Journal
PLANT JOURNAL
Volume 105, Issue 3, Pages 708-720Publisher
WILEY
DOI: 10.1111/tpj.15065
Keywords
Arabidopsis; autophagy; colocalization analysis; functional module; gene expression; protein– protein interaction
Categories
Funding
- National Natural Science Foundation of China [31670179, 91854201]
- Research Grants Council of Hong Kong [AoE/M-05/12, CUHK14130716, 14102417, 14100818, 14101219, C4012-16E, C400217G, C4033-19E, R4005-18]
- CUHK Research Committee
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This study identified autophagy-related modules in Arabidopsis using a systems-level algorithm, revealing that newly identified genes in these modules are upregulated and coexpressed during senescence. Additionally, the Golgi apparatus autophagy-related module, ARM13, was found to function in the autophagy process through module clustering and functional analysis.
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.
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