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Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
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Revisiting the evolution of the yeast Atg1 complex.

Kha M Nguyen1, Hannah R Shariati1, Calvin K Yip1

  • 1Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada.

Autophagy Reports
|October 2, 2025
PubMed
Summary

The yeast Atg1 complex evolved differently between budding and fission yeasts. Budding yeasts with Atg101 show a rod-shaped Atg17 scaffold, suggesting alternative evolutionary paths for autophagy-related proteins.

Keywords:
AlphaFold3Atg1 complexAtg17budding yeastfission yeast

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Area of Science:

  • Molecular and Cellular Biology
  • Evolutionary Biology
  • Yeast Genetics

Background:

  • The autophagy-related (ATG) protein complex, specifically Atg1, is crucial for initiating nonselective autophagy in yeast.
  • Distinct compositions of the Atg1 complex exist between budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe), with differing scaffold proteins (Atg17, Atg29, Atg31 vs. Atg17, Atg101).
  • The evolutionary timeline and structural impact of these compositional differences on Atg17 remain largely unknown.

Purpose of the Study:

  • To investigate the evolutionary divergence of the Atg1 complex in yeast.
  • To determine the structural variations in the Atg17 scaffold across different yeast species.
  • To explore the potential functional implications of Atg101 incorporation and the Atg13 HORMA domain.

Main Methods:

  • Systematic composition analysis of the Atg1 complex across various yeast species.
  • Structural modeling and negative stain electron microscopy (EM) for scaffold structure determination.
  • Analysis of the Atg13 HORMA domain in Schizosaccharomyces pombe.

Main Results:

  • Atg101 was identified in the Atg1 complex of several budding yeast species, with some co-occurring with Atg29/Atg31.
  • Budding yeast species possessing Atg101 exhibited a rod-shaped Atg17 scaffold, contrasting with the S-shaped scaffold in species lacking Atg101.
  • The Atg13 HORMA domain in Schizosaccharomyces pombe may have a stabilizing cap, hinting at a distinct role for Atg101.

Conclusions:

  • The presence of Atg101 correlates with a rod-shaped Atg17 structure in budding yeasts, indicating a significant evolutionary shift.
  • These findings suggest alternative evolutionary pathways for the Atg1 complex structure and function within the yeast lineage.
  • The study delineates potential evolutionary trajectories for the core autophagy initiation complex.