The proppin Bcas3 and its interactor KinkyA localize to the early phagophore and regulate autophagy

References

• Schink KO, Tan KW, Stenmark H. Phosphoinositides in Control of Membrane Dynamics. Annu Rev Cell Dev Biol. 2016;32:143–171.
   PubMed Web of Science ®Google Scholar
• Stirnimann CU, Petsalaki E, Russell RB, et al. WD40 proteins propel cellular networks. Trends Biochem Sci. 2010;35:565–574.
   PubMed Web of Science ®Google Scholar
• Krick R, Busse RA, Scacioc A, et al. Structural and functional characterization of the two phosphoinositide binding sites of PROPPINs, a beta-propeller protein family. Proc Natl Acad Sci U S A. 2012;109:E2042–9.
   PubMed Web of Science ®Google Scholar
• Krick R, Henke S, Tolstrup J, et al. Dissecting the localization and function of Atg18, Atg21 and Ygr223c. Autophagy. 2008;4:896–910.
   PubMed Web of Science ®Google Scholar
• Krick R, Thumm M. Atg8 lipidation is coordinated in a PtdIns3P-dependent manner by the PROPPIN Atg21. Autophagy. 2016;12:2260–2261.
   PubMed Web of Science ®Google Scholar
• Guan J, Stromhaug PE, George MD, et al. Cvt18/Gsa12 is required for cytoplasm-to-vacuole transport, pexophagy, and autophagy in Saccharomyces cerevisiae and Pichia pastoris. Mol Biol Cell. 2001;12:3821–3838.
   PubMed Web of Science ®Google Scholar
• Gómez-Sánchez R, Rose J, Guimarães R, et al. Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores. J Cell Biol. 2018;217:2743–2763.
   PubMed Web of Science ®Google Scholar
• Kotani T, Kirisako H, Koizumi M, et al. The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation. Proc Natl Acad Sci U S A. 2018;115:10363–10368.
   PubMed Web of Science ®Google Scholar
• Gopaldass N, Fauvet B, Lashuel H, et al. Membrane scission driven by the PROPPIN Atg18. Embo J. 2017;36:3274–3291.
   PubMed Web of Science ®Google Scholar
• Polson HE, de Lartigue J, Rigden DJ, et al. Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. Autophagy. 2010;6:506–522.
   PubMed Web of Science ®Google Scholar
• Yamada Y, Schaap P. Cyclic AMP induction of Dictyostelium prespore gene expression requires autophagy. Dev Biol. 2019;452:114–126.
   PubMed Web of Science ®Google Scholar
• Yamada Y, Cassidy A, Schaap P. The transcription factor Spores Absent A is a PKA dependent inducer of Dictyostelium sporulation. Sci Rep. 2018;8:6643.
   PubMed Web of Science ®Google Scholar
• Rukova B, Staneva R, Hadjidekova S, et al. Whole genome methylation analyses of schizophrenia patients before and after treatment. Biotechnol Biotechnol Equip. 2014;28:518–524.
   PubMed Web of Science ®Google Scholar
• Ko HW, Norman RX, Tran J, et al. Broad-minded links cell cycle-related kinase to cilia assembly and hedgehog signal transduction. Dev Cell. 2010;18:237–247.
   PubMed Web of Science ®Google Scholar
• West CM. Comparative analysis of spore coat formation, structure, and function in Dictyostelium. Int Rev Cytol. 2003;222:237–293.
   PubMedGoogle Scholar
• Wang M, Van Driel R, Schaap P. Cyclic AMP-phosphodiesterase induces dedifferentiation of prespore cells in Dictyostelium discoideum slugs: evidence that cyclic AMP is the morphogenetic signal for prespore differentiation. Development. 1988;103:611–618.
   Web of Science ®Google Scholar
• Schaap P, Van Driel R. Induction of post-aggregative differentiation in Dictyostelium discoideum by cAMP. Evidence of involvement of the cell surface cAMP receptor. Exp Cell Res. 1985;159:388–398.
