Structural Biology and Electron Microscopy of the Autophagy Molecular Machinery

Abstract

Autophagy is a highly regulated bulk degradation process that plays a key role in the maintenance of cellular homeostasis. During autophagy, a double membrane-bound compartment termed the autophagosome is formed through de novo nucleation and assembly of membrane sources to engulf unwanted cytoplasmic components and targets them to the lysosome or vacuole for degradation. Central to this process are the autophagy-related (ATG) proteins, which play a critical role in plant fitness, immunity, and environmental stress response. Over the past few years, cryo-electron microscopy (cryo-EM) and single-particle analysis has matured into a powerful and versatile technique for the structural determination of protein complexes at high resolution and has contributed greatly to our current understanding of the molecular mechanisms underlying autophagosome biogenesis. Here we describe the plant-specific ATG proteins and summarize recent structural and mechanistic studies on the protein machinery involved in autophagy initiation with an emphasis on those by single-particle analysis.

Autophagy in the retinal pigment epithelium: a new vision and future challenges

“…Studies have focused on the molecular mechanisms behind these processes highlighting the importance of autophagy receptors and key adaptor proteins, which link substrates to autophagy machinery. So far, a number of landmark papers have reviewed autophagy in different fields including selective cargo recognition and degradation [ 2 , 3 ]; transcriptional and post‐transcriptional regulation of autophagy [ 4 , 5 ]; dynamic molecular mechanisms participating in the formation of core autophagic machinery and its fusion with lysosomes [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]; and related processes governing final cargo degradation [ 17 , 29 ]. The initiation of autophagy requires a UNC51‐like kinase (ULK1) that forms a complex with autophagy‐related 13 (ATG13) and family‐interacting protein of 200 KDa (FIP200), driving autophagosomes formation.…”

Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels

“…In yeast bulk autophagy, the early PAS is formed by high-order assemblies of the Atg1 kinase complex with other Atg proteins to form a so-called Atg-complex condensate ( Hawkins and Klionsky, 2020 ; Fujioka and Noda, 2021 ) ( Figure 9C ) where LLPS organizes the site of autophagosome formation ( Fujioka et al, 2020 ). In the past years crystallography and cryo-EM have provided considerable insights into the molecular interactions between Atg proteins and membranes at the heart of PAS formation and autophagosome biogenesis ( Lai et al, 2019 ). Still in yeast, protein Vps13 is found at vacuole-mitochondria (vCLAMP) and vacuole-ER (NVJ, the nuclear envelope derives from the ER) contact sites ( Lang et al, 2015 ) and also promotes the formation of another double membrane structure, the prospore ( Park and Neiman, 2012 ).…”

Advances in Plant Autophagy

“…The structural and mechanistic studies on the protein machinery involved in autophagy initiation and autophagosome biogenesis, are summarized in the review by Lai et al [ 14 ]. Structural data mainly obtained by X-ray crystallography, are mostly only available for the yeast and mammalian proteins and complexes.…”