AVT2 (YEL064C) is a 480-residue polytopic integral membrane protein of budding yeast, one of seven paralogous AVT proteins (AVT1-7) belonging to the amino acid/auxin permease (AAAP) superfamily (TCDB 2.A.18; Pfam Aa_trans PF01490; InterPro IPR013057; PANTHER PTHR22950), the same solute-carrier clan (SLC32/SLC36/SLC38-like) as the neuronal vesicular GABA/glycine transporters. It has nine predicted transmembrane helices and a disordered cytoplasmic N-terminus, and its fold is that of an amino acid transmembrane transporter. Unlike several of its paralogs, AVT2 has no experimentally demonstrated transported substrate, transport direction, or driving force: in the founding biochemical survey of the family, transport activity was demonstrated for AVT1 (vacuolar uptake of large neutral amino acids) and for AVT3, AVT4 and AVT6 (vacuolar amino acid efflux), whereas AVT2 was not among the members with measurable activity. AVT2 has been directly localized to the endoplasmic reticulum, while the vacuolar-membrane localization typical of the family is inferred rather than directly shown for this paralog. Its physiological role remains undetermined and its null mutant is viable.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0015179 L-amino acid transmembrane transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: Generic amino-acid transmembrane transporter molecular function assigned by phylogenetic (IBA) inference across the AAAP/AVT tree. This is the most specific molecular function that can be defended for AVT2: the Aa_trans (PF01490 / AAAP; PANTHER PTHR22950) fold with nine predicted TM helices supports amino-acid transporter activity, but AVT2 has no demonstrated substrate and no demonstrated transport direction, so it must stay at this generic level. A more specific term (particular substrate, or uptake vs. efflux) is not supported: the paralogs split between uptake (AVT1) and efflux (AVT3/AVT4/AVT6) of different amino-acid classes, so paralogy does not pin AVT2's specificity. Reason: The AAAP/Aa_trans transporter fold justifies a generic amino-acid transmembrane transporter molecular function; no substrate or direction is assignable for AVT2 (it was among the AVT members with no demonstrated transport activity), so the annotation should remain generic and must not be specialized. Supporting Evidence: PMID:11274162 Seven genes in Saccharomyces cerevisiae are predicted to code for membrane-spanning proteins (designated AVT1-7) that are related to the neuronal gamma-aminobutyric acid-glycine vesicular transporters. |
| GO:0003333 amino acid transmembrane transport | IBA GO_REF:0000033 | ACCEPT | Summary: Generic amino-acid transmembrane transport biological process, assigned by phylogenetic inference and consistent with the transporter fold and the demonstrated function of the AVT family. The specific amino-acid substrate and the direction of transport for AVT2 are unknown, so the annotation is kept at this generic BP level rather than specialized to a particular vacuolar uptake or efflux process. Reason: A generic amino-acid transmembrane transport process is the appropriate biological-process annotation for a member of a demonstrated amino-acid transporter family whose own substrate and direction are undetermined; specializing it would over-annotate. Supporting Evidence: PMID:11274162 We have now demonstrated that four of these proteins mediate amino acid transport in vacuoles. |
| GO:1902475 L-alpha-amino acid transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: Amino-acid transmembrane transport biological process reached automatically by inter-ontology (logical) inference from the GO:0015179 L-amino acid transmembrane transporter molecular function. It is consistent with the IBA-supported generic transport process above and with the transporter fold; the specific substrate and direction remain unknown, so it is retained at this generic level. Reason: Auto-derived, internally consistent generic amino-acid transport process; correct at this generality for a fold-confirmed amino-acid transporter of undetermined specificity. Supporting Evidence: PMID:11274162 This function is consistent with the role of the vacuole in protein degradation, whereby accumulated amino acids are exported to the cytosol. |
| GO:0005783 endoplasmic reticulum | IDA PMID:11274162 A family of yeast proteins mediating bidirectional vacuolar ... | ACCEPT | Summary: Direct-assay (IDA) localization of AVT2 to the endoplasmic reticulum, curated by SGD from the founding AVT-family paper. This is the only experimentally determined localization for AVT2 specifically and is accepted as the authoritative cellular-component call. It is notable that this differs from the vacuole-membrane localization typical of the family and inferred by UniProt from the same paper (see the vacuolar membrane annotation), leaving the in-vivo site of action of AVT2 an open question. Reason: Experimental (IDA) localization curated from the primary paper; per curation guidance a direct-assay curator call is not overruled from an abstract-only cache. This is the core, directly demonstrated localization for AVT2. Supporting Evidence: PMID:11274162 A family of yeast proteins mediating bidirectional vacuolar amino acid transport. |
