Ilt1 (YDR090C; Ionic Liquid Tolerance 1) is a 310-residue budding-yeast protein with seven predicted membrane spans and two PQ-loop repeats. Chromosomal GFP fusions localize to the plasma membrane. It belongs to a conserved PQ-loop lineage with inferred basic-amino-acid transmembrane transport, vacuolar export and intracellular amino-acid homeostasis functions; its target-specific transport substrate, direction and possible vacuolar pool have not been directly measured. Loss of ILT1 sensitizes the BY background to imidazolium ionic liquids and crystal violet, and complementation or additional gene copies improve tolerance. This effect depends on strain background and does not require that Ilt1 be a component of the Sge1 efflux mechanism. How its inherited transport role relates to cationic-xenobiotic tolerance remains unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005774 vacuolar membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved PAINT inheritance is supported by the actual target lineage below PTN001044753. Reason: The actual PTHR16201 tree explicitly maps Q03193/YDR090C to leaf PTN000415976 in SF37 below annotated ancestor PTN001044753. Different characterized subfamilies do not invalidate this ancestral assertion, and no loss was found along the target lineage. The primary study establishes plasma-membrane localization and background-dependent xenobiotic tolerance but does not test or exclude a vacuolar pool, basic-amino-acid transport, or intracellular amino-acid homeostasis. Accept as an inherited function/location, distinguishing it from direct target assay evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001044753 SUPPORTS TRANSFER Accession-mapped target lineage is inspected and below this ancestor. PM imaging does not exclude a vacuolar pool or establish loss of inherited transport/homeostasis. Supporting Evidence: file:yeast/ILT1/ILT1-paint-lineage.md All four disputed inherited annotations originate at PTN001044753 and remain positive on target leaf PTN000415976. PMID:30045857 Ilt1 may also function at the plasma membrane and through a mechanism distinct from Sge1, but whether it directly exports ionic liquids and cationic compounds out of the cell remains unclear. |
| GO:0034488 basic amino acid transmembrane export from vacuole | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved PAINT inheritance is supported by the actual target lineage below PTN001044753. Reason: The actual PTHR16201 tree explicitly maps Q03193/YDR090C to leaf PTN000415976 in SF37 below annotated ancestor PTN001044753. Different characterized subfamilies do not invalidate this ancestral assertion, and no loss was found along the target lineage. The primary study establishes plasma-membrane localization and background-dependent xenobiotic tolerance but does not test or exclude a vacuolar pool, basic-amino-acid transport, or intracellular amino-acid homeostasis. Accept as an inherited function/location, distinguishing it from direct target assay evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001044753 SUPPORTS TRANSFER Accession-mapped target lineage is inspected and below this ancestor. PM imaging does not exclude a vacuolar pool or establish loss of inherited transport/homeostasis. Supporting Evidence: file:yeast/ILT1/ILT1-paint-lineage.md All four disputed inherited annotations originate at PTN001044753 and remain positive on target leaf PTN000415976. PMID:30045857 Ilt1 may also function at the plasma membrane and through a mechanism distinct from Sge1, but whether it directly exports ionic liquids and cationic compounds out of the cell remains unclear. |
| GO:0080144 intracellular amino acid homeostasis | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved PAINT inheritance is supported by the actual target lineage below PTN001044753. Reason: The actual PTHR16201 tree explicitly maps Q03193/YDR090C to leaf PTN000415976 in SF37 below annotated ancestor PTN001044753. Different characterized subfamilies do not invalidate this ancestral assertion, and no loss was found along the target lineage. The primary study establishes plasma-membrane localization and background-dependent xenobiotic tolerance but does not test or exclude a vacuolar pool, basic-amino-acid transport, or intracellular amino-acid homeostasis. Accept as an inherited function/location, distinguishing it from direct target assay evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001044753 SUPPORTS TRANSFER Accession-mapped target lineage is inspected and below this ancestor. PM imaging does not exclude a vacuolar pool or establish loss of inherited transport/homeostasis. Supporting Evidence: file:yeast/ILT1/ILT1-paint-lineage.md All four disputed inherited annotations originate at PTN001044753 and remain positive on target leaf PTN000415976. PMID:30045857 Ilt1 may also function at the plasma membrane and through a mechanism distinct from Sge1, but whether it directly exports ionic liquids and cationic compounds out of the cell remains unclear. |
| GO:0015174 basic amino acid transmembrane transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved PAINT inheritance is supported by the actual target lineage below PTN001044753. Reason: The actual PTHR16201 tree explicitly maps Q03193/YDR090C to leaf PTN000415976 in SF37 below annotated ancestor PTN001044753. Different characterized subfamilies do not invalidate this ancestral assertion, and no loss was found along the target lineage. The primary study establishes plasma-membrane localization and background-dependent xenobiotic tolerance but does not test or exclude a vacuolar pool, basic-amino-acid transport, or intracellular amino-acid homeostasis. Accept as an inherited function/location, distinguishing it from direct target assay evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001044753 SUPPORTS TRANSFER Accession-mapped target lineage is inspected and below this ancestor. PM imaging does not exclude a vacuolar pool or establish loss of inherited transport/homeostasis. Supporting Evidence: file:yeast/ILT1/ILT1-paint-lineage.md All four disputed inherited annotations originate at PTN001044753 and remain positive on target leaf PTN000415976. PMID:30045857 Ilt1 may also function at the plasma membrane and through a mechanism distinct from Sge1, but whether it directly exports ionic liquids and cationic compounds out of the cell remains unclear. file:yeast/ILT1/ILT1-deep-research-falcon.md the specific substrate and physiological role of YDR090C have **not yet been established directly** in the available primary literature |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic location from UniProt Subcellular Location mapping (UniProt SUBCELLULAR LOCATION: Cell membrane). Concordant with experimental IDA. Reason: Plasma-membrane localization is independently supported experimentally (Ilt1-GFP; Huh et al. GFP dataset). This IEA annotation is correct and redundant with the IDA below. Supporting Evidence: PMID:30045857 both Sge1PLL-GFP and Ilt1-GFP fusion proteins localized to the plasma membrane |
