Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signaling Pathways

Appelhoff, 2004, Differential function of the prolyl hydroxylases PHD1, PHD2, and PHD3 in the regulation of hypoxia-inducible factor, J. Biol. Chem., 279, 38458, 10.1074/jbc.M406026200 Baek, 2005, OS-9 interacts with hypoxia-inducible factor 1alpha and prolyl hydroxylases to promote oxygen-dependent degradation of HIF-1alpha, Mol. Cell, 17, 503, 10.1016/j.molcel.2005.01.011 Barrett, 2011, Pharmacological characterization of 1-(5-chloro-6-(trifluoromethoxy)-1H-benzoimidazol-2-yl)-1H-pyrazole-4-carboxylic acid (JNJ-42041935), a potent and selective hypoxia-inducible factor prolyl hydroxylase inhibitor, Mol. Pharmacol., 79, 910, 10.1124/mol.110.070508 Bertrand, 2011, cIAP1/2 are direct E3 ligases conjugating diverse types of ubiquitin chains to receptor interacting proteins kinases 1 to 4 (RIP1-4), PLoS ONE, 6, e22356, 10.1371/journal.pone.0022356 Chen, 2005, Ubiquitin signalling in the NF-kappaB pathway, Nat. Cell Biol., 7, 758, 10.1038/ncb0805-758 Cockman, 2006, Posttranslational hydroxylation of ankyrin repeats in IkappaB proteins by the hypoxia-inducible factor (HIF) asparaginyl hydroxylase, factor inhibiting HIF (FIH), Proc. Natl. Acad. Sci. USA, 103, 14767, 10.1073/pnas.0606877103 Cockman, 2009, Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins, Mol. Cell. Proteomics, 8, 535, 10.1074/mcp.M800340-MCP200 Coulombe, 2003, Rapid turnover of extracellular signal-regulated kinase 3 by the ubiquitin-proteasome pathway defines a novel paradigm of mitogen-activated protein kinase regulation during cellular differentiation, Mol. Cell. Biol., 23, 4542, 10.1128/MCB.23.13.4542-4558.2003 Cox, 2014, Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ, Mol. Cell. Proteomics, 13, 2513, 10.1074/mcp.M113.031591 Cummins, 2006, Prolyl hydroxylase-1 negatively regulates IkappaB kinase-beta, giving insight into hypoxia-induced NFkappaB activity, Proc. Natl. Acad. Sci. USA, 103, 18154, 10.1073/pnas.0602235103 Fabre, 2014, Label-free quantitative proteomics reveals the dynamics of proteasome complexes composition and stoichiometry in a wide range of human cell lines, J. Proteome Res., 13, 3027, 10.1021/pr500193k Farrell, 2014, HGF induces epithelial-to-mesenchymal transition by modulating the mammalian hippo/MST2 and ISG15 pathways, J. Proteome Res., 13, 2874, 10.1021/pr5000285 Foxler, 2012, The LIMD1 protein bridges an association between the prolyl hydroxylases and VHL to repress HIF-1 activity, Nat. Cell Biol., 14, 201, 10.1038/ncb2424 González-Pacheco, 2006, Mechanisms of endothelial response to oxidative aggression: protective role of autologous VEGF and induction of VEGFR2 by H2O2, Am. J. Physiol. Heart Circ. Physiol., 291, H1395, 10.1152/ajpheart.01277.2005 Hauri, 2013, Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1, Mol. Syst. Biol., 9, 713, 10.1002/msb.201304750 Hewitson, 2002, Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family, J. Biol. Chem., 277, 26351, 10.1074/jbc.C200273200 Huang, 2013, Phosphorylation of Dishevelled by protein kinase RIPK4 regulates Wnt signaling, Science, 339, 1441, 10.1126/science.1232253 Ivan, 2001, HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing, Science, 292, 464, 10.1126/science.1059817 Jaakkola, 2001, Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation, Science, 292, 468, 10.1126/science.1059796 Janke, 2013, Factor inhibiting HIF-1 (FIH-1) modulates protein interactions of apoptosis-stimulating p53 binding protein 2 (ASPP2), J. Cell Sci., 126, 2629, 10.1242/jcs.117564 Köditz, 2007, Oxygen-dependent