MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v03/MSV000086357/primary200OK0000ProteomicsOlivier JulienBasil HubbardQ ExactiveHomo Sapiens (ncbitaxon:9606)https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=3955019027d54539b1ac5fd22104b1fbojulien@ualberta.cabphubbar@ualberta.caUniversity of AlbertaMassIVE5UNIMOD:4 - "Iodoacetamide derivative."UNIMOD:7 - "Deamidation."UNIMOD:35 - "Oxidation or Hydroxylation."Tubby-like proteins (TULPs) are characterized by a conserved C-terminal domain that binds phosphoinositides. Collectively, mammalian TULP1-4 proteins play essential roles in intracellular transport, cell differentiation, signaling, and motility. Yet, little is known about how the function of these proteins is regulated in cells. Here, we present the protein-protein interaction network of TULP3, a protein that is responsible for the trafficking of G-protein-coupled receptors to cilia and whose aberrant expression is associated with severe developmental disorders and polycystic kidney disease. We identify several protein interaction nodes linked to TULP3 that include enzymes involved in acetylation and ubiquitination. We show that acetylation of two key lysine residues on TULP3 by p300 increases TULP3 protein abundance and that deacetylation of these sites by HDAC1 decreases protein levels. Furthermore, we show that one of these sites is ubiquitinated in the absence of acetylation and that acetylation inversely correlates with ubiquitination of TULP3. This mechanism is evidently conserved across species and is active in zebrafish during development. Finally, we identify this same regulatory module in TULP1, TULP2, and TULP4 and demonstrate that the stability of these proteins is similarly modulated by an acetylation switch. This study unveils a signaling pathway that links nuclear enzymes to ciliary membrane receptors via TULP3, describes a dynamic mechanism for the regulation of all tubby-like proteins, and explores how to exploit it pharmacologically using drugs.A conserved acetylation switch enables pharmacological control of tubby-like protein stability.Kerek Evan M EM, Yoon Kevin H KH, Luo Shu Y SY, Chen Jerry J, Valencia Robert R, Julien Olivier O, Waskiewicz Andrew J AJ, Hubbard Basil P BPProtein Gene Products, AI316887, Gene., Gene Proteins, protein polypeptide chains, native protein, natural protein, polypeptide chain, protein complex, 2310022L06Rik, Protein, TUBL3, Gene Products, Proteins, proteins, protein, protein aggregate, protein-containing complexHEK293T, Co-Immunoprecipitations, 293 T cell, TUBL3., Human Embryonic Kidney 293T, 293-T, HEK293T cell, 293tsA1609neo, 2310022L06Rik, Co-Immunoprecipitation, Precipitation, HEK 293 T, 293 T, 293T cell, 293T, Co Immunoprecipitation, Hek 293T, AI316887, Table, Immune, HEK-293T, Immune Precipitations, Precipitations, Immune Precipitation, HEK-293-T, 293-T cellpreventive measures, Stabilities, Stability, Controlling, Protein Stabilities., preventive therapy, reference sample, control, prophylaxis, Protein, acetylation, Acetylations, prevention and control, Controlled, prevention, macromolecular stability of proteinMotch A, Ghrfr, Product, Lysine Hydrochloride, Hdac1-ps, postnatal development, Receptors, Cilium, CBP/p300, growth and development, protein, sci, PtdIns, "Polycystic kidney" EXACT [SNOMEDCT_2005_07_31:204954005], Social Controls, Interaction Network, Protein-Protein Interaction Network, DmelCG7471, unspecified type" EXACT [ICD9CM_2006:753.12], Renal Disease, Primary Cilia, protein polypeptide chains, Lysine Acetate, DmelCG7467, diseases, Roles, Pharmaceutical Product, DHDAC1, Concepts, HOW, How, 2, diseases and disorders, deacetylation, dRPD3, protein aggregate, dRpd3, DmelCG15319, hdac1, Formal Social Controls, l(3)j5D5, IKKg, D. rerios, Protein Interaction Map, KEY, Key, L Lysine, HDAC, 24B, signal transduction by protein phosphorylation, Notch 1 extracellular truncation, human disease, Ubiquitylation, Notch 1, enzymes, K, PKD - Polycystic Kidney Disease, Zebrafishes, "PCK - Polycystic kidney disease" EXACT [SNOMEDCT_2005_07_31:82525005], stru, epsilon-diaminocaproic acid, proteins, Fishes, l(3)S053606, Polycystic Renal Diseases, Notch 1 intracellular domain, CG10293, Phosphatidyl Inositol, fibrocystic renal disease, Polycystic Renal Disease, Social, Inositol Phospholipids, l(3)j5B5, anon-WO0172774.126, RGD1564487, LYS, medicine, Pharmaceutical, Lysin, Role Concepts, Zebra Fishes, Nodal, Homo sapiens