AIM6 (YDL237W) is an uncharacterized protein of the budding yeast Saccharomyces cerevisiae whose molecular function and subcellular location are not established. It is a 390-residue protein synthesized with a predicted N-terminal signal peptide (residues 1-17), suggesting entry into the secretory pathway, and the bulk of the mature protein adopts the PLC-like phosphodiesterase TIM (beta/alpha)8-barrel fold shared by phosphoinositide-specific phospholipase C and glycerophosphodiester phosphodiesterase enzymes. It defines its own narrow sequence family (the AIM6 family) within a divergent, uncharacterized branch of this phosphodiesterase-like superfamily, and no catalytic activity, substrate, or physiological reaction has been demonstrated for it. The only experimental phenotype reported is that deletion impairs respiratory (non-fermentable-carbon) growth and alters mitochondrial transmission, the observation from which the gene took its name (Altered Inheritance of Mitochondria); whether this reflects a direct or an indirect role in mitochondrial function is unresolved. The gene is non-essential and is conserved among fungi.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006629 lipid metabolic process | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Electronic InterPro2GO annotation transferred from the PLC-like phosphodiesterase superfamily match (IPR017946). Phosphoinositide-specific phospholipase C acts on membrane lipids, but AIM6 belongs to a divergent, uncharacterized subgroup of the fold with no demonstrated lipid substrate or lipid-related activity, and InterPro itself states its function is unclear. Reason: This over-extrapolates the lipid role of characterized PI-PLC enzymes to a divergent uncharacterized domain. There is no experimental evidence that AIM6 participates in lipid metabolism; the phosphodiesterase-like superfamily also contains glycerophosphodiester phosphodiesterases and many non-lipid activities, so "lipid metabolic process" is an unsupported specialization from a fold-only match. Not a confident biological process for this gene. |
| GO:0008081 phosphoric diester hydrolase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Electronic InterPro2GO annotation from the PLC-like phosphodiesterase TIM-barrel superfamily match (IPR017946 / IPR039559, CDD cd08577 "PI-PLCc_GDPD_SF_unchar3"). The mature protein does adopt this catalytic fold and retains some conserved His/Asp residues consistent with it, so the annotation is not demonstrably wrong; however the assignment is a distant, fold-level prediction from a subgroup that CDD and InterPro explicitly label uncharacterized, with no demonstrated activity, substrate, or assay. Reason: Keep awareness of the fold-based phosphodiesterase prediction, but it should not be treated as an established molecular function. It rests solely on membership in a divergent, uncharacterized branch of the PI-PLC/GDPD superfamily; no catalytic activity or substrate has ever been shown for AIM6. This is the central molecular-function knowledge gap for the gene (see knowledge_gaps), not a curated core function. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: SGD records the molecular function as ND (no biological data available). This correctly states that no experimentally supported molecular function is known for AIM6; the only molecular-function claim in GOA is the fold-based IEA phosphodiesterase prediction above. Reason: Appropriate use of the root term with ND to signal that AIM6's molecular function is genuinely unknown. Consistent with SGD's summary that the protein's biological role and cellular location are unknown. |
| GO:0005575 cellular_component | ND GO_REF:0000015 | ACCEPT | Summary: SGD records the cellular component as ND (no biological data available). UniProt provides no subcellular-location statement; the only localization-relevant feature is a predicted N-terminal signal peptide implying secretory-pathway entry, which is not sufficient to assign a compartment. Reason: Correct use of the root term with ND: AIM6's localization is unresolved. The predicted signal peptide and the indirect nature of the mitochondrial deletion phenotype mean a specific compartment cannot be asserted. |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: SGD records the biological process as ND (no biological data available). The one experimental handle is that deletion impairs respiratory growth / alters mitochondrial transmission (PMID:19300474), but the screen authors caution this may be indirect, so a specific biological process is not assignable with confidence. Reason: Correct use of the root term with ND. While the AIM screen phenotype hints at a role connected to mitochondrial biogenesis/respiration, the effect may be indirect and no mechanism is known, so no specific BP term is warranted. The unknown biological role is captured in knowledge_gaps. |
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Download this section (compressed HTML)Q: Does the AIM6 PLC-like phosphodiesterase-fold domain have any catalytic activity in vitro, and if so, on what substrate (a phosphoinositide, a glycerophosphodiester, a cyclic phosphate, or another phosphodiester)?
Q: Where does AIM6 localize? Is the predicted N-terminal signal peptide cleaved and does the protein enter the secretory pathway (ER/Golgi/cell surface/vacuole), which would argue that its respiratory phenotype is indirect rather than a direct mitochondrial role?
