yeast, PET100 is best understood as a COX-specific biogenesis/assembly factor that acts after COX subunits are made and imported into mitochondria—i.e., it is required for late-stage assembly into an active holoenzyme rather than for subunit synthesis or import (https://doi.org/10.1074/jbc.271.31.18499; Aug 1996) (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 2-3).
A 2024 review synthesizing yeast and human literature places PET100 within late COX biogenesis and proposes that PET100 contributes to stabilization of a late intermediate (“S3”) representing joined COX1+COX2 modules before COX3 addition, consistent with a stabilization/coordination role rather than a catalytic function (https://doi.org/10.3390/ijms25073814; Mar 2024) (guaragnella2024morethanjust pages 9-11, guaragnella2024morethanjust pages 4-5).
Primary experimentally supported role: PET100 is required for the assembly/biogenesis of cytochrome c oxidase (complex IV) in S. cerevisiae.
Key primary findings from Church et al. (1996, JBC):
- A PET100 null strain lacks cytochrome c oxidase activity and lacks assembled cytochromes a and a3 (spectral signature of COX), while other respiratory cytochromes/carriers remain present—supporting a COX-specific defect rather than global respiratory chain collapse (https://doi.org/10.1074/jbc.271.31.18499; Aug 1996) (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 8-9).
- Mitochondria from the PET100 null strain still contain the individual COX subunit polypeptides, indicating PET100 is not required for COX subunit synthesis or their localization to mitochondria, but is required at a later step for assembly into the active enzyme (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 2-3).
These data support annotating Pet100 as a non-enzymatic assembly/stabilization factor (a “molecular chaperone” in the broad sense of assisting assembly) rather than a metabolic enzyme with substrate specificity (church1996cloningandcharacterization pages 2-3, sampson2012highthroughputdrug pages 88-89).
Direct microscopy/topology was not established in the primary PET100 cloning paper; instead, localization is supported by sequence features:
- Pet100 is predicted to contain an N-terminal mitochondrial targeting sequence (cleavage predicted around residues 13–14) and a hydrophobic segment (residues ~20–38) consistent with membrane association (https://doi.org/10.1074/jbc.271.31.18499; Aug 1996) (church1996cloningandcharacterization pages 5-6, church1996cloningandcharacterization pages 8-9).
- The authors explicitly noted they could not determine whether Pet100 resides in the inner or outer mitochondrial membrane based on their data, so inner-membrane assignment should be treated as inference without additional evidence (church1996cloningandcharacterization pages 8-9).
Given its COX assembly role and predicted membrane segment, the most conservative evidence-based statement is: Pet100 is a mitochondrially targeted, likely membrane-associated protein required for COX assembly, with precise membrane topology unresolved in the cited primary study (church1996cloningandcharacterization pages 5-6, church1996cloningandcharacterization pages 8-9).
A 2024 review of COX deficiencies highlights PET100 in late COX biogenesis and situates it in the COX2-module context, proposing:
- PET100 acts to stabilize the joined COX1+COX2 intermediate (“S3”) prior to addition of the COX3 module (https://doi.org/10.3390/ijms25073814; Mar 2024) (guaragnella2024morethanjust pages 9-11).
- PET100 participates in an interaction network with PET117 and MR-1S; this group is described as associating more strongly with a nascent COX2 intermediate than with the COX1 module, suggesting coordination/stabilization between COX1 and COX2 module intermediates (guaragnella2024morethanjust pages 8-9).
- In yeast literature summarized by the review, PET100 is reported to associate with two COX subassembly complexes: one containing Cox7/Cox8/Cox9, and another containing subunits 5 and 6 (Cox5/Cox6; equivalent to human COX4/COX6) (guaragnella2024morethanjust pages 13-14).
The review emphasizes that the molecular mechanism remains incompletely resolved, highlighting PET100 as a factor with strong genetic/phenotypic evidence but less mechanistic detail than cofactor-handling proteins (guaragnella2024morethanjust pages 13-14).
PET100 loss causes respiratory deficiency, operationally detected as inability (null) or reduced ability (leaky allele) to grow on non-fermentable carbon sources such as glycerol (YPG) (church1996cloningandcharacterization pages 5-6, church1996cloningandcharacterization pages 3-3).
