iLIR Autophagy Database

Click here for: Documented LIRCPs

Reviews

Birgisdottir, A. B., et al. (2013). "The LIR motif - crucial for selective autophagy." J Cell Sci 126(Pt 15): 3237-3247.

Cebollero, E., et al. (2012). "Reticulophagy and ribophagy: regulated degradation of protein production factories." Int J Cell Biol 2012: 182834.

Dunn, W. A., Jr., et al. (2005). "Pexophagy: the selective autophagy of peroxisomes." Autophagy 1(2): 75-83.

Galluzzi, L., et al. (2015). "Autophagy in malignant transformation and cancer progression." EMBO J.

Knodler, L. A. and J. Celli (2011). "Eating the strangers within: host control of intracellular bacteria via xenophagy." Cell Microbiol 13(9): 1319-1327.

Lamark, T. and T. Johansen (2012). "Aggrephagy: selective disposal of protein aggregates by macroautophagy." Int J Cell Biol 2012: 736905.

Noda, N. N., et al. (2010). "Atg8-family interacting motif crucial for selective autophagy." FEBS Lett 584(7): 1379-1385.

Stotland, A. and R. A. Gottlieb (2015). "Mitochondrial quality control: Easy come, easy go." Biochim Biophys Acta.

Weidberg, H., et al. (2009). "Lipophagy: selective catabolism designed for lipids." Dev Cell 16(5): 628-630.

Wild, P., et al. (2014). "The LC3 interactome at a glance." J Cell Sci 127(Pt 1): 3-9.

Bioinformatics studies and tools

Behrends, C., et al. (2010). "Network organization of the human autophagy system." Nature 466(7302): 68-76.

Kalvari, I., et al. (2014). "iLIR: A web resource for prediction of Atg8-family interacting proteins." Autophagy 10(5): 913-925.

Selective autophagy

Alemu, E. A., et al. (2012). "ATG8 family proteins act as scaffolds for assembly of the ULK complex: sequence requirements for LC3-interacting region (LIR) motifs." J Biol Chem 287(47): 39275-39290.

Bellelli R, et al. (2016). "NCOA4 Deficiency Impairs Systemic Iron Homeostasis." Cell reports 14:411-21.

Bjorkoy, G., et al. (2005). "p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death." J Cell Biol 171(4): 603-614.

Bourke, L. T., et al. (2013). "Signal transducer and activator of transcription-1 localizes to the mitochondria and modulates mitophagy." JAKSTAT 2(4): e25666.

Hanna, R. A., et al. (2012). "Microtubule-associated protein 1 light chain 3 (LC3) interacts with Bnip3 protein to selectively remove endoplasmic reticulum and mitochondria via autophagy." J Biol Chem 287(23): 19094-19104.

Ichimura, Y., et al. (2008). "Structural basis for sorting mechanism of p62 in selective autophagy." J Biol Chem 283(33): 22847-22857.

Jiang, S., et al. (2011). "Starch-binding domain-containing protein 1 (Stbd1) and glycogen metabolism: Identification of the Atg8 family interacting motif (AIM) in Stbd1 required for interaction with GABARAPL1." Biochem. Biophys. Res. Commun. 413, 420-425.

Kirkin, V., et al. (2009). "A role for NBR1 in autophagosomal degradation of ubiquitinated substrates." Mol Cell 33(4): 505-516.

Kondo-Okamoto, N., et al. (2012). A"utophagy-related protein 32 acts as autophagic degron and directly initiates mitophagy." J. Biol. Chem. 287, 10631-10638.

Liu, L., et al. (2012). "Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells." Nat. Cell Biol. 14, 177-185.

Mancias, J. D., et al. (2014). "Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy." Nature 509(7498): 105-109.

Mohrlülder, J., et al. (2007a). "Identification of clathrin heavy chain as a direct interaction partner for the gamma- aminobutyric acid type A receptor associated protein." Biochemistry 46, 14537-14543.

