The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Primary fission-yeast literature explicitly identifies SPBC660.08 (syn. mug167) as Atg38 and characterizes it as a subunit of the autophagy-specific phosphatidylinositol 3-kinase (PtdIns3K/PI3K) complex I in Schizosaccharomyces pombe, matching the UniProt accession O94427 description (Atg38 family; N-terminal MIT domain; C-terminal coiled-coil) (yu2020atg38atg8interactionin pages 1-2, yu2020atg38atg8interactionin pages 2-4). Reviews on fission-yeast autophagy also summarize Atg38 as the fifth PI3K complex I subunit identified in 2020 and highlight its species-specific interaction properties (xu2022fissionyeastautophagy pages 7-8).
Macroautophagy (autophagy) is a conserved pathway in which cytoplasmic material is engulfed by a double-membrane autophagosome and delivered to the vacuole/lysosome for degradation. In fission yeast, early autophagy initiation requires production of phosphatidylinositol 3-phosphate (PtdIns3P) at an initiation site (the PAS/phagophore) by the class III PI3K Vps34, acting in PtdIns3K complex I (xu2022fissionyeastautophagy pages 4-5).
In S. pombe, PtdIns3K complex I contains core components Vps34, Vps15, Atg6, Atg14, plus the additional fifth subunit Atg38 (fernandez2025cellularadaptationto pages 30-35, xu2022fissionyeastautophagy pages 7-8). Atg38 is therefore best understood as an accessory/scaffolding/regulatory subunit of the autophagy-initiating PI3K complex rather than as an enzyme itself.
Atg38/NRBF2 family proteins are characterized by:
- An N-terminal MIT domain (microtubule-interacting and targeting domain fold), widely implicated in binding PI3K complex I (ohashi2016characterizationofatg38 pages 1-6, ohashi2021classiiiphosphatidylinositol pages 1-3).
- A C-terminal coiled-coil / homodimerization region that supports complex association and punctate autophagy-site localization (ohashi2016characterizationofatg38 pages 11-15, ohashi2016characterizationofatg38 pages 48-56).
An AIM (Atg8-family-interacting motif) (also called LIR in mammals) is a short linear motif that binds Atg8-family proteins. In fission yeast, Atg38 contains an AIM that enables direct binding to Atg8, coupling a “downstream” autophagosome protein to an “upstream” PI3K initiation complex (yu2020atg38atg8interactionin pages 2-4, xu2022fissionyeastautophagy pages 7-8).
Biochemical co-purification shows S. pombe Atg38 associates with complex I components (Vps34, Vps15, Atg6, Atg14) but not with the complex II-specific subunit Vps38, supporting complex I-specific incorporation (yu2020atg38atg8interactionin pages 1-2, yu2020atg38atg8interactionin pages 2-4).
A fission-yeast-specific feature highlighted in a review is that Atg38 in S. pombe binds directly to Vps34, unlike budding yeast and mammals where Atg38/NRBF2 are often described as associating via other subunits (xu2022fissionyeastautophagy pages 7-8).
Direct experimental mapping in living S. pombe cells using the Pil1 co-tethering assay shows Atg38 is incorporated into PtdIns3K complex I via Atg38–Vps34 interaction (yu2021visualdetectionof pages 8-9, yu2021visualdetectionof pages 9-11). Key interface mapping includes:
- A short conserved Atg38 region (~residues 152–161); deletion Δ153–160 or point mutation F157A strongly reduces Vps34 binding (yu2021visualdetectionofa pages 10-13, yu2021visualdetectionof pages 8-9).
- Vps34 residues 251–801 (helical + lipid kinase domain region) mediate binding to Atg38, whereas Vps34 residues 1–250 mediate Vps15 binding—consistent with a model where Vps34 simultaneously connects Vps15 and Atg38 to assemble complex I (yu2021visualdetectionofa pages 10-13, yu2021visualdetectionof pages 9-11).
Functionally, disrupting this interface (Atg38F157A) diminishes starvation-induced autophagy measured by Pho8Δ60, and forcibly tethering Vps34 to Atg38F157A restores autophagic activity—supporting a causal role for Atg38 incorporation into complex I via Vps34 (yu2021visualdetectionofa pages 10-13, yu2021visualdetectionof pages 8-9).
Yu et al. (2020) established that Atg38 directly binds Atg8 via a defined AIM and that this binding recruits Atg38 to Atg8-positive autophagy initiation structures (PAS/phagophore), thereby enhancing the accumulation of PtdIns3K complex I and downstream factors at the PAS (yu2020atg38atg8interactionin pages 1-2, yu2020atg38atg8interactionin pages 5-8).
AIM mapping and key residues:
- AIM localized around aa 173–185.
