Post-translational modifications in signal integration (original) (raw)

• Kho, Y. et al. A tagging-via-substrate technology for detection and proteomics of farnesylated proteins. Proc. Natl. Acad. Sci. USA 101, 12479–12484 (2004).
  CAS PubMed PubMed Central Google Scholar
• Mann, M. & Jensen, O.N. Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21, 255–261 (2003).
  CAS PubMed Google Scholar
• Fischer, E.H. & Krebs, E.G. Conversion of phosphorylase b to phosphorylase a in muscle extracts. J. Biol. Chem. 216, 121–132 (1955).
  CAS PubMed Google Scholar
• Walsh, D.A., Perkins, J.P. & Krebs, E.G. An adenosine 3′,5′-monophosphate-dependant protein kinase from rabbit skeletal muscle. J. Biol. Chem. 243, 3763–3765 (1968).
  CAS PubMed Google Scholar
• Hershko, A. Some lessons from my work on the biochemistry of the ubiquitin system. J. Biol. Chem. 284, 10291–10295 (2009).
  CAS PubMed PubMed Central Google Scholar
• Schmidt, E.E. & Davies, C.J. The origins of polypeptide domains. Bioessays 29, 262–270 (2007).
  CAS PubMed PubMed Central Google Scholar
• Jin, J. et al. Eukaryotic protein domains as functional units of cellular evolution. Sci. Signal. 2, ra76 (2009).
  PubMed Google Scholar
• Hunter, T. & Cooper, J.A. Protein-tyrosine kinases. Annu. Rev. Biochem. 54, 897–930 (1985).
  CAS PubMed Google Scholar
• Manning, G., Plowman, G.D., Hunter, T. & Sudarsanam, S. Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci. 27, 514–520 (2002).
  CAS PubMed Google Scholar
• Nurse, P. A long twentieth century of the cell cycle and beyond. Cell 100, 71–78 (2000).
  CAS PubMed Google Scholar
• Ullrich, A. & Schlessinger, J. Signal transduction by receptors with tyrosine kinase activity. Cell 61, 203–212 (1990).
  CAS PubMed Google Scholar
• Narayanan, A. & Jacobson, M.P. Computational studies of protein regulation by post-translational phosphorylation. Curr. Opin. Struct. Biol. 19, 156–163 (2009).
  CAS PubMed Google Scholar
• Johnson, L.N. & Lewis, R.J. Structural basis for control by phosphorylation. Chem. Rev. 101, 2209–2242 (2001).
  CAS PubMed Google Scholar
• Pawson, T. Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 116, 191–203 (2004).
  CAS PubMed Google Scholar
• Kuriyan, J. & Cowburn, D. Modular peptide recognition domains in eukaryotic signaling. Annu. Rev. Biophys. Biomol. Struct. 26, 259–288 (1997).
  CAS PubMed Google Scholar
• Filippakopoulos, P. et al. Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation. Cell 134, 793–803 (2008).
  CAS PubMed PubMed Central Google Scholar
• Bae, J.H. et al. The selectivity of receptor tyrosine kinase signaling is controlled by a secondary SH2 domain binding site. Cell 138, 514–524 (2009).
  CAS PubMed PubMed Central Google Scholar
• Hershko, A. & Ciechanover, A. The ubiquitin system. Annu. Rev. Biochem. 67, 425–479 (1998).
  CAS PubMed Google Scholar
• Ikeda, F. & Dikic, I. Atypical ubiquitin chains: new molecular signals. 'Protein modifications: beyond the usual suspects' review series. EMBO Rep. 9, 536–542 (2008).
  CAS PubMed PubMed Central Google Scholar
• Rahighi, S. et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-κB activation. Cell 136, 1098–1109 (2009).
  CAS PubMed Google Scholar
• Tokunaga, F. et al. Involvement of linear polyubiquitylation of NEMO in NF-κB activation. Nat. Cell Biol. 11, 123–132 (2009).
  CAS PubMed Google Scholar
• Dikic, I., Wakatsuki, S. & Walters, K.J. Ubiquitin-binding domains — from structures to functions. Nat. Rev. Mol. Cell Biol. 10, 659–671 (2009).
  CAS PubMed PubMed Central Google Scholar
• Hirano, S. et al. Double-sided ubiquitin binding of Hrs-UIM in endosomal protein sorting. Nat. Struct. Mol. Biol. 13, 272–277 (2006).
  CAS PubMed Google Scholar
• Bienko, M. et al. Regulation of translesion synthesis DNA polymerase η by monoubiquitination. Mol. Cell 37, 396–407 (2010).
  CAS PubMed Google Scholar
• Husnjak, K. et al. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 453, 481–488 (2008).
