TPC Lecture 9 & 10 Module 4073 Autophagy & Longevity Summer Semester 2024 PDF

Module 4073 „Autophagy & Longevity“ Lecture 9 & 10: Selective autophagy and non- canonical autophagy Prof. Dr. Tassula Proikas-Cezanne 24th June & 1st July 2024 Twitter: @TassulaPC  History of Autophagy Photo: Mari Honda...

Module 4073 „Autophagy & Longevity“ Lecture 9 & 10: Selective autophagy and non- canonical autophagy Prof. Dr. Tassula Proikas-Cezanne 24th June & 1st July 2024 Twitter: @TassulaPC  History of Autophagy Photo: Mari Honda From: Kwon YT, Ciechanover A (2017) Trends Biochem Sci. 42(11):873-886.  History of Autophagy Photo: Mari Honda Autophagy receptors UBD LIR p62 NBR1 (neighbor of BRCA1 gene 1) … Modified: Kwon YT, Ciechanover A (2017) Trends Biochem Sci. 42(11):873-886.  Selective autophagy (1) Functions of autophagy receptors and adaptors in selective autophagy Photo: Mari Honda Stolz and Dikic, Nat Cell Biol. 2014;16(6):495-501.  Selective autophagy (1) Functions of autophagy receptors and adaptors in selective autophagy Photo: Mari Honda Stolz and Dikic, Nat Cell Biol. 2014;16(6):495-501.  Selective autophagy (1) The selective recruitment of phagophores to cargos through the interaction of autophagy receptors with LC3II Photo: Mari Honda Stolz and Dikic, Nat Cell Biol. 2014;16(6):495-501.  Selective autophagy (1) Selective autophagy types and corresponding receptors Gubas and Dikic, FEBS J. 2022, 289(1):75-89.  Selective autophagy (1) Regulatory modifications reported for selective autophagy receptors SAR: Selective Autophagy Receptor Gubas and Dikic, FEBS J. 2022, 289(1):75-89.  Selective autophagy (1) The selective recruitment of phagophores to cargos through the interaction of autophagy receptors with LC3II Photo: Mari Honda LIR: LC3-interacting region Stolz and Dikic, Nat Cell Biol. 2014;16(6):495-501.  Selective autophagy (1) The selective recruitment of phagophores to cargos through the interaction of autophagy receptors with LC3II Photo: Mari Honda LIR: LC3-interacting region GIM: GABARAP-interacting motif Stolz and Dikic, Nat Cell Biol. 2014;16(6):495-501.  Selective autophagy (1) LC3/GABARAPs Microtubule-associated protein-1 light chain 3 (MAP1LC3) family (MAP1LC3A, MAP1LC3B, MAP1LC3C; short names LC3A, LC3B, LC3C) LC3A LC3B LC3C GABARAP GABARAPL1 GABARAPL2 γ-aminobutyric acid (GABA)-receptor-associated proteins (GABARAP, GABARAPL1, GABARAPL2)  Selective autophagy (1) LC3/GABARAPs Photo: Mari Honda Jacquet et al., Autophagy. 2021;17(3):599-611.  Selective autophagy (1) The selective recruitment of phagophores to cargos through the interaction of autophagy receptors with LC3II Photo: Mari Honda LIR: LC3-interacting region GIM: GABARAP-interacting motif Stolz and Dikic, Nat Cell Biol. 2014;16(6):495-501.  Selective autophagy (1) Types of cargo recognition in selective autophagy I. In ubiquitin-dependent autophagy, cargo is polyubiquitinated, which serves as a signal for its degradation. Cargo receptors can simultaneously bind ATG8 proteins and polyubiquitin on the cargo, providing a strong link between autophagy machinery and the cargo itself. SAR: Selective Autophagy Receptor Gubas and Dikic, FEBS J. 2022, 289(1):75-89.  Selective autophagy (1) Types of cargo recognition in selective autophagy II. Cargo receptors can also bind sugars, such as lectins, that are recruited to the cargo, as is the case during lysophagy, where galectin 3 decorates damaged lysosomes and is able to bind the receptors. SAR: Selective Autophagy Receptor Gubas and Dikic, FEBS J. 2022, 289(1):75-89.  