References
- Galluzzi L, Baehrecke EH, Ballabio A, et al. Molecular definitions of autophagy and related processes. Embo J. 2017;36(13):1811–1836.
- Onodera J, Ohsumi Y. Autophagy is required for maintenance of amino acid levels and protein synthesis under nitrogen starvation. J Biol Chem. 2005;280(36):31582–31586.
- Rich KA, Burkett C, Webster P. Cytoplasmic bacteria can be targets for autophagy. Cell Microbiol. 2003;5(7):455–468.
- Klionsky DJ, Cregg JM, Dunn WA, et al. A unified nomenclature for yeast autophagy-related genes. Dev Cell. 2003;5(4):539–545.
- Liu R, Zhi X, Zhong Q. ATG14 controls SNARE-mediated autophagosome fusion with a lysosome. Autophagy. 2015;11(5):847–849.
- Axe EL, Walker SA, Manifava M, et al. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol. 2008;182(4):685–701.
- Proikas-Cezanne T, Takacs Z, Donnes P, et al. WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome. J Cell Sci. 2015;128(2):207–217.
- Lystad AH, Simonsen A. Phosphoinositide-binding proteins in autophagy. FEBS Lett. 2016;590(15):2454–2468.
- Cao Y, Klionsky DJ. Physiological functions of Atg6/Beclin 1: a unique autophagy-related protein. Cell Res. 2007;17(10):839–849.
- Furuya N, Yu J, Byfield M, et al. The evolutionarily conserved domain of Beclin 1 is required for Vps34 binding, autophagy and tumor suppressor function. Autophagy. 2005;1(1):46–52.
- Itakura E, Mizushima N. Atg14 and UVRAG: mutually exclusive subunits of mammalian Beclin 1-PI3K complexes. Autophagy. 2009;5(4):534–536.
- Fimia GM, Stoykova A, Romagnoli A, et al. Ambra1 regulates autophagy and development of the nervous system. Nature. 2007;447(7148):1121–1125.
- Li X, He L, Che KH, et al. Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG. Nat Commun. 2012;3:662.
- Mei Y, Su M, Sanishvili R, et al. Identification of BECN1 and ATG14 coiled-coil interface residues that are important for starvation-induced autophagy. Biochemistry. 2016;55(30):4239–4253.
- Matsunaga K, Saitoh T, Tabata K, et al. Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat Cell Biol. 2009;11(4):385–396.
- Maiuri MC, Criollo A, Tasdemir E, et al. BH3-only proteins and BH3 mimetics induce autophagy by competitively disrupting the interaction between Beclin 1 and Bcl-2/Bcl-X(L). Autophagy. 2007;3(4):374–376.
- Maiuri MC, Le Toumelin G, Criollo A, et al. Functional and physical interaction between Bcl-X(L) and a BH3-like domain in Beclin-1. Embo J. 2007;26(10):2527–2539.
- 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.
- Ravikumar B, Berger Z, Vacher C, et al. Rapamycin pre-treatment protects against apoptosis. Hum Mol Genet. 2006;15(7):1209–1216.
- Mochizuki T, Wu G, Hayashi T, et al. PKD2, a gene for polycystic kidney disease that encodes an integral membrane protein. Science. 1996;272(5266):1339–1342.
- Luo Y, Vassilev PM, Li X, et al. Native polycystin 2 functions as a plasma membrane Ca2+-permeable cation channel in renal epithelia. Mol Cell Biol. 2003;23(7):2600–2607.
- Criollo A, Altamirano F, Pedrozo Z, et al. Polycystin-2-dependent control of cardiomyocyte autophagy. J Mol Cell Cardiol. 2018;118:110–121.
- Orhon I, Dupont N, Zaidan M, et al. Primary-cilium-dependent autophagy controls epithelial cell volume in response to fluid flow. Nat Cell Biol. 2016;18(6):657–667.
- Grieben M, Pike ACW, Shintre CA, et al. Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2). Nat Struct Mol Biol. 2017;24(2):114–122.
- Yang Y, Ehrlich BE. Structural studies of the C-terminal tail of polycystin-2 (PC2) reveal insights into the mechanisms used for the functional regulation of PC2. J Physiol. 2016;594(15):4141–4149.
- Feng S, Okenka GM, Bai C-X, et al. Identification and functional characterization of an N-terminal oligomerization domain for polycystin-2. J Biol Chem. 2008;283(42):28471–28479.
- Somlo S, Ehrlich B. Human disease: calcium signaling in polycystic kidney disease. Curr Biol. 2001;11(9):R356–60.
- Gainullin VG, Hopp K, Ward CJ, et al. Polycystin-1 maturation requires polycystin-2 in a dose-dependent manner. J Clin Invest. 2015;125(2):607–620.
- Ravichandran K, Edelstein CL. Polycystic kidney disease: a case of suppressed autophagy? Semin Nephrol. 2014;34(1):27–33.