- F178 and V181 are critical for binding; mutations (e.g., F178A/V181A or Δ176–181) disrupt Atg8 coimmunoprecipitation/binding; reciprocal Atg8 mutations (P52A/R67A) weaken binding (yu2020atg38atg8interactionin pages 2-4, yu2020atg38atg8interactionin pages 4-5).
Localization dependency: Atg38 forms starvation-induced puncta that colocalize with Atg8 at the PAS, and Atg14 is required for Atg38 puncta formation, consistent with complex I-dependent targeting (yu2020atg38atg8interactionin pages 2-4).
Mechanistic consequence: AIM disruption does not substantially affect upstream PAS proteins (e.g., Atg13, Atg9) but reduces PAS accumulation of complex I and downstream factors (Atg14, Atg18b, Atg24b, Atg2, Atg5, Atg16, Atg8), supporting a model in which Atg38–Atg8 binding amplifies PI3K complex I presence and downstream assembly at the PAS (yu2020atg38atg8interactionin pages 5-8, yu2020atg38atg8interactionin pages 4-5).
Atg38’s primary biological role is in autophagosome formation efficiency, by promoting PI3K complex I recruitment/accumulation at the PAS and supporting downstream assembly steps, including Atg8 lipidation and autophagosome growth (yu2020atg38atg8interactionin pages 5-8, yu2020atg38atg8interactionin pages 4-5).
Experimental microscopy shows Atg38 localizes to starvation-induced puncta colocalizing with Atg8, i.e., the PAS/phagophore assembly site. This localization is mediated by the complex I context and reinforced by direct Atg8 binding via the AIM (yu2020atg38atg8interactionin pages 1-2, yu2020atg38atg8interactionin pages 2-4).
Loss of Atg38 (atg38Δ) or disruption of its Atg8-binding AIM impairs nitrogen-starvation-induced autophagy readouts:
- CFP-Atg8 processing assay: atg38Δ reduces accumulation of vacuolar free CFP (a flux indicator) (yu2020atg38atg8interactionin pages 1-2, yu2020atg38atg8interactionin pages 2-4).
- Pho8Δ60 assay: atg38Δ abolishes starvation-induced Pho8Δ60 activation; Atg38F157A diminishes Pho8Δ60 induction (yu2020atg38atg8interactionin pages 4-5, yu2021visualdetectionof pages 8-9).
- Tdh1-YFP processing: Atg38 AIM mutant yields ~50% of WT flux (yu2020atg38atg8interactionin pages 4-5).
AIM-mediated Atg38–Atg8 binding affects autophagosome size:
- In an fsc1Δ background, mean autophagosome diameter was 451 nm (WT Atg38 condition) versus 271 nm in cells expressing Atg38[AIM mut]; analyses reported sample sizes n=45 and n=30 in the size measurements (yu2020atg38atg8interactionin pages 5-8, yu2020atg38atg8interactionin pages 4-5).
Atg38 loss was reported to cause autophagy defects without broad vacuolar sorting phenotypes (e.g., normal vacuole size and no Cpy1 mistargeting in the cited excerpt), supporting a more specific role in autophagy machinery organization rather than general vacuolar trafficking (yu2020atg38atg8interactionin pages 2-4).
A 2023 mechanistic study in budding yeast described PI3K complex I recruitment to the PAS via multiple interactions, including association with the Atg1 complex via the Atg38 C-terminal region, and cooperation with Atg9 and Vac8; these recruitment routes are regulated by Atg1 kinase activity and phosphorylation of PI3K complex I subunits (hitomi2023theatg1complex pages 2-3, hitomi2023theatg1complex pages 8-8). While this work is not in S. pombe, it provides an updated conserved framework in which an Atg38/NRBF2-like subunit helps integrate the PI3K complex with upstream scaffolds and phosphorylation control.
A 2024 review synthesizes current structural/biochemical models in which NRBF2 (Atg38 ortholog) binds VPS15 and can trigger conformational rearrangements in VPS34’s catalytic region, relieving VPS15-imposed inhibition and activating complex I; it also emphasizes layered regulation by Rab GTPases and ULK1/Atg1-dependent phosphorylation (lee2024regulatorymechanismsgoverning pages 4-5). These models provide mechanistic hypotheses for how Atg38-family binding may influence PI3K complex activity beyond mere recruitment/stability.
In yeast-cell biology and autophagy research, Atg38 is used as a defined module to probe autophagy initiation mechanisms:
Fluorescent processing assays (e.g., CFP-Atg8 processing; Tdh1-YFP processing) to quantify cargo delivery/proteolysis in the vacuole (yu2020atg38atg8interactionin pages 2-4, yu2020atg38atg8interactionin pages 4-5).
Protein–protein interaction mapping in living fission yeast
The Pil1 co-tethering assay is used to test binary/ternary/quaternary interactions among autophagy proteins, including mapping the Atg38–Vps34 incorporation interface and quantifying colocalization by Pearson correlation coefficient (PCC; n=10 cells in reported quantifications) (yu2021visualdetectionof pages 8-9).
