The carboxy terminus of yeast Atg13 binds phospholipid membrane via motifs that overlap with the Vac8-interacting domain

Autophagy. 2020 Jun;16(6):1007-1020. doi: 10.1080/15548627.2019.1648117. Epub 2019 Aug 2.


Macroautophagy/autophagy is a conserved catabolic recycling pathway involving the sequestration of cytoplasmic components within double-membrane vesicles termed autophagosomes. The autophagy-related (Atg) protein Atg13 is a key member of the autophagy initiation complex. The Atg13 C terminus is an intrinsically disordered region (IDR) harboring a binding site for the vacuolar membrane protein Vac8. Recent reports suggest Atg13 acts as a hub to assemble the initiation complex, and also participates in membrane recognition. Here we show that the Atg13 C terminus directly binds to lipid membranes via electrostatic interactions between positively charged residues in Atg13 and negatively charged phospholipids as well as a hydrophobic insertion of a Phe residue. We identified 2 sets of residues in the Atg13 IDR that affect its phospholipid-binding properties; these residues overlap with the Vac8-binding domain of Atg13. Our data indicate that Atg13 binding to phospholipids and Vac8 is mutually exclusive, and both are required for efficient autophagy.

Abbreviations: Atg: autophagy-related; CD: circular dichroism; Cvt: cytoplasm-to-vacuole targeting; IDR: intrinsically disordered region; ITC: isothermal calorimetry; MIM: MIT-interacting motif; MKO: multiple-knockout; PAS: phagophore assembly site; PC: phosphatidylcholine; PS: phosphatidylserine; PtdIns: phosphatidylinositol; PtdIns3P: phosphatidylinositol-3-phosphate.

Keywords: Autophagy; intrinsically disordered region; membrane binding; phospholipids; structure.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry*
  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism*
  • Amino Acid Motifs
  • Autophagosomes / metabolism
  • Autophagy* / genetics
  • Autophagy-Related Proteins / chemistry*
  • Autophagy-Related Proteins / genetics
  • Autophagy-Related Proteins / metabolism*
  • Calorimetry
  • Gene Expression
  • Hydrophobic and Hydrophilic Interactions
  • Liposomes
  • Membrane Proteins / metabolism*
  • Phospholipids / chemistry*
  • Protein Binding
  • Protein Domains
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Static Electricity
  • Vacuoles / metabolism
  • Vesicular Transport Proteins / metabolism*


  • ATG13 protein, S cerevisiae
  • Adaptor Proteins, Signal Transducing
  • Autophagy-Related Proteins
  • Liposomes
  • Membrane Proteins
  • Phospholipids
  • Saccharomyces cerevisiae Proteins
  • VAC8 protein, S cerevisiae
  • Vesicular Transport Proteins