References
- Sakin V, Richter SM, Hsiao HH, et al. Sumoylation of the GTPase ran by the RanBP2 SUMO E3 ligase complex. J Biol Chem. 2015;290(39):23589–23602.
- Cho MH, Cho K, Kang HJ, et al. Autophagy in microglia degrades extracellular beta-amyloid fibrils and regulates the NLRP3 inflammasome. Autophagy. 2014;10(10):1761–1775.
- Pichler A, Knipscheer P, Oberhofer E, et al. SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat Struct Mol Biol. 2005;12(3):264–269.
- Luo HB, Xia YY, Shu XJ, et al. SUMOylation at K340 inhibits tau degradation through deregulating its phosphorylation and ubiquitination. Proc Natl Acad Sci U S A. 2014;111(46):16586–16591.
- De La Cruz-Herrera CF, Baz-Martinez M, Lang V, et al. Conjugation of SUMO to p85 leads to a novel mechanism of PI3K regulation. Oncogene. 2016;35(22):2873–2880.
- Schuldt A. Post-translational modification: a SUMO protease for stress protection. Nat Rev Mol Cell Biol. 2013;14(5):263.
- Gareau JR, Lima CD. The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Mol Cell Biol. 2010;11(12):861–871.
- Yu L, Chen Y, Tooze SA. Autophagy pathway: cellular and molecular mechanisms. Autophagy. 2018;14(2):207–215.
- Yang Z, Klionsky DJ. Mammalian autophagy: core molecular machinery and signaling regulation. Curr Opin Cell Biol. 2010;22(2):124–131.
- Mizushima N. Autophagy: process and function. Genes Dev. 2007;21(22):2861–2873.
- Dall’armi C, Devereaux KA, Di Paolo G. The role of lipids in the control of autophagy. Curr Biol. 2013;23(1):R33–45.
- Lamb CA, Yoshimori T, Tooze SA. The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol. 2013;14(12):759–774.
- Carlsson SR, Simonsen A. Membrane dynamics in autophagosome biogenesis. J Cell Sci. 2015;128(2):193–205.
- Alessi DR, Kozlowski MT, Weng QP, et al. 3-Phosphoinositide-dependent protein kinase 1 (PDK1) phosphorylates and activates the p70 S6 kinase in vivo and in vitro. Curr Biol. 1998;8(2):69–81.
- Frodin M, Jensen CJ, Merienne K, et al. A phosphoserine-regulated docking site in the protein kinase RSK2 that recruits and activates PDK1. Embo J. 2000;19(12):2924–2934.
- Jensen CJ, Buch MB, Krag TO, et al. 90-kDa ribosomal S6 kinase is phosphorylated and activated by 3-phosphoinositide-dependent protein kinase-1. J Biol Chem. 1999;274(38):27168–27176.
- Pullen N, Dennis PB, Andjelkovic M, et al. Phosphorylation and activation of p70s6k by PDK1. Science. 1998;279(5351):707–710.
- Balendran A, Hare GR, Kieloch A, et al. Further evidence that 3-phosphoinositide-dependent protein kinase-1 (PDK1) is required for the stability and phosphorylation of protein kinase C (PKC) isoforms. FEBS Lett. 2000;484(3):217–223.
- Chou MM, Hou W, Johnson J, et al. Regulation of protein kinase C zeta by PI 3-kinase and PDK-1. Curr Biol. 1998;8(19):1069–1077.
- Dutil EM, Toker A, Newton AC. Regulation of conventional protein kinase C isozymes by phosphoinositide-dependent kinase 1 (PDK-1). Curr Biol. 1998;8(25):1366–1375.
- Le Good JA, Ziegler WH, Parekh DB, et al. Protein kinase C isotypes controlled by phosphoinositide 3-kinase through the protein kinase PDK1. Science. 1998;281(5385):2042–2045.
- Biondi RM, Kieloch A, Currie RA, et al. The PIF-binding pocket in PDK1 is essential for activation of S6K and SGK, but not AKT. Embo J. 2001;20(16):4380–4390.
