20S蛋白酶体快速分离和异质性研究及蛋白质体外甲基化修饰和行为表征
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摘要
20S蛋白酶体(core particle, CP)是一个相对分子量约为700 kDa的蛋白质复合体,由14种不同亚基组成,分别称为α1～α7,β1～β7,并共同形成一个桶状结构α7β7β7α7。在先前的研究中,CP的分离主要依赖抗体、液相色谱以及亲合标签纯化等技术。在本研究中,我们报道了一种简单快速、经济、有效的CP分离方法。该方法主要涉及多步超速离心和非变性聚丙烯酰胺凝胶电泳技术；然后,利用二维电泳结合质谱技术对分离得到的CP进行了鉴定和分析,并对不同组织细胞来源的CP进行了蛋白酶体异质性探讨。该方法不仅适合于大通量(来自红细胞)和小规模的CP(来自培养细胞)纯化,亦适合于分离不同组织细胞来源的CP。此外,我们在纯化过程中发展了一种新型的直接三维凝胶电泳技术(direct three-dimensional gel electrophoresis, d3-DE)。实验结果表明,该分离方法对CP以及其它蛋白复合体的分离具有较大的学术价值。
蛋白质甲基化修饰对蛋白质行使特定功能具有重要作用。除常见的精氨酸和赖氨酸甲基化修饰之外,发生在天冬氨酸和谷氨酸侧链的甲基化修饰亦被认为具有非常重要的的调节功能。然而,能引起蛋白质体外甲基化(in vitro methylation)修饰的甲醇正被广泛地使用。本研究建立了一种蛋白质体外甲基化的质谱检测方法,并将其应用于牛血清白蛋白、鸡卵清白蛋白以及20S蛋白酶体复合体的体外甲基化修饰位点筛选。该质谱检测方法主要利用了峰标签技术(4P tag)以及质谱数据人工筛选(manual inspection of spectral data)方法。本研究旨在建立一种能有效地筛选蛋白质体外甲基化的质谱方法,揭示体外甲基化修饰的特点和反应特征,提出建议以尽量避免蛋白质体外甲基化修饰对体内甲基化(in vivo methylation)修饰研究的干扰,为今后蛋白质体内甲基化研究提供一定的参考价值。
The 20S core particle (CP) is composed of 28 subunits arranged in four stacked heptameric rings (a7(37(37a7) forming a symmetrical barrel-shaped structure. Typically, in previous reports, the purification of CP mainly relied on the antibody, liquid chromatography and affinity tag-based strategies. In this study, we report a relatively simple, economical and effective protocol for proteomic analyses of CP, which only combines differential centrifugations with native-PAGE. Furthermore, it is compatible with both scaled-up purification from erythrocytes and scaled-down purification from low to around 3.0×10'pancreatic cancer cells, SW1990. This protocol was also applied for CP isolation from different species, such as yeast and mouse liver. In addition, a direct three-dimensional gel electrophoresis (d3-DE) approach that omits the interval procedure between native-PAGE and IEF/SDS-PAGE was developed. The results obtained in this study show that this protocol has a valuable potential for the studies of CP and other protein complexes.
It is assumed that much more functional importance for protein activity than expected may be granted by methylation that occurs at the side-chain of aspartate or glutamate residue. In vitro methylation mainly comes from the use of methanol in sample preparation prior to MS analysis. In this study, we first performed the methylation site-directed proteomic screening of bovine serum albumin, ovalbumin and 20S proteasome for gel staining using a meaningfully indicative MS-pattern of peak tag (termed as 4P tag) and manual inspection for mass spectral data. As a result, there were seventeen proteolytic peptides with twenty modified sites confirmed to be in vitro methylated. Subsequently, the prevalence investigation was performed, focusing on the reaction kinetic behavior and characteristics of in vitro methylation. This study provided a simple and robust approach for confirmation of in vitro methylation by methanol, thus complementary confirmation for in vivo methylation, as well as the precautious guide for the use of methanol in proteomic and in vivo methylation studies.
蛋白质甲基化修饰对蛋白质行使特定功能具有重要作用。除常见的精氨酸和赖氨酸甲基化修饰之外,发生在天冬氨酸和谷氨酸侧链的甲基化修饰亦被认为具有非常重要的的调节功能。然而,能引起蛋白质体外甲基化(in vitro methylation)修饰的甲醇正被广泛地使用。本研究建立了一种蛋白质体外甲基化的质谱检测方法,并将其应用于牛血清白蛋白、鸡卵清白蛋白以及20S蛋白酶体复合体的体外甲基化修饰位点筛选。该质谱检测方法主要利用了峰标签技术(4P tag)以及质谱数据人工筛选(manual inspection of spectral data)方法。本研究旨在建立一种能有效地筛选蛋白质体外甲基化的质谱方法,揭示体外甲基化修饰的特点和反应特征,提出建议以尽量避免蛋白质体外甲基化修饰对体内甲基化(in vivo methylation)修饰研究的干扰,为今后蛋白质体内甲基化研究提供一定的参考价值。
The 20S core particle (CP) is composed of 28 subunits arranged in four stacked heptameric rings (a7(37(37a7) forming a symmetrical barrel-shaped structure. Typically, in previous reports, the purification of CP mainly relied on the antibody, liquid chromatography and affinity tag-based strategies. In this study, we report a relatively simple, economical and effective protocol for proteomic analyses of CP, which only combines differential centrifugations with native-PAGE. Furthermore, it is compatible with both scaled-up purification from erythrocytes and scaled-down purification from low to around 3.0×10'pancreatic cancer cells, SW1990. This protocol was also applied for CP isolation from different species, such as yeast and mouse liver. In addition, a direct three-dimensional gel electrophoresis (d3-DE) approach that omits the interval procedure between native-PAGE and IEF/SDS-PAGE was developed. The results obtained in this study show that this protocol has a valuable potential for the studies of CP and other protein complexes.
