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Review

Putting proteomics on target: activity-based profiling of ubiquitin and ubiquitin-like processing enzymes

Pages 213-221 | Published online: 09 Jan 2014

References

  • Wilkinson KD. The discovery of ubiquitin-dependent proteolysis. Proc. Natl Acad. Sci. USA102, 15280–15282 (2005).
  • Glickman MH, Ciechanover A. The ubiquitin–proteasome proteolytic pathway: destruction for the sake of construction. Physiol. Rev.82, 373–428 (2002).
  • Hershko A, Ciechanover A, Rose IA. Resolution of the ATP-dependent proteolytic system from reticulocytes: a component that interacts with ATP. Proc. Natl Acad. Sci. USA76, 3107–3110 (1979).
  • Passmore LA, Barford D. Getting into position: the catalytic mechanisms of protein ubiquitylation. Biochem. J.379, 513–525 (2004).
  • Jin J, Cardozo T, Lovering RC, Elledge SJ, Pagano M, Harper JW. Systematic analysis and nomenclature of mammalian F-box proteins. Genes Dev.18, 2573–2580 (2004).
  • Berndt C, Bech-Otschir D, Dubiel W, Seeger M. Ubiquitin system: JAMMing in the name of the lid. Curr. Biol.12, R815–R817 (2002).
  • Borodovsky A, Kessler BM, Casagrande R, Overkleeft HS, Wilkinson KD, Ploegh HL. A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14. EMBO J.20, 5187–5196 (2001).
  • Lam YA, Xu W, DeMartino GN, Cohen RE. Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome. Nature385, 737–740 (1997).
  • Wilkinson CR. Ubiquitin-like proteins: meet the family. Semin. Cell Dev. Biol.15, 199–200 (2004).
  • Denison C, Kirkpatrick DS, Gygi SP. Proteomic insights into ubiquitin and ubiquitin-like proteins. Curr. Opin. Chem. Biol.9, 69–75 (2005).
  • Kirkpatrick DS, Denison C, Gygi SP. Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nature Cell Biol.7, 750–757 (2005).
  • Peng J, Schwartz D, Elias JE et al. A proteomics approach to understanding protein ubiquitination. Nature Biotechnol.21, 921–926 (2003).
  • Wang D, Xu W, McGrath SC, Patterson C, Neckers L, Cotter RJ. Direct identification of ubiquitination sites on ubiquitin-conjugated CHIP using MALDI mass spectrometry. J. Proteome Res.4, 1554–1560 (2005).
  • Warren MR, Parker CE, Mocanu V, Klapper D, Borchers CH. Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination. Rapid Commun. Mass Spectrom.19, 429–437 (2005).
  • Hemelaar J, Lelyveld VS, Kessler BM, Ploegh HL. A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L. J. Biol. Chem.278, 51841–51850 (2003).
  • Ichimura Y, Kirisako T, Takao T et al. A ubiquitin-like system mediates protein lipidation. Nature408, 488–492 (2000).
  • Dao CT, Zhang DE. ISG15: a ubiquitin-like enigma. Front. Biosci.10, 2701–2722 (2005).
  • Giannakopoulos NV, Luo JK, Papov V et al. Proteomic identification of proteins conjugated to ISG15 in mouse and human cells. Biochem. Biophys. Res. Commun.336, 496–506 (2005).
  • Nijman MB, Luna-Vargas MPA, Velda A et al. A gemomic and functional inventory of deubiquitinating enzymes. Cell123, 773–786 (2005).
  • Hershko A, Rose IA. Ubiquitin-aldehyde: a general inhibitor of ubiquitin-recycling processes. Proc. Natl Acad. Sci. USA84, 1829–1833 (1987).
  • Pickart CM, Rose IA. Mechanism of ubiquitin carboxyl-terminal hydrolase. Borohydride and hydroxylamine inactivate in the presence of ubiquitin. J. Biol. Chem.261, 10210–10217 (1986).
  • Wing SS. Deubiquitinating enzymes – the importance of driving in reverse along the ubiquitin–proteasome pathway. Int. J. Biochem. Cell Biol.35, 590–605 (2003).