   PubMed Web of Science ®Google Scholar
• Hopper NA, Sanders GM, Fosnaugh KL, et al. Protein kinase A is a positive regulator of spore coat gene transcription in Dictyostelium. Differentiation. 1995;58:183–188.
   PubMed Web of Science ®Google Scholar
• Ceccarelli A, Mahbubani H, Williams JG. Positively and negatively acting signals regulating stalk cell and anterior-like cell differentiation in Dictyostelium. Cell. 1991;65:983–989.
   PubMed Web of Science ®Google Scholar
• Chen ZH, Singh R, Cole C, et al. Adenylate cyclase A acting on PKA mediates induction of stalk formation by cyclic diguanylate at the Dictyostelium organizer. Proc Natl Acad Sci U S A. 2017;114:516–521.
   PubMed Web of Science ®Google Scholar
• Bärlund M, Monni O, Weaver JD, et al. Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer†. Genes Chromosomes Cancer. 2002;35:311–317.
   PubMed Web of Science ®Google Scholar
• Ehrbrecht A, Muller U, Wolter M, et al. Comprehensive genomic analysis of desmoplastic medulloblastomas: identification of novel amplified genes and separate evaluation of the different histological components. J Pathol. 2006;208:554–563.
   PubMed Web of Science ®Google Scholar
• Shetty R, Joshi D, Jain M, et al. Rudhira/BCAS3 is essential for mouse development and cardiovascular patterning. Sci Rep. 2018;8:5632.
   PubMed Web of Science ®Google Scholar
• Jain M, Bhat GP, VijayRaghavan K, et al. Rudhira/BCAS3 is a cytoskeletal protein that controls Cdc42 activation and directional cell migration during angiogenesis. Exp Cell Res. 2012;318:753–767.
   PubMed Web of Science ®Google Scholar
• Joshi D, Inamdar MS. Rudhira/BCAS3 couples microtubules and intermediate filaments to promote cell migration for angiogenic remodeling. Mol Biol Cell. 2019;30:1437–1450.
   PubMed Web of Science ®Google Scholar
• Bakula D, Mueller AJ, Proikas-Cezanne T. WIPI beta-propellers function as scaffolds for STK11/LKB1-AMPK and AMPK-related kinase signaling in autophagy. Autophagy. 2018;14:1082–1083.
   PubMed Web of Science ®Google Scholar
• Jain BP, Pandey S. WD40 repeat proteins: signalling scaffold with diverse functions. Protein J. 2018;37:391–406.
   PubMed Web of Science ®Google Scholar
• Baskaran S, Ragusa MJ, Boura E, et al. Two-site recognition of phosphatidylinositol 3-phosphate by PROPPINs in autophagy. Mol Cell. 2012;47:339–348.
   PubMed Web of Science ®Google Scholar
• Liang R, Ren J, Zhang Y, et al. Structural conservation of the two phosphoinositide-binding sites in WIPI proteins. J Mol Biol. 2019;431:1494–1505.
   PubMed Web of Science ®Google Scholar
• Gloeckner G, Lawal HM, Felder M, et al. The multicellularity genes of dictyostelid social amoebas. Nat Commun. 2016;7:12085.
   PubMed Web of Science ®Google Scholar
• Muller-Taubenberger A. Calreticulin and calnexin in the endoplasmic reticulum are important for phagocytosis. Embo J. 2001;20:6772–6782.
   PubMed Web of Science ®Google Scholar
• Schneider N, Schwartz JM, Kohler J, et al. Golvesin-GFP fusions as distinct markers for golgi and post-golgi vesicles in dictyostelium cells. Biology of the Cell. 2000;92:495–511.
   PubMed Web of Science ®Google Scholar
• Gabriel D, Hacker U, Kohler J, et al. The contractile vacuole network of Dictyostelium as a distinct organelle: its dynamics visualized by a GFP marker protein. J Cell Sci. 1999;112(Pt 22):3995–4005.