It is assumed that much more functional importance for protein activity than expected may be granted by methylation that occurs at the side-chain of aspartate or glutamate residue. In vitro methylation mainly comes from the use of methanol in sample preparation prior to MS analysis. In this study, we first performed the methylation site-directed proteomic screening of bovine serum albumin, ovalbumin and 20S proteasome for gel staining using a meaningfully indicative MS-pattern of peak tag (termed as 4P tag) and manual inspection for mass spectral data. As a result, there were seventeen proteolytic peptides with twenty modified sites confirmed to be in vitro methylated. Subsequently, the prevalence investigation was performed, focusing on the reaction kinetic behavior and characteristics of in vitro methylation. This study provided a simple and robust approach for confirmation of in vitro methylation by methanol, thus complementary confirmation for in vivo methylation, as well as the precautious guide for the use of methanol in proteomic and in vivo methylation studies.
引文
[1]Baumeister, W., Walz, J., Zuhl, F., et al. The proteasome:paradigm of a self-compartmentalizing protease [J]. Cell,1998,92(3):367-380.
[2]Fruh, K., Gossen, M., Wang, K., et al. Displacement of housekeeping proteasome subunits by MHC-encoded LMPs:a newly discovered mechanism for modulating the multicatalytic proteinase complex [J]. EMBO J,1994,13(14):3236-3244.
[3]Morel, S., Levy, F., Burlet-Schiltz,O., et al. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells [J]. Immunity,2000,12(1):107-117.
[4]Drews, O., Zong, C., Ping, P. Exploring proteasome complexes by proteomic approaches [J]. Proteomics,2007,7(7):1047-1058.
[5]Lu, H., Zong, C., Wang, Y., et al. Revealing the dynamics of 20S proteasome phosphoproteome:A combined CID and ETD approach [J]. Mol Cell Proteomics,2008.
[6]Ducoux-Petit, M., Uttenweiler-Joseph, S., Brichory, F., et al. Scaled-down purification protocol to access proteomic analysis of 20S proteasome from human tissue samples:comparison of normal and tumor colorectal cells [J]. J Proteome Res,2008,7(7): 2852-2859.
[7]Bousquet-Dubouch, M. P., Uttenweiler-Joseph, S., Ducoux-Petit, M., et al. Purification and proteomic analysis of 20S proteasomes from human cells [J]. Methods Mol Biol,2008,432301-320.
[8]Elsasser, S., Schmidt, M., Finley, D. Characterization of the proteasome using native gel electrophoresis [J]. Methods Enzymol,2005,398353-363.
[9]Candiano, G., Bruschi, M., Musante, L., et al. Blue silver:a very sensitive colloidal Coomassie G-250 staining for proteome analysis [J]. Electrophoresis,2004,25(9):1327-1333.
[10]Mortz, E., Krogh, T. N., Vorum, H., et al. Improved silver staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis [J]. Proteomics,2001,1(11):1359-1363.
[11]Leggett, D. S., Glickman, M. H., Finley, D. Purification of proteasomes, proteasome subcomplexes, and proteasome-associated proteins from budding yeast [J]. Methods Mol Biol,2005,30157-70.
[12]Zong, C., Gomes, A. V., Drews, O., et al. Regulation of murine cardiac 20S proteasomes:role of associating partners [J]. Circ Res,2006,99(4):372-380.
[13]Groll, M., Bajorek, M., Kohler, A., et al. A gated channel into the proteasome core particle [J]. Nat Struct Biol,2000,7(11):1062-1067.
[14]Werhahn, W., Braun, H. P. Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis [J]. Electrophoresis, 2002,23(4):640-646.
[15]Wittig, I., Braun, H. P., Schagger, H. Blue native PAGE [J]. Nat Protoc,2006,1(1): 418-428.
[16]Kleijnen, M. F., Roelofs, J., Park, S., et al. Stability of the proteasome can be regulated allosterically through engagement of its proteolytic active sites [J]. Nat Struct Mol Biol,2007,14(12):1180-1188.
[17]Gillette, T. G., Kumar, B., Thompson, D., et al. Differential roles of the C-termini of AAA subunits of PA700 (19S regulator) in asymmetric assembly and activation of the 26s proteasome [J]. J Biol Chem,2008.
[18]Drews, O., Wildgruber, R., Zong, C., et al. Mammalian proteasome subpopulations with distinct molecular compositions and proteolytic activities [J]. Mol Cell Proteomics, 2007,6(11):2021-2031.
[19]Rubinsztein, D. C. The roles of intracellular protein-degradation pathways in neurodegeneration [J]. Nature,2006,443(7113):780-786.
[20]Mani, A., Gelmann, E. P. The ubiquitin-proteasome pathway and its role in cancer [J]. J Clin Oncol,2005,23(21):4776-4789.
