Post-translationally-modified structures in the autophagy machinery: an integrative perspective

Autophagy is a self-cleaning process that occurs at a constitutive basal level, and is upregulated in response to stress. Macroautophagy (hereafter autophagy) is the most robust type of autophagy, where cargo (specific or nonspecific) is engulfed within a double-membrane structure termed an autophagosome. This process needs to be tightly regulated to maintain normal cellular homeostasis and prevent dysfunction; therefore, a fuller knowledge of the mechanisms of autophagy regulation is crucial for understanding the entire pathway. The autophagy-related proteins are the primary components that carry out autophagy. Many of these proteins are conserved from yeast to humans. A number of significant discoveries with regard to protein functional domains, protein-protein interactions or post-translational modifications of proteins involved in autophagy have been reported in parallel with, or followed by, solving the NMR or crystal structures of autophagy proteins or their protein domains. In the present review, we summarize structural insights gathered to date on the proteins of the autophagy machinery that are modulated by a post-translational modification, specifically phosphorylation, acetylation, ubiquitination and/or SUMOylation. For each protein, we link the reported results with information on the propensity of the corresponding amino acid sequence toward order/disorder. This integrative approach yields a comprehensive overview for each post-translationally modified protein, and also reveals areas for further investigation.