Ubiquitin and proteasomes

Molecular dissection of autophagy: two ubiquitin-like systems

Key Points

  • This review discusses recent analyses of the genes required for autophagy ? intracellular bulk protein degradation ? in yeast, where two ubiquitin-like systems have now been revealed.

  • Light microscopy studies show that starved yeast cells take up their own cytoplasm into vacuoles through autophagic bodies. Closer analysis using electron microscopy show that these bodies form a double-membraned structure called the autophagosome, which subsequently fuses with the vacuole/lysosome. The whole process is topologically the same in mammals.

  • Screens in yeast defective in autophagy morphologically and biochemically revealed two sets of genes, the APG and AUT genes, respectively. A specific vacuolar enzyme biosynthetic pathway requires the cytosol-to-vacuole-targeting (CVT) genes. There is extensive overlap between the CVT genes and the APG/AUT genes.All apg mutants have defects at or before formation of the autophagosome.

  • Two ubiquitin-like systems have been discovered. The first ? the Apg12 conjugation system ? is unique in that Apg12 is synthesized as a mature form; it seems to have just one target, Apg5, and at steady state almost all Apg12 molecules are conjugated with Apg5.

  • The second ? Apg8/Aut7 ? is processed at its carboxy-terminal region by Aut2/Apg4. Apg8 exists in two forms, one of which is membrane bound through a phospholipid. This lipidation is mediated by ubiqutin-like system; Apg8 is activated by Apg7 and transferred to Apg3 and finally forms a conjugate with phosphatidylethaolamine (PE). Apg4 cleaves Apg8?PE, releasing Apg8 from membrane.

  • Morphological studies show that Apg8 localizes on the membrane of intermediate structures of the autophagosome; this transient association seems to be essential for formation of the autophagosome.

  • Both Apg12 and Apg8 are highly conserved, with apparent homologues in the worm, mammals and plants. In higher eukaryotes, Apg8 consists of a multigene family.


Recent analyses of the genes required for autophagy ? intracellular bulk protein degradation ? in yeast have revealed two ubiquitin-like systems, both of which are involved in the membrane dynamics of the process. Molecular dissection of these systems is now revealing some surprises.

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Figure 1: Electron microscopic images of autophagy in yeast.
Figure 2: Two ubiquitin-like systems are required for autophagy.


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    *Macroautophagy is generally a non-selective sequestration.But in some physiological situations, excess or unnecessary organelles areselectively degraded in a lysosome/vacuole. The best-studied case is peroxisomedegradation, called pexophagy by Daniel Klionsky. In the yeast Pichia pastoris, peroxisomes are sequestered through either macroautophagy or microautophagy,depending on the nutrient conditions40.


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Thanks to T. Noda and N. Mizushima for critical discussion and reading of this manuscript.

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Lysosomal degradation of proteins



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Ohsumi, Y. Molecular dissection of autophagy: two ubiquitin-like systems. Nat Rev Mol Cell Biol 2, 211–216 (2001). https://doi.org/10.1038/35056522

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