SIA1 (YOR137C) is a poorly characterized 622-residue protein of the budding yeast Saccharomyces cerevisiae. It carries an N-terminal signal peptide and a single calcineurin-like metallophosphoesterase (metallophosphatase/purple acid phosphatase-like) domain, placing it in a family that also contains the yeast paralog Dcr2 and several plant "probable inactive purple acid phosphatases". Genetic evidence shows that SIA1 is required for the glucose-triggered, post-translational activation of the plasma membrane proton pump Pma1: cells lacking SIA1 have normal Pma1 protein levels at the plasma membrane but fail to show the full glucose-induced increase in Pma1 maximal velocity, identifying SIA1 as a positive regulator of H+-ATPase activation rather than a component of the pump itself. SIA1 was independently isolated as a multicopy suppressor of a temperature-sensitive allele of the essential translation factor eIF5A (the source of its name, "Suppressor of eIF5A"), a screen that linked eIF5A to the WSC/PKC1 cell-wall-integrity signalling pathway. SIA1 transcription is induced by ethanol stress. Its molecular activity is unresolved: although the metallophosphatase fold and phylogenetic assignment suggest a possible phosphatase, no catalytic activity or substrate has been demonstrated, and its closest relatives are predicted to be catalytically inactive.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004721 phosphoprotein phosphatase activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Family-level phylogenetic (IBA) inference of phosphatase activity from the calcineurin-like metallophosphatase fold. SIA1 has the domain, but no phosphatase activity or substrate has ever been demonstrated for it, and its nearest orthologs include "probable inactive purple acid phosphatases". Retained as a plausible family-level hypothesis but not treated as an established (core) function. Reason: SIA1 is assigned to PANTHER PTHR32440:SF0 (phosphatase DCR2-related), a metallophosphoesterase / purple acid phosphatase-like family, so an IBA phosphatase annotation is a defensible domain-based hypothesis and should not be removed. However, the only experimental data on SIA1 concern its requirement for glucose activation of Pma1, with no assay of phosphatase activity; SGD lists molecular function as Unknown; and several reviewed SF0 members are annotated as inactive purple acid phosphatases. The catalytic activity of SIA1 is therefore an open knowledge gap, so this term is kept as non-core rather than accepted as a core function. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTHR32440 · phosphatase DCR2-related (SF0) SOURCE WEAK OR INFERRED Family includes yeast Dcr2 and plant PAP14/16/28/29 annotated as probable INACTIVE purple acid phosphatases; SIA1 catalytic activity unverified. Supporting Evidence: file:yeast/SIA1/SIA1-uniprot.txt |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Generic hydrolase parent term inferred electronically (InterPro2GO) from the metallophosphatase domain IPR004843. Consistent with the fold but uninformative and subsumed by the more specific (also inferential) phosphatase term; not wrong. Reason: This IEA annotation is a direct domain-to-GO mapping (IPR004843 -> hydrolase activity) and is consistent with the metallophosphatase fold. It is far more general than the family-level phosphatase inference and carries the same (unverified) assumption that the domain is catalytically active. It is retained as non-core background rather than removed, since the fold is genuinely present, but it does not describe a demonstrated SIA1 function. Supporting Evidence: file:yeast/SIA1/SIA1-uniprot.txt |
| GO:1902600 proton transmembrane transport | IMP PMID:9450541 Yeast gene YOR137c is involved in the activation of the yeas... | MODIFY | Summary: Based on the SIA1 deletion phenotype (loss of glucose-triggered Pma1 Vmax increase), SGD annotated SIA1 to proton transmembrane transport (IMP). The experimental evidence is sound, but SIA1 does not itself transport protons; it is required for activation of the Pma1 proton pump. A regulatory process term better captures the biology. Reason: The experimental support (PMID:9450541, IMP) is solid and must be retained - the paper shows SIA1 is required for the glucose-induced Vmax increase of Pma1. However, the term "proton transmembrane transport" attributes the ion-translocation process to SIA1, whereas SIA1 is a regulator required for activation of the transporter, not a transporter or channel. The essence is sound but a better term exists, so MODIFY to a regulatory term ("regulation of proton transport", GO:0010155) that preserves the experimental support while stating the biology accurately. Proposed replacements: regulation of proton transport Supporting Evidence: PMID:9450541 Deletion of YOR137c does not affect the level of Pma1 at the plasma membrane, but disturbs the glucose-triggered Vmax increase of the enzyme. file:yeast/SIA1/SIA1-deep-research-falcon.md Within this pathway, SIA1 is genetically implicated alongside PTK2 as a positive factor in Pma1 activation. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: SGD ND placeholder recording that no molecular-function data are available for SIA1. This is accurate: SIA1's molecular activity is genuinely unresolved (see knowledge_gaps). Reason: The root molecular_function ND annotation correctly records the absence of curated molecular-function evidence. Given that SIA1 has no experimentally demonstrated activity and its family assignment is ambiguous (possible pseudophosphatase), the ND placeholder is an honest reflection of the state of knowledge and should be retained until an activity is established. |
| GO:0005575 cellular_component | ND GO_REF:0000015 | ACCEPT | Summary: SGD ND placeholder recording that no cellular-component data are available for SIA1. SIA1 has a predicted signal peptide (secretory-pathway entry) but no experimentally verified subcellular localization is curated. Reason: The root cellular_component ND annotation correctly records the absence of curated localization evidence. Although a signal peptide predicts membrane/secretory-pathway entry and SIA1 functionally regulates the plasma-membrane Pma1, no experimental localization is available, so retaining the honest ND placeholder is appropriate. |
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Download this section (compressed HTML)Q: Does SIA1 act directly on Pma1 (physical interaction / activator or scaffold) or indirectly through a signalling or lipid-mediated route to promote glucose activation of the H+-ATPase?