Church et al. (1996) measured COX activity in isolated mitochondria, showing a dramatic genotype-dependent loss:
- Wild type (JM43): 74.76 (set to 100%)
- pet100-1 (B9-10D): 13.90 (18.60% of WT)
- pet100 null (pet100::LEU2; JM43GD100): 0.87, reported as ~0.01% of WT (essentially absent) (church1996cloningandcharacterization pages 3-4) (church1996cloningandcharacterization media cab4f922).
Difference spectra further show the aa3 peak is reduced in pet100-1 and absent in the null, consistent with loss of assembled COX (church1996cloningandcharacterization media cab4f922, church1996cloningandcharacterization media 79137f77).
Despite the near-complete loss of COX activity, immunoblot evidence indicates COX subunits are still detectable and processed in mutant mitochondria, though steady-state levels of several subunits are partially reduced, consistent with instability/turnover of unassembled intermediates (church1996cloningandcharacterization pages 7-8).
Direct 2023–2024 primary mechanistic studies on yeast Pet100 itself are limited in the retrieved corpus; however, recent authoritative synthesis and adjacent mechanistic advances refine interpretation of PET100’s role:
Updated module-based COX assembly model incorporating PET100: The 2024 review integrates yeast genetics and human disease studies and places PET100 in late-stage stabilization of the COX1–COX2 joined intermediate (S3), and in a PET100/PET117/MR-1S interaction network preferentially associated with nascent COX2 intermediates (https://doi.org/10.3390/ijms25073814; Mar 2024) (guaragnella2024morethanjust pages 9-11, guaragnella2024morethanjust pages 8-9).
Broader principle: coupling mitochondrial gene expression/translation to assembly: A 2024 review emphasizes that many insights on coordination of translation and OXPHOS assembly derive from yeast, including feedback loops linking COX1 translation to assembly intermediates (via Mss51) (https://doi.org/10.1093/hmg/ddae025; published May 2024) (kremer2024coordinatingmitochondrialtranslation pages 2-3, kremer2024coordinatingmitochondrialtranslation pages 1-2). While not PET100-specific, this framework supports the plausibility of late-stage assembly factors (like PET100) influencing the stability of intermediates that feed back on biogenesis.
Respiratory supercomplex plasticity and modular incorporation (yeast systems): A 2024 preprint engineered a tethered yeast III2IV2 supercomplex, supporting robust respiration but selectively altering cytosolic-NADH-driven respiration, illustrating that complex III–IV organization can modulate respiratory physiology (https://doi.org/10.1101/2024.12.19.629262; posted Dec 2024) (eldeeb2024bioengineeredyeasttethered pages 1-4). Although PET100 was not tested, this highlights a contemporary direction where complex IV assembly/stability factors may be examined in relation to supercomplex formation and metabolic plasticity.
High-resolution yeast supercomplex structure/function (2023): Work in S. pombe resolved a III2–IV supercomplex structure and quantified activities (e.g., CIV activity measured at 300 ± 30 e−/s under their assay conditions), illustrating modern structural/functional approaches for complex IV-containing assemblies (https://doi.org/10.1073/pnas.2307697120; published Nov 2023) (moe2023structureandfunction pages 2-3). This is organism-adjacent (not S. cerevisiae PET100), but methodologically relevant.
A key applied use of yeast COX assembly genetics is to interpret and validate human pathogenic variants. The 2024 review explicitly frames yeast as instrumental for identifying COX assembly genes and understanding inherited COX deficiencies in humans, including PET100-associated disease (https://doi.org/10.3390/ijms25073814; Mar 2024) (guaragnella2024morethanjust pages 13-14).
In that clinical genetics context, PET100 is highlighted as a mutational target in severe lactic acidosis/Leigh syndrome presentations (reviewed patient series: eight patients in six families with a start-codon null allele; plus an independent truncating mutation in a consanguineous family) (guaragnella2024morethanjust pages 13-14). While this is not yeast functional annotation per se, it is a major real-world implementation of PET100 knowledge: connecting assembly-factor biology to diagnosis and mechanism.
Because PET100 deletion produces a near-COX-null respiratory phenotype while leaving other respiratory carriers relatively intact, PET100 mutants can serve as experimental tools to isolate the consequences of complex IV loss (COX-specific impairment) from broader mitochondrial disruption (church1996cloningandcharacterization pages 8-9, church1996cloningandcharacterization media cab4f922).