[21]Zoeger, A., Blau, M., Egerer, K., et al. Circulating proteasomes are functional and have a subtype pattern distinct from 20S proteasomes in major blood cells [J]. Clin Chem, 2006,52(11):2079-2086.
[22]Sixt, S. U., Dahlmann, B. Extracellular, circulating proteasomes and ubiquitin incidence and relevance [J]. Biochim Biophys Acta,2008,1782(12):817-823.
[23]Ma, W., Kantarjian, H., O'Brien, S., et al. Enzymatic activity of circulating proteasomes correlates with clinical behavior in patients with chronic lymphocytic leukemia [J]. Cancer,2008,112(6):1306-1312.
[24]Rajkumar, S. V., Richardson, P. G., Hideshima, T., et al. Proteasome inhibition as a novel therapeutic target in human cancer [J]. J Clin Oncol,2005,23(3):630-639.
[25]Claverol, S., Burlet-Schiltz, O., Girbal-Neuhauser, E., et al. Mapping and structural dissection of human 20 S proteasome using proteomic approaches [J]. Mol Cell Proteomics,2002,1(8):567-578.
[26]Froment, C., Uttenweiler-Joseph, S., Bousquet-Dubouch, M. P., et al. A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity [J]. Proteomics,2005, 5(9):2351-2363.
[27]Castro-Borges, W., Cartwright, J., Ashton, P. D., et al. The 20S proteasome of Schistosoma mansoni:a proteomic analysis [J]. Proteomics,2007,7(7):1065-1075.
[28]Schmidt, F., Dahlmann, B., Janek, K., et al. Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches [J]. Proteomics,2006,6(16):4622-4632.
[29]Arribas, J., Arizti, P., Castano, J. G. Antibodies against the C2 COOH-terminal region discriminate the active and latent forms of the multicatalytic proteinase complex [J]. J Biol Chem,1994,269(17):12858-12864.
[30]Bousquet-Dubouch, M. P., Baudelet, E., Guerin, F., et al. Affinity purification strategy to capture human endogenous proteasome complexes diversity and to identify proteasome-interacting proteins [J]. Mol Cell Proteomics,2009,8(5):1150-1164.
[1]Jenuwein, T., Allis, C. D. Translating the histone code [J]. Science,2001,293(5532): 1074-1080.
[2]Linggi, B. E., Brandt, S. J., Sun, Z. W., et al. Translating the histone code into leukemia [J]. J Cell Biochem,2005,96(5):938-950.
[3]Walsh, C. T., Garneau-Tsodikova, S., Gatto, G. J., Jr. Protein posttranslational modifications:the chemistry of proteome diversifications [J]. Angew Chem Int Ed Engl, 2005,44(45):7342-7372.
[4]Xie, H., Clarke, S. Methyl esterification of C-terminal leucine residues in cytosolic 36-kDa polypeptides of bovine brain. A novel eucaryotic protein carboxyl methylation reaction [J]. J Biol Chem,1993,268(18):13364-13371.
[5]Perna, A. F., Ingrosso, D., Zappia, V., et al. Enzymatic methyl esterification of erythrocyte membrane proteins is impaired in chronic renal failure. Evidence for high levels of the natural inhibitor S-adenosylhomocysteine [J]. J Clin Invest,1993,91(6): 2497-2503.
[6]Ingrosso, D., D'Angelo, S., di Carlo, E., et al. Increased methyl esterification of altered aspartyl residues in erythrocyte membrane proteins in response to oxidative stress [J]. Eur J Biochem,2000,267(14):4397-4405.
[7]Djordjevic, S., Stock, A. M. Chemotaxis receptor recognition by protein methyltransferase CheR [J]. Nat Struct Biol,1998,5(6):446-450.
[8]Sprung, R., Chen, Y., Zhang, K., et al. Identification and validation of eukaryotic aspartate and glutamate methylation in proteins [J]. J Proteome Res,2008,7(3):1001-1006.
[9]Candiano, G., Bruschi, M., Musante, L., et al. Blue silver:a very sensitive colloidal Coomassie G-250 staining for proteome analysis [J]. Electrophoresis,2004,25(9):1327-1333.
[10]Carmella, S. G., Chen, M., Villalta, P. W., et al. Ethylation and methylation of hemoglobin in smokers and non-smokers [J]. Carcinogenesis,2002,23(11):1903-1910.
[11]Xing, G., Zhang, J., Chen, Y., et al. Identification of four novel types of in vitro protein modifications [J]. J Proteome Res,2008,7(10):4603-4608.
[12]Zhu, J. X., Doyle, H. A., Mamula, M. J., et al. Protein repair in the brain, proteomic analysis of endogenous substrates for protein L-isoaspartyl methyltransferase in mouse brain [J]. J Biol Chem,2006,281(44):33802-33813.
[13]Sarioglu, H., Lottspeich, F., Walk, T., et al. Deamidation as a widespread phenomenon in two-dimensional polyacrylamide gel electrophoresis of human blood plasma proteins [J]. Electrophoresis,2000,21(11):2209-2218.
[14]Lanthier, J., Desrosiers, R. R. Protein L-isoaspartyl methyltransferase repairs abnormal aspartyl residues accumulated in vivo in type-I collagen and restores cell migration [J]. Exp Cell Res,2004,293(1):96-105.
[15]Lou, L. L., Clarke, S. Enzymatic methylation of band 3 anion transporter in intact human erythrocytes [J]. Biochemistry,1987,26(1):52-59.