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) endoplasmic-reticulum localization. It agrees with, and independently corroborates, the same ER compartment established for AVT2 by direct assay (the IDA annotation from PMID:11274162). Accepted as consistent with the experimentally determined localization; the IDA remains the primary, directly grounded evidence. Reason: Points to the same ER compartment that is experimentally demonstrated for AVT2 by direct assay (IDA, PMID:11274162); the phylogenetic call is concordant with that evidence and is accepted as corroborating rather than contradicting it. Supporting Evidence: PMID:11274162 A family of yeast proteins mediating bidirectional vacuolar amino acid transport. |
| GO:0016020 membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Broad membrane localization from phylogenetic inference. Correct and consistent with the experimentally supported multi-pass topology (nine predicted TM helices); retained as a general, non-core localization statement, since the more informative compartment identity (ER by IDA, vacuole membrane by UniProt) is captured by the specific annotations. Reason: AVT2 is unambiguously an integral multi-pass membrane protein, so the generic membrane term is directly supported and correct; it is broad but accurate for a polytopic transporter. Supporting Evidence: PMID:11274162 Seven genes in Saccharomyces cerevisiae are predicted to code for membrane-spanning proteins (designated AVT1-7) |
| GO:0005774 vacuolar membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Vacuolar-membrane localization from the UniProt Subcellular Location mapping (SL-0271). In the UniProt record this location is attributed to the same primary paper (PubMed:11274162) as the AVT2-specific ER localization curated by SGD, so the two databases interpret the same study differently: the family is canonically tonoplast/vacuolar, but AVT2 was directly observed in the ER. This annotation is retained as a plausible, family-consistent location but is not treated as an established core fact, because it conflicts with the direct-assay ER localization. Whether AVT2 acts at the vacuole membrane, is ER-resident, or is a vacuolar transporter caught in the secretory pathway is an open question. Reason: Family-expected/UniProt-mapped location that conflicts with the AVT2-specific ER IDA; retained as plausible but non-core rather than removed, since the underlying subcellular location mapping is not overruled and the ER-vs-vacuole question is genuinely unresolved. Supporting Evidence: PMID:11274162 A family of yeast proteins mediating bidirectional vacuolar amino acid transport. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | REMOVE | Summary: Root molecular_function placeholder (No Data) assigned by SGD. It is superseded by the generic but informative L-amino acid transmembrane transporter activity (GO:0015179) annotation already present from the IBA route, so the uninformative root term should be removed. Reason: ND root-term placeholder that is now redundant: the molecular-function aspect is already covered, more informatively, by the GO:0015179 transporter activity annotation. |
| GO:0008150 biological_process | ND GO_REF:0000015 | REMOVE | Summary: Root biological_process placeholder (No Data) assigned by SGD. It is superseded by the generic amino-acid transmembrane transport (GO:0003333) biological-process annotation already present, so the uninformative root term should be removed. Reason: ND root-term placeholder that is now redundant: the biological-process aspect is already covered by the GO:0003333 amino acid transmembrane transport annotation. |
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Download this section (compressed HTML)Q: What amino acid(s) does AVT2 transport, and in which direction (vacuolar uptake or efflux), given that it was inactive in the assay that characterized AVT1/AVT3/AVT4/AVT6?
Q: Does AVT2 function at the endoplasmic reticulum (where it was directly localized) or at the vacuole membrane (as expected for the family and mapped by UniProt), and is its localization conditional?
Q: Are the seven AVT paralogs functionally redundant, and does AVT2 have any dedicated phenotype under conditions (e.g. nitrogen starvation, autophagy) that stress vacuolar amino-acid flux?