Mohrlülder, J., et al. (2007b). "Identification of calreticulin as a ligand of GABARAP by phage display screening of a peptide library." FEBS J. 274, 5543-5555.

Newman, A. C., Set al. (2012). "TBK1 kinase addiction in lung cancer cells is mediated via autophagy of Tax1bp1/Ndp52 and non-canonical NF-kB signalling." PLoS ONE 7, e50672.

Noda, N. N., et al. (2008). "Structural basis of target recognition by Atg8/LC3 during selective autophagy." Genes Cells 13(12): 1211-1218.

Novak, I., et al. (2010). "Nix is a selective autophagy receptor for mitochondrial clearance." EMBO Rep 11(1): 45-51.

Ochaba, J., et al. (2014). "Potential function for the Huntingtin protein as a scaffold for selective autophagy." Proc Natl Acad Sci U S A.

Okamoto, K., et al. (2009). "Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy." Dev. Cell 17, 87-97.

Pankiv, S., et al. (2007). "p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy." J Biol Chem 282(33): 24131-24145.

Sandilands, E., . et al. (2012). A"utophagic targeting of Src promotes cancer cell survival following reduced FAK signalling." Nat. Cell Biol. 14, 51-60.

Schwarten, M., et al. (2009). "Nix directly binds to GABARAP: a possible crosstalk between apoptosis and autophagy." Autophagy 5(5):690-8

Schweers, R. L., et al. (2007). N"IX is required for programmed mitochondrial clearance during reticulocyte maturation." Proc. Natl. Acad. Sci. USA 104, 19500-19505.

Suzuki, K., et al. (2010). S"elective transport of alpha-mannosidase by autophagic pathways: identification of a novel receptor, Atg34p." J. Biol. Chem. 285, 30019-30025.

Svenning, S., et al. (2011). "Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1." Autophagy 7, 993-1010.

Tang, Z., et al. (2013). "Autophagy promotes primary ciliogenesis by removing OFD1 from centriolar satellites." Nature 502(7470): 254-257.

Thurston, T. L., et al. (2009). "The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria." Nat Immunol 10(11): 1215-1221.

Tian, Y., et al. (2013). "Adaptor complex AP2/PICALM, through interaction with LC3, targets Alzheimer's APP-CTF for terminal degradation via autophagy." Proc Natl Acad Sci U S A 110(42): 17071-17076.

von Muhlinen, et al. (2012). "LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy." Mol. Cell 48, 329-342.

Wild, P., et al. (2011). "Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth." Science 333(6039): 228-233.

Zhu, Y., et al. (2013). "Modulation of serines 17 and 24 in the LC3-interacting region of Bnip3 determines pro-survival mitophagy versus apoptosis." J Biol Chem 288(2): 1099-1113.

Regulation of the autophagy process

Buraschi, S., et al. (2013). "Decorin causes autophagy in endothelial cells via Peg3." Proc Natl Acad Sci U S A 110(28): E2582-2591.

Colecchia, D., et al. (2012). "MAPK15/ERK8 stimulates autophagy by interacting with LC3 and GABARAP proteins." Autophagy 8, 1724-1740.

Dunlop, E. A., et al. (2014). "FLCN, a novel autophagy component, interacts with GABARAP and is regulated by ULK1 phosphorylation." Autophagy 10(10): 1749-1760.

Garcia-Marcos, M., et al. (2011). "A GDI (AGS3) and a GEF (GIV) regulate autophagy by balancing G protein activity and growth factor signals." Mol Biol Cell 22(5): 673-686.

Hain, A. U., et al. (2012). "Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction." J. Struct. Biol. 180, 551-562.

Jiang K, et al.(2016). "Tumor suppressor Spred2 interaction with LC3 promotes autophagosome maturation and induces autophagy-dependent cell death. Oncotarget.

Kraft, C., et al. (2012). "Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy." EMBO J 31(18): 3691-3703.