[16]Springer, W. R., Koshland, D. E., Jr. Identification of a protein methyltransferase as the cheR gene product in the bacterial sensing system [J]. Proc Natl Acad Sci U S A, 1977,74(2):533-537.
[17]Galletti, P., Ciardiello, A., Ingrosso, D., et al. Repair of isopeptide bonds by protein carboxyl O-methyltransferase:seminal ribonuclease as a model system [J]. Biochemistry, 1988,27(5):1752-1757.
[18]Galletti, P., Iardino, P., Ingrosso, D., et al. Enzymatic methyl esterification of a deamidated form of mouse epidermal growth factor [J]. Int J Pept Protein Res,1989, 33(6):397-402.
[19]Jung, S. Y., Li, Y., Wang, Y, et al. Complications in the assignment of 14 and 28 Da mass shift detected by mass spectrometry as in vivo methylation from endogenous proteins [J]. Anal Chem,2008,80(5):1721-1729.
[20]Haebel, S., Albrecht, T., Sparbier, K., et al. Electrophoresis-related protein modification:alkylation of carboxy residues revealed by mass spectrometry [J]. Electrophoresis,1998,19(5):679-686.
[21]Winkler, C., Denker, K., Wortelkamp, S., et al. Silver-and Coomassie-staining protocols:detection limits and compatibility with ESI MS [J]. Electrophoresis,2007, 28(12):2095-2099.
[22]Sauer, G., Korner, R., Hanisch, A., et al. Proteome analysis of the human mitotic spindle [J]. Mol Cell Proteomics,2005,4(1):35-43.
[23]Lawlor, K., Nazarian, A., Lacomis, L., et al. Pathway-Based Biomarker Search by High-Throughput Proteomics Profiling of Secretomes [J]. J Proteome Res,2009.
[24]Pahlich, S., Zakaryan, R. P., Gehring, H. Protein arginine methylation:Cellular functions and methods of analysis [J]. Biochim Biophys Acta,2006,1764(12):1890-1903.
[25]Ren, H., Tai, S. K., Khuri, F., et al. Farnesyltransferase inhibitor SCH66336 induces rapid phosphorylation of eukaryotic translation elongation factor 2 in head and neck squamous cell carcinoma cells [J]. Cancer Res,2005,65(13):5841-5847.
[26]Rietschel, B., Arrey, T. N., Meyer, B., et al. Elastase digests:new ammunition for shotgun membrane proteomics [J]. Mol Cell Proteomics,2009,8(5):1029-1043.
[27]Brame, C. J., Boutaud, O., Davies, S. S., et al. Modification of proteins by isoketal-containing oxidized phospholipids [J]. J Biol Chem,2004,279(14):13447-13451.
[28]Mi, J., Kirchner, E., Cristobal, S. Quantitative proteomic comparison of mouse peroxisomes from liver and kidney [J]. Proteomics,2007,7(11):1916-1928.
[29]Buggiotti, L., Primmer, C. R., Kouvonen, P., et al. Identification of differentially expressed proteins in Ficedula flycatchers [J]. Proteomics,2008,8(10):2150-2153.
[30]Xu, S., Ye, M., Xu, D., et al. Matrix with high salt tolerance for the analysis of peptide and protein samples by desorption/ionization time-of-flight mass spectrometry [J]. Anal Chem,2006,78(8):2593-2599.
[31]Williams, T. L., Andrzejewski, D., Lay, J. O., et al. Experimental factors affecting the quality and reproducibility of MALDI TOF mass spectra obtained from whole bacteria cells [J]. J Am Soc Mass Spectrom,2003,14(4):342-351.
[32]Zheng, J., Li, N., Ridyard, M., et al. Simple and robust two-layer matrix/sample preparation method for MALDI MS/MS analysis of peptides [J]. J Proteome Res,2005, 4(5):1709-1716.
[33]Mohring, T., Kellmann, M., Jurgens, M., et al. Top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry [J]. J Mass Spectrom,2005,40(2):214-226.
[34]Jakubiec, A., Tournier, V., Drugeon, G., et al. Phosphorylation of viral RNA-dependent RNA polymerase and its role in replication of a plus-strand RNA virus [J]. J Biol Chem,2006,281(30):21236-21249.
[35]Lin, C. Y., Wang, V., Shui, H. A., et al. A comprehensive evaluation of imidazole-zinc reverse stain for current proteomic researches [J]. Proteomics,2009,9(3):696-709.
[36]Lee, C., Levin, A., Branton, D. Copper staining:a five-minute protein stain for sodium dodecyl sulfate-polyacrylamide gels [J]. Anal Biochem,1987,166(2):308-312.
[1]Hershko A., Ciechanover A. The ubiquitin system[J]. Annu Rev Biochem,1998,67: 425-479.
[2]Voges D., Zwickl P., Baumeister W. The 26S proteasome:A molecular machine designed for controlled proteolysis[J]. Annu Rev Biochem,1999,68:1015-1068.
[3]Beers E. P., Callis J. Utility of polyhistidine-tagged ubiquitin in the purification of ubiquitin-protein conjugates and as an affinity ligand for the purification of ubiquitin-specific hydrolases[J]. J Biol Chem,1993,268:21645-21649.
[4]Peng J., Schwartz D., Elias J.E., et al. A proteomics approach to understanding protein ubiquitination[J]. Nat Biotechnol,2003,21:921-926.