- Park J, Leong ML, Buse P, et al. Serum and glucocorticoid-inducible kinase (SGK) is a target of the PI 3-kinase-stimulated signaling pathway. Embo J. 1999;18(11):3024–3033.
- Wang X, Hills LB, Huang YH. Lipid and protein co-regulation of PI3K effectors AKT and itk in lymphocytes. Front Immunol. 2015;6:117.
- Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005;33(WebServer issue):W244–8.
- Holmstrom S, Van Antwerp ME, Iniguez-Lluhi JA. Direct and distinguishable inhibitory roles for SUMO isoforms in the control of transcriptional synergy. Proc Natl Acad Sci U S A. 2003;100(26):15758–15763.
- Yurchenko V, Xue Z, Sadofsky MJ. SUMO modification of human XRCC4 regulates its localization and function in DNA double-strand break repair. Mol Cell Biol. 2006;26(5):1786–1794.
- Ross S, Best JL, Zon LI, et al. SUMO-1 modification represses Sp3 transcriptional activation and modulates its subnuclear localization. Mol Cell. 2002;10(4):831–842.
- Wen D, Wu J, Wang L, et al. SUMOylation promotes nuclear import and stabilization of polo-like kinase 1 to support its mitotic function. Cell Rep. 2017;21(8):2147–2159.
- Komander D, Fairservice A, Deak M, et al. Structural insights into the regulation of PDK1 by phosphoinositides and inositol phosphates. Embo J. 2004;23(20):3918–3928.
- Gao X, Lowry PR, Zhou X, et al. PI3K/AKT signaling requires spatial compartmentalization in plasma membrane microdomains. Proc Natl Acad Sci U S A. 2011;108(35):14509–14514.
- Jaber N, Dou Z, Chen JS, et al. Class III PI3K Vps34 plays an essential role in autophagy and in heart and liver function. Proc Natl Acad Sci U S A. 2012;109(6):2003–2008.
- Panaretou C, Domin J, Cockcroft S, et al. Characterization of p150, an adaptor protein for the human phosphatidylinositol (PtdIns) 3-kinase. Substrate presentation by phosphatidylinositol transfer protein to the p150.Ptdins 3-kinase complex. J Biol Chem. 1997;272(4):2477–2485.
- Kolesar P, Sarangi P, Altmannova V, et al. Dual roles of the SUMO-interacting motif in the regulation of Srs2 sumoylation. Nucleic Acids Res. 2012;40(16):7831–7843.
- Casamayor A, Morrice NA, Alessi DR. Phosphorylation of Ser-241 is essential for the activity of 3-phosphoinositide-dependent protein kinase-1: identification of five sites of phosphorylation in vivo. Biochem J. 1999;342(Pt 2):287–292.
- Russell RC, Tian Y, Yuan H, et al. ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol. 2013;15(7):741–750.
- Jaber N, Zong WX. Class III PI3K Vps34: essential roles in autophagy, endocytosis, and heart and liver function. Ann N Y Acad Sci. 2013;1280:48–51.
- Yu X, Long YC, Shen HM. Differential regulatory functions of three classes of phosphatidylinositol and phosphoinositide 3-kinases in autophagy. Autophagy. 2015;11(10):1711–1728.
- Nobukuni T, Joaquin M, Roccio M, et al. Amino acids mediate mTOR/raptor signaling through activation of class 3 phosphatidylinositol 3OH-kinase. Proc Natl Acad Sci U S A. 2005;102(40):14238–14243.
- Kim J, Kim YC, Fang C, et al. Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell. 2013;152(1–2):290–303.
- Stjepanovic G, Baskaran S, Lin MG, et al. Vps34 kinase domain dynamics regulate the autoPhagic PI 3-kinase complex. Mol Cell. 2017;67(3):528–534 e3.
- Hamasaki M, Furuta N, Matsuda A, et al. Autophagosomes form at ER-mitochondria contact sites. Nature. 2013;495(7441):389–393.
- Ge L, Melville D, Zhang M, et al. The ER-Golgi intermediate compartment is a key membrane source for the LC3 lipidation step of autophagosome biogenesis. Elife. 2013;2:e00947.