  CAS PubMed PubMed Central Google Scholar
• Brzovic, P.S., Lissounov, A., Christensen, D.E., Hoyt, D.W. & Klevit, R.E.A. UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination. Mol. Cell 21, 873–880 (2006).
  CAS PubMed Google Scholar
• Hoeller, D. et al. Regulation of ubiquitin-binding proteins by monoubiquitination. Nat. Cell Biol. 8, 163–169 (2006).
  CAS PubMed Google Scholar
• Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41–45 (2000).
  CAS PubMed Google Scholar
• Kouzarides, T. Acetylation: a regulatory modification to rival phosphorylation? EMBO J. 19, 1176–1179 (2000).
  CAS PubMed PubMed Central Google Scholar
• Kovacs, J.J. et al. HDAC6 regulates Hsp90 acetylation and chaperone-dependent activation of glucocorticoid receptor. Mol. Cell 18, 601–607 (2005).
  CAS PubMed Google Scholar
• Yang, X.J. Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays 26, 1076–1087 (2004).
  CAS PubMed Google Scholar
• Ianari, A., Gallo, R., Palma, M., Alesse, E. & Gulino, A. Specific role for p300/CREB-binding protein-associated factor activity in E2F1 stabilization in response to DNA damage. J. Biol. Chem. 279, 30830–30835 (2004).
  CAS PubMed Google Scholar
• Simonsson, M., Heldin, C.H., Ericsson, J. & Gronroos, E. The balance between acetylation and deacetylation controls Smad7 stability. J. Biol. Chem. 280, 21797–21803 (2005).
  CAS PubMed Google Scholar
• Zippo, A. et al. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 138, 1122–1136 (2009).
  CAS PubMed Google Scholar
• Choudhary, C. et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834–840 (2009).
  CAS PubMed Google Scholar
• Wang, Q. et al. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327, 1004–1007 (2010).
  CAS PubMed PubMed Central Google Scholar
• Zhao, S. et al. Regulation of cellular metabolism by protein lysine acetylation. Science 327, 1000–1004 (2010).
  CAS PubMed PubMed Central Google Scholar
• Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).
  CAS PubMed Google Scholar
• Kirmizis, A. et al. Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 449, 928–932 (2007).
  CAS PubMed PubMed Central Google Scholar
• Huang, J. & Berger, S.L. The emerging field of dynamic lysine methylation of non-histone proteins. Curr. Opin. Genet. Dev. 18, 152–158 (2008).
  CAS PubMed Google Scholar
• Nielsen, P.R. et al. Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416, 103–107 (2002).
  CAS PubMed Google Scholar
• Chen, C. et al. Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Proc. Natl. Acad. Sci. USA 106, 20336–20341 (2009).
  CAS PubMed PubMed Central Google Scholar
• Cote, J. & Richard, S. Tudor domains bind symmetrical dimethylated arginines. J. Biol. Chem. 280, 28476–28483 (2005).
  CAS PubMed Google Scholar
• Kirino, Y. et al. Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization. RNA 16, 70–78 (2010).
  CAS PubMed PubMed Central Google Scholar
• Kaelin, W.G. Proline hydroxylation and gene expression. Annu. Rev. Biochem. 74, 115–128 (2005).
  CAS PubMed Google Scholar
• Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 103, 211–225 (2000).
  CAS PubMed Google Scholar
• Marshall, M.S. Ras target proteins in eukaryotic cells. FASEB J. 9, 1311–1318 (1995).
  CAS PubMed Google Scholar
• Engelman, J.A., Luo, J. & Cantley, L.C. The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nat. Rev. Genet. 7, 606–619 (2006).
  CAS PubMed Google Scholar
• Cantley, L.C. The phosphoinositide 3-kinase pathway. Science 296, 1655–1657 (2002).
  CAS PubMed Google Scholar
• Offterdinger, M., Georget, V., Girod, A. & Bastiaens, P.I. Imaging phosphorylation dynamics of the epidermal growth factor receptor. J. Biol. Chem. 279, 36972–36981 (2004).
  CAS PubMed Google Scholar
• Yudushkin, I.A. et al. Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B. Science 315, 115–119 (2007).
  CAS PubMed Google Scholar
• Chen, P., Xie, H. & Wells, A. Mitogenic signaling from the EGF receptor is attenuated by a phospholipase C-γ/protein kinase C feedback mechanism. Mol. Biol. Cell 7, 871–881 (1996).
  CAS PubMed PubMed Central Google Scholar
• Damke, H., Gossen, M., Freundlieb, S., Bujard, H. & Schmid, S.L. Tightly regulated and inducible expression of dominant interfering dynamin mutant in stably transformed HeLa cells. Methods Enzymol. 257, 209–220 (1995).
  CAS PubMed Google Scholar
• Burgess, A.W. et al. An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol. Cell 12, 541–552 (2003).
