Interactions between Autophagy Receptors and Ubiquitin-like Proteins Form the Molecular Basis for Selective Autophagy  Vladimir Rogov, Volker Dötsch, Terje Johansen, Vladimir Kirkin  Molecular Cell  Volume 53, Issue 2, Pages 167-178 (January 2014) DOI: 10.1016/j.molcel.2013.12.014 Copyright © 2014 Elsevier Inc. Terms and Conditions

Figure 1 Types of Selective Autophagy in Mammalian Cells The terms aggrephagy, glycophagy, ribophagy, etc. reflect recognition and degradation of a particular type of cargo: protein aggregates, glycogen, ribosomes, etc. Established (black) and putative (red) selective autophagy receptors for the respective processes are listed. Question marks indicate as-of-yet unidentified receptor proteins. Molecular Cell 2014 53, 167-178DOI: (10.1016/j.molcel.2013.12.014) Copyright © 2014 Elsevier Inc. Terms and Conditions

Figure 2 Overview of the Autophagy Pathway In canonical (nonselective) autophagy, the ULK1 and Vps34 complexes serve as integrators of starvation and stress signaling. mTOR, AMPK, and PKA kinases modulate ULK1 complex activity, while ER stress, hypoxia, and infection act via the Vps34 complex. The net result of the signaling is production of the autophagosome that fuses with a lysosome for cargo degradation. Proteins are presented as surfaces generated from existing structures. Molecular Cell 2014 53, 167-178DOI: (10.1016/j.molcel.2013.12.014) Copyright © 2014 Elsevier Inc. Terms and Conditions

Figure 3 Structure of Ub, LC3B, ATG12, and UBL Domains of ATG5 and Structural Determinants of the LIR:Atg8/LC3/GABARAP Interaction Structures of Ub (A), LC3B (B), ATG12 (C), and ATG5 (D) are shown as ribbon diagrams, with Protein Data Bank (PDB) accession codes in brackets. Two hydrophobic pockets of LC3B, HP1 (gray) and HP2 (light brown), are shown in (E). In (F), p62-LIR:LC3B complex (PDB ID 2ZJD) is shown, with elements of the LC3B structure depicted as a ribbon diagram and the structure of the core part of p62-LIR as orange sticks. W340 of p62-LIR oriented to HP1 and L343 oriented to HP2 are represented by a mesh. Molecular Cell 2014 53, 167-178DOI: (10.1016/j.molcel.2013.12.014) Copyright © 2014 Elsevier Inc. Terms and Conditions

Figure 4 Atg8/LC3/GABARAP-Binding Proteins and Their LIR Sequences LC3-Interacting Regions (LIRs) of known Atg8/LC3/GABARAP-interacting proteins are grouped with respect to the aromatic residue (W, F, or Y) at the central position. The conserved aromatic and hydrophobic residues are in bold and underlined; negatively charged residues within and immediately before (at positions −3, −2, or −1) the LIR core are in red; positively charged residues are in blue; and amino acid residues that can potentially be phosphorylated (Ser/Thr) are in green. Atypical LIRs are shown below the consensus sequence. The invariant residues in these sequences are in underlined bold. Only one representative protein from the respective phylogenic tree is shown (priority is given to the highest organism). The pictograms give schematic representations of the Atg8/LC3/GABARAP-interacting proteins. The LIR motifs are shown as arrows (magenta, characterized; yellow, potential); yellow cylinders indicate autophagy-related UBDs or segments of direct cargo recognition; blue cylinders represent characterized functional domains and motifs within proteins; and green connections are any other elements. Abbreviations: H. sapiens, Homo sapiens; S. cerevisiae, Saccharomyces cerevisiae; P. pastoris, Pichia pastoris; aa, amino acids; HC, heavy chain. Molecular Cell 2014 53, 167-178DOI: (10.1016/j.molcel.2013.12.014) Copyright © 2014 Elsevier Inc. Terms and Conditions

Figure 5 ATG5-Binding Proteins The pictograms give schematic representations of the ATG5-interacting proteins. Blue cylinders represent characterized functional domains and motifs within proteins; green connections are any other elements. Abbreviations: H. sapiens, Homo sapiens; aa, amino acids; seq., sequence; pos., position. Molecular Cell 2014 53, 167-178DOI: (10.1016/j.molcel.2013.12.014) Copyright © 2014 Elsevier Inc. Terms and Conditions

Figure 6 The Model of Selective Autophagosome Formation (1) Cargo is modified (e.g., by ubiquitination). (2) Polymeric autophagy receptors (e.g., p62) bind to the cargo either via Ub or directly. (3) Preexisting phagophores are recruited to the cargo-receptor complex via PE-conjugated Atg8/LC3/GABARAPs and ATG5-ATG12-ATG16 bound to Ub or autophagic receptors (e.g., via Alfy). (4) ULK1 complex is recruited via Atg8/LC3/GABARAPs and/or ATG16, while VPS34 complex may be recruited via ULK1, so that the nucleation complex is established at the cargo. (5) The phagophore expands to form an autophagosome around the cargo. (6) The completed autophagosome fuses with a lysosome, leading to cargo and receptor degradation. Molecular Cell 2014 53, 167-178DOI: (10.1016/j.molcel.2013.12.014) Copyright © 2014 Elsevier Inc. Terms and Conditions