ATF-4 stability is mediated by the PHD3 oxygen sensor, Blood, 110, 3610, 10.1182/blood-2007-06-094441 Lee, 2016, An ID2-dependent mechanism for VHL inactivation in cancer, Nature, 529, 172, 10.1038/nature16475 Lenihan, 2013, The impact of hypoxia on cell death pathways, Biochem. Soc. Trans., 41, 657, 10.1042/BST20120345 Loenarz, 2008, Expanding chemical biology of 2-oxoglutarate oxygenases, Nat. Chem. Biol., 4, 152, 10.1038/nchembio0308-152 Luo, 2011, Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1, Cell, 145, 732, 10.1016/j.cell.2011.03.054 Metzen, 2003, Intracellular localisation of human HIF-1 alpha hydroxylases: implications for oxygen sensing, J. Cell Sci., 116, 1319, 10.1242/jcs.00318 Meylan, 2002, RIP4 (DIK/PKK), a novel member of the RIP kinase family, activates NF-kappa B and is processed during apoptosis, EMBO Rep., 3, 1201, 10.1093/embo-reports/kvf236 Moser, 2013, PHD1 links cell-cycle progression to oxygen sensing through hydroxylation of the centrosomal protein Cep192, Dev. Cell, 26, 381, 10.1016/j.devcel.2013.06.014 Nguyen, 2013, A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network, J. Cell Sci., 126, 1454, 10.1242/jcs.119974 Olsen, 2013, Status of large-scale analysis of post-translational modifications by mass spectrometry, Mol. Cell. Proteomics, 12, 3444, 10.1074/mcp.O113.034181 Rose, 2011, Inhibition of 2-oxoglutarate dependent oxygenases, Chem. Soc. Rev., 40, 4364, 10.1039/c0cs00203h Scholz, 2013, Regulation of IL-1β-induced NF-κB by hydroxylases links key hypoxic and inflammatory signaling pathways, Proc. Natl. Acad. Sci. USA, 110, 18490, 10.1073/pnas.1309718110 Shin, 2009, Inhibitor of nuclear factor-kappaB alpha derepresses hypoxia-inducible factor-1 during moderate hypoxia by sequestering factor inhibiting hypoxia-inducible factor from hypoxia-inducible factor 1alpha, FEBS J., 276, 3470, 10.1111/j.1742-4658.2009.07069.x Taipale, 2013, Chaperones as thermodynamic sensors of drug-target interactions reveal kinase inhibitor specificities in living cells, Nat. Biotechnol., 31, 630, 10.1038/nbt.2620 Tate, 2013, Label-free quantitative proteomics trends for protein-protein interactions, J. Proteomics, 81, 91, 10.1016/j.jprot.2012.10.027 Turriziani, 2014, On-beads digestion in conjunction with data-dependent mass spectrometry: a shortcut to quantitative and dynamic interaction proteomics, Biology (Basel), 3, 320 Ulyatt, 2011, Hypoxia differentially regulates VEGFR1 and VEGFR2 levels and alters intracellular signaling and cell migration in endothelial cells, Biochem. Biophys. Res. Commun., 404, 774, 10.1016/j.bbrc.2010.12.057 van Uden, 2011, Evolutionary conserved regulation of HIF-1β by NF-κB, PLoS Genet., 7, e1001285, 10.1371/journal.pgen.1001285 Wang, 2014, ERK3 promotes endothelial cell functions by upregulating SRC-3/SP1-mediated VEGFR2 expression, J. Cell. Physiol., 229, 1529, 10.1002/jcp.24596 Winston, 1999, The SCFbeta-TRCP-ubiquitin ligase complex associates specifically with phosphorylated destruction motifs in IkappaBalpha and beta-catenin and stimulates IkappaBalpha ubiquitination in vitro, Genes Dev., 13, 270, 10.1101/gad.13.3.270 Xie, 2012, PHD3-dependent hydroxylation of HCLK2 promotes the DNA damage response, J. Clin. Invest., 122, 2827, 10.1172/JCI62374 Yuan, 2011, Cell-to-cell variability in PI3K protein level regulates PI3K-AKT pathway activity in cell populations, Curr. Biol., 21, 173, 10.1016/j.cub.2010.12.047 Zheng, 2014, Prolyl hydroxylation by EglN2 destabilizes FOXO3a by blocking its interaction with the USP9x deubiquitinase, Genes Dev., 28, 1429, 10.1101/gad.242131.114