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NVJ3 (systematic name YDR179W-A; UniProt Q03983) encodes a protein in Saccharomyces cerevisiae (strain ATCC 204508 / S288c) that was originally annotated as an uncharacterized open reading frame. It has since been identified as a component of the nucleus-vacuole junction (NVJ) and designated NVJ3 based on its localization and functional context (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24). The protein contains a Phox-associated (PXA) domain (IPR003114 / PF02194), which is consistent with its classification as a paralog of the sorting nexin-related protein Mdm1 (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24). The gene identity is confirmed across multiple independent studies.
Nvj3 is a soluble protein and a paralog of the ER membrane protein Mdm1 (vladimir2019investigatingsphingolipidmetabolism pages 21-24). Unlike Mdm1, which possesses a full multi-domain architecture consisting of an N-terminal transmembrane domain (for ER anchoring), a PXA domain, an RGS (regulator of G-protein signaling) domain, a PX (Phox homology) domain (for vacuolar PI3P binding), and a C-terminal nexin/PXC domain (bohnert2020tetheringfattethers pages 2-3, bandyopadhyay2024lysosomalmembranecontact pages 3-4, bandyopadhyay2024lysosomalmembranecontact pages 4-6), Nvj3 retains primarily the PXA domain but lacks the integral membrane domains and the PX domain that anchor Mdm1 in the ER membrane and target it to the vacuole, respectively (vladimir2019investigatingsphingolipidmetabolism pages 21-24).
The PXA domain is a critical functional element shared among sorting nexin-RGS family members (Mdm1 in yeast; SNX13, SNX14, SNX19, and SNX25 in mammals) (amatya2021snxpxargspxcsubfamilyof pages 5-7, bandyopadhyay2024lysosomalmembranecontact pages 3-4). Structural studies on the mammalian orthologs reveal that the PXA domain, together with the PXC domain, forms a tightly intertwined tunnel-like structure approximately 80 Å in length with a hydrophobic interior lined by residues from both domains (bandyopadhyay2024lysosomalmembranecontact pages 3-4, bandyopadhyay2024lysosomalmembranecontact pages 4-6). In Mdm1, the PXA domain binds free fatty acids in vitro and is sufficient on its own to drive lipid droplet (LD) targeting and biogenesis (vladimir2019investigatingsphingolipidmetabolism pages 21-24, bohnert2020tetheringfattethers pages 2-3). The mammalian ortholog Snx14 similarly requires its PXA domain for fatty acid binding and proper saturated fatty acid metabolism; deletion of the PXA domain abrogates Snx14's ability to rescue cell viability following palmitate exposure (datta2020snx14proximitylabeling pages 10-11). Given that Nvj3 possesses a PXA domain, it is inferred to have the capacity for lipid or fatty acid binding at the NVJ, though direct biochemical characterization of Nvj3's PXA domain has not been reported.
The following table summarizes the key properties of NVJ3:
| Property | NVJ3 summary |
|---|---|
| Gene name | NVJ3 (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24) |
| Systematic name | YDR179W-A; corresponds to the UniProt target protein for S. cerevisiae S288c described in the research context (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24) |
| UniProt accession | Q03983 |
| Organism | Saccharomyces cerevisiae (strain ATCC 204508 / S288c), budding yeast (kohler2020closingthegap pages 3-5, vrijsen2022interorganellarcommunicationin pages 7-8) |
| Protein type | Soluble protein; described as a soluble paralog of the ER membrane protein Mdm1 (vladimir2019investigatingsphingolipidmetabolism pages 21-24) |
| Key domain | PXA / Phox-associated domain; by family inference, PXA domains in Mdm1/SNX14-family proteins are lipid-associated and linked to fatty-acid handling (bohnert2020tetheringfattethers pages 2-3, datta2020snx14proximitylabeling pages 10-11, bandyopadhyay2024lysosomalmembranecontact pages 3-4, bandyopadhyay2024lysosomalmembranecontact pages 4-6) |