Li, M., et al. (2011). "Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates." J. Biol. Chem. 286, 7327-7338.

N'Diaye, E. N., et al. (2009). "PLIC proteins or ubiquilins regulate autophagy-dependent cell survival during nutrient starvation." EMBO Rep 10(2): 173-179.

Nakatogawa, H., et al. (2012). "The autophagy-related protein kinase Atg1 interacts with the ubiquitin-like protein Atg8 via the Atg8 family interacting motif to facilitate autophagosome formation." J Biol Chem 287(34): 28503-28507.

Pattingre, S., et al. (2003). "The G-protein regulator AGS3 controls an early event during macroautophagy in human intestinal HT-29 cells." J Biol Chem 278(23): 20995-21002.

Poluzzi, C., et al. (2014). "Endorepellin evokes autophagy in endothelial cells." J Biol Chem 289(23): 16114-16128.

Popovic, D., et al. (2012). "Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers." Mol Cell Biol 32(9): 1733-1744.

Rothenberg, C., et al. (2010). "Ubiquilin functions in autophagy and is degraded by chaperone-mediated autophagy." Hum Mol Genet 19(16): 3219-3232.

Sancho, A., et al. (2012). "DOR/Tp53inp2 and Tp53inp1 constitute a metazoan gene family encoding dual regulators of autophagy and transcription." PLoS ONE 7, e34034.

Satoo, K., et al. (2009). "The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy." EMBO J 28(9): 1341-1350.

Seillier, M., et al. (2012). "TP53INP1, a tumor suppressor, interacts with LC3 and ATG8-family proteins through the LC3-interacting region (LIR) and promotes autophagy-dependent cell death." Cell Death Differ. 19, 1525-1535.

Ulbricht, A., et al. (2013). "Cellular mechanotransduction relies on tension-induced and chaperone-assisted autophagy." Curr Biol 23(5): 430-435.

Wilkinson, D. S., et al. (2015) "Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy." Molecular cell 57:55-68.

Xie, R., et al. (2011). "Microtubule-associated protein 1S (MAP1S) bridges autophagic components with microtubules and mitochondria to affect autophagosomal biogenesis and degradation." J Biol Chem 286(12): 10367-10377.

Yamaguchi, M., et al. (2010). "Autophagy-related protein 8 (Atg8) family interacting motif in Atg3 mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-to-vacuole targeting pathway." J Biol Chem 285(38): 29599-29607.

Vesicular transport

Fu, M. M., et al. (2014). "LC3 binding to the scaffolding protein JIP1 regulates processive dynein-driven transport of autophagosomes." Dev Cell 29(5): 577-590.

Itoh, T., et al. (2008). "Golgi-resident small GTPase Rab33B interacts with Atg16L and modulates autophagosome formation." Mol. Biol. Cell 19, 2916-2925.

Pankiv, S., et al. (2010). "FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport." J Cell Biol 188(2): 253-269.

Xie, R., et al. (2011). "Microtubule-associated protein 1S (MAP1S) bridges autophagic components with microtubules and mitochondria to affect autophagosomal biogenesis and degradation." J Biol Chem 286(12): 10367-10377.

Proteins targeted to autophagosomes for degradation

Gao, C., et al. (2010). "Autophagy negatively regulates Wnt signalling by promoting Dishevelled degradation." Nat Cell Biol 12(8): 781-790.

Paul, S., et al. (2012). "Selective autophagy of the adaptor protein Bcl10 modulates T cell receptor activation of NF-kappaB." Immunity 36(6): 947-958.

Petherick, K. J., et al. (2013). "Autolysosomal beta-catenin degradation regulates Wnt-autophagy-p62 crosstalk." EMBO J 32(13): 1903-1916.

Zhang, Y., et al. (2011). "GABARAPL1 negatively regulates Wnt/beta-catenin signaling by mediating Dvl2 degradation through the autophagy pathway." Cell Physiol Biochem 27(5): 503-512.