  CAS PubMed Google Scholar
• Huang, F., Khvorova, A., Marshall, W. & Sorkin, A. Analysis of clathrin-mediated endocytosis of epidermal growth factor receptor by RNA interference. J. Biol. Chem. 279, 16657–16661 (2004).
  CAS PubMed Google Scholar
• Sorkin, A., Waters, C., Overholser, K.A. & Carpenter, G. Multiple autophosphorylation site mutations of the epidermal growth factor receptor. Analysis of kinase activity and endocytosis. J. Biol. Chem. 266, 8355–8362 (1991).
  CAS PubMed Google Scholar
• Schmidt, M.H. & Dikic, I. The Cbl interactome and its functions. Nat. Rev. Mol. Cell Biol. 6, 907–918 (2005).
  CAS PubMed Google Scholar
• Seaman, M.N. Endosome protein sorting: motifs and machinery. Cell. Mol. Life Sci. 65, 2842–2858 (2008).
  CAS PubMed Google Scholar
• Piper, R.C. & Katzmann, D.J. Biogenesis and function of multivesicular bodies. Annu. Rev. Cell Dev. Biol. 23, 519–547 (2007).
  CAS PubMed PubMed Central Google Scholar
• Haglund, K. et al. Multiple monoubiquitination of RTKs is sufficient for their endocytosis and degradation. Nat. Cell Biol. 5, 461–466 (2003).
  CAS PubMed Google Scholar
• Huang, F., Kirkpatrick, D., Jiang, X., Gygi, S. & Sorkin, A. Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. Mol. Cell 21, 737–748 (2006).
  CAS PubMed Google Scholar
• Raiborg, C., Bache, K.G., Mehlum, A., Stang, E. & Stenmark, H. Hrs recruits clathrin to early endosomes. EMBO J. 20, 5008–5021 (2001).
  CAS PubMed PubMed Central Google Scholar
• Raiborg, C. et al. Hrs sorts ubiquitinated proteins into clathrin-coated microdomains of early endosomes. Nat. Cell Biol. 4, 394–398 (2002).
  CAS PubMed Google Scholar
• Raiborg, C., Malerod, L., Pedersen, N.M. & Stenmark, H. Differential functions of Hrs and ESCRT proteins in endocytic membrane trafficking. Exp. Cell Res. 314, 801–813 (2008).
  CAS PubMed Google Scholar
• Shih, S.C. et al. Epsins and Vps27p/Hrs contain ubiquitin-binding domains that function in receptor endocytosis. Nat. Cell Biol. 4, 389–393 (2002).
  CAS PubMed Google Scholar
• Deribe, Y.L. et al. Regulation of epidermal growth factor receptor trafficking by lysine deacetylase HDAC6. Sci. Signal. 2, ra84 (2009).
  PubMed Google Scholar
• Bodmer, J.L., Schneider, P. & Tschopp, J. The molecular architecture of the TNF superfamily. Trends Biochem. Sci. 27, 19–26 (2002).
  CAS PubMed Google Scholar
• Bianchi, K. & Meier, P. A tangled web of ubiquitin chains: breaking news in TNF-R1 signaling. Mol. Cell 36, 736–742 (2009).
  CAS PubMed Google Scholar
• Karin, M. & Gallagher, E. TNFR signaling: ubiquitin-conjugated TRAFfic signals control stop-and-go for MAPK signaling complexes. Immunol. Rev. 228, 225–240 (2009).
  CAS PubMed Google Scholar
• Vallabhapurapu, S. & Karin, M. Regulation and function of NF-κB transcription factors in the immune system. Annu. Rev. Immunol. 27, 693–733 (2009).
  CAS PubMed Google Scholar
• Wertz, I.E. et al. De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling. Nature 430, 694–699 (2004).
  CAS PubMed Google Scholar
• Ea, C.K., Deng, L., Xia, Z.P., Pineda, G. & Chen, Z.J. Activation of IKK by TNFα requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO. Mol. Cell 22, 245–257 (2006).
  CAS PubMed Google Scholar
• Chen, Z.J. Ubiquitin signalling in the NF-κB pathway. Nat. Cell Biol. 7, 758–765 (2005).
  CAS PubMed PubMed Central Google Scholar
• Wang, C. et al. TAK1 is a ubiquitin-dependent kinase of MKK and IKK. Nature 412, 346–351 (2001).
  CAS PubMed Google Scholar
• Yaron, A. et al. Identification of the receptor component of the IκBα-ubiquitin ligase. Nature 396, 590–594 (1998).
  CAS PubMed Google Scholar
• Karin, M. & Ben-Neriah, Y. Phosphorylation meets ubiquitination: the control of NF-κB activity. Annu. Rev. Immunol. 18, 621–663 (2000).