| Paralog | Mdm1 (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24) |
| Subcellular localization | Nucleus-vacuole junction (NVJ), an ER-vacuole/nuclear envelope-vacuole membrane contact site (karnebeck2019newinsightsinto pages 36-40, santanasosa2023ayeastmitotic pages 9-11, vrijsen2022interorganellarcommunicationin pages 7-8) |
| Localization dependency | Mdm1-dependent, Nvj1-independent: Nvj3 localizes to NVJs independently of Nvj1, but in mdm1Δ cells it redistributes from the NVJ to the cytoplasm (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24) |
| Primary function | Accessory NVJ protein / tether-associated factor implicated in lipid droplet biogenesis and lipid metabolic organization at a subset of NVJs, rather than being the core structural tether itself (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 3-5) |
| NOT involved in | Piecemeal microautophagy of the nucleus (PMN); Nvj3-containing NVJs are described as distinct from PMN-active Nvj1-Vac8 junctions (santanasosa2023ayeastmitotic pages 9-11) |
| Broader pathway context | Part of a larger NVJ protein network that can include Nvj1, Vac8, Nvj2, Mdm1, Osh1, Tsc13, Lam5, Lam6, and Vps13 and contributes to lipid/sterol/FA organization at ER-vacuole contacts (kohler2020closingthegap pages 3-5, karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) |
| Phenotype/context from broader NVJ loss | In a nvj1Δ nvj2Δ nvj3Δ mdm1Δ mutant, ER-vacuole contacts are lost by EM, while cells still grow comparably to wild type under the tested conditions; altered ceramide-related lipid flux was also reported (vladimir2019investigatingsphingolipidmetabolism pages 75-81) |
| Related mammalian orthologs of Mdm1 | The Mdm1/SNX-RGS family is represented in mammals by SNX13, SNX14, SNX19, and SNX25; these are relevant evolutionary comparators for inferring PXA-family function, not direct demonstrated orthologs of yeast Nvj3 (bandyopadhyay2024lysosomalmembranecontact pages 3-4, amatya2021snxpxargspxcsubfamilyof pages 5-7) |
Table: This table summarizes the verified identity, localization, inferred molecular role, and pathway context of yeast NVJ3/YDR179W-A. It is useful as a compact reference because the direct literature on NVJ3 is limited and much of its function is inferred from its Mdm1 relationship and PXA-domain family biology.
Nvj3 localizes to the nucleus-vacuole junction (NVJ), the membrane contact site formed between the nuclear envelope (outer nuclear membrane/perinuclear ER) and the vacuolar membrane in budding yeast (karnebeck2019newinsightsinto pages 36-40, santanasosa2023ayeastmitotic pages 9-11, vladimir2019investigatingsphingolipidmetabolism pages 21-24). This localization was initially reported by Henne et al. (2015) and has been confirmed in multiple subsequent studies.
Critically, Nvj3's localization to the NVJ is Mdm1-dependent but Nvj1-independent (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24). In wild-type cells, Nvj3 is found concentrated at NVJ contact sites. However, in mdm1Δ cells, Nvj3 redistributes from the NVJ to the cytoplasm, indicating that Mdm1 serves as the anchor or recruitment factor that retains Nvj3 at the ER-vacuole interface (karnebeck2019newinsightsinto pages 36-40). By contrast, deletion of NVJ1 does not affect Nvj3 localization, demonstrating that the Mdm1-Nvj3 module operates independently of the canonical Nvj1-Vac8 NVJ tethering system (vladimir2019investigatingsphingolipidmetabolism pages 21-24).
A central finding is that Nvj3, together with Mdm1 and Nvj2, is associated with a subset of NVJ contact sites that are specifically dedicated to lipid droplet (LD) biogenesis in response to nutrient stress (santanasosa2023ayeastmitotic pages 9-11). These LD biogenesis-associated NVJs are functionally and spatially distinct from the NVJs involved in piecemeal microautophagy of the nucleus (PMN), which are established through the canonical Nvj1-Vac8 interaction (santanasosa2023ayeastmitotic pages 9-11).