Q: Is the SIA1 metallophosphatase domain catalytically active, and if so what is its physiological substrate - or is SIA1 a pseudophosphatase like its closest relatives?
Q: Is SIA1's role in glucose activation of Pma1 mechanistically connected to its genetic identity as an eIF5A suppressor and to WSC/PKC1 cell-wall-integrity signalling, or are these independent activities?
Experiment: Co-immunoprecipitation / proximity labelling of tagged SIA1 and Pma1 before and after glucose addition to test for direct interaction; phosphoproteomic comparison of Pma1 (especially the C-terminal autoinhibitory Ser/Thr residues) in wild-type versus sia1-delta cells upon glucose refeeding.
Hypothesis: SIA1 promotes glucose activation of Pma1 by directly modulating Pma1's activity or phosphorylation state.
Type: interaction and phosphorylation analysis
Experiment: Recombinant expression of the SIA1 metallophosphatase domain and in vitro phosphatase assays (para-nitrophenyl phosphate and phosphopeptide substrates) with metal-dependence controls; parallel assay of catalytic-residue point mutants to test whether any activity requires the predicted metal-binding scaffold.
Hypothesis: The SIA1 metallophosphatase domain is (or is not) catalytically active.
Type: enzymology
Experiment: Determine the subcellular localization of endogenously tagged SIA1 by fluorescence microscopy and membrane fractionation, and test signal-peptide dependence, to place SIA1 relative to Pma1 in the secretory pathway / plasma membrane.
Hypothesis: SIA1 localizes to a compartment consistent with acting on Pma1 (plasma membrane or secretory pathway).
Type: cell biology / localization
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: SIA1's molecular activity is undetermined. Although it has a calcineurin-like metallophosphatase fold and carries a family-level IBA "phosphoprotein phosphatase activity" annotation, no catalytic activity or substrate has ever been demonstrated for SIA1, and its closest relatives include probable inactive purple acid phosphatases, so it is unknown whether SIA1 is an active phosphatase or a pseudoenzyme.
OPEN BIOLOGY MF_DARK
What is known: Established: SIA1 contains a single metallophosphatase domain (Pfam PF00149; InterPro IPR004843) and belongs to PANTHER PTHR32440:SF0. Not established: any measured enzymatic activity, substrate, or metal dependence; SGD lists molecular function as Unknown.
Significance: Whether SIA1 is an active phosphatase determines the class of mechanism by which it could regulate Pma1 (direct enzymatic modification versus non-catalytic scaffolding), and would resolve whether the family-level IBA/IEA activity annotations reflect real biology.
What would resolve it: In vitro phosphatase assays on recombinant SIA1 (and catalytic-residue mutants) with phosphoprotein/phosphopeptide and generic substrates; structural comparison of the SIA1 active site with active metallophosphatases.
Provenance (the field's own admissions):
Gap: The mechanism linking SIA1 to glucose activation of Pma1 is unknown - whether SIA1 acts directly on the pump or through an intermediate signalling/lipid step, and which of the "at least two independent mechanisms" of Pma1 glucose activation SIA1 belongs to.
OPEN BIOLOGY MF_DARK
What is known: Established: sia1-delta cells retain normal plasma-membrane Pma1 levels but fail the glucose-triggered Vmax increase (PMID:9450541). Not established: the molecular step or partner through which SIA1 exerts this effect.
Significance: Identifies how a central metabolic signal (glucose) is transduced to the master plasma-membrane proton pump; SIA1 is a genetic entry point into this poorly understood activation pathway.
What would resolve it: Epistasis and interaction studies placing SIA1 relative to known Pma1 glucose-activation inputs (Ptk1/2 kinases, Glc7 phosphatase, sphingolipid/ergosterol requirements) and direct interaction tests.
Provenance (the field's own admissions):
Gap: SIA1's direct physical partners and its subcellular localization are unknown. No validated Pma1 physical interaction is curated, and there is no experimentally determined localization despite a predicted N-terminal signal peptide.
OPEN BIOLOGYCURATION CC_DARK
What is known: Established: SIA1 has a predicted signal peptide (UniProt residues 1-27) and low-throughput interaction records exist, but SGD lists cellular component as Unknown and no direct Pma1 interaction is curated. Not established: where SIA1 resides and what it binds.
Significance: Knowing whether SIA1 reaches the plasma membrane / secretory pathway and what it binds is prerequisite to any mechanistic model of how it acts on Pma1.
What would resolve it: Endogenous-tag localization microscopy and membrane fractionation; affinity-purification mass spectrometry / proximity labelling to define the SIA1 interactome.
Provenance (the field's own admissions):
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