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Proteomic Profiling of Autophagosome Cargo in Saccharomyces cerevisiae

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Listed:
  • Kuninori Suzuki
  • Shingo Nakamura
  • Mayumi Morimoto
  • Kiyonaga Fujii
  • Nobuo N Noda
  • Fuyuhiko Inagaki
  • Yoshinori Ohsumi

Abstract

Macroautophagy (autophagy) is a bulk protein-degradation system ubiquitously conserved in eukaryotic cells. During autophagy, cytoplasmic components are enclosed in a membrane compartment, called an autophagosome. The autophagosome fuses with the vacuole/lysosome and is degraded together with its cargo. Because autophagy is important for the maintenance of cellular homeostasis by degrading unwanted proteins and organelles, identification of autophagosome cargo proteins (i.e., the targets of autophagy) will aid in understanding the physiological roles of autophagy. In this study, we developed a method for monitoring intact autophagosomes ex vivo by detecting the fluorescence of GFP-fused aminopeptidase I, the best-characterized selective cargo of autophagosomes in Saccharomyces cerevisiae. This method facilitated optimization of a biochemical procedure to fractionate autophagosomes. A combination of LC-MS/MS with subsequent statistical analyses revealed a list of autophagosome cargo proteins; some of these are selectively enclosed in autophagosomes and delivered to the vacuole in an Atg11-independent manner. The methods we describe will be useful for analyzing the mechanisms and physiological significance of Atg11-independent selective autophagy.

Suggested Citation

  • Kuninori Suzuki & Shingo Nakamura & Mayumi Morimoto & Kiyonaga Fujii & Nobuo N Noda & Fuyuhiko Inagaki & Yoshinori Ohsumi, 2014. "Proteomic Profiling of Autophagosome Cargo in Saccharomyces cerevisiae," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-9, March.
    • Handle: RePEc:plo:pone00:0091651
    DOI: 10.1371/journal.pone.0091651
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    1. Yoshinobu Ichimura & Takayoshi Kirisako & Toshifumi Takao & Yoshinori Satomi & Yasutsugu Shimonishi & Naotada Ishihara & Noboru Mizushima & Isei Tanida & Eiki Kominami & Mariko Ohsumi & Takeshi Noda &, 2000. "A ubiquitin-like system mediates protein lipidation," Nature, Nature, vol. 408(6811), pages 488-492, November.
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