Mdm1 functions as the primary tri-organellar molecular tether at these sites, connecting the ER, the vacuole, and lipid droplets (choudhary2021auniquejunctional pages 7-9). It is anchored to the ER through its N-terminal integral membrane domain, targets the vacuolar membrane via its PX domain binding to phosphatidylinositol 3-phosphate (PI3P), and associates with lipid droplets through its PXA domain (vladimir2019investigatingsphingolipidmetabolism pages 21-24, choudhary2021auniquejunctional pages 7-9). Mdm1 recruits the fatty acyl-CoA synthetase Faa1, linking it to the conversion of free fatty acids into storage-competent neutral lipids and thereby promoting LD formation (vladimir2019investigatingsphingolipidmetabolism pages 21-24). As a soluble Mdm1 paralog that is recruited to the NVJ by Mdm1, Nvj3 likely functions as an accessory factor in this lipid metabolic hub, potentially contributing to fatty acid handling or lipid organization through its PXA domain (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 3-5).
Despite its localization at the NVJ — the site where PMN occurs — Nvj3 is not involved in piecemeal microautophagy of the nucleus. The NVJ contact sites at which Nvj3, Mdm1, and Nvj2 are found do not participate in the PMN autophagy pathway (santanasosa2023ayeastmitotic pages 9-11). PMN instead depends on the Nvj1-Vac8 interaction, with additional contributions from Osh1 (essential for proper PMN bleb formation) and Tsc13 (whose absence reduces PMN bleb size) (kohler2020closingthegap pages 9-11, karnebeck2019newinsightsinto pages 36-40). This functional segregation underscores that the NVJ is not a monolithic structure but rather comprises functionally distinct subdomains.
The quadruple deletion mutant nvj1Δ nvj2Δ nvj3Δ mdm1Δ (ΔNVJ) was found to grow normally under standard conditions, comparable to wild-type cells (vladimir2019investigatingsphingolipidmetabolism pages 75-81). However, electron microscopy confirmed that this ΔNVJ mutant completely lacks ER-vacuole contacts (vladimir2019investigatingsphingolipidmetabolism pages 75-81). Analysis of sphingolipid metabolism in the quadruple mutant revealed reduced levels of PHC-B ceramide species and lower mean amounts of C17-ceramides and C17-IPCs at certain time points, suggesting that the collective loss of NVJ proteins affects ceramide metabolism and lipid flux between the ER and vacuole (vladimir2019investigatingsphingolipidmetabolism pages 75-81). In a separate study examining α-synuclein toxicity in yeast, Nvj3 was described as "a protein of unknown function" that is a paralog of Mdm1 and localizes to the NVJ depending on Mdm1 (vecchio2023multipletethersof pages 3-4).
Nvj3 operates within a larger network of NVJ-resident proteins that collectively coordinate lipid metabolism, sterol transport, and interorganellar communication at the nuclear envelope-vacuole interface. The following table summarizes the major NVJ proteins and their functional roles:
| Protein name | Membrane association | Primary function at NVJ | Role in PMN | Role in LD biogenesis | Key domains/features |
|---|---|---|---|---|---|
| Nvj1 | Integral membrane protein of the outer nuclear membrane / perinuclear ER | Core NVJ tether with Vac8; organizes canonical nucleus-vacuole junctions and recruits PMN-related factors (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 3-5, kohler2020closingthegap pages 9-11) | Direct, essential structural component of PMN sites (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 9-11) | Not the main LD-biogenesis factor; distinct from Mdm1/Nvj2/Nvj3 LD-producing NVJs (santanasosa2023ayeastmitotic pages 9-11) | Transmembrane tether; binds Vac8; interacts with Osh1 and Tsc13 functionally at NVJs (kohler2020closingthegap pages 3-5, kohler2020closingthegap pages 9-11) |
| Vac8 | Vacuolar membrane-associated, highly palmitoylated protein | Core vacuolar-side NVJ tether with Nvj1; scaffold for vacuole contact organization (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 3-5, kohler2020closingthegap pages 9-11) | Direct, essential structural component of PMN sites; conformational state linked to PMN/Cvt functions (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 9-11) | Not the principal LD-biogenesis determinant, though present at NVJ-related contact systems (diep2024thevacuolelipid pages 2-3, kohler2020closingthegap pages 9-11) | Armadillo-repeat scaffold; palmitoylated vacuolar surface protein (kohler2020closingthegap pages 3-5, kohler2020closingthegap pages 9-11) |