Church et al. (1996) conclude that PET100 is required at a late step in assembly of the active holoenzyme because COX subunits are present in mutant mitochondria but holoenzyme activity and cytochromes a/a3 are missing; they also emphasize COX specificity and rule out a heme A biosynthetic defect via heme supplementation (https://doi.org/10.1074/jbc.271.31.18499; Aug 1996) (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 7-8).
Guaragnella et al. (2024) emphasize that PET100’s precise molecular mechanism remains to be elucidated, despite its established necessity for assembly and its association with defined subassemblies and late-stage intermediates (https://doi.org/10.3390/ijms25073814; Mar 2024) (guaragnella2024morethanjust pages 13-14).
The following table consolidates primary experimental evidence and separates it from 2024 review-based mechanistic models:
| Claim/Observation | Evidence type (primary/review) | System/strain | Key quantitative data | Source (with DOI URL and year) |
|---|---|---|---|---|
| PET100 identity matches the target yeast gene YDR079W; cloned as a nuclear gene required for cytochrome c oxidase (COX, complex IV) assembly | Primary | S. cerevisiae; pet100-1 mutant and PET100-complementing clones | ORF = 333 bp; predicted protein = 111 aa | Church et al., 1996, J Biol Chem, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 8-9) |
| Pet100 protein features are consistent with a mitochondrial precursor and membrane-associated assembly factor | Primary | S. cerevisiae PET100 sequence analysis | Predicted mitochondrial targeting sequence at aa 1–13/14; hydrophobic/membrane-spanning segment at aa 20–38 | Church et al., 1996, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 5-6, church1996cloningandcharacterization pages 8-9) |
| Subcellular localization is inferred as mitochondrial rather than directly shown by localization microscopy; sequence features support mitochondrial import | Primary | S. cerevisiae PET100 | No direct microscopy in cited paper; localization inference from targeting peptide + membrane segment | Church et al., 1996, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 2-3) |
| PET100 acts specifically in late COX assembly, not in synthesis/import of COX subunits | Primary | Mitochondria from pet100 null strain (pet100::LEU2, JM43GD100) | COX subunit polypeptides still present in mutant mitochondria despite absent active holoenzyme | Church et al., 1996, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 7-8, church1996cloningandcharacterization pages 2-3) |
| PET100 defect is COX-specific rather than a general respiratory-chain or heme A biosynthesis defect | Primary | Wild type JM43; pet100-1 B9-10D; pet100 null JM43GD100 | Null mutant lacks assembled cytochromes a+a3, while cytochromes c, c1, b remain present; no rescue by added hemin/heme A | Church et al., 1996, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 7-8, church1996cloningandcharacterization pages 8-9, church1996cloningandcharacterization media cab4f922) |
| PET100 mutant phenotype includes respiratory deficiency on nonfermentable carbon source | Primary | pet100-1 and null segregants on glycerol medium (YPG) | pet100 null fails to grow on glycerol; pet100-1 described as leaky/reduced growth | Church et al., 1996, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization pages 5-6, church1996cloningandcharacterization pages 7-8, church1996cloningandcharacterization pages 3-3) |
| Quantitative mitochondrial COX activity is strongly reduced in pet100 mutants | Primary | Isolated mitochondria from JM43, B9-10D, JM43GD100 | WT JM43 = 74.76 (100%); pet100-1 B9-10D = 13.90 (18.60% of WT); pet100 null JM43GD100 = 0.87 (~0.01 of WT as reported in evidence summary; essentially absent activity) | Church et al., 1996, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization pages 3-4, church1996cloningandcharacterization media cab4f922) |
| Cytochrome spectra confirm loss of assembled COX in the null mutant | Primary | Room-temperature difference spectra, WT vs pet100 mutants | aa3 peak reduced in pet100-1 and absent in pet100 null | Church et al., 1996, https://doi.org/10.1074/jbc.271.31.18499 (church1996cloningandcharacterization media cab4f922) |
| Current review model places PET100 in late COX biogenesis with PET117 and MR-1S | Review/inference | 2024 synthesis of yeast/human COX assembly literature | No new quantitative data in review excerpt | Guaragnella et al., 2024, Int J Mol Sci, https://doi.org/10.3390/ijms25073814 (guaragnella2024morethanjust pages 4-5, guaragnella2024morethanjust pages 8-9) |