[5]Hitchcock A. L., Auld K., Gygi S.P., et al. A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery[J]. Proc Natl Acad Sci USA,2003,100:12735-12740.
[6]Tsirigotis M., Thurig S., Dube M., et al. Analysis of ubiquitination in vivo using a transgenic mouse model [J]. Biotechniques,2001,31:120-126,128,130.
[7]Kirkpatrick D. S., Weldonl S. F., Tsaprailis G., et al. Liebler and A. Jay Gandolfi, Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin[J]. Proteomics,2005,5:2104-2111.
[8]Ricolleau G., Charbonnel C., Lode L., et al. Surface-enhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node-negative breast cancer tumors[J]. Proteomics,2006,6:1963-1975.
[9]Mayor T., Russell-Lipford J., Graumann J., et al. Analysis of poly-ubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets[J]. Mol Cell Proteomics,2005,4:741-751.
[10]Johnson E. S. Protein modification by sumo[J]. Annu. Rev. Biochem,2004,73: 355-382.
[11]Wohlschlegel J. A., Johnson E. S., Reed S. I., et al. Global analysis of protein sumoylation in Saccharomyces cerevisiae[J]. J Biol Chem,2004,279:45662-45668.
[12]Zhao Y., Kwon S. W., Anselmo A., et al. Broad spectrum identification of cellular small ubiquitin-related modifier (SUMO) substrate proteins[J]. J Biol Chem,2004, 279:20999-21002.
[13]Vertegaal A. C., Ogg S. C., Jaffray E., et al. A proteomic study of SUMO-2 target proteins[J]. J Biol Chem,2004,279:33791-33798.
[14]Rosas-Acosta G., Russell W. K., Deyrieux A., et al. A Universal Strategy for Proteomic Studies of SUMO and Other Ubiquitin-like Modifiers[J]. Mol Cell Proteomics,2005,4:56-72.
[15]Panse V. G., Hardeland U., Werner T., et al. A proteome-wide approach identifies sumoylated substrate proteins in yeast[J]. J Biol Chem,2004,279:41346-41351.
[16]Nalepa G., Rolfe M., Harper J.W. Drug discovery in the ubiquitin-proteasome system[J]. Nat Rev Drug Dis,2006,5:596-613
[17]Zachariae W. Mass spectrometric analysis of the anaphase-promoting complex from yeast:identification of a subunit related to cullins[J]. Science,1998,279:1216-1219.
[18]Yoon H. J. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes[J]. Curr Biol,2002,12:2048-2054.
[19]Seol J. H., Feldman R. M., Zachariae W., et al. Cdc53/cullin and the essential Hrtl RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34[J]. Genes Dev,1999,13:1614-1626.
[20]Seol J. H., Shevchenko A., Deshaies R. J. Skpl forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly[J]. Nat Cell Biol,2001,3:384-391.
[21]Peters J. M. The anaphase promoting complex/cyclosome:a machine designed to destroy [J]. Nat Rev Mol Cell Biol,2006,7:644-656.
[22]Reed S. I. The ubiquitin-proteasome pathway in cell cycle control[J]. Results Probl Cell Differ,2006,42:147-81
[23]Lechner E., Achard P., Vansiri A., et al. F-box proteins everywhere[J]. Curr Opin Plant Biol,2006,25. [Epub ahead of print].
[24]Hemelaar J., Galardy P. J., Borodovsky A., et al. Chemistry-based functional proteomics:mechanismbased activity-profiling tools for ubiquitin and ubiquitin-like specific proteases[J]. J Proteome Res,2004,3:268-276.
[25]Borodovsky A., Ovaa H., Kolli N., et al. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family[J]. Chem Biol,2002, 9:1149-1159.
[26]Gururaja T., Li W., Noble W. S., et al. Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing[J]. J Proteome Res,2003,2:394-404.
[27]Li T., Evdokimov E., Shen R. F., et al. Sumoylation of heterogeneous nuclear ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins:a proteomic analysis[J]. Proc Natl Acad Sci,2004,101:8551-8556.
[28]Sato K., Hayami R., Wu W., et al. Nucleophosmin/B23 is a candidate substrate for the BRCA1-BARD1 ubiquitin ligase[J]. J Biol Chem,2004,279:30919-30922.
[29]Starita L. M., Machida Y., Sankaran S., et al. BRCA1-dependent ubiquitination of y-tubulin regulates centrosome number[J]. Mol Cell Biol,2004,24:8457-8466.
[30]Chang T. L., Cubillos F. F., Kakhniashvili D. G., et al. Ankyrin is a target of spectrin's E2/E3 ubiquitin-conjugating/ligating activity[J]. Cell Mol Biol,2004, 50:59-66.
[31]Chung T. L., Hsiao H. H., Yeh Y. Y., et al. In vitro modification of human centromere protein CENP-C fragments by small ubiquitinlike modifier (SUMO) protein:definitive identification of the modification sites by tandem mass spectrometry analysis of isopeptides[J]. J Biol Chem,2004,279:39653-39662.
[32]Marotti L. A. Jr., Newitt R., Wang Y., et al. Direct identification of a G protein ubiquitination site by mass spectrometry [J]. Biochem,2002,41:5067-5074.
[33]Moren A., Hellman U., Inada Y., et al. Differential ubiquitination defines the functional status of the tumor suppressor Smad4[J]. J Biol Chem 2003,278:33571-33582.