Mechanistic engineering/rescue
Cross-species reviews emphasize that some details remain contested in the broader field, such as the precise subunit contact sites for MIT domains in different organisms, stoichiometry dynamics (especially in mammals), and whether NRBF2 activates or inhibits complex I under certain assay conditions (ohashi2021classiiiphosphatidylinositol pages 1-3, ohashi2021classiiiphosphatidylinositol pages 4-6). These open issues matter when extrapolating beyond S. pombe, but in S. pombe the primary mechanism (Vps34 binding + Atg8 AIM feedback) is experimentally defined (yu2021visualdetectionof pages 8-9, yu2020atg38atg8interactionin pages 4-5).
Atg38 (SPBC660.08; Mug167) is a non-enzymatic autophagy factor that acts as a PtdIns3K/PI3K complex I subunit at the PAS/phagophore, promoting efficient autophagy initiation and autophagosome growth. Two experimentally supported molecular features underlie this role: (i) incorporation into complex I via direct binding to Vps34 (interface centered on Atg38 F157 and Vps34 residues 251–801) and (ii) a direct AIM-mediated interaction with Atg8 (AIM around aa 173–185; key residues F178/V181) that creates a positive-feedback loop to increase PAS accumulation of PI3K complex I and downstream factors. Disrupting these interactions reduces autophagic flux and yields smaller autophagosomes (e.g., ~451 nm vs ~271 nm in a TEM assay context) (yu2021visualdetectionof pages 8-9, yu2020atg38atg8interactionin pages 4-5).
| Claim/Function | Evidence type | Key experimental details/quantitative results | Cellular location | Source (authors, year, journal, DOI URL) |
|---|---|---|---|---|
| SPBC660.08/mug167 is the bona fide S. pombe Atg38 and a PtdIns3K/PI3K complex I subunit | AP-MS/co-purification, domain analysis | SPBC660.08 co-purified with Vps34, Vps15, Atg6, and Atg14, but not the complex II-specific subunit Vps38; protein architecture reported as N-terminal MIT domain plus C-terminal coiled-coil, matching Atg38 family assignment | Autophagy-specific PI3K complex at the PAS/phagophore | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 1-2) |
| Atg38 is an auxiliary/regulatory PI3K complex I subunit with conserved MIT and C-terminal homodimerization/coiled-coil regions | HDX-MS, X-ray crystallography, EM, SEC-MALS | Structural work showed Atg38 binds complex I through its MIT domain; the C-terminal region forms a homodimeric “mushroom-like” structure and supports PAS localization/complex association; yeast complex I engages one Atg38 homodimer | Base of PI3K complex I; PAS/autophagic puncta | Ohashi et al., 2016, Autophagy, https://doi.org/10.1080/15548627.2016.1226736 (ohashi2016characterizationofatg38 pages 1-6, ohashi2016characterizationofatg38 pages 11-15, ohashi2016characterizationofatg38 pages 48-56) |
| Atg38 directly binds Atg8 through an AIM | Co-IP, GST pull-down, yeast two-hybrid, mutagenesis | AIM mapped to a conserved region around aa 173-185; F178 and V181 are critical; deleting aa 176-181 or mutating F178A/V181A abolished or strongly weakened Atg8 binding; reciprocal Atg8 P52A/R67A mutations weakened binding | PAS/phagophore assembly site (Atg8-positive puncta) | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 2-4, yu2020atg38atg8interactionin pages 4-5) |
| Atg38 localization to starvation-induced puncta depends on the autophagy machinery and supports recruitment to Atg8-positive structures | Fluorescence microscopy/colocalization | Atg38 formed starvation-induced puncta that colocalized with Atg8; Atg14 was required for Atg38 puncta formation, consistent with complex I-dependent PAS targeting | PAS/phagophore | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 2-4) |
| Atg38-Atg8 interaction establishes a positive feedback loop that increases PAS accumulation of PI3K complex I and downstream Atg factors | Mutagenesis, fluorescence microscopy, FLIP | AIM-disrupting mutations did not alter upstream PAS factors (Atg13, Atg9) but reduced PAS accumulation of Atg14 and downstream factors Atg18b, Atg24b, Atg2, Atg5, Atg16, Atg8; authors conclude the primary defect is reduced PAS accumulation of Atg38 itself | PAS/phagophore | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 1-2, yu2020atg38atg8interactionin pages 5-8, xu2022fissionyeastautophagy pages 7-8) |