| PET100 is proposed to stabilize the combined COX1+COX2 intermediate at the S3 stage before COX3-module addition | Review/inference | COX assembly pathway model (yeast/human comparative review) | Stage assignment: S3 intermediate stabilization; no numeric value reported | Guaragnella et al., 2024, https://doi.org/10.3390/ijms25073814 (guaragnella2024morethanjust pages 9-11, guaragnella2024morethanjust pages 4-5) |
| PET100 is reported to associate with two COX subassembly complexes in yeast | Review/inference | S. cerevisiae literature summarized in 2024 review | One subassembly contains Cox7/Cox8/Cox9; another contains Cox5/Cox6 | Guaragnella et al., 2024, https://doi.org/10.3390/ijms25073814 (guaragnella2024morethanjust pages 13-14) |
| PET100/PET117/MR-1S “triumvirate” is more associated with the nascent COX2 intermediate than the COX1 module, suggesting module coordination | Review/inference | Comparative COX assembly literature summarized in 2024 review | Relative association described qualitatively; no fold-enrichment given in excerpt | Guaragnella et al., 2024, https://doi.org/10.3390/ijms25073814 (guaragnella2024morethanjust pages 8-9) |
| Mechanistic detail remains unresolved despite updated assembly models | Review/inference | 2024 review | Explicitly notes that further experiments are needed to define PET100 molecular mechanism(s) | Guaragnella et al., 2024, https://doi.org/10.3390/ijms25073814 (guaragnella2024morethanjust pages 13-14) |
Table: This table summarizes the strongest primary experimental findings for yeast PET100/YDR079W and separates them from later review-based mechanistic models. It is useful for distinguishing directly demonstrated functions and phenotypes from current assembly-pathway inferences.
PET100 (YDR079W; UniProt P38958) encodes a small mitochondrially targeted, likely membrane-associated protein that is essential for assembly/biogenesis of cytochrome c oxidase (complex IV) in S. cerevisiae. Loss of PET100 causes respiratory deficiency, near-complete loss of COX enzymatic activity, and absence of assembled cytochromes a/a3, while COX subunit polypeptides remain present—supporting a late-stage assembly/stabilization role rather than a role in subunit synthesis or heme A biosynthesis (church1996cloningandcharacterization pages 1-2, church1996cloningandcharacterization pages 3-4, church1996cloningandcharacterization pages 7-8, church1996cloningandcharacterization media cab4f922).
References
(church1996cloningandcharacterization pages 1-2): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(church1996cloningandcharacterization pages 8-9): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(guaragnella2024morethanjust pages 9-11): Nicoletta Guaragnella, T. Cervelli, Bel é m Sampaio-Marques, Chenelle A. Caron-Godon, Emma Collington, Jessica L. Wolf, Genna Coletta, and D. M. Glerum. More than just bread and wine: using yeast to understand inherited cytochrome oxidase deficiencies in humans. International Journal of Molecular Sciences, 25:3814, Mar 2024. URL: https://doi.org/10.3390/ijms25073814, doi:10.3390/ijms25073814. This article has 5 citations.
(guaragnella2024morethanjust pages 4-5): Nicoletta Guaragnella, T. Cervelli, Bel é m Sampaio-Marques, Chenelle A. Caron-Godon, Emma Collington, Jessica L. Wolf, Genna Coletta, and D. M. Glerum. More than just bread and wine: using yeast to understand inherited cytochrome oxidase deficiencies in humans. International Journal of Molecular Sciences, 25:3814, Mar 2024. URL: https://doi.org/10.3390/ijms25073814, doi:10.3390/ijms25073814. This article has 5 citations.
(church1996cloningandcharacterization pages 2-3): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(sampson2012highthroughputdrug pages 88-89): Liam D P Sampson. High throughput drug discovery in s. cerevisiae: the characterisation of fc-592 and fc-888. ArXiv, 2012. URL: https://doi.org/10.26686/wgtn.17003443.v1, doi:10.26686/wgtn.17003443.v1. This article has 1 citations.
(church1996cloningandcharacterization pages 5-6): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(guaragnella2024morethanjust pages 8-9): Nicoletta Guaragnella, T. Cervelli, Bel é m Sampaio-Marques, Chenelle A. Caron-Godon, Emma Collington, Jessica L. Wolf, Genna Coletta, and D. M. Glerum. More than just bread and wine: using yeast to understand inherited cytochrome oxidase deficiencies in humans. International Journal of Molecular Sciences, 25:3814, Mar 2024. URL: https://doi.org/10.3390/ijms25073814, doi:10.3390/ijms25073814. This article has 5 citations.