| GO:0016020 membrane | IEA GO_REF:0000117 | ACCEPT | Summary: Broad membrane localization is directly compatible with the target membrane topology and GFP microscopy. Reason: This correct broader term describes the core location; a more specific plasma-membrane annotation does not make it non-core. |
| GO:0005886 plasma membrane | IDA PMID:30045857 Natural Variation in the Multidrug Efflux Pump SGE1 Underlie... | ACCEPT | Summary: Direct experimental localization: Ilt1-GFP fusion protein localizes to the plasma membrane. This is the core, well-supported cellular location for Ilt1. Reason: Supported by direct fluorescence-microscopy evidence (Ilt1-GFP), and corroborated by the Huh et al. genome-wide GFP-localization study (UniProt SUBCELLULAR LOCATION: Cell membrane, ECO:0000269|PubMed:14562095). This is a core annotation. Supporting Evidence: PMID:30045857 both Sge1PLL-GFP and Ilt1-GFP fusion proteins localized to the plasma membrane |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: ND records the absence of an experimentally established target molecular activity. Reason: Retain the original curator-supplied placeholder while distinguishing direct knowledge from the independently supported phylogenetic transporter inference. ND does not negate that inferred activity. |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: Retain the original ND process placeholder as source provenance; the phenotype study leaves the direct xenobiotic-response mechanism unresolved. Reason: Deletion sensitivity, complementation and dosage effects establish toxin-tolerance dependence but do not show which response step Ilt1 performs. The earlier authored NEW xenobiotic-response assertion is withdrawn; this does not remove the separately supported inherited amino-acid-homeostasis processes. Supporting Evidence: PMID:30045857 ILT1 functions in tolerance to a range of cationic toxins in the BY strain background |
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Download this section (compressed HTML)Q: Does Ilt1 directly transport the imidazolium ionic-liquid cation (or a protective solute) across the plasma membrane, or does it act indirectly (e.g. by modulating another transporter or membrane property)?
Suggested experts: Trey K. Sato, Audrey P. Gasch
Q: What accounts for the background-dependence of the ilt1 phenotype (required in BY but not in strain 378)?
Q: How does the inherited basic-amino-acid transport/homeostasis role contribute to cationic-toxin tolerance, and does Ilt1 itself perform a xenobiotic-response step? The previous authored NEW response term is withdrawn pending participation evidence; necessity and rescue alone do not identify that step.
Experiment: Reconstitute purified Ilt1 into proteoliposomes (or express in a heterologous transport-null system) and assay uptake/efflux of candidate solutes, including the [C2C1im]+ cation, cationic dyes, and cationic amino acids, under a range of pH and ion gradients.
Hypothesis: Ilt1 is a plasma-membrane transporter whose substrate is a cation relevant to ionic-liquid/cationic-dye tolerance.
Type: transport assay
Experiment: Measure Ilt1 protein level, localization, and PTM state (including the reported Ser229 phosphorylation) with and without [C2C1im]Cl / crystal violet treatment.
Hypothesis: Ilt1 abundance or plasma-membrane residence changes upon exposure to cationic xenobiotics.
Type: quantitative fluorescence microscopy and immunoblotting
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Direct biochemical substrate, direction and transport mechanism of Ilt1 remain undetermined despite a supported inherited basic-amino-acid transporter assignment. The contribution of its plasma-membrane and any vacuolar pool to toxin tolerance requires testing.
OPEN BIOLOGY MF_DARK
What is known: Seven predicted membrane spans and two PQ-loop repeats support a transporter architecture. Actual PAINT descent establishes that the basic-amino-acid inference is ancestral inheritance, not a pairwise mis-transfer from another subfamily. Target-specific assays have demonstrated PM localization and toxin-tolerance dependence, but have not measured amino-acid flux or excluded vacuolar localization.
Significance: Ilt1 is a conserved PQ-loop membrane protein of unknown activity whose only characterized role is in tolerance to industrially relevant ionic liquids; resolving its molecular function would clarify a plasma-membrane detoxification/transport mechanism and inform engineering of ionic-liquid-tolerant biofuel strains.
What would resolve it: Direct transport assays (e.g. radiolabelled-substrate uptake/efflux in reconstituted proteoliposomes or heterologous cells) across candidate solutes including the ionic-liquid cation itself and cationic amino acids; substrate screens; and structure-guided identification of the translocation pathway.
Provenance (the field's own admissions):
Gap: The mechanistic relationship between inherited amino-acid homeostasis and strain-dependent xenobiotic tolerance is unknown.
OPEN BIOLOGY BP_DARK
What is known: ILT1 deletion impairs tolerance to cationic compounds in BY but not strain 378 under the tested conditions. This does not by itself identify a xenobiotic-response step, exclude the inherited homeostasis role, or imply absence of other physiological functions.
Significance: Distinguishing an incidental xenobiotic-tolerance effect from a native transport/homeostasis function is required to place ILT1 in a pathway.
What would resolve it: Systematic phenotyping (growth across ion/nutrient/stress conditions, metabolomics of ilt1 mutants), genetic-interaction mapping, and testing candidate native substrates.
Provenance (the field's own admissions):
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