| Nvj2 | Accessory NVJ protein; membrane-associated SMP protein at NE-vacuole contacts | Accessory/regulatory NVJ factor that adapts contact abundance and function; part of a subset of NVJs linked to lipid handling (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 3-5, vrijsen2022interorganellarcommunicationin pages 7-8) | Not defined as a core PMN factor; PMN mainly depends on Nvj1-Vac8 (santanasosa2023ayeastmitotic pages 9-11, kohler2020closingthegap pages 3-5) | Yes, associated with LD-biogenesis NVJs together with Mdm1 and Nvj3 (santanasosa2023ayeastmitotic pages 9-11) | SMP lipid-transfer domain (vrijsen2022interorganellarcommunicationin pages 7-8) |
| Nvj3 | Soluble protein; Mdm1-dependent peripheral resident at NVJ | Accessory NVJ factor and soluble paralog of Mdm1; likely supports lipid/fatty-acid handling at a subset of NVJs (karnebeck2019newinsightsinto pages 36-40, vladimir2019investigatingsphingolipidmetabolism pages 21-24) | No clear evidence for direct PMN role; Nvj3-positive NVJs are described as distinct from PMN junctions (santanasosa2023ayeastmitotic pages 9-11) | Yes, associated with LD-biogenesis NVJs under nutrient stress (santanasosa2023ayeastmitotic pages 9-11) | PXA domain; lacks the ER-anchoring/TM and PX architecture described for Mdm1, consistent with being soluble (vladimir2019investigatingsphingolipidmetabolism pages 21-24, bohnert2020tetheringfattethers pages 2-3, bandyopadhyay2024lysosomalmembranecontact pages 3-4) |
| Mdm1 | ER/nuclear ER integral membrane protein with vacuole-binding PX domain | Interorganelle tether at NVJ and ER-vacuole contacts; recruits lipid-metabolic machinery and organizes FA/ceramide handling (vladimir2019investigatingsphingolipidmetabolism pages 21-24, choudhary2021auniquejunctional pages 7-9) | Not the canonical PMN tether; Mdm1-positive NVJs can be distinct from PMN-active junctions (santanasosa2023ayeastmitotic pages 9-11) | Major positive regulator of LD biogenesis; tri-organellar tether linking ER, vacuole, and LDs (vladimir2019investigatingsphingolipidmetabolism pages 21-24, choudhary2021auniquejunctional pages 7-9) | N-terminal membrane anchor, PXA domain, RGS domain, PX domain binding PI3P, C-terminal nexin/PXC region (choudhary2021auniquejunctional pages 7-9, bohnert2020tetheringfattethers pages 2-3, bandyopadhyay2024lysosomalmembranecontact pages 3-4, bandyopadhyay2024lysosomalmembranecontact pages 4-6) |
| Osh1 | Peripheral lipid-transfer protein recruited to NVJ/PMN blebs | Sterol/oxysterol transport factor at NVJ; links Nvj1 to lipid trafficking (vladimir2019investigatingsphingolipidmetabolism pages 21-24, kohler2020closingthegap pages 3-5, kohler2020closingthegap pages 9-11) | Yes; essential for proper PMN vesicle/bleb formation (kohler2020closingthegap pages 9-11, karnebeck2019newinsightsinto pages 36-40) | No specific direct LD-biogenesis role established here (vladimir2019investigatingsphingolipidmetabolism pages 21-24, kohler2020closingthegap pages 9-11) | Oxysterol-binding protein family member (OSBP-related protein) (vladimir2019investigatingsphingolipidmetabolism pages 21-24, karnebeck2019newinsightsinto pages 36-40) |
| Tsc13 | Integral ER membrane enzyme enriched at NVJ | Very-long-chain fatty acid elongation enzyme contributing to NVJ lipid environment and membrane properties (vladimir2019investigatingsphingolipidmetabolism pages 21-24, kohler2020closingthegap pages 3-5, karnebeck2019newinsightsinto pages 36-40) | Supports PMN efficiency; loss reduces PMN bleb size rather than abolishing PMN (karnebeck2019newinsightsinto pages 36-40) | Indirect/supportive via FA elongation and local lipid metabolism, not established as a dedicated LD tether (vladimir2019investigatingsphingolipidmetabolism pages 21-24, karnebeck2019newinsightsinto pages 36-40) | Enoyl-CoA reductase of VLCFA synthesis pathway (vladimir2019investigatingsphingolipidmetabolism pages 21-24, karnebeck2019newinsightsinto pages 36-40) |
