THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy

Autophagy. 2018;14(2):296-310. doi: 10.1080/15548627.2017.1402990.

Abstract

Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org ), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of ATG genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.

Keywords: ATG; autophagy; phosphorylation; post-translational modification; ubiquitin.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Autophagy / physiology*
  • Autophagy-Related Proteins
  • Databases, Protein*
  • Datasets as Topic
  • Humans
  • Phosphorylation / physiology*
  • Protein Kinases / genetics
  • Protein Kinases / metabolism*
  • Protein Processing, Post-Translational / physiology*
  • Signal Transduction
  • Ubiquitins / genetics
  • Ubiquitins / metabolism*

Substances

  • Autophagy-Related Proteins
  • Ubiquitins
  • Protein Kinases

Grant support

This work was supported by grants from the Special Project on Precision Medicine under the National Key R&D Program (2017YFC0906600), the National Basic Research Program (973 project) (2013CB933900), Natural Science Foundation of China (31671360), and International Science & Technology Cooperation Program of China (2014DFB30020).