[34]Lee J. S., Hong U. S., Lee T. H., et al. Mass spectrometry analysis of tumor necrosis factor receptor-associated factor 1 ubiquitinatin mediated by cellular inhibitor of apoptosis 2[J]. Proteomics,2004,4:3376-3382.
[35]Flick K., Ouni I., Wohlschlegel J. A., et al. Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain[J]. Nat Cell Biol, 2004,6:634-641.
[36]Kirkpatrick D. S., Gerber S. A., Gygi S. P. The absolute quantification strategy:a general procedure for the quantification of proteins and post-translational modifications[J]. Methods,2005,35:265-273.
[37]Li M., Brooks C. L., Wu-Baer F., et al. Mono-versus polyubiquitination: differential control of p53 fate by mdm2[J]. Science,2003,302:1972-1975.
[38]Haglund K., Sigismund S., Polo S., et al. Multiple monoubiquitination of RTKs is sufficient for their endocytosis and degradation[J]. Nat Cell Biol,2003,5:461-466.
[39]Coux O., Tanaka K., Goldberg A. L. Structure and functions of the 20S and 26S proteasomes[J]. Ann Rev Biochem,1996,65,801-847.
[40]Voges D., Zwickl P., Baumeister W. The 26S proteasome:a molecular machine
designed for controlled proteolysis[J]. Annu Rev Biochem,1999,68,1015-1068.
[41]Tanaka K. Proteasomes:structure and biology[J]. J Biochem(tokyo),1998,123, 195-204.
[42]Fruh K., Gossen M., Wang K., et al. Displacement of housekeeping proteasome subunits by MHC encoded LMPs:a newly discovered mechanism for modulating the multicatalytic proteinase complex[J]. EMBO J,1994,13:3236-3244
[43]Morel S., Levy F., Burlet-Schiltz O., et al. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells[J]. Immunity,2000,12:107-117
[44]Dahlmann B., Ruppert T., Kuehn L., et al., Different proteasome subtypes in a single tissue exhibit different enzymatic properties [J]. J Mol Biol,2000,303:643-653.
[45]Merforth S., Kuehn L., Osmers A., et al. Alteration of 20S proteasome-subtypes and proteasome activator PA28 in skeletal muscle of rat after induction of diabetes mellitus[J]. Int J Biochem Cell Biol,2003,35:740-748.
[46]Froment C., Uttenweiler-Joseph S., ousquet-Dubouch M. P., et al. A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity[J]. Proteomics, 2005,5:2351-2363
[47]Tokunaga F., Aruga R., Iwanaga S., et al. The NH2-terminal residues of rat liver proteasome (multicatalytic proteinase complex) subunits, C2,. C3 and C8, are N-acetylated[J]. FEBS Lett,1990,263:373-375.
[48]Kimura J., Takaoka M., Tanaka S., et al., N -Acetylation and Proteolytic Activity of the Yeast 20 S Proteasome[J]. J Biol Chem,2000,275:4635-4639.
[49]Mason G. G. F., Hendil K. B., Rivett A. J. Phosphorylation of proteasomes in mammalian cells:identification of two phosphorylated subunits and the effect of phosphorylation on activity[J]. Eur J Biochem,1996,238:453-462.
[50]Bose S., Stratford F. L. L., Broadfoot K. I., et al. Phosphorylation of 20S proteasome alpha subunit C8[J]. Biochem. J.2004,378:177-184.
[51]Schmid H. P., Vallon R., Tomek W., et al. Glycosylation and deglycosylation of proteasomes (prosomes) from calf-liver cells:high abundance of neuraminic acid[J]. Biochimie,1993,75:905-910.
[52]Sumegi M., Hunyadi-Gulyas e., Medzihradszky K. F., et al.26S proteasome subunits are O-linked N-acetylglucosamine-modified in Drosophila melanogaster[J]. Biochem Biophys Res Commun,2003,312:1284-1289.
[53]Schmidt F., Dahlmann B., Janek K., et al. Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches[J]. Proteomics,2006,6:4622-4632.
[54]Claverol S., Burlet-Schiltz O., Girbal-Neuhauser E., et al. Structural Dissection of Human 20 S Proteasome Using Proteomic Approaches [J]. Mol. Cell. Proteomics, 1:567-578.
[55]Huang L., Burlingame A. L. Comprehensive mass spectrometric analysis of the 20S proteasome complex[J]. Methods Enzymol,2005,405:187-236.
[56]Sone T., Saeki Y., Toh-e A., et al. Semlp is a Novel Subunit of the 26S Proteasome from Saccharomyces cerevisiae[J]. J Bio Chem,2004,279:28807-28816.
[57]Verma R., Chen S., Feldman R. Proteasomal Proteomics:Identification of Nucleotidesensitive Proteasome-interacting Proteins by Mass Spectrometric Analysis of Affinity-purified Proteasomes[J]. Mol Biol Cell,2000,11:3425-3439.
[58]Guerrero C., Tagwerker C., Kaiser P., Huang L. An Integrated Mass Spectrometry-Based Proteomics Approach-QTAX to Decipher the 26S Proteasome Interacting Network[J]. Mol Cell Proteomics,2006,5:366-378.
[59]Hannich J. T. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae[J]. J Biol Chem 2005,280:4102-4110.
[60]Wykoff D. D., O'Shea E. K. Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome[J]. Mol Cell Proteomics,2005,4: 73-83.