  CAS PubMed Google Scholar
• Yamamoto, M. et al. Key function for the Ubc13 E2 ubiquitin-conjugating enzyme in immune receptor signaling. Nat. Immunol. 7, 962–970 (2006).
  CAS PubMed Google Scholar
• Xu, M., Skaug, B., Zeng, W. & Chen, Z.J. A ubiquitin replacement strategy in human cells reveals distinct mechanisms of IKK activation by TNFα and IL-1β. Mol. Cell 36, 302–314 (2009).
  CAS PubMed PubMed Central Google Scholar
• Haas, T.L. et al. Recruitment of the linear ubiquitin chain assembly complex stabilizes the TNF-R1 signaling complex and is required for TNF-mediated gene induction. Mol. Cell 36, 831–844 (2009).
  CAS PubMed Google Scholar
• Lee, J.H. & Paull, T.T. ATM activation by DNA double-strand breaks through the Mre11-Rad50-Nbs1 complex. Science 308, 551–554 (2005).
  CAS PubMed Google Scholar
• Bakkenist, C.J. & Kastan, M.B. DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation. Nature 421, 499–506 (2003).
  CAS PubMed Google Scholar
• Matsuoka, S. et al. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316, 1160–1166 (2007).
  CAS PubMed Google Scholar
• Ahn, J., Urist, M. & Prives, C. The Chk2 protein kinase. DNA Repair (Amst.) 3, 1039–1047 (2004).
  CAS Google Scholar
• Bassermann, F. & Pagano, M. Dissecting the role of ubiquitylation in the DNA damage response checkpoint in G2. Cell Death Differ. 17, 78–85 (2010).
  CAS PubMed Google Scholar
• Busino, L. et al. Degradation of Cdc25A by β-TrCP during S phase and in response to DNA damage. Nature 426, 87–91 (2003).
  CAS PubMed Google Scholar
• Jin, J. et al. SCFβ-TRCP links Chk1 signaling to degradation of the Cdc25A protein phosphatase. Genes Dev. 17, 3062–3074 (2003).
  CAS PubMed PubMed Central Google Scholar
• Hu, J., McCall, C.M., Ohta, T. & Xiong, Y. Targeted ubiquitination of CDT1 by the DDB1–CUL4A-ROC1 ligase in response to DNA damage. Nat. Cell Biol. 6, 1003–1009 (2004).
  CAS PubMed Google Scholar
• Hoege, C., Pfander, B., Moldovan, G.L., Pyrowolakis, G. & Jentsch, S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419, 135–141 (2002).
  CAS PubMed Google Scholar
• Bienko, M. et al. Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science 310, 1821–1824 (2005).
  CAS PubMed Google Scholar
• Guo, C. et al. Ubiquitin-binding motifs in REV1 protein are required for its role in the tolerance of DNA damage. Mol. Cell. Biol. 26, 8892–8900 (2006).
  CAS PubMed PubMed Central Google Scholar
• Hofmann, R.M. & Pickart, C.M. Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair. Cell 96, 645–653 (1999).
  CAS PubMed Google Scholar
• Ivan, M. et al. HIFα targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing. Science 292, 464–468 (2001).
  CAS PubMed Google Scholar
• Jaakkola, P. et al. Targeting of HIF-α to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292, 468–472 (2001).
  CAS PubMed Google Scholar
• Kamura, T. et al. Activation of HIF1α ubiquitination by a reconstituted von Hippel-Lindau (VHL) tumor suppressor complex. Proc. Natl. Acad. Sci. USA 97, 10430–10435 (2000).
  CAS PubMed PubMed Central Google Scholar
• MacKenzie, E.D. et al. Cell-permeating α-ketoglutarate derivatives alleviate pseudohypoxia in succinate dehydrogenase-deficient cells. Mol. Cell. Biol. 27, 3282–3289 (2007).
  CAS PubMed PubMed Central Google Scholar
• Boulahbel, H., Duran, R.V. & Gottlieb, E. Prolyl hydroxylases as regulators of cell metabolism. Biochem. Soc. Trans. 37, 291–294 (2009).
  CAS PubMed Google Scholar
• Hardy, W.R. et al. Combinatorial ShcA docking interactions support diversity in tissue morphogenesis. Science 317, 251–256 (2007).
  CAS PubMed PubMed Central Google Scholar
• Johnson, S.A., You, Z. & Hunter, T. Monitoring ATM kinase activity in living cells. DNA Repair (Amst.) 6, 1277–1284 (2007).
  CAS Google Scholar
• Violin, J.D., Zhang, J., Tsien, R.Y. & Newton, A.C. A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C. J. Cell Biol. 161, 899–909 (2003).
  CAS PubMed PubMed Central Google Scholar