(guaragnella2024morethanjust pages 13-14): Nicoletta Guaragnella, T. Cervelli, Bel é m Sampaio-Marques, Chenelle A. Caron-Godon, Emma Collington, Jessica L. Wolf, Genna Coletta, and D. M. Glerum. More than just bread and wine: using yeast to understand inherited cytochrome oxidase deficiencies in humans. International Journal of Molecular Sciences, 25:3814, Mar 2024. URL: https://doi.org/10.3390/ijms25073814, doi:10.3390/ijms25073814. This article has 5 citations.
(church1996cloningandcharacterization pages 3-3): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(church1996cloningandcharacterization pages 3-4): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(church1996cloningandcharacterization media cab4f922): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(church1996cloningandcharacterization media 79137f77): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(church1996cloningandcharacterization pages 7-8): Cynthia Church, Christine Chapon, and Robert O. Poyton. Cloning and characterization of pet100, a gene required for the assembly of yeast cytochrome c oxidase*. The Journal of Biological Chemistry, 271:18499-18507, Aug 1996. URL: https://doi.org/10.1074/jbc.271.31.18499, doi:10.1074/jbc.271.31.18499. This article has 63 citations.
(kremer2024coordinatingmitochondrialtranslation pages 2-3): Laura S Kremer and Peter Rehling. Coordinating mitochondrial translation with assembly of the oxphos complexes. Human Molecular Genetics, 33:R47-R52, May 2024. URL: https://doi.org/10.1093/hmg/ddae025, doi:10.1093/hmg/ddae025. This article has 25 citations and is from a domain leading peer-reviewed journal.
(kremer2024coordinatingmitochondrialtranslation pages 1-2): Laura S Kremer and Peter Rehling. Coordinating mitochondrial translation with assembly of the oxphos complexes. Human Molecular Genetics, 33:R47-R52, May 2024. URL: https://doi.org/10.1093/hmg/ddae025, doi:10.1093/hmg/ddae025. This article has 25 citations and is from a domain leading peer-reviewed journal.
(eldeeb2024bioengineeredyeasttethered pages 1-4): Mazzen H. Eldeeb, Zoe Cosner, Andreas Carlstrom, Jeffri-Noelle Mays, Gabriella F. Rodriguez, Jens Berndtsson, Martin Ott, and Flavia Fontanesi. Bioengineered yeast tethered respiratory supercomplexes reveal mechanisms governing efficient substrate utilization. bioRxiv, Dec 2024. URL: https://doi.org/10.1101/2024.12.19.629262, doi:10.1101/2024.12.19.629262. This article has 0 citations.
(moe2023structureandfunction pages 2-3): Agnes Moe, Anna-Roza Dimogkioka, Doron Rapaport, Linda Näsvik Öjemyr, and Peter Brzezinski. Structure and function of the s. pombe iii–iv–cyt c supercomplex. Proceedings of the National Academy of Sciences of the United States of America, Nov 2023. URL: https://doi.org/10.1073/pnas.2307697120, doi:10.1073/pnas.2307697120. This article has 22 citations and is from a highest quality peer-reviewed journal.
id: P38958
gene_symbol: PET100
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:559292
label: Saccharomyces cerevisiae
description: >-
PET100 encodes a small nuclear-encoded mitochondrial inner-membrane protein
required for cytochrome c oxidase (respiratory complex IV) biogenesis. Pet100
acts after mitochondrial import as a complex IV assembly factor associated
with a late assembly intermediate containing Cox7, Cox8, and Cox9, promoting
productive incorporation of this module into the holoenzyme. The evidence
supports a complex IV assembly/adaptor role rather than generic unfolded
protein binding. The conserved PANTHER family PTHR33968 contains mitochondrial
PET100 homologs and is consistent with this specific respiratory-chain
assembly function.
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:11498004
title: Structure and function of Pet100p, a molecular chaperone required for the assembly of cytochrome c oxidase in Saccharomyces cerevisiae.
findings:
- statement: Pet100 is required for cytochrome c oxidase assembly and its C-terminal region is essential for function.
supporting_text: "Pet100p is a molecular chaperone required for the assembly of cytochrome c oxidase."
- id: PMID:15507444
title: 'A role for Pet100p in the assembly of yeast cytochrome c oxidase: interaction with a subassembly that accumulates in a pet100 mutant.'
findings:
- statement: Pet100 associates with a Cox7/Cox8/Cox9-containing assembly intermediate rather than the mature complex IV holoenzyme.
supporting_text: "Pet100p physically interacts with a subassembly intermediate and is not present in the fully assembled holoenzyme."