- Lu J, Boheler KR, Jiang L, et al. Polycystin-2 plays an essential role in glucose starvation-induced autophagy in human embryonic stem cell-derived cardiomyocytes. Stem Cells. 2018;36(4):501–513.
- Pena-Oyarzun D, Troncoso R, Kretschmar C, et al. Hyperosmotic stress stimulates autophagy via polycystin-2. Oncotarget. 2017;8(34):55984–55997.
- Shillingford JM, Leamon CP, Vlahov IR, et al. Folate-conjugated rapamycin slows progression of polycystic kidney disease. J Am Soc Nephrol. 2012;23(10):1674–1681.
- Li Y, Wright JM, Qian F, et al. Polycystin 2 interacts with type I inositol 1,4,5-trisphosphate receptor to modulate intracellular Ca2+ signaling. J Biol Chem. 2005;280(50):41298–41306.
- Pazour GJ, San Agustin JT, Follit JA, et al. Polycystin-2 localizes to kidney cilia and the ciliary level is elevated in orpk mice with polycystic kidney disease. Curr Biol. 2002;12(11):R378–80.
- Pampliega O, Orhon I, Patel B, et al. Functional interaction between autophagy and ciliogenesis. Nature. 2013;502(7470):194–200.
- Hamasaki M, Furuta N, Matsuda A, et al. Autophagosomes form at ER-mitochondria contact sites. Nature. 2013;495(7441):389–393.
- Mousavi SA, Kjeken R, Berg TO, et al. Effects of inhibitors of the vacuolar proton pump on hepatic heterophagy and autophagy. Biochim Biophys Acta. 2001;1510(1–2):243–257.
- Klionsky DJ, Abdelmohsen K, Abe A, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 2016;12(1):1–222.
- Tanida I, Ueno T, Kominami E. Human light chain 3/MAP1LC3B is cleaved at its carboxyl-terminal Met121 to expose Gly120 for lipidation and targeting to autophagosomal membranes. J Biol Chem. 2004;279(46):47704–47710.
- Hanada T, Noda NN, Satomi Y, et al. The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. J Biol Chem. 2007;282(52):37298–37302.
- Yoshii SR, Mizushima N. Monitoring and measuring autophagy. Int J Mol Sci. 2017;18(9):1865.
- Proikas-Cezanne T, Ruckerbauer S, Stierhof Y-D, et al. Human WIPI-1 puncta-formation: a novel assay to assess mammalian autophagy. FEBS Lett. 2007;581(18):3396–3404.
- Lindmo K, Brech A, Finley KD, et al. The PI 3-kinase regulator Vps15 is required for autophagic clearance of protein aggregates. Autophagy. 2008;4(4):500–506.
- Behn D, Bosk S, Hoffmeister H, et al. Quantifying the interaction of the C-terminal regions of polycystin-2 and polycystin-1 attached to a lipid bilayer by means of QCM. Biophys Chem. 2010;150(1–3):47–53.
- Anyatonwu GI, Estrada M, Tian X, et al. Regulation of ryanodine receptor-dependent calcium signaling by polycystin-2. Proc Natl Acad Sci U S A. 2007;104(15):6454–6459.
- Geng L, Boehmerle W, Maeda Y, et al. Syntaxin 5 regulates the endoplasmic reticulum channel-release properties of polycystin-2. Proc Natl Acad Sci U S A. 2008;105(41):15920–15925.
- Dudko OK, Hummer G, Szabo A. Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc Natl Acad Sci U S A. 2008;105(41):15755–15760.
- Burgos-Bravo F, Figueroa NL, Casanova-Morales N, et al. Single-molecule measurements of the effect of force on Thy-1/αvβ3-integrin interaction using nonpurified proteins. Mol Biol Cell. 2018;29(3):326–338.
- Hoffmeister H, Babinger K, Gürster S, et al. Polycystin-2 takes different routes to the somatic and ciliary plasma membrane. J Cell Biol. 2011;192(4):631–645.
- Gao W, Ding W-X, Stolz DB, et al. Induction of macroautophagy by exogenously introduced calcium. Autophagy. 2008;4(6):754–761.
- Brady NR, Hamacher-Brady A, Yuan H, et al. The autophagic response to nutrient deprivation in the hl-1 cardiac myocyte is modulated by Bcl-2 and sarco/endoplasmic reticulum calcium stores. Febs J. 2007;274(12):3184–3197.
- Hoyer-Hansen M, Bastholm L, Szyniarowski P, et al. Control of macroautophagy by calcium, calmodulin-dependent kinase kinase-beta, and Bcl-2. Mol Cell. 2007;25(2):193–205.
- Kuo IY, DesRochers TM, Kimmerling EP, et al. Cyst formation following disruption of intracellular calcium signaling. Proc Natl Acad Sci U S A. 2014;111(39):14283–14288.
- Li A, Tian X, Zhang X, et al. Human polycystin-2 transgene dose-dependently rescues ADPKD phenotypes in Pkd2 mutant mice. Am J Pathol. 2015;185(10):2843–2860.