- Nascimbeni AC, Giordano F, Dupont N, et al. ER-plasma membrane contact sites contribute to autophagosome biogenesis by regulation of local PI3P synthesis. Embo J. 2017;36(14):2018–2033.
- Nishimura T, Tamura N, Kono N, et al. Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains. Embo J. 2017;36(12):1719–1735.
- Tooze SA. Current views on the source of the autophagosome membrane. Essays Biochem. 2013;55:29–38.
- Turco E, Martens S. Insights into autophagosome biogenesis from in vitro reconstitutions. J Struct Biol. 2016;196(1):29–36.
- Rosonina E, Akhter A, Dou Y, et al. Regulation of transcription factors by sumoylation. Transcription. 2017;8(4):220–231.
- Dou H, Huang C, Singh M, et al. Regulation of DNA repair through deSUMOylation and SUMOylation of replication protein A complex. Mol Cell. 2010;39(3):333–345.
- Wan J, Subramonian D, Zhang XD. SUMOylation in control of accurate chromosome segregation during mitosis. Curr Protein Pept Sci. 2012;13(5):467–481.
- Cremona CA, Sarangi P, Zhao X. Sumoylation and the DNA damage response. Biomolecules. 2012;2(3):376–388.
- Zhang J, Goodson ML, Hong Y, et al. MEL-18 interacts with HSF2 and the SUMO E2 UBC9 to inhibit HSF2 sumoylation. J Biol Chem. 2008;283(12):7464–7469.
- Yang Y, Fiskus W, Yong B, et al. Acetylated hsp70 and KAP1-mediated Vps34 SUMOylation is required for autophagosome creation in autophagy. Proc Natl Acad Sci U S A. 2013;110(17):6841–6846.
- Wang L, Zhou K, Fu Z, et al. Brain development and AKT signaling: the crossroads of signaling pathway and neurodevelopmental diseases. J Mol Neurosci. 2017;61(3):379–384.
- Cordon-Barris L, Pascual-Guiral S, Yang S, et al. Mutation of the 3-phosphoinositide-dependent protein kinase 1 (PDK1) substrate-docking site in the developing brain causes microcephaly with abnormal brain morphogenesis independently of AKT, leading to impaired cognition and disruptive behaviors. Mol Cell Biol. 2016;36(23):2967–2982.
- Xu C, Yu L, Hou J, et al. Conditional deletion of PDK1 in the forebrain causes neuron loss and increased apoptosis during cortical development. Front Cell Neurosci. 2017;11:330.
- Kilic U, Caglayan AB, Beker MC, et al. Particular phosphorylation of PI3K/AKT on Thr308 via PDK-1 and PTEN mediates melatonin’s neuroprotective activity after focal cerebral ischemia in mice. Redox Biol. 2017;12:657–665.
- Lee YJ, Mou Y, Maric D, et al. Elevated global SUMOylation in Ubc9 transgenic mice protects their brains against focal cerebral ischemic damage. PLoS One. 2011;6(10):e25852.
- Gwizdek C, Casse F, Martin S. Protein sumoylation in brain development, neuronal morphology and spinogenesis. Neuromolecular Med. 2013;15(4):677–691.
- Martin S, Wilkinson KA, Nishimune A, et al. Emerging extranuclear roles of protein SUMOylation in neuronal function and dysfunction. Nat Rev Neurosci. 2007;8(12):948–959.
- Naito T, Kuma A, Mizushima N. Differential contribution of insulin and amino acids to the mTORC1-autophagy pathway in the liver and muscle. J Biol Chem. 2013;288(29):21074–21081.
- Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using modeller. Curr Protoc Bioinf. 2006;Chapter 5 Unit–5 6.
- Conway P, Tyka MD, Dimaio F, et al. Relaxation of backbone bond geometry improves protein energy landscape modeling. Protein Sci. 2014;23(1):47–55.
- Huang PS, Ban YE, Richter F, et al. RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS One. 2011;6(8):e24109.
- Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612.
- Yang Y, Fu W, Chen J, et al. SIRT1 sumoylation regulates its deacetylase activity and cellular response to genotoxic stress. Nat Cell Biol. 2007;9(11):1253–1262.