  • Galardy P, Ploegh HL, Ovaa H. Mechanism-based proteomics tools based on ubiquitin and ubiquitin-like proteins: crystallography, activity profiling, and protease identification. Methods Enzymol.399, 120–131 (2005).
  • Ovaa H, Galardy PJ, Ploegh HL. Mechanism-based proteomics tools based on ubiquitin and ubiquitin-like proteins: synthesis of active site-directed probes. Methods Enzymol.399, 468–478 (2005).
  • Wilkinson KD, Gan-Erdene T, Kolli N. Derivitization of the C-terminus of ubiquitin and ubiquitin-like proteins using intein chemistry: methods and uses. Methods Enzymol.399, 37–51 (2005).
  • Hemelaar J, Galardy PJ, Borodovsky A, Kessler BM, Ploegh HL, Ovaa H. Chemistry-based functional proteomics: mechanism-based activity-profiling tools for ubiquitin and ubiquitin-like specific proteases. J. Proteome Res.3, 268–276 (2004).
  • Hemelaar J, Borodovsky A, Kessler BM et al. Specific and covalent targeting of conjugating and deconjugating enzymes of ubiquitin-like proteins. Mol. Cell Biol.24, 84–95 (2004).
  • Ovaa H, Kessler BM, Rolen U, Galardy PJ, Ploegh HL, Masucci MG. Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells. Proc. Natl Acad. Sci. USA101, 2253–2258 (2004).
  • Gan-Erdene T, Nagamalleswari K, Yin L, Wu K, Pan ZQ, Wilkinson KD. Identification and characterization of DEN1, a deneddylase of the ULP family. J. Biol. Chem.278, 28892–28900 (2003).
  • Wu K, Yamoah K, Dolios G et al. DEN1 is a dual function protease capable of processing the C terminus of Nedd8 and deconjugating hyper-neddylated CUL1. J. Biol. Chem.278, 28882–28891 (2003).
  • Borodovsky A, Ovaa H, Kolli N et al. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem. Biol.9, 1149–1159 (2002).
  • Iyer LM, Koonin EV, Aravind L. Novel predicted peptidases with a potential role in the ubiquitin signaling pathway. Cell Cycle3(11), 1440–1450 (2004).
  • Kattenhorn LM, Korbel GA, Kessler BM, Spooner E, Ploegh HL. A deubiquitinating enzyme encoded by HSV-1 belongs to a family of cysteine proteases that is conserved across the family Herpesviridae. Mol. Cell19, 547–557 (2005).
  • Schlieker C, Korbel GA, Kattenhorn LM, Ploegh HL. A deubiquitinating activity is conserved in the large tegument protein of the Herpesviridae. J. Virol.79, 15582–15585 (2005).
  • Shackelford J, Pagano JS. Tumor viruses and cell signaling pathways: deubiquitination versus ubiquitination. Mol. Cell Biol.24, 5089–5093 (2004).
  • Balakirev MY, Jaquinod M, Haas AL, Chroboczek J. Deubiquitinating function of adenovirus proteinase. J. Virol.76, 6323–6331 (2002).
  • Andres G, Alejo A, Simon-Mateo C, Salas ML. African swine fever virus protease, a new viral member of the SUMO-1-specific protease family. J. Biol. Chem.276, 780–787 (2001).
  • Honig JE, Osborne JC, Nichol ST. Crimean–Congo hemorrhagic fever virus genome L RNA segment and encoded protein. Virology321, 29–35 (2004).
  • Kinsella E, Martin SG, Grolla A, Czub M, Feldmann H, Flick R. Sequence determination of the Crimean–Congo hemorrhagic fever virus L segment. Virology321, 23–28 (2004).
  • Barretto N, Jukneliene D, Ratia K, Chen Z, Mesecar AD, Baker SC. The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity. J. Virol.79, 15189–15198 (2005).