Experiment: Perform substrate- and direction-resolved transport assays of AVT2 (uptake and efflux, with and without a proton gradient/ATP) in isolated vacuoles/vesicles or a heterologous system, mirroring the assays used to characterize AVT1/AVT3/AVT4/AVT6.
Hypothesis: AVT2 transports a specific amino acid or amino-acid class in a defined direction; its previous apparent inactivity reflects assay conditions (e.g. wrong substrate, mislocalization, or a requirement for a partner/condition) rather than a genuine lack of transport capability.
Experiment: Determine the subcellular localization of endogenously tagged AVT2 by high-resolution imaging and fractionation, co-stained with ER and vacuole-membrane markers, across growth conditions.
Hypothesis: AVT2 localizes at least partly to the ER rather than exclusively to the vacuole membrane, and its distribution changes with growth/nutrient condition.
Experiment: Construct combinatorial avt single and multiple deletions (including avt2) and phenotype them for vacuolar amino-acid pools and growth under nitrogen limitation, autophagy induction, and diverse amino-acid conditions.
Hypothesis: AVT2 is partially redundant with other AVT paralogs and contributes to vacuolar amino-acid homeostasis only in combination with, or under conditions that stress, the rest of the family.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The physiological substrate, transport direction, driving force, and biological role of AVT2 are all undetermined. It is one of the functionally dark members of the yeast AVT family: a bona fide amino-acid-transporter-fold protein with no demonstrated cargo, no assigned transport direction, and no dedicated loss-of-function phenotype (the null is viable).
OPEN BIOLOGY WHOLLY_DARK
What is known: What is established: AVT2 is a nine-TM AAAP/Aa_trans (PF01490) amino-acid-transporter-fold protein, a paralog of the demonstrated vacuolar amino-acid transporters AVT1/AVT3/AVT4/AVT6. What is excluded/unknown: in the family's founding biochemical survey only four of the seven AVT proteins (AVT1, AVT3, AVT4, AVT6) had measurable transport activity, and AVT2 was not among them, so no substrate or direction is established for AVT2. The paralogs are functionally split between uptake and efflux of different amino-acid classes, so paralogy does not resolve AVT2's function.
Significance: AVT2 is a conserved AVT-family transporter that has remained functionally unassigned since the family was described; closing this gap would remove a dark node from yeast vacuolar/amino-acid transport biology and clarify whether the AVT paralogs are redundant or specialized.
What would resolve it: Direct transport assays (substrate screens and uptake/efflux/driving-force measurements) of AVT2 in isolated vacuoles or a heterologous expression system; comparative metabolomics and combinatorial avt deletions (with and without AVT1/AVT3/AVT4/AVT5/AVT6/AVT7) to resolve redundancy and any AVT2-specific phenotype.
Provenance (the field's own admissions):
Gap: The in-vivo compartment where AVT2 acts is unresolved. AVT2 has been directly localized to the endoplasmic reticulum, yet the family is canonically vacuolar (tonoplast) and UniProt maps AVT2 to the vacuole membrane. It is unknown whether AVT2 is a genuine ER-resident transporter, an ER-retained (e.g. unassembled/regulated) family member, or a vacuolar transporter observed in the secretory pathway.
OPEN BIOLOGY CC_DARK
What is known: Established: an experimental (IDA) localization of AVT2 to the endoplasmic reticulum, and a UniProt Subcellular Location mapping to the vacuole membrane; both are attributed to the same primary study. Unknown: which localization reflects AVT2's site of function, and whether its localization is conditional or regulated.
Significance: The compartment where a transporter resides constrains its possible substrates and biological role; the ER-versus-vacuole ambiguity is a barrier to interpreting AVT2's function and to deciding whether the family-level vacuolar-transport annotations apply to this paralog.
What would resolve it: High-resolution live-cell imaging of endogenously tagged AVT2 with ER and vacuole-membrane markers under multiple growth conditions; subcellular fractionation and, if warranted, mutational analysis of putative ER-retention/trafficking signals.
Provenance (the field's own admissions):
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