Generation and physiological roles of linear ubiquitin chains
Tóm tắt
Ubiquitination now ranks with phosphorylation as one of the best-studied post-translational modifications of proteins with broad regulatory roles across all of biology. Ubiquitination usually involves the addition of ubiquitin chains to target protein molecules, and these may be of eight different types, seven of which involve the linkage of one of the seven internal lysine (K) residues in one ubiquitin molecule to the carboxy-terminal diglycine of the next. In the eighth, the so-called linear ubiquitin chains, the linkage is between the amino-terminal amino group of methionine on a ubiquitin that is conjugated with a target protein and the carboxy-terminal carboxy group of the incoming ubiquitin. Physiological roles are well established for K48-linked chains, which are essential for signaling proteasomal degradation of proteins, and for K63-linked chains, which play a part in recruitment of DNA repair enzymes, cell signaling and endocytosis. We focus here on linear ubiquitin chains, how they are assembled, and how three different avenues of research have indicated physiological roles for linear ubiquitination in innate and adaptive immunity and suppression of inflammation.
Tài liệu tham khảo
Pickart CM: Back to the future with ubiquitin. Cell. 2004, 116: 181-190. 10.1016/S0092-8674(03)01074-2.
Hershko A, Ciechanover A: The ubiquitin system. Annu Rev Biochem. 1998, 67: 425-479. 10.1146/annurev.biochem.67.1.425.
Varshavsky A: Regulated protein degradation. Trends Biochem Sci. 2005, 30: 283-286. 10.1016/j.tibs.2005.04.005.
Hershko A: Ubiquitin: roles in protein modification and breakdown. Cell. 1983, 34: 11-12. 10.1016/0092-8674(83)90131-9.
Hershko A, Heller H, Elias S, Ciechanover A: Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown. J Biol Chem. 1983, 258: 8206-8214.
Karin M, Ben-Neriah Y: Phosphorylation meets ubiquitination: the control of NF-[kappa]B activity. Annu Rev Immunol. 2000, 18: 621-663. 10.1146/annurev.immunol.18.1.621.
Hunter T: Signaling - 2000 and beyond. Cell. 2000, 100: 113-127. 10.1016/S0092-8674(00)81688-8.
Cohen P: The origins of protein phosphorylation. Nat Cell Biol. 2002, 4: E127-130. 10.1038/ncb0502-e127.
Ciechanover A, Elias S, Heller H, Hershko A: "Covalent affinity" purification of ubiquitin-activating enzyme. J Biol Chem. 1982, 257: 2537-2542.
Harper JW, Schulman BA: Structural complexity in ubiquitin recognition. Cell. 2006, 124: 1133-1136. 10.1016/j.cell.2006.03.009.
Ye Y, Rape M: Building ubiquitin chains: E2 enzymes at work. Nat Rev Mol Cell Biol. 2009, 10: 755-764. 10.1038/nrm2780.
Ikeda F, Dikic I: Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' review series. EMBO Rep. 2008, 9: 536-542. 10.1038/embor.2008.93.
Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP: A proteomics approach to understanding protein ubiquitination. Nat Biotechnol. 2003, 21: 921-926. 10.1038/nbt849.
Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, Robert J, Rush J, Hochstrasser M, Finley D, Peng J: Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell. 2009, 137: 133-145. 10.1016/j.cell.2009.01.041.
Kirisako T, Kamei K, Murata S, Kato M, Fukumoto H, Kanie M, Sano S, Tokunaga F, Tanaka K, Iwai K: A ubiquitin ligase complex assembles linear polyubiquitin chains. EMBO J. 2006, 25: 4877-4887. 10.1038/sj.emboj.7601360.
Haas TL, Emmerich CH, Gerlach B, Schmukle AC, Cordier SM, Rieser E, Feltham R, Vince J, Warnken U, Wenger T, Koschny R, Komander D, Silke J, Walczak H: Recruitment of the linear ubiquitin chain assembly complex stabilizes the TNF-R1 signaling complex and is required for TNF-mediated gene induction. Mol Cell. 2009, 36: 831-844. 10.1016/j.molcel.2009.10.013.