disease, ubiquitination, single organism signaling, Kidney Diseases, 0904/17, leopard danio, aberrant, CG7471, acetylation, KAT3B, signal transduction by conformational transition, cilial membrane, G-Protein-Coupled Receptor, DRpd3, CG7467, lit, Tusp, Polycystic Kidneys, eld, rpd[3], signal transduction by trans-phosphorylation, Protein-Protein Interaction Maps, DmIKKgamma, signaling cascade, G Protein Coupled Receptor, Motch, Role Concept, Playthings and Play, SZ1, dIKK, Diseases, Kenny, dmHDA401, Role, lysine, Plaything, CBP_, Brachydanio rerio, HD1, Pharmaceutic, Phosphoglyceride, Su(var)3-26, 1110057P05Rik, TUSP, little, l(1)G0112, single organism intracellular transport, dCBP, l(1)G0350, l(1)G0470, RP14, Motile, drpd3, Danio rerio, 2210038L17Rik, Kidney, Motile Cilia, "Polycystic kidney disease NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:268233005], IKK-gamma, Toys, Nejire, Control, gon-10, alpha, NEXT, Controls, E(var)3-64BC, A730011L11, Osa, OSA, G Protein Coupled, Phosphoinositides, disease, Kidneys, single-organism intracellular transport, DmelCG16910, nej CBP, signaling pathway, Renal Diseases, E(E2F)3C, Protein Protein Interaction Map, Inositide Phospholipids, Biocatalyst, CT65, D. rerio, anon-EST:Liang-2.39, TAN1, Tulp1l, Regulation, HDAC-1, zebrafish, LCA15, zebra fish, Regulations, protein levels, atypia, other disease, A430090G16, Inositide, Plays, l(3)64Cc, RPD3, Biocatalysts, P62, 2310022L06Rik, dHDAC-1, Phosphatidylinositol, Gene, Polycystic Renal, Network, RSTS2, protein-containing complex, l(3)04539, dmCBP, dIKK-gamma, CG15321, "Polycystic kidney disease NOS" EXACT [SNOMEDCT_2005_07_31:204956007], Polycystic Kidney, p300 HAT, Protein Interaction Networks, C819, RPD3L1, "Polycystic kidney, CG15319, zebra danio, polypeptide chain, DmIKK-gamma, Gene Products, p300, disease or disorder, Phosphatidyl, atypical, Lysine, dmIKKgamma, Inositide Phospholipid, IKK[[gamma]], rpd3, Cyprinus rerio, Map, Crbp, dKAT3, Protein-Protein, Toy, Polycystic Kidney Disease, Drugs, study, l(3)j9C3, GON-10, Phospholipid, l(3)s2612, Playthings, Nodal Cilium, Acetylations, dHDAC1, PKD - polycystic kidney disease, l(3)04556, non-neoplastic, AI316887, "polycystic kidney" EXACT [CSP2005:0725-1693], signalling pathway, Enzyme, drugs, Puppets, IKK, l(3)00090, Pharmaceuticals., "Polycystic kidney" EXACT [SNOMEDCT_2005_07_31:268332003], B. rerio, DmelCG10293, en(lz)4F/4H, Play, disorder, Nej, signal transduction by cis-phosphorylation, Protein-Protein Interaction Map, species, T14, Preparation, NICD, Differentiation, Puppet, Interaction Map, Brachydanio rerio frankei, Protein Interaction Network, Products, Disease, Inositol Phosphoglyceride, cilium membrane, Zebra Fish, anon-WO03040301.89, Formal Social Control, clone 2.39, protein complex, Proteins, disorders, polycystic kidney disease, enzyme activity, Hdac1, Phosphoglycerides, function, Primary, defective, medical condition, qkr, Medications, G-Protein-Coupled Receptors, l(3)S090417, Cell, Nodal Cilia, G-Protein-Coupled, Concept, Inositol, Polycystic, development, IKKgamma, native protein, MommeD5, Inositol Phosphoglycerides, natural protein, Social Control, Acetate, Su(var)326, KH93F, Protein, Danio rerio frankei, condition, Su(var)328, signalling cascade, L-Lysine, flagellum membrane, Differentiations, who, Polycystic kidney disease, TUBL2, flagellar membrane, TUBL1, p300/CBP, Phosphoinositide, G Protein Coupled Receptors, HDAC1, Zebra, Kidney Disease, hdac1b, Phospholipids, Pharmaceutic Preparations, Dmikkgamma, Danio frankei, TUBL3, CBP, Cbp, postnatal growth, Cell Differentiations, Dmel_CG15321, Who/How, "Polycystic kidney disease" EXACT [SNOMEDCT_2005_07_31:204955006], mT14, danio, CG16910, Zebra danios, Rpd3/HDAC, Cilia, Protein Gene Products, Drug, Gene Proteins, Zebra danio, "Polycystic kidney" EXACT [SNOMEDCT_2005_07_31:156973002], Preparations, Protein Interaction, Protein-Protein Interaction, Pdet, Inositol Phospholipid, signalling process, Protein Protein Interaction Network, anon-WO0147981.11, Primary Cilium, Fibrocystic Renal Disease, cbp, qkr[93F], anon-WO0118547.314, rpd3l1, DmHDAC1, regulation, Receptor, Motile Cilium, 6-diaminohexanoic acid, Pharmaceutical Products, Protein-Protein Interaction Networks, growth, Enisyl, Severe, Pharmaceutical Preparation0falseIdentification of TULP3 protein interactionsTable S1: Anti-FLAG immunoprecipitation on HEK293T cell lysates stably expressing FLAG-TULP3 .Thu Oct 22 10:22:00 BST 2020MSV00008635733187986