Systematic prediction of autophagy-related proteins using Arabidopsis thaliana interactome data

Lixin Cheng*, Yonglun Zeng, Shuai Hu, Ning Zhang, Kenneth C.P. Cheung, Baiying Li, Kwong-Sak Leung, Liwen Jiang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

Autophagy is a self-degradative process that is crucial for maintaining cellular homeostasis by removing damaged cytoplasmic components and recycling nutrients. Such an evolutionary conserved proteolysis process is regulated by the autophagy-related (Atg) proteins. The incomplete understanding of plant autophagy proteome and the importance of a proteome-wide understanding of the autophagy pathway prompted us to predict Atg proteins and regulators in Arabidopsis. Here, we developed a systems-level algorithm to identify autophagy-related modules (ARMs) based on protein subcellular localization, protein–protein interactions, and known Atg proteins. This generates a detailed landscape of the autophagic modules in Arabidopsis. We found that the newly identified genes in each ARM tend to be upregulated and coexpressed during the senescence stage of Arabidopsis. We also demonstrated that the Golgi apparatus ARM, ARM13, functions in the autophagy process by module clustering and functional analysis. To verify the in silico analysis, the Atg candidates in ARM13 that are functionally similar to the core Atg proteins were selected for experimental validation. Interestingly, two of the previously uncharacterized proteins identified from the ARM analysis, AGD1 and Sec14, exhibited bona fide association with the autophagy protein complex in plant cells, which provides evidence for a cross-talk between intracellular pathways and autophagy. Thus, the computational framework has facilitated the identification and characterization of plant-specific autophagy-related proteins and novel autophagy proteins/regulators in higher eukaryotes.
Original languageEnglish
Pages (from-to)708-720
Number of pages13
JournalPlant Journal
Volume105
Issue number3
DOIs
Publication statusPublished - Feb 2021

Scopus Subject Areas

  • Genetics
  • Plant Science
  • Cell Biology

User-Defined Keywords

  • Arabidopsis
  • autophagy
  • colocalization analysis
  • functional module
  • gene expression
  • protein–protein interaction

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