   PubMed Web of Science ®Google Scholar
• von Lohneysen K. A Dictyostelium long chain fatty acyl coenzyme A-synthetase mediates fatty acid retrieval from endosomes. Eur J Cell Biol. 2003;82:505–514.
   PubMed Web of Science ®Google Scholar
• Tekinay T, Wu MY, Otto GP, et al. Function of the Dictyostelium discoideum Atg1 kinase during autophagy and development. Eukaryot Cell. 2006;5:1797–1806.
   PubMed Web of Science ®Google Scholar
• 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;182:685–701.
   PubMed Web of Science ®Google Scholar
• King JS, Veltman DM, Insall RH. The induction of autophagy by mechanical stress. Autophagy. 2011;7:1490–1499.
   PubMed Web of Science ®Google Scholar
• Kimura S, Noda T, Yoshimori T. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy. 2007;3:452–460.
   PubMed Web of Science ®Google Scholar
• Yu L, Chen Y, Tooze SA. Autophagy pathway: cellular and molecular mechanisms. Autophagy. 2018;14:207–215.
   PubMed Web of Science ®Google Scholar
• Otto GP, Wu MY, Kazgan N, et al. Dictyostelium macroautophagy mutants vary in the severity of their developmental defects. J Biol Chem. 2004;279:15621–15629.
   PubMed Web of Science ®Google Scholar
• Stege JT, Laub MT, Loomis WF. tip genes act in parallel pathways of early Dictyostelium development. Dev Genet. 1999;25:64–77.
   PubMedGoogle Scholar
• Mesquita A, Tabara LC, Martinez-Costa O, et al. Dissecting the function of Atg1 complex in Dictyostelium autophagy reveals a connection with the pentose phosphate pathway enzyme transketolase. Open Biol. 2015;5:150088.
   Web of Science ®Google Scholar
• Muñoz-Braceras S, Calvo R, Escalante R. TipC and the chorea-acanthocytosis protein VPS13A regulate autophagy in Dictyostelium and human HeLa cells. Autophagy. 2015;11:918–927.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43:D447–52.
   PubMed Web of Science ®Google Scholar
• Siva K, Inamdar MS. Rudhira is a cytoplasmic WD40 protein expressed in mouse embryonic stem cells and during embryonic erythropoiesis. Gene Expression Patterns GEP. 2006;6:225–234.
   PubMed Web of Science ®Google Scholar
• Dingermann T, Reindl N, Werner H, et al. Optimization and in situ detection of Escherichia coli beta-galactosidase gene expression in Dictyostelium discoideum. Gene. 1989;85:353–362.
   PubMed Web of Science ®Google Scholar
• Faix J. A rapid and efficient method to generate multiple gene disruptions in Dictyostelium discoideum using a single selectable marker and the Cre-loxP system. Nucleic Acids Res. 2004;32:e143.
   PubMed Web of Science ®Google Scholar
• Meima ME, Weening KE, Schaap P. Vectors for expression of proteins with single or combinatorial fluorescent protein and tandem affinity purification tags in Dictyostelium. Protein Expr Purif. 2007;53:283–288.
   PubMed Web of Science ®Google Scholar
• Paschke P, Knecht DA, Silale A, et al. Rapid and efficient genetic engineering of both wild type and axenic strains of Dictyostelium discoideum. PLoS One. 2018;13:e0196809.
   PubMed Web of Science ®Google Scholar
• Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc. 2016;11:2301–2319.
   PubMed Web of Science ®Google Scholar
• Tyanova S, Temu T, Sinitcyn P, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016;13:731–740.
   PubMed Web of Science ®Google Scholar
• Ihaka R, Gentleman R. R: a language for data analysis and graphics. J Comput Graph Statist. 1996;5:299–314.
   Google Scholar