NVJ3 (YDR179W-A) is a soluble Saccharomyces cerevisiae protein that resides at the nucleus-vacuole junction (NVJ), the membrane contact site where the nuclear endoplasmic reticulum apposes the vacuole. It is a paralog of the ER-anchored tether Mdm1 (the yeast member of the SNX13/14/19/25 sorting-nexin family) and shares with Mdm1 a single recognizable domain, the Phox-associated (PXA) domain; unlike Mdm1 it lacks a transmembrane anchor and a phosphoinositide-binding PX domain. Nvj3 is recruited to ER-vacuole contacts by direct association with Mdm1 and, in cells lacking Mdm1, redistributes to the cytoplasm; its contact-site localization does not require the canonical NVJ tether Nvj1. Functionally, Nvj3 acts together with Mdm1 in neutral-lipid (triacylglycerol) metabolism and lipid-droplet dynamics at ER-vacuole contacts, particularly during nutritional stress: loss of NVJ3 (with MDM1) increases triacylglycerol and lipid-droplet content in a manner dependent on the fatty acyl-CoA synthetase Faa1. Its own biochemical (molecular) activity has not been established.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006629 lipid metabolic process | IMP PMID:29146766 Lipid droplet biogenesis is spatially coordinated at ER-vacu... | ACCEPT | Summary: Supported by loss-of-function evidence: deletion of NVJ3 (together with MDM1) increases triacylglycerol and lipid-droplet content, an effect suppressed by deletion of the fatty acyl-CoA synthetase Faa1. Nvj3 therefore participates in NVJ-associated neutral-lipid metabolism. The term is general but correctly reflects the demonstrated biological process, and the acts_upstream_of_or_within qualifier is appropriate for a modulatory role established genetically. Retained as a core biological process; the specific molecular step remains a gap. Supporting Evidence: PMID:29146766 deleting MDM1, NVJ3, or both causes accumulation of LDs in yeast, and a ~2βfold increase in TAG PMID:29146766 Deletion of Faa1 in addition to Mdm1 and Nvj3 suppresses the increase in TAG we see in the mdm1 Ξ nvj3 Ξ double knockout |
| GO:0071561 nucleus-vacuole junction | IDA PMID:26283797 Mdm1/Snx13 is a novel ER-endolysosomal interorganelle tether... | ACCEPT | Summary: Well supported by direct imaging: GFP-tagged Nvj3 localizes to the nucleus-vacuole junction and colocalizes with Mdm1 there. This is a core, experimentally established localization of the protein. Supporting Evidence: PMID:26283797 both it and Mdm1 localize specifically to NVJs in an Nvj1-independent manner |
| GO:0098853 endoplasmic reticulum-vacuole membrane contact site | IDA PMID:26283797 Mdm1/Snx13 is a novel ER-endolysosomal interorganelle tether... | ACCEPT | Summary: Well supported and more precise than the NVJ term for the underlying structure. Nvj3 localizes to the ER-vacuole membrane contact site, retaining this localization even in nvj1-deletion cells, where it is enriched at the tips of ER tubules contacting the vacuole. Core localization annotation. Supporting Evidence: PMID:26283797 both Mdm1 and Nvj3 retained ERβvacuole MCS localizations in nvj1Ξ yeast but were no longer restricted to NVJ patches PMID:26283797 Nvj3 was clearly enriched at the tips of ER tubules making contact with the vacuole, confirming ERβvacuole tethering does not require Nvj1 |
| GO:0032266 phosphatidylinositol-3-phosphate binding | ISS PMID:26283797 Mdm1/Snx13 is a novel ER-endolysosomal interorganelle tether... | MARK AS OVER ANNOTATED | Summary: This is an ISS annotation transferred from the paralog Mdm1 (with/from SGD:S000004572). The sequence basis for the transfer is weak: in Mdm1 the high-affinity PI3P-binding activity is a property of its C-terminal PX domain, whereas the source paper states that the PXA domain is the ONLY domain shared between Mdm1 and Nvj3. Nvj3 has no PX domain (InterPro/Pfam for Q03983 returns only the PXA domain, PF02194) and is predicted to be soluble with no transmembrane anchor (max Kyte-Doolittle hydropathy ~1.1, below a TM threshold). There is no direct biochemical evidence that Nvj3 itself binds PI3P, and the domain that would confer that activity is absent, so this is likely an over-annotation by similarity. A specific molecular function for Nvj3 remains undetermined (see knowledge_gaps). Supporting Evidence: PMID:26283797 the PXA domain is the only domain shared between Mdm1 and Nvj3 PMID:26283797 its C-terminal PX domain, which binds PI3P with high affinity |
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Download this section (compressed HTML)Q: Does Nvj3 bind or transfer a specific lipid through its PXA domain, or does it act solely as an Mdm1-recruited scaffold at ER-vacuole contacts?