Rahighi S, Ikeda F, Kawasaki M, Akutsu M, Suzuki N, Kato R, Kensche T, Uejima T, Bloor S, Komander D, Randow F, Wakatsuki S, Dikic I: Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell. 2009, 136: 1098-1109. 10.1016/j.cell.2009.03.007.
Tokunaga F, Sakata S, Saeki Y, Satomi Y, Kirisako T, Kamei K, Nakagawa T, Kato M, Murata S, Yamaoka S, Yamamoto M, Akira S, Takao T, Tanaka K, Iwai K: Involvement of linear polyubiquitylation of NEMO in NF-kappaB activation. Nat Cell Biol. 2009, 11: 123-132. 10.1038/ncb1821.
Gerlach B, Cordier SM, Schmukle AC, Emmerich CH, Rieser E, Haas TL, Webb AI, Rickard JA, Anderton H, Wong WW, Nachbur U, Gangoda L, Warnken U, Purcell AW, Silke J, Walczak H: Linear ubiquitination prevents inflammation and regulates immune signalling. Nature. 2011, 471: 591-596. 10.1038/nature09816.
Ikeda F, Deribe YL, Skånland SS, Stieglitz B, Grabbe C, Franz-Wachtel M, van Wijk SJ, Goswami P, Nagy V, Terzic J, Tokunaga F, Androulidaki A, Nakagawa T, Pasparakis M, Iwai K, Sundberg JP, Schaefer L, Rittinger K, Macek B, Dikic I: SHARPIN forms a linear ubiquitin ligase complex regulating NF-kappaB activity and apoptosis. Nature. 2011, 471: 637-641. 10.1038/nature09814.
Tokunaga F, Nakagawa T, Nakahara M, Saeki Y, Taniguchi M, Sakata S, Tanaka K, Nakano H, Iwai K: SHARPIN is a component of the NF-kappaB-activating linear ubiquitin chain assembly complex. Nature. 2011, 471: 633-636. 10.1038/nature09815.
Nagy V, Dikic I: Ubiquitin ligase complexes: from substrate selectivity to conjugational specificity. Biol Chem. 2010, 391: 163-169. 10.1515/BC.2010.021.
de Bie P, Ciechanover A: Ubiquitination of E3 ligases: self-regulation of the ubiquitin system via proteolytic and non-proteolytic mechanisms. Cell Death Differ. 2011, 18: 1393-1402. 10.1038/cdd.2011.16.
Hatakeyama S, Yada M, Matsumoto M, Ishida N, Nakayama KI: U box proteins as a new family of ubiquitin-protein ligases. J Biol Chem. 2001, 276: 33111-33120. 10.1074/jbc.M102755200.
Tokunaga C, Kuroda S, Tatematsu K, Nakagawa N, Ono Y, Kikkawa U: Molecular cloning and characterization of a novel protein kinase C-interacting protein with structural motifs related to RBCC family proteins. Biochem Biophys Res Commun. 1998, 244: 353-359. 10.1006/bbrc.1998.8270.
Eisenhaber B, Chumak N, Eisenhaber F, Hauser MT: The ring between ring fingers (RBR) protein family. Genome Biol. 2007, 8: 209-10.1186/gb-2007-8-3-209.
Marin I, Lucas JI, Gradilla AC, Ferrus A: Parkin and relatives: the RBR family of ubiquitin ligases. Physiol Genomics. 2004, 17: 253-263. 10.1152/physiolgenomics.00226.2003.
Marin I, Ferrus A: Comparative genomics of the RBR family, including the Parkinson's disease-related gene parkin and the genes of the ariadne subfamily. Mol Biol Evol. 2002, 19: 2039-2050. 10.1093/oxfordjournals.molbev.a004029.
Chaugule VK, Burchell L, Barber KR, Sidhu A, Leslie SJ, Shaw GS, Walden H: Autoregulation of Parkin activity through its ubiquitin-like domain. EMBO J. 2011, 30: 2853-2867. 10.1038/emboj.2011.204.
