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Updated: Dec 30, 2025

Study of Protein-protein Interactions in Autophagy Research
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Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy

Jonathan A Stefely1,2,3, Yu Zhang3, Elyse C Freiberger4,5,6,7

  • 1Morgridge Institute for Research , Madison, WI, USA.

Autophagy
|January 24, 2020
PubMed

Insights

Researchers identified CALCOCO1 as a key protein in MTOR-regulated autophagy, specifically in the selective removal of endoplasmic reticulum components (reticulophagy). This discovery advances understanding of the MTOR-autophagy axis and its potential as an anticancer target.

Area of Science:

  • Cellular Biology
  • Molecular Biology
  • Cancer Research

Background:

  • Macroautophagy/autophagy is a crucial cellular process suppressed by MTOR (mechanistic target of rapamycin kinase).
  • MTOR-regulated autophagy is a significant target in cancer therapy, but its molecular mechanisms are not fully understood.
  • Identifying novel proteins within the MTOR-autophagy signaling pathway is essential for therapeutic development.

Purpose of the Study:

  • To identify novel proteins involved in the MTOR-autophagy axis using proteomic profiling.
  • To elucidate the role of identified proteins, particularly CALCOCO1 (calcium binding and coiled-coil domain protein 1), in MTOR-regulated autophagy.
  • To investigate the involvement of CALCOCO1 in selective autophagy, such as reticulophagy (autophagy of the endoplasmic reticulum).

Main Methods:

  • Proteomic profiling was employed on wild-type and autophagy-gene knockout (Atg5 or Ulk1/Ulk2) mouse embryonic fibroblast (MEF) cell lines.
  • Cells were treated with an MTOR inhibitor (MLN0128) and cultured in media with either glucose or galactose to modulate autophagy.
  • Mass spectrometry was used to analyze protein expression, followed by co-immunoprecipitation and genetic deletion experiments to confirm protein interactions and functions.

Main Results:

  • Proteomic analysis identified known autophagy proteins and novel candidates, including CALCOCO1.
  • CALCOCO1 was shown to physically interact with MAP1LC3C, a critical component of the autophagy machinery.
  • Genetic deletion of CALCOCO1 impaired reticulophagy, demonstrating its role in selective endoplasmic reticulum turnover.

Conclusions:

  • CALCOCO1 plays a significant role in MTOR-regulated selective autophagy, particularly reticulophagy.
  • This study provides a valuable proteomic resource for understanding the MTOR-autophagy axis and identifying new pathway components.
  • The findings contribute to the ongoing investigation of autophagy as an anticancer target.
Keywords:
ATG5CALCOCO1MAP1LC3MTORULK1ULK2mass spectrometry proteomicsreticulophagyselective autophagy

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