Suggested experts: W. Mike Henne
Q: What is the mechanistic step by which Nvj3 couples Dga1-dependent triacylglycerol synthesis to efficient lipid-droplet packaging?
Suggested experts: W. Mike Henne
Experiment: Express and purify recombinant Nvj3 (and its isolated PXA domain) and perform protein-lipid overlay, liposome flotation/co-sedimentation, and lipid-transfer assays against a panel of phospholipids, phosphoinositides, DAG, and sterols to identify any direct lipid ligand or transfer activity.
Hypothesis: The Nvj3 PXA domain binds a specific lipid that contributes to its function at ER-vacuole contacts.
Type: in vitro lipid-binding/transfer biochemistry
Experiment: Combine quantitative lipidomics of nvj3Ξ and PXA-domain point/deletion mutants with live-cell imaging of DAG and lipid-droplet biogenesis during diauxic shift or glucose depletion to map Nvj3's step in TAG synthesis and lipid-droplet packaging.
Hypothesis: Nvj3 organizes DAG/TAG conversion at ER-vacuole contacts and its PXA domain is required for this role.
Type: genetics + lipidomics + live-cell imaging
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The direct molecular/biochemical activity of Nvj3 is undetermined: it is unknown whether Nvj3 binds or transfers a specific lipid, senses a lipid, or acts purely as a scaffold/adaptor recruited by Mdm1. Its only recognizable domain is the PXA (Phox-associated) domain, whose biochemical function is itself uncharacterized.
OPEN BIOLOGY MF_DARK
What is known: Nvj3's localization (NVJ / ER-vacuole contact site) and its genetic contribution to triacylglycerol/lipid-droplet homeostasis are experimentally established, and it is known to depend on Mdm1 for recruitment; but no in vitro activity, ligand, or catalytic step has been assigned to the protein or its PXA domain. (Fatty-acid binding has been shown for the PXA domains of the paralog Mdm1 and of human SNX14, but not for Nvj3 itself.)
Significance: Nvj3 is the only yeast protein besides Mdm1 to carry a PXA domain; defining its activity would clarify the function of the conserved PXA domain and the mechanism by which ER-vacuole contacts regulate neutral-lipid metabolism.
What would resolve it: Biochemical characterization of recombinant Nvj3 and its PXA domain (lipid-binding / lipid-transfer assays, ligand identification) and structure determination, combined with separation-of-function alleles tested for lipid-droplet phenotypes.
Provenance (the field's own admissions):
Gap: Whether Nvj3 itself possesses membrane-tethering activity, or is only a passenger recruited to Mdm1-formed ER-vacuole contacts, is unresolved.
OPEN BIOLOGY MF_DARK
What is known: Mdm1 is an ER-anchored transmembrane protein that tethers the ER to the vacuole via its PI3P-binding PX domain; Nvj3 is predicted soluble, lacks a PX domain, and requires Mdm1 for contact-site localization. Independent tethering by Nvj3 alone has not been demonstrated.
Significance: Distinguishing tether from passenger determines whether Nvj3 should be annotated with a contact-site tether activity or an accessory/adaptor role.
What would resolve it: Test ER-vacuole contact formation and reconstituted tethering with Nvj3 in the absence of Mdm1 (e.g. synthetic tethering assays, in vitro membrane binding).
Provenance (the field's own admissions):
Gap: The specific molecular step by which Nvj3 influences triacylglycerol synthesis and lipid-droplet packaging is unknown, as is the physiological consequence of its loss beyond a mild neutral-lipid imbalance.
NARROWING BIOLOGY BP_DARK
What is known: nvj3Ξ (with mdm1Ξ) increases TAG and lipid droplets in an Faa1-dependent manner, and a 2026 preprint links Nvj3 to Dga1-dependent TAG synthesis and DAG localization; but no peer-reviewed mechanism, direct partner in TAG synthesis, or robust growth phenotype has been reported (no hits in 10 CRISPR screens per BioGRID-ORCS).
Significance: Resolving the step would connect ER-vacuole contact-site biology to the enzymology of lipid-droplet biogenesis and to the conserved SNX13/14-family lipid roles in mammals.
What would resolve it: Peer-reviewed, mechanistic dissection of the Nvj3-Dga1/DAG relationship (e.g. the findings reported in the preprint PMID:41542480), with lipidomics and separation-of-function alleles.
Provenance (the field's own admissions):
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