| Lam5/Lam6 | Lipid-transfer/contact-site proteins associated with NVJ and other MCSs | Accessory sterol-transfer/contact expansion factors at NVJ; Lam6 especially linked to MCS expansion (karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) | No direct PMN-specific role established in gathered evidence (karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) | Potential indirect role through sterol organization and contact remodeling; no direct dedicated LD-biogenesis function shown here (karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) | StART-like sterol-transfer proteins / contact-site regulators (karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) |
| Vps13 | Large peripheral lipid transporter recruited to NVJ | Bulk lipid transporter at NVJ and other contact sites; contributes to lipid exchange and contact-site function (karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) | No direct PMN-core role established in gathered evidence (karnebeck2019newinsightsinto pages 36-40) | Possible indirect role through lipid supply/transport at NVJ, but not identified here as the principal LD-biogenesis factor (karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) | Large Vps13-family bridge-like lipid transport protein (karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8) |
Table: This table compares major nucleus-vacuole junction proteins in budding yeast, emphasizing which proteins form the core PMN tether versus those associated with lipid-droplet biogenesis and lipid handling. It is useful for placing NVJ3 in the broader NVJ functional network.
Key interacting partners and co-residents at the NVJ include: Nvj1 and Vac8 (core tethers), Osh1 (oxysterol-binding protein for sterol transport), Tsc13 (enoyl-CoA reductase for very-long-chain fatty acid biosynthesis), Nvj2 (SMP domain lipid transfer protein), Lam5 and Lam6 (sterol transport proteins), and Vps13 (bulk lipid transporter) (kohler2020closingthegap pages 3-5, karnebeck2019newinsightsinto pages 36-40, vrijsen2022interorganellarcommunicationin pages 7-8). NVJ contacts are known to expand upon nutrient stress, and this expansion is associated with increased lipid droplet formation at adjacent ER subdomains (choudhary2021auniquejunctional pages 7-9, kohler2020closingthegap pages 3-5).
Mdm1, the functional partner of Nvj3, belongs to the SNX-PXA-RGS-PXC subfamily of sorting nexins (amatya2021snxpxargspxcsubfamilyof pages 5-7, bandyopadhyay2024lysosomalmembranecontact pages 3-4). The mammalian orthologs of Mdm1 include SNX13 (involved in endolysosomal cholesterol export), SNX14 (linked to SCAR20 cerebellar ataxia disease when mutated), SNX19, and SNX25 (amatya2021snxpxargspxcsubfamilyof pages 5-7, datta2020snx14proximitylabeling pages 10-11, bandyopadhyay2024lysosomalmembranecontact pages 3-4). The Drosophila homolog Snazarus similarly regulates lipid droplet populations at plasma membrane-droplet contacts in adipocytes (bohnert2020tetheringfattethers pages 2-3). Nvj3 appears to be a yeast-specific soluble derivative of this sorting nexin family, retaining the PXA domain but having lost the membrane-anchoring and vacuole-targeting domains present in Mdm1. No direct mammalian ortholog of Nvj3 has been identified.
NVJ3 (YDR179W-A) encodes a soluble, PXA domain-containing protein that functions as an accessory component of the nucleus-vacuole junction in S. cerevisiae. It is a paralog of the ER membrane tether Mdm1 and depends on Mdm1 for its localization to the NVJ, but is independent of the canonical NVJ tether Nvj1. Nvj3 resides at a subset of NVJ contact sites that are dedicated to lipid droplet biogenesis under nutrient stress, rather than at those involved in piecemeal microautophagy of the nucleus. Through its PXA domain — which in the related Mdm1 and SNX14 proteins has been shown to bind free fatty acids and promote lipid droplet formation — Nvj3 is inferred to participate in fatty acid handling or lipid organization at the ER-vacuole interface. Collectively, the NVJ proteins including Nvj3 maintain ER-vacuole contacts that are essential for ceramide metabolism and lipid homeostasis. The precise biochemical function of Nvj3 remains incompletely characterized, and much of its functional annotation is inferred from its domain architecture, localization, and relationship to the better-studied Mdm1.
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