- Litvinov RI, Bennett JS, Weisel JW, et al. Multi-step fibrinogen binding to the integrin (alpha)IIb(beta)3 detected using force spectroscopy. Biophys J. 2005;89(4):2824–2834.
- Litvinov RI, Barsegov V, Schissler AJ, et al. Dissociation of bimolecular alphaIIbbeta3-fibrinogen complex under a constant tensile force. Biophys J. 2011;100(1):165–173.
- Rinko LJ, Lawrence MB, Guilford WH. The molecular mechanics of P- and L-selectin lectin domains binding to PSGL-1. Biophys J. 2004;86(1 Pt 1):544–554.
- Litvinov RI, Vilaire G, Shuman H, et al. Quantitative analysis of platelet alpha v beta 3 binding to osteopontin using laser tweezers. J Biol Chem. 2003;278(51):51285–51290.
- Cantero Mdel R, Velázquez IF, Streets AJ, et al. The cAMP signaling pathway and direct protein kinase A phosphorylation regulate polycystin-2 (TRPP2) channel function. J Biol Chem. 2015;290(39):23888–23896.
- Streets AJ, Needham AJ, Gill SK, et al. Protein kinase D-mediated phosphorylation of polycystin-2 (TRPP2) is essential for its effects on cell growth and calcium channel activity. Mol Biol Cell. 2010;21(22):3853–3865.
- Streets AJ, Wessely O, Peters DJM, et al. Hyperphosphorylation of polycystin-2 at a critical residue in disease reveals an essential role for polycystin-1-regulated dephosphorylation. Hum Mol Genet. 2013;22(10):1924–1939.
- Hill SM, Wrobel L, Rubinsztein DC. Post-translational modifications of Beclin 1 provide multiple strategies for autophagy regulation. Cell Death Differ. 2019;26(4):617–629.
- Celic A, Petri ET, Demeler B, et al. Domain mapping of the polycystin-2 C-terminal tail using de novo molecular modeling and biophysical analysis. J Biol Chem. 2008;283(42):28305–28312.
- Medina DL, Di Paola S, Peluso I, et al. Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. Nat Cell Biol. 2015;17(3):288–299.
- Luyten T, Welkenhuyzen K, Roest G, et al. Resveratrol-induced autophagy is dependent on IP3Rs and on cytosolic Ca(2). Biochim Biophys Acta Mol Cell Res. 2017;1864(6):947–956.
- Pfisterer SG, Mauthe M, Codogno P, et al. Ca2+/calmodulin-dependent kinase (CaMK) signaling via CaMKI and AMP-activated protein kinase contributes to the regulation of WIPI-1 at the onset of autophagy. Mol Pharmacol. 2011;80(6):1066–1075.
- Choi S, Kim HJ. The Ca2+ channel TRPML3 specifically interacts with the mammalian ATG8 homologue GATE16 to regulate autophagy. Biochem Biophys Res Commun. 2014;443(1):56–61.
- Ghislat G, Patron M, Rizzuto R, et al. Withdrawal of essential amino acids increases autophagy by a pathway involving Ca2+/calmodulin-dependent kinase kinase-β (CaMKK-β). J Biol Chem. 2012;287(46):38625–38636.
- Cardenas C, Miller RA, Smith I, et al. Essential regulation of cell bioenergetics by constitutive InsP3 receptor Ca2+ transfer to mitochondria. Cell. 2010;142(2):270–283.
- Petri ET, Celic A, Kennedy SD, et al. Structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity. Proc Natl Acad Sci U S A. 2010;107(20):9176–9181.
- Kuo IY, Keeler C, Corbin R, et al. The number and location of EF hand motifs dictates the calcium dependence of polycystin-2 function. Faseb J. 2014;28(5):2332–2346.
- Kuo IY, Kwaczala AT, Nguyen L, et al. Decreased polycystin 2 expression alters calcium-contraction coupling and changes beta-adrenergic signaling pathways. Proc Natl Acad Sci U S A. 2014;111(46):16604–16609.
- Paavola J, Schliffke S, Rossetti S, et al. Polycystin-2 mutations lead to impaired calcium cycling in the heart and predispose to dilated cardiomyopathy. J Mol Cell Cardiol. 2013;58:199–208.
- Peintner L, Borner C. Role of apoptosis in the development of autosomal dominant polycystic kidney disease (ADPKD). Cell Tissue Res. 2017;369(1):27–39.
- Sweeney WE Jr., Avner ED. Pathophysiology of childhood polycystic kidney diseases: new insights into disease-specific therapy. Pediatr Res. 2014;75(1–2):148–157.
- Sammels E, Devogelaere B, Mekahli D, et al. Polycystin-2 activation by inositol 1,4,5-trisphosphate-induced Ca2+release requires its direct association with the inositol 1,4,5-trisphosphate receptor in a signaling microdomain. J Biol Chem. 2010;285(24):18794–18805.
- Smith SB, Cui Y, Bustamante C. Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol. 2003;361:134–162.