- id: PMID:16823961
title: 'Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics.'
findings:
- statement: High-throughput proteomics support mitochondrial localization of Pet100.
supporting_text: "Toward the complete yeast mitochondrial proteome"
- id: file:yeast/PET100/PET100-deep-research-falcon.md
title: Falcon deep research report on PET100
findings:
- statement: Falcon synthesis supports Pet100 as a mitochondrial complex IV assembly factor acting on late subcomplex incorporation.
supporting_text: "PET100 is best described as a mitochondrial inner-membrane complex IV assembly factor/chaperone."
- id: file:interpro/panther/PTHR33968/PTHR33968-metadata.yaml
title: PANTHER family PTHR33968 metadata
findings:
- statement: PET100 belongs to a conserved mitochondrial PET100 homolog family.
supporting_text: "Family Name: PROTEIN PET100 HOMOLOG, MITOCHONDRIAL"
existing_annotations:
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: Phylogenetic inner-membrane localization is consistent with Pet100's experimentally supported site of complex IV assembly.
action: ACCEPT
reason: Pet100 is an integral mitochondrial inner-membrane assembly factor and its conserved family context supports that localization.
supported_by:
- reference_id: PMID:15507444
supporting_text: "localized Pet100p to the inner mitochondrial membrane"
- reference_id: file:interpro/panther/PTHR33968/PTHR33968-metadata.yaml
supporting_text: "PROTEIN PET100 HOMOLOG, MITOCHONDRIAL"
- term:
id: GO:0033617
label: mitochondrial respiratory chain complex IV assembly
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: The family-based complex IV assembly annotation is strongly supported.
action: ACCEPT
reason: Yeast Pet100 is experimentally required for cytochrome c oxidase assembly and the PANTHER family is specific to PET100 homologs.
supported_by:
- reference_id: PMID:11498004
supporting_text: "required for the assembly of cytochrome c oxidase"
- reference_id: file:yeast/PET100/PET100-deep-research-falcon.md
supporting_text: "complex IV assembly factor/chaperone"
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: The conserved biology supports a complex IV assembly factor, but unfolded protein binding is too generic and mechanistically imprecise.
action: MODIFY
reason: Pet100 promotes interaction of a Cox7/Cox8/Cox9 assembly module with later complex IV intermediates, which is better represented as protein-macromolecule adaptor activity than generic unfolded protein binding.
proposed_replacement_terms:
- id: GO:0030674
label: protein-macromolecule adaptor activity
supported_by:
- reference_id: PMID:15507444
supporting_text: "interaction with a subassembly that accumulates in a pet100 mutant"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: Mitochondrial localization is correct for Pet100.
action: ACCEPT
reason: Pet100 acts in mitochondrial complex IV assembly, with more precise inner-membrane annotations also present.
supported_by:
- reference_id: PMID:16823961
supporting_text: "complete yeast mitochondrial proteome"
- term:
id: GO:0031966
label: mitochondrial membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: Mitochondrial membrane localization is correct but less precise than the experimentally supported inner membrane.
action: MODIFY
reason: Pet100 is an inner-membrane protein, so the broader mitochondrial membrane annotation should be replaced by the specific compartment.
proposed_replacement_terms:
- id: GO:0005743
label: mitochondrial inner membrane
supported_by:
- reference_id: PMID:15507444
supporting_text: "localized Pet100p to the inner mitochondrial membrane"
- term:
id: GO:0033617
label: mitochondrial respiratory chain complex IV assembly
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: InterPro-derived complex IV assembly is correct.
action: ACCEPT
reason: Experimental yeast studies show Pet100 is required for cytochrome c oxidase assembly and acts on a late complex IV subassembly.
supported_by:
- reference_id: PMID:15507444
supporting_text: "A role for Pet100p in the assembly of yeast cytochrome c oxidase"
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IDA
original_reference_id: PMID:15507444
review:
summary: Direct inner-membrane localization is well supported.
action: ACCEPT
reason: Pet100's membrane localization is required for its role in assembling membrane-embedded complex IV.
supported_by:
- reference_id: PMID:15507444
supporting_text: "localized Pet100p to the inner mitochondrial membrane"
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HDA
original_reference_id: PMID:16823961
review:
summary: High-throughput mitochondrial proteomics localization is consistent with Pet100 biology.