Q: Is the respiratory-growth / altered-mitochondrial-transmission phenotype of aim6-delta a direct consequence of AIM6 activity, or an indirect/pleiotropic effect (e.g. via lipid or secretory-pathway homeostasis)?
Experiment: Purify recombinant mature AIM6 (residues 18-390) and assay phosphodiesterase activity against a panel of candidate substrates (phosphoinositides, glycerophosphodiesters such as glycerophosphocholine, cyclic nucleotides, and generic bis-p-nitrophenyl phosphate) with and without divalent cations; test predicted catalytic-residue point mutants (e.g. the His118/His120 pair) to establish whether the retained fold is enzymatically functional or a pseudoenzyme.
Hypothesis: The AIM6 PLC-like domain is a catalytically active phosphodiesterase acting on a specific phosphodiester substrate.
Type: in vitro enzyme assay / structure-function mutagenesis
Experiment: Determine AIM6 subcellular localization by tagging the endogenous locus (C-terminal fluorescent tag, and separately an internal tag preserving the signal peptide) and by subcellular fractionation / signal-peptide cleavage assays, to test whether AIM6 is secreted/ER-Golgi resident versus mitochondrial.
Hypothesis: AIM6 enters the secretory pathway and is not a resident mitochondrial protein, implying its respiratory phenotype is indirect.
Type: fluorescence microscopy / subcellular fractionation
Experiment: Characterize aim6-delta with quantitative respiratory-growth and petite-frequency assays, lipidomic profiling, and epistasis / synthetic-genetic-array analysis against mitochondrial- biogenesis and lipid/secretory-pathway mutants to place AIM6 in a functional module and distinguish a direct from an indirect mitochondrial role.
Hypothesis: The aim6-delta respiratory phenotype reports a defined pathway that can be identified by genetic and physiological profiling.
Type: quantitative genetics / metabolic profiling
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The molecular function of AIM6 is unknown. Although the mature protein adopts the PLC-like phosphodiesterase (PI-PLC/GDPD-type) TIM-barrel fold, it is undetermined whether AIM6 has any catalytic activity at all, and if so what its substrate and reaction are. No enzymatic activity, substrate, or partner has ever been measured for it.
OPEN BIOLOGY WHOLLY_DARK
What is known: AIM6 is a verified, non-essential, expressed 390-aa protein (protein-level evidence) with a predicted N-terminal signal peptide (1-17). Its C-terminal domain (~residues 115-385) matches the PLC-like phosphodiesterase TIM-barrel superfamily (IPR017946) and an AIM6-specific PI-PLC-like catalytic-domain entry (IPR039559) built on CDD cd08577, a group explicitly labelled "uncharacterized." Some conserved His/Asp residues consistent with the fold are retained. The only functional label in GOA beyond root/ND terms is the fold-based IEA phosphodiesterase prediction.
Significance: AIM6 is a conserved fungal protein that defines its own family within a divergent branch of the ubiquitous phosphoinositide-phospholipase-C / glycerophosphodiester-phosphodiesterase superfamily. Establishing whether it is an active phosphodiesterase (and on what substrate) or a pseudoenzyme would assign a first molecular function to a member of the fungal unknome and clarify a poorly explored corner of a large, biomedically important enzyme fold.
What would resolve it: In vitro phosphodiesterase assays on purified AIM6 against a substrate panel, with catalytic-residue mutagenesis to test whether the fold is functional; structural determination of the domain to inspect the active-site geometry.
Provenance (the field's own admissions):
Gap: The biological role of AIM6 and the mechanism behind its deletion phenotype are unknown. It is unresolved whether AIM6 acts directly in mitochondrial biogenesis/respiration or whether the respiratory-growth defect of the deletion is an indirect consequence of some other cellular activity.
OPEN BIOLOGY BP_DARK
What is known: The one experimental phenotype is that aim6-delta impairs respiratory (non-fermentable-carbon) growth and alters mitochondrial transmission (the basis of the AIM name), reported in the quantitative petite-frequency screen of PMID:19300474. That study explicitly cautions that many genes with such phenotypes are not mitochondrial and may affect biogenesis indirectly. AIM6's localization is unknown, and its predicted signal peptide points toward the secretory pathway rather than the mitochondrion.
Significance: Assigning AIM6 to a specific pathway would explain a reproducible respiratory-growth phenotype in a model eukaryote and determine whether it is a genuine (if unusual, secretory-pathway-linked) contributor to mitochondrial function or an indirect effector — a distinction the original screen flagged as generally unresolved for its hits.
What would resolve it: Determine AIM6 localization; run epistasis / synthetic-genetic and metabolic (lipidomic) profiling of aim6-delta against mitochondrial-biogenesis and lipid/secretory-pathway mutants to place AIM6 in a functional module and test direct vs indirect models.
Provenance (the field's own admissions):
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