| Loss of Atg38 or disruption of its Atg8 AIM reduces autophagic flux | CFP-Atg8 processing, Pho8Δ60, Tdh1-YFP processing | atg38Δ blocked starvation-induced CFP-Atg8 processing and abolished starvation-induced increase in Pho8Δ60 activity; Atg38[AIM mut] gave about 50% of WT autophagic flux in the Tdh1-YFP processing assay | Vacuole-directed autophagic pathway; PAS-phagophore initiation step | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 2-4, yu2020atg38atg8interactionin pages 4-5) |
| The Atg38-Atg8 interaction promotes normal autophagosome size | TEM, FLIP, mutagenesis | In an fsc1Δ background, average autophagosome diameter was 451 nm with WT Atg38 versus 271 nm with Atg38[AIM mut]; reported sample sizes included n=45 and n=30 in the size analyses | Autophagosome/phagophore | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 5-8, yu2020atg38atg8interactionin pages 4-5) |
| AIM-dependent Atg8 binding is the key autophagy-promoting function tested in this study | Rescue by engineered interaction | Inserting an exogenous AIM (3×EEEWEEL) into Atg38[AIM mut] restored autophagy and autophagosome size to near-WT levels, showing that Atg8 binding per se is functionally important | PAS/phagophore | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 4-5) |
| In S. pombe, Atg38 is incorporated into PI3K complex I through Vps34 | Pil1 co-tethering assay, ternary/quaternary interaction mapping | Pil1 assays showed Atg38-Vps34 association; CFP-Vps34 could bridge Vps15 and Atg38, indicating Vps34 links Atg38 to the rest of complex I; Vps34 aa 1-250 mediated Vps15 interaction, whereas aa 251-801 mediated Atg38 binding | PI3K complex I at the PAS | Yu et al., 2021, Journal of Cell Science, https://doi.org/10.1242/jcs.258774 (yu2021visualdetectionofa pages 10-13, yu2021visualdetectionof pages 8-9, yu2021visualdetectionof pages 13-14, yu2021visualdetectionof pages 9-11) |
| A short conserved Atg38 region centered on F157 is required for Vps34 binding | Mutagenesis, Pil1 co-tethering, quantitative colocalization | Deleting aa 153-160 or mutating F157A largely blocked the Atg38-Vps34 interaction; colocalization was quantified by PCC (mean ± s.d., n=10 cells) in the assay framework | PI3K complex I/PAS | Yu et al., 2021, Journal of Cell Science, https://doi.org/10.1242/jcs.258774 (yu2021visualdetectionofa pages 10-13, yu2021visualdetectionof pages 8-9, yu2021visualdetectionofa pages 32-34) |
| Disrupting the Atg38-Vps34 interface impairs autophagy, and forced linkage to Vps34 rescues function | Pho8Δ60 autophagy assay, fusion-rescue experiment | Atg38F157A diminished starvation-induced Pho8Δ60 activation (assayed after 4 h nitrogen starvation; normalized to +N = 1); fusion of Vps34 to Atg38F157A restored autophagic activity, supporting a direct incorporation role for the Vps34-Atg38 interaction | PAS/autophagy initiation pathway | Yu et al., 2021, Journal of Cell Science, https://doi.org/10.1242/jcs.258774 (yu2021visualdetectionofa pages 10-13, yu2021visualdetectionof pages 8-9, yu2021visualdetectionofa pages 32-34) |
| Atg38 has a relatively specific autophagy role rather than a broad vacuolar sorting defect | Phenotypic assays | atg38Δ cells showed autophagy defects but were reported as not temperature sensitive, with normal vacuole size and no Cpy1 mistargeting, supporting a relatively specific defect in autophagy initiation/efficiency | Autophagy pathway, not general vacuolar trafficking | Yu et al., 2020, Autophagy, https://doi.org/10.1080/15548627.2020.1713644 (yu2020atg38atg8interactionin pages 2-4) |
| Current fission-yeast consensus places Atg38 as the fifth subunit of PI3K complex I and highlights a species-specific mechanism | Review synthesis from primary data | Review notes that in S. pombe, unlike budding yeast and mammals, Atg38 binds directly to Vps34 and also carries an AIM/LIR that creates a positive-feedback loop to enhance PAS accumulation of PI3K complex I and downstream factors | PAS/phagophore, autophagy initiation machinery | Xu & Du, 2022, Cells, https://doi.org/10.3390/cells11071086; Ohashi, 2021, Autophagy, https://doi.org/10.1080/15548627.2021.1872240 (xu2022fissionyeastautophagy pages 7-8, ohashi2021classiiiphosphatidylinositol pages 4-6, ohashi2021classiiiphosphatidylinositol pages 3-4) |
Table: This table summarizes experimentally supported functional annotation for Schizosaccharomyces pombe Atg38/O94427, including complex I membership, interaction interfaces, localization, autophagy phenotypes, and rescue experiments. It highlights the main primary evidence and key quantitative findings useful for gene/protein annotation.
References
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