Skip to main page content
U.S. flag
See More

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Sep 29;4(1):2555835.
doi: 10.1080/27694127.2025.2555835. eCollection 2025.

Revisiting the evolution of the yeast Atg1 complex

Kha M Nguyen  1 , Hannah R Shariati  1 , Calvin K Yip  1
Affiliations

Revisiting the evolution of the yeast Atg1 complex

Kha M Nguyen et al. Autophagy Rep. .

Abstract

The budding yeast Saccharomyces cerevisiae Atg1 complex coordinates the initiation of nonselective autophagy and consists of the Atg1 kinase, Atg13 regulatory subunit, and an S-shaped scaffold formed by Atg17, Atg29, and Atg31. In contrast, the fission yeast Schizosaccharomyces pombe Atg1 complex incorporates Atg101 instead of Atg29 and Atg31 and features a rod-shaped Atg17 scaffold. The timing of this divergence and its impact on the structural evolution of Atg17 remain unclear. Our systematic composition analysis revealed that Atg101 is found in the Atg1 complex of several budding yeast species, including two that contain both Atg29/Atg31 and Atg101. Structural modeling and negative stain EM analysis indicated that budding yeast species with Atg101 exhibit a rod-shaped Atg17. Additionally, we found that the Atg13 HORMA domain of S. pombe may possess a stabilizing cap, suggesting an alternative function for Atg101. Collectively, our findings delineate the potential evolutionary trajectories of the Atg1 complex in yeast. Abbreviations: ATG, autophagy-related; BLAST, basic local alignment search tool; C-Mad2, closed Mad2; EAT, Early Autophagy Targeting/Tethering; EM, electron microscopy; His-MBP, histidine-maltose binding protein; HORMA, Hop1, Rev7, and Mad2; IDR, intrinsically disordered region; O-Mad2, open Mad2; iTOL, Interactive Tree of Life; PAS, phagophore assembly site; PI3K, phosphatidylinositol 3-kinase; PMSF, phenylmethylsulfonyl fluoride; pTM, predicted template modeling; RMSD, root mean square deviation; TOR, target of rapamycin; TORC1, TOR complex 1.

Keywords: AlphaFold3; Atg1 complex; Atg17; budding yeast; fission yeast.

PubMed Disclaimer

Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Atg1 complex composition during nonselective autophagy. (A) Diagram of Atg1 complex formation in relation to the PAS in S. cerevisiae. In nutrient-abundant conditions, TORC1 inhibits assembly of the Atg1 complex by hyperphosphorylating Atg13 at its disordered tail. In nutrient-deprived conditions, TORC1 is inactivated, which leads to dephosphorylation of Atg13, followed by binding of this protein to Atg1 and the Atg17 scaffolding complex (Atg17-Atg31-Atg29) and the initiation of the phagophore. (B) A comparison of Atg1 complex composition in S. cerevisiae and S. pombe during non-selective autophagy. Notably, S. cerevisiae consists of Atg13, Atg1, Atg17 (S-shaped), Atg31, and Atg29, while S. pombe consists of Atg13, Atg1, Atg17 (Rod-shaped), and Atg101.
Figure 2.
Figure 2.
Phylogenetic tree of Atg17 from the Saccharomycetes and Schizosaccharomycetes class. The phylogeny was based on Atg17 sequence of species in the Saccharomycetes and Schizosaccharomycetes class obtained from Uniprot. Light blue and pink Atg17 entries have predicted rod-shaped and curved architecture, respectively. Blue, magenta and yellow squares indicate whether the yeast species has an annotated Atg101, Atg31 and/or Atg29 on Uniprot, respectively.
Figure 3.
Figure 3.
Comparison of the overall architecture of AlphaFold3 predicted models and experimentally determined structures of dimeric Atg17. (A) Alphafold3 predicted model of dimeric S. cerevisiae Atg17 (colored by pLDDT score) showcasing its curved S-shaped architecture. (B) Alphafold3 predicted model of dimeric S. pombe Atg17 (colored by pLDDT score) showcasing its rod-shaped architecture. (C) Alphafold3 predicted model of dimeric L. thermotolerans Atg17 (colored by pLDDT score) aligned onto the crystallographic structure of the L. thermotolerans Atg17-Atg31-Atg29 subassembly shown in white (PDB 4HPQ). (D) Alphafold3 predicted model of dimeric N. fulvescens’s Atg17 (colored by pLDDT score). (E) Alignment of the Alphafold3 predicted models of dimeric S. pombe (light blue) and N. fulvescens (beige) Atg17 dimers. (F) Representative negative stain EM 2D class average of recombinant S. cerevisiae Atg17. (G) Representative negative stain EM 2D class average of recombinant S. pombe Atg17. (H) Representative negative stain EM 2D class average of recombinant N. fulvescens Atg17 (I) Representative negative stain EM 2D class average of short dimer population of recombinant N. fulvescens Atg17 (J) Alphafold3 predicted model of N. fulvescens Atg17 (purple) in complex with Atg31 (red pink) and Atg29 (yellow) (K) comparison of the Alphafold3 predicted model of N. fulvescens Atg17 monomer (purple), Atg31 (red pink) and Atg29 (yellow) to the predicted model of N. fulvescens Atg17 dimer.
Figure 4.
Figure 4.
Predicted Atg13 cap regions and multiple sequence alignment (A) Alphafold3 predicted model of N. fulvescens Atg13 (dark green) and Atg101 (dark blue) in complex. (B) Alphafold3 predicted model of L. thermotolerans Atg13 (light green). (C) Alphafold3 predicted model of S. pombe Atg13 (green) and Atg101 (blue) in complex. (D) Alphafold3 predicted model of S. cerevisiae Atg13 (sea green). Predicted cap regions are represented in pink in (A-D). (E) Multiple sequence alignment of selected yeast Atg13. Light blue and pink species have predicted rod-shaped and curved Atg17 architecture, respectively. Blue, magenta and yellow squares indicate whether the yeast species has an annotated Atg101, Atg31 and/or Atg29 on Uniprot, respectively. Residues predicted to form the Atg13 cap are highlighted in pink.
See this image and copyright information in PMC

References

    1. Wen X, Klionsky DJ.. An overview of macroautophagy in yeast. J Mol Biol. 2016;428(9):1681–14. doi: 10.1016/j.jmb.2016.02.021 - DOI - PMC - PubMed
    1. Yamamoto H, Zhang S, Mizushima N. Autophagy genes in biology and disease. Nat Rev Genet. 2023;24(6):382–400. doi: 10.1038/s41576-022-00562-w - DOI - PMC - PubMed
    1. Levine B, Kroemer G. Biological functions of autophagy genes: a disease perspective. Cell. 2019;176(1–2):11–42. doi: 10.1016/j.cell.2018.09.048 - DOI - PMC - PubMed
    1. Russell RC, Yuan H-X, Guan K-L. Autophagy regulation by nutrient signaling. Cell Res. 2014;24(1):42–57. doi: 10.1038/cr.2013.166 - DOI - PMC - PubMed
    1. Scaffold proteins in bulk and selective autophagy. Prog mol biol transl sci [Internet]. Elsevier; 2020. [cited 2025 Jul 25]. p. 15–35. Available from: https://linkinghub.elsevier.com/retrieve/pii/S187711732030020X - PubMed

LinkOut - more resources