Wenzel DM, Lissounov A, Brzovic PS, Klevit RE: UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature. 2011, 474: 105-108. 10.1038/nature09966.
Lim KL, Dawson VL, Dawson TM: Parkin-mediated lysine 63-linked polyubiquitination: a link to protein inclusions formation in Parkinson's and other conformational diseases?. Neurobiol Aging. 2006, 27: 524-529. 10.1016/j.neurobiolaging.2005.07.023.
Doss-Pepe EW, Chen L, Madura K: Alpha-synuclein and parkin contribute to the assembly of ubiquitin lysine 63-linked multiubiquitin chains. J Biol Chem. 2005, 280: 16619-16624. 10.1074/jbc.M413591200.
Dynek JN, Goncharov T, Dueber EC, Fedorova AV, Izrael-Tomasevic A, Phu L, Helgason E, Fairbrother WJ, Deshayes K, Kirkpatrick DS, Vucic D: c-IAP1 and UbcH5 promote K11-linked polyubiquitination of RIP1 in TNF signalling. EMBO J. 2011, 29: 4198-4209.
Lo YC, Lin SC, Rospigliosi CC, Conze DB, Wu CJ, Ashwell JD, Eliezer D, Wu H: Structural basis for recognition of diubiquitins by NEMO. Mol Cell. 2009, 33: 602-615. 10.1016/j.molcel.2009.01.012.
Ikeda F, Crosetto N, Dikic I: What determines the specificity and outcomes of ubiquitin signaling?. Cell. 2010, 143: 677-681. 10.1016/j.cell.2010.10.026.
Ea CK, Deng L, Xia ZP, Pineda G, Chen ZJ: Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO. Mol Cell. 2006, 22: 245-257. 10.1016/j.molcel.2006.03.026.
Zhou H, Wertz I, O'Rourke K, Ultsch M, Seshagiri S, Eby M, Xiao W, Dixit VM: Bcl10 activates the NF-kappaB pathway through ubiquitination of NEMO. Nature. 2004, 427: 167-171. 10.1038/nature02273.
Ni CY, Wu ZH, Florence WC, Parekh VV, Arrate MP, Pierce S, Schweitzer B, Van Kaer L, Joyce S, Miyamoto S, Ballard DW, Oltz EM: Cutting edge: K63-linked polyubiquitination of NEMO modulates TLR signaling and inflammation in vivo. J Immunol. 2008, 180: 7107-7111.
Abbott DW, Wilkins A, Asara JM, Cantley LC: The Crohn's disease protein, NOD2, requires RIP2 in order to induce ubiquitinylation of a novel site on NEMO. Curr Biol. 2004, 14: 2217-2227. 10.1016/j.cub.2004.12.032.
HogenEsch H, Gijbels MJ, Offerman E, van Hooft J, van Bekkum DW, Zurcher C: A spontaneous mutation characterized by chronic proliferative dermatitis in C57BL mice. Am J Pathol. 1993, 143: 972-982.
Degterev A, Yuan J: Expansion and evolution of cell death programmes. Nat Rev Mol Cell Biol. 2008, 9: 378-390. 10.1038/nrm2393.
Van Herreweghe F, Festjens N, Declercq W, Vandenabeele P: Tumor necrosis factor-mediated cell death: to break or to burst, that's the question. Cell Mol Life Sci. 2010, 67: 1567-1579. 10.1007/s00018-010-0283-0.
Sato Y, Fujita H, Yoshikawa A, Yamashita M, Yamagata A, Kaiser SE, Iwai K, Fukai S: Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex. Proc Natl Acad Sci USA. 2011, 108: 20520-20525. 10.1073/pnas.1109088108.
Walczak H: TNF and ubiquitin at the crossroads of gene activation, cell death, inflammation, and cancer. Immunol Rev. 2011, 244: 9-28. 10.1111/j.1600-065X.2011.01066.x.
Micheau O, Tschopp J: Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes. Cell. 2003, 114: 181-190. 10.1016/S0092-8674(03)00521-X.