[61]Zhou W., Ryan J. J., Zhou H. Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses[J]. J Biol Chem,2004,279:32262-32268.
[62]Denison C., Rudner A. D., Gerber S. A., et al. A Proteomic strategy for gaining insights into protein sumoylation in yeast[J]. Mol Cell Proteomics,2005,4:246-254.
[2]Fruh, K., Gossen, M., Wang, K., et al. Displacement of housekeeping proteasome subunits by MHC-encoded LMPs:a newly discovered mechanism for modulating the multicatalytic proteinase complex [J]. EMBO J,1994,13(14):3236-3244.
[3]Morel, S., Levy, F., Burlet-Schiltz,O., et al. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells [J]. Immunity,2000,12(1):107-117.
[4]Drews, O., Zong, C., Ping, P. Exploring proteasome complexes by proteomic approaches [J]. Proteomics,2007,7(7):1047-1058.
[5]Lu, H., Zong, C., Wang, Y., et al. Revealing the dynamics of 20S proteasome phosphoproteome:A combined CID and ETD approach [J]. Mol Cell Proteomics,2008.
[6]Ducoux-Petit, M., Uttenweiler-Joseph, S., Brichory, F., et al. Scaled-down purification protocol to access proteomic analysis of 20S proteasome from human tissue samples:comparison of normal and tumor colorectal cells [J]. J Proteome Res,2008,7(7): 2852-2859.
[7]Bousquet-Dubouch, M. P., Uttenweiler-Joseph, S., Ducoux-Petit, M., et al. Purification and proteomic analysis of 20S proteasomes from human cells [J]. Methods Mol Biol,2008,432301-320.
[8]Elsasser, S., Schmidt, M., Finley, D. Characterization of the proteasome using native gel electrophoresis [J]. Methods Enzymol,2005,398353-363.
[9]Candiano, G., Bruschi, M., Musante, L., et al. Blue silver:a very sensitive colloidal Coomassie G-250 staining for proteome analysis [J]. Electrophoresis,2004,25(9):1327-1333.
[10]Mortz, E., Krogh, T. N., Vorum, H., et al. Improved silver staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis [J]. Proteomics,2001,1(11):1359-1363.
[11]Leggett, D. S., Glickman, M. H., Finley, D. Purification of proteasomes, proteasome subcomplexes, and proteasome-associated proteins from budding yeast [J]. Methods Mol Biol,2005,30157-70.
[12]Zong, C., Gomes, A. V., Drews, O., et al. Regulation of murine cardiac 20S proteasomes:role of associating partners [J]. Circ Res,2006,99(4):372-380.
[13]Groll, M., Bajorek, M., Kohler, A., et al. A gated channel into the proteasome core particle [J]. Nat Struct Biol,2000,7(11):1062-1067.
[14]Werhahn, W., Braun, H. P. Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis [J]. Electrophoresis, 2002,23(4):640-646.
[15]Wittig, I., Braun, H. P., Schagger, H. Blue native PAGE [J]. Nat Protoc,2006,1(1): 418-428.
[16]Kleijnen, M. F., Roelofs, J., Park, S., et al. Stability of the proteasome can be regulated allosterically through engagement of its proteolytic active sites [J]. Nat Struct Mol Biol,2007,14(12):1180-1188.
[17]Gillette, T. G., Kumar, B., Thompson, D., et al. Differential roles of the C-termini of AAA subunits of PA700 (19S regulator) in asymmetric assembly and activation of the 26s proteasome [J]. J Biol Chem,2008.
[18]Drews, O., Wildgruber, R., Zong, C., et al. Mammalian proteasome subpopulations with distinct molecular compositions and proteolytic activities [J]. Mol Cell Proteomics, 2007,6(11):2021-2031.
[19]Rubinsztein, D. C. The roles of intracellular protein-degradation pathways in neurodegeneration [J]. Nature,2006,443(7113):780-786.
[20]Mani, A., Gelmann, E. P. The ubiquitin-proteasome pathway and its role in cancer [J]. J Clin Oncol,2005,23(21):4776-4789.
[21]Zoeger, A., Blau, M., Egerer, K., et al. Circulating proteasomes are functional and have a subtype pattern distinct from 20S proteasomes in major blood cells [J]. Clin Chem, 2006,52(11):2079-2086.
[22]Sixt, S. U., Dahlmann, B. Extracellular, circulating proteasomes and ubiquitin incidence and relevance [J]. Biochim Biophys Acta,2008,1782(12):817-823.
[23]Ma, W., Kantarjian, H., O'Brien, S., et al. Enzymatic activity of circulating proteasomes correlates with clinical behavior in patients with chronic lymphocytic leukemia [J]. Cancer,2008,112(6):1306-1312.
[24]Rajkumar, S. V., Richardson, P. G., Hideshima, T., et al. Proteasome inhibition as a novel therapeutic target in human cancer [J]. J Clin Oncol,2005,23(3):630-639.
[25]Claverol, S., Burlet-Schiltz, O., Girbal-Neuhauser, E., et al. Mapping and structural dissection of human 20 S proteasome using proteomic approaches [J]. Mol Cell Proteomics,2002,1(8):567-578.
[26]Froment, C., Uttenweiler-Joseph, S., Bousquet-Dubouch, M. P., et al. A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity [J]. Proteomics,2005, 5(9):2351-2363.