Selective autophagy (1) Types of cargo recognition in selective autophagy III. SARs can also bind directly to the cargo and deliver it to the forming phagophore through the ATG8 binding. SAR: Selective Autophagy Receptor Gubas and Dikic, FEBS J. 2022, 289(1):75-89.  Selective autophagy (1) Types of cargo recognition in selective autophagy IV. Some lipids (such as cardiolipin) can bind ATG8s and provide a direct link between cargo and autophagy machinery in a receptor-independent manner. SAR: Selective Autophagy Receptor Gubas and Dikic, FEBS J. 2022, 289(1):75-89. Canonical and non-canonical autophagy Pathways of canonical and non- canonical autophagy: Canonical autophagy: initiation (1), nucleation (2), elongation and closure (3), recycling (4) and degradation (5) Non-canonical autophagy: bypass some of the canonical steps Photo: Mari Honda Proteins that may be bypassed during non-canonical autophagy are highlighted in red boxes. From: Codogno, Mehrpour, Proikas-Cezanne (2012) Nat Rev Mol Cell Biol. 13:7-12. Canonical and non-canonical autophagy Non-canonical autophagy is characterized by the following hallmarks: Autophagosome formation does not require the hierarchical intervention of all of the ATG proteins. The double membrane does not necessarily elongate from a single Photo: Mari Honda source. A set of ATG proteins can be recruited to a pre-existing membrane that is different from the phagophore. From: Codogno, Mehrpour, Proikas-Cezanne (2012) Nat Rev Mol Cell Biol. 13:7-12. Atg8s are dispensable for autophagosome formation but regulate autophagosome expansion Hexa KO cell deficient for all ATG8/GABARAP members: 3D rendering Reconstructed autophagosomal compartment (green) Sequestered mitochondrion (red) Photo: Mari Honda Endoplasmic reticulum (purple) From: Nguyen et al. (2018) J Cell Biol. 215(6):857-874. Non-canonical functions of ATG16L1 Model for the recruitment of ATG16L1 to membranes: (Left) Induction of LC3 lipidation during autophagy depends on the ULK1 complex subunit FIP200 and WIPI2, which recruit ATG16L1 to the site of autophagosome formation via the FBD. LC3 becomes conjugated to the isolation membrane. (Right) During autophagy-unrelated, non-canonical pathways involving LC3 lipidation, ATG16L1 is recruited via its C-terminal WD40 domain and promotes the lipidation of LC3 to single membranes. From: Fracchiolla, Martens (2018) EMBO J 37(4): e98895. Canonical and non-canonical autophagy Examples of non-canonical autophagy structures a | The hallmarks of canonical autophagosomes. b | ATG-dependent autophagic pathway with noncanonical structures: In some cases of xenophagy the envelope membrane does not display canonical hallmarks. Example, group A Streptococcus (GAS) is sequestered by a double-membraned Photo: Mari Honda autophagosome that is formed from multiple isolation membranes. c | ATG-dependent, non-autophagic pathway: Engagement of Toll-like receptors (TLRs) with their ligand at the cell surface leads to the non-canonical recruitment of ATG proteins to the single-membrane bound phagosome. From: Codogno, Mehrpour, Proikas-Cezanne (2012) Nat Rev Mol Cell Biol. 13:7-12. Autophagy as an anti-bacterial mechanism Autophagy targets intracellular bacteria After invasion of host cells, the bacterium resides in a bacterium- containing vacuole (or phagosome). Some bacteria damage the vacuolar or phagosomal membrane and eventually escape into the cytosol. Autophagy can target bacteria in damaged vacuoles or phagosomes: e.g. Mycobacterium tuberculosis, Salmonella enterica subsp. enterica serovar Typhimurium Autophagy can also target bacteria in the cytosol: e.g. Group A Streptococcus From: Huang , Brumell (2014) Nat Rev Microbiol. 