  • Roden J, Eardley L, Hotson A, Cao Y, Mudgett MB. Characterization of the Xanthomonas AvrXv4 effector, a SUMO protease translocated into plant cells. Mol. Plant Microbe Interact.17, 633–643 (2004).
  • Orth K, Xu Z, Mudgett MB et al. Disruption of signaling by Yersinia effector YopJ, a ubiquitin-like protein protease. Science290, 1594–1597 (2000).
  • Zhou H, Monack DM, Kayagaki N et al. Yersinia virulence factor YopJ acts as a deubiquitinase to inhibit NF-κB activation. J. Exp. Med.202, 1327–1332 (2005).
  • Leggett DS, Hanna J, Borodovsky A et al. Multiple associated proteins regulate proteasome structure and function. Mol. Cell10, 495–507 (2002).
  • Hu M, Li P, Song L et al. Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14. EMBO J.24, 3747–3756 (2005).
  • Misaghi S, Galardy PJ, Meester WJ, Ovaa H, Ploegh HL, Gaudet R. Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J. Biol. Chem.280, 1512–1520 (2005).
  • Johnston SC, Riddle SM, Cohen RE, Hill CP. Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J.18, 3877–3887 (1999).
  • Johnston SC, Larsen CN, Cook WJ, Wilkinson KD, Hill CP. Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution. EMBO J.16, 3787–3796 (1997).
  • Hu M, Li P, Li M et al. Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell111, 1041–1054 (2002).
  • Oliveira AM, Chou MM, Perez-Atayde AR, Rosenberg AE. Aneurysmal bone cyst: a neoplasm driven by upregulation of the USP6 oncogene. J. Clin. Oncol.24, e1; author reply e2 (2006).
  • Shen C, Ye Y, Robertson SE, Lau AW, Mak DO, Chou MM. Calcium/calmodulin regulates ubiquitination of the ubiquitin-specific protease TRE17/USP6. J. Biol. Chem.280, 35967–35973 (2005).
  • Nanao MH, Tcherniuk SO, Chroboczek J, Dideberg O, Dessen A, Balakirev MY. Crystal structure of human otubain 2. EMBO Rep.5, 783–788 (2004).
  • Reverter D, Wu K, Erdene TG, Pan ZQ, Wilkinson KD, Lima CD. Structure of a complex between Nedd8 and the Ulp/Senp protease family member Den1. J. Mol. Biol.345, 141–151 (2005).
  • Mossessova E, Lima CD. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol. Cell5, 865–876 (2000).
  • Powers JC, Asgian JL, Ekici OD, James KE. Irreversible inhibitors of serine, cysteine and threonine proteases. Chem. Rev.102, 4639–4750 (2002).
  • Rasnick D. Perspect. Drug Discov.6, 47 (1996).
  • Palmer JT, Rasnick D, Klaus JL, Bromme D. Vinyl sulfones as mechanism-based cysteine protease inhibitors. J. Med. Chem.38, 3193–3196 (1995).
  • Borodovsky A, Ovaa H, Meester WJ et al. Small-molecule inhibitors and probes for ubiquitin- and ubiquitin-like-specific proteases. Chembiochem6, 287–291 (2005).
  • Mason DE, Ek J, Peters EC, Harris JL. Substrate profiling of deubiquitin hydrolases with a positional scanning library and mass spectrometry. Biochemistry43, 6535–6544 (2004).
  • Ritchie KJ, Hahn CS, Kim KI et al. Role of ISG15 protease UBP43 (USP18) in innate immunity to viral infection. Nature Med.10, 1374–1378 (2004).
  • Wilkinson KD. Regulation of ubiquitin-dependent processes by deubiquitinating enzymes. FASEB J.11, 1245–1256 (1997).
  • Shokat K, Velleca M. Novel chemical genetic approaches to the discovery of signal transduction inhibitors. Drug Discov. Today7, 872–879 (2002).
  • Bishop AC, Ubersax JA, Petsch DT et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature407, 395–401 (2000).
  • Evans PC, Ovaa H, Hamon M et al. Zinc-finger protein A20, a regulator of inflammation and cell survival, has de-ubiquitinating activity. Biochem. J.378, 727–734 (2004).