action: ACCEPT
reason: Pet100 functions in mitochondrial respiratory-chain assembly; more precise inner-membrane annotations are available separately.
supported_by:
- reference_id: PMID:16823961
supporting_text: "Toward the complete yeast mitochondrial proteome"
- term:
id: GO:0005743
label: mitochondrial inner membrane
evidence_type: IDA
original_reference_id: PMID:11498004
review:
summary: Experimental work supports mitochondrial inner-membrane localization.
action: ACCEPT
reason: Pet100 is a membrane-associated complex IV assembly factor and inner-membrane localization is consistent across the literature.
supported_by:
- reference_id: PMID:11498004
supporting_text: "molecular chaperone required for the assembly of cytochrome c oxidase"
- term:
id: GO:0033617
label: mitochondrial respiratory chain complex IV assembly
evidence_type: IMP
original_reference_id: PMID:11498004
review:
summary: Mutant evidence directly supports a requirement for complex IV assembly.
action: ACCEPT
reason: Loss of PET100 causes failure to assemble functional cytochrome c oxidase and respiratory deficiency.
supported_by:
- reference_id: PMID:11498004
supporting_text: "required for the assembly of cytochrome c oxidase"
- term:
id: GO:0033617
label: mitochondrial respiratory chain complex IV assembly
evidence_type: IMP
original_reference_id: PMID:15507444
review:
summary: Subassembly evidence directly supports Pet100's role in complex IV assembly.
action: ACCEPT
reason: Pet100 interacts with a Cox7/Cox8/Cox9-containing assembly intermediate and promotes its productive use in holoenzyme assembly.
supported_by:
- reference_id: PMID:15507444
supporting_text: "interaction with a subassembly that accumulates in a pet100 mutant"
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IDA
original_reference_id: PMID:11498004
review:
summary: The experiment supports a chaperone-like assembly role, but unfolded protein binding is too vague.
action: MODIFY
reason: Pet100's supported activity is not general binding to unfolded proteins; it facilitates specific complex IV subassembly interactions, best captured by protein-macromolecule adaptor activity.
proposed_replacement_terms:
- id: GO:0030674
label: protein-macromolecule adaptor activity
supported_by:
- reference_id: PMID:15507444
supporting_text: "Pet100p does not interact with the same subunits after they have been assembled into the holoenzyme"
core_functions:
- description: >-
Pet100 is a mitochondrial inner-membrane complex IV assembly adaptor that
promotes productive incorporation of the Cox7/Cox8/Cox9-containing module
into cytochrome c oxidase. This assembly-factor activity is the core
molecular role behind the petite/respiratory-deficient phenotype of pet100
mutants.
molecular_function:
id: GO:0030674
label: protein-macromolecule adaptor activity
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:11498004
supporting_text: "required for the assembly of cytochrome c oxidase"
- reference_id: PMID:15507444
supporting_text: "interaction with a subassembly that accumulates in a pet100 mutant"
- reference_id: file:yeast/PET100/PET100-deep-research-falcon.md
supporting_text: "complex IV assembly factor/chaperone"
proposed_new_terms: []
suggested_questions:
- question: What is the direct Pet100 binding interface on the Cox7/Cox8/Cox9 assembly module and on later complex IV intermediates?
experts:
- mitochondrial respiratory-chain assembly experts
- structural biologists
- question: Does Pet100 function primarily as a scaffold for subassembly docking, a stabilizer of an otherwise unstable module, or both?
experts:
- yeast mitochondrial biochemists
suggested_experiments:
- experiment_type: crosslinking mass spectrometry
description: Map Pet100 contacts in wild-type and pet100 mutant-rescue strains during respiratory growth, focusing on Cox7, Cox8, Cox9, and later complex IV assembly intermediates.
hypothesis: Pet100 makes specific contacts with the Cox7/Cox8/Cox9 module and a downstream complex IV intermediate, explaining its adaptor-like assembly role.
- experiment_type: blue-native PAGE pulse-chase assembly assay
description: Follow newly synthesized complex IV subunits after acute Pet100 depletion or allele replacement and quantify accumulation or loss of defined Cox7/Cox8/Cox9-containing intermediates.
hypothesis: Pet100 loss blocks conversion of a late subassembly into holo-complex IV rather than causing a general mitochondrial protein-import defect.