12(2):101-14. Autophagy as an anti-bacterial mechanism Model of the antibacterial autophagy of S. Typhimurium The bacterium resides in a Salmonella-containing vacuole (SCV) after invading epithelial cells. Early after infection (~1 hour), the membrane of a subset of SCVs is damaged and the bacterium is exposed to the cytoplasm Ubiquitination by E3 ligase LRSAM1 and autophagy receptors (p62, NDP52, OPTN) recruitment. The damaged SCV membrane also exposes β-glycans and recruits galectin 8 (GAL8), which binds to NDP52 and further recruits LC3. T3SS, type III secretion system From: Huang , Brumell (2014) Nat Rev Microbiol. 12(2):101-14. Autophagy as an anti-bacterial mechanism Model of the antibacterial autophagy of S. Typhimurium At ~1 hour post-infection, a subset of bacteria recruits diacylglycerol (DAG) to the undamaged SCVs. DAG activates protein kinase Cδ (PKCδ), which activates NADPH oxidase (NOX) and promotes reactive oxygen species (ROS) production This induces LC3-associated phagocytosis (LAP) of bacteria. T3SS, type III secretion system From: Huang , Brumell (2014) Nat Rev Microbiol. 12(2):101-14. Autophagy as an anti-bacterial mechanism Model of the antibacterial autophagy of S. Typhimurium At ~4 hours post-infection, mammalian target of rapamycin (mTOR) is redistributed to the SCV membrane Inhibition of autophagy Autophagy escape and bacterial replication in SCVs. T3SS, type III secretion system From: Huang , Brumell (2014) Nat Rev Microbiol. 12(2):101-14. LC3-associated phagocytosis (LAP) Photo: Mari Honda From: Heckmann, Green (2019) J Cell Sci. 132(5):jcs222984. LC3-associated phagocytosis (LAP) LAP uses a portion of the canonical autophagy machinery LAP: Non-canonical ATG function LAP is characterized by the conjugation of LC3 family proteins to phagosome membranes LAP cargos: pathogens, dying cells, soluble ligands, protein aggregates. LAP pathway involved in immune activation and inflammatory responses. From: Heckmann, Green (2019) J Cell Sci. 132(5):jcs222984. LC3-associated phagocytosis (LAP) LAP is not dependent on the AMPK– mTORC1–ULK1 axis LAP is not responsive to nutrient status or intracellular stress sensing Activating stimulus from the cell exterior: ligands, pathogens, dying cells, immune complexes From: Heckmann, Green (2019) J Cell Sci. 132(5):jcs222984. LC3-associated phagocytosis (LAP) ULK complex (ULK1, FIP200, ATG13, ATG101) is dispensable for LAP Required is the PI3KC3 complex composed of VPS34, VPS15, BECN1, ATG14L, UVRAG, RUBCN From: Heckmann, Green (2019) J Cell Sci. 132(5):jcs222984. LC3-associated phagocytosis (LAP) Photo: Mari Honda From: Heckmann, Green (2019) J Cell Sci. 132(5):jcs222984. LC3-associated phagocytosis (LAP) From: Heckmann, Green (2019) J Cell Sci. 132(5):jcs222984. LC3-associated phagocytosis (LAP) ULK complex (ULK1, FIP200, ATG13, ATG101) is dispensable for LAP Required is the PI3KC3 complex composed of VPS34, VPS15, BECN1, ATG14L, UVRAG, RUBCN LC3 lipidation occurs faster LC3 lipidation occurs upon phagosome sealing LC3 not involved in cargo selection From: Heckmann, Green (2019) J Cell Sci. 132(5):jcs222984. Thank you.