  • Liu Y, Lashuel HA, Choi S et al. Discovery of inhibitors that elucidate the role of UCH-L1 activity in the H1299 lung cancer cell line. Chem. Biol.10, 837–846 (2003).
  • Liu Y, Fallon L, Lashuel HA, Liu Z, Lansbury PT Jr. The UCH-L1 gene encodes two opposing enzymatic activities that affect α-synuclein degradation and Parkinson’s disease susceptibility. Cell111, 209–218 (2002).
  • Mullally JE, Moos PJ, Edes K, Fitzpatrick FA. Cyclopentenone prostaglandins of the J series inhibit the ubiquitin isopeptidase activity of the proteasome pathway. J. Biol. Chem.276, 30366–30373 (2001).
  • Matsumoto M, Hatakeyama S, Oyamada K, Oda Y, Nishimura T, Nakayama KI. Large-scale analysis of the human ubiquitin-related proteome. Proteomics5, 4145–4151 (2005).
  • Schwartz DC, Hochstrasser M. A superfamily of protein tags: ubiquitin, SUMO and related modifiers. Trends Biochem. Sci.28, 321–328 (2003).
  • Staub O. Ubiquitylation and isgylation: overlapping enzymatic cascades do the job. Sci. STKE2004, pe43 (2004).
  • Hipp MS, Kalveram B, Raasi S, Groettrup M, Schmidtke G. FAT10, a ubiquitin-independent signal for proteasomal degradation. Mol. Cell Biol.25, 3483–3491 (2005).
  • Raasi S, Schmidtke G, Groettrup M. The ubiquitin-like protein FAT10 forms covalent conjugates and induces apoptosis. J. Biol. Chem.276, 35334–35343 (2001).
  • Zhang DW, Jeang KT, Lee CQ. p53 negatively regulates the expression of FAT10, a gene upregulated in various cancers. Oncogene (2006) (In Press).
  • Goehring AS, Rivers DM, Sprague GF. Attachment of the ubiquitin-related protein Urm1p to the antioxidant protein Ahp1p urmylation: a ubiquitin-like pathway that functions during invasive growth and budding in yeast. Mol. Biol. Cell14, 4329–4341 (2003).
  • Goehring AS, Rivers DM, Sprague GF Jr. Attachment of the ubiquitin-related protein Urm1p to the antioxidant protein Ahp1p. Eukaryot. Cell2, 930–936 (2003).
  • Wilkinson CR, Dittmar GA, Ohi MD, Uetz P, Jones N, Finley D. Ubiquitin-like protein Hub1 is required for pre-mRNA splicing and localization of an essential splicing factor in fission yeast. Curr. Biol.14, 2283–2288 (2004).
  • McNally T, Huang Q, Janis RS, Liu Z, Olejniczak ET, Reilly RM. Structural analysis of UBL5, a novel ubiquitin-like modifier. Protein Sci.12, 1562–1566 (2003).
  • Dittmar GA, Wilkinson CR, Jedrzejewski PT, Finley D. Role of a ubiquitin-like modification in polarized morphogenesis. Science295, 2442–2446 (2002).
  • Rossman TG, Visalli MA, Komissarova EV. Fau and its ubiquitin-like domain (FUBI) transforms human osteogenic sarcoma (HOS) cells to anchorage-independence. Oncogene22, 1817–1821 (2003).
  • Hiemstra PS, van den Barselaar MT, Roest M, Nibbering PH, van Furth R. Ubiquicidin, a novel murine microbicidal protein present in the cytosolic fraction of macrophages. J. Leukoc. Biol.66, 423–428 (1999).
  • Kas K, Stickens D, Merregaert J. Characterization of a processed pseudogene of human FAU1 on chromosome 18. Gene160, 273–276 (1995).
  • Rolen U, Kobzeva V, Gasparjan N et al. Activity profiling of deubiquitinating enzymes in cervical carcinoma biopsies and cell lines. Mol. Carcinog.45(4), 260–269 (2006).

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