[27]Castro-Borges, W., Cartwright, J., Ashton, P. D., et al. The 20S proteasome of Schistosoma mansoni:a proteomic analysis [J]. Proteomics,2007,7(7):1065-1075.
[28]Schmidt, F., Dahlmann, B., Janek, K., et al. Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches [J]. Proteomics,2006,6(16):4622-4632.
[29]Arribas, J., Arizti, P., Castano, J. G. Antibodies against the C2 COOH-terminal region discriminate the active and latent forms of the multicatalytic proteinase complex [J]. J Biol Chem,1994,269(17):12858-12864.
[30]Bousquet-Dubouch, M. P., Baudelet, E., Guerin, F., et al. Affinity purification strategy to capture human endogenous proteasome complexes diversity and to identify proteasome-interacting proteins [J]. Mol Cell Proteomics,2009,8(5):1150-1164.
[1]Jenuwein, T., Allis, C. D. Translating the histone code [J]. Science,2001,293(5532): 1074-1080.
[2]Linggi, B. E., Brandt, S. J., Sun, Z. W., et al. Translating the histone code into leukemia [J]. J Cell Biochem,2005,96(5):938-950.
[3]Walsh, C. T., Garneau-Tsodikova, S., Gatto, G. J., Jr. Protein posttranslational modifications:the chemistry of proteome diversifications [J]. Angew Chem Int Ed Engl, 2005,44(45):7342-7372.
[4]Xie, H., Clarke, S. Methyl esterification of C-terminal leucine residues in cytosolic 36-kDa polypeptides of bovine brain. A novel eucaryotic protein carboxyl methylation reaction [J]. J Biol Chem,1993,268(18):13364-13371.
[5]Perna, A. F., Ingrosso, D., Zappia, V., et al. Enzymatic methyl esterification of erythrocyte membrane proteins is impaired in chronic renal failure. Evidence for high levels of the natural inhibitor S-adenosylhomocysteine [J]. J Clin Invest,1993,91(6): 2497-2503.
[6]Ingrosso, D., D'Angelo, S., di Carlo, E., et al. Increased methyl esterification of altered aspartyl residues in erythrocyte membrane proteins in response to oxidative stress [J]. Eur J Biochem,2000,267(14):4397-4405.
[7]Djordjevic, S., Stock, A. M. Chemotaxis receptor recognition by protein methyltransferase CheR [J]. Nat Struct Biol,1998,5(6):446-450.
[8]Sprung, R., Chen, Y., Zhang, K., et al. Identification and validation of eukaryotic aspartate and glutamate methylation in proteins [J]. J Proteome Res,2008,7(3):1001-1006.
[9]Candiano, G., Bruschi, M., Musante, L., et al. Blue silver:a very sensitive colloidal Coomassie G-250 staining for proteome analysis [J]. Electrophoresis,2004,25(9):1327-1333.
[10]Carmella, S. G., Chen, M., Villalta, P. W., et al. Ethylation and methylation of hemoglobin in smokers and non-smokers [J]. Carcinogenesis,2002,23(11):1903-1910.
[11]Xing, G., Zhang, J., Chen, Y., et al. Identification of four novel types of in vitro protein modifications [J]. J Proteome Res,2008,7(10):4603-4608.
[12]Zhu, J. X., Doyle, H. A., Mamula, M. J., et al. Protein repair in the brain, proteomic analysis of endogenous substrates for protein L-isoaspartyl methyltransferase in mouse brain [J]. J Biol Chem,2006,281(44):33802-33813.
[13]Sarioglu, H., Lottspeich, F., Walk, T., et al. Deamidation as a widespread phenomenon in two-dimensional polyacrylamide gel electrophoresis of human blood plasma proteins [J]. Electrophoresis,2000,21(11):2209-2218.
[14]Lanthier, J., Desrosiers, R. R. Protein L-isoaspartyl methyltransferase repairs abnormal aspartyl residues accumulated in vivo in type-I collagen and restores cell migration [J]. Exp Cell Res,2004,293(1):96-105.
[15]Lou, L. L., Clarke, S. Enzymatic methylation of band 3 anion transporter in intact human erythrocytes [J]. Biochemistry,1987,26(1):52-59.
[16]Springer, W. R., Koshland, D. E., Jr. Identification of a protein methyltransferase as the cheR gene product in the bacterial sensing system [J]. Proc Natl Acad Sci U S A, 1977,74(2):533-537.
[17]Galletti, P., Ciardiello, A., Ingrosso, D., et al. Repair of isopeptide bonds by protein carboxyl O-methyltransferase:seminal ribonuclease as a model system [J]. Biochemistry, 1988,27(5):1752-1757.
[18]Galletti, P., Iardino, P., Ingrosso, D., et al. Enzymatic methyl esterification of a deamidated form of mouse epidermal growth factor [J]. Int J Pept Protein Res,1989, 33(6):397-402.
[19]Jung, S. Y., Li, Y., Wang, Y, et al. Complications in the assignment of 14 and 28 Da mass shift detected by mass spectrometry as in vivo methylation from endogenous proteins [J]. Anal Chem,2008,80(5):1721-1729.
[20]Haebel, S., Albrecht, T., Sparbier, K., et al. Electrophoresis-related protein modification:alkylation of carboxy residues revealed by mass spectrometry [J]. Electrophoresis,1998,19(5):679-686.
[21]Winkler, C., Denker, K., Wortelkamp, S., et al. Silver-and Coomassie-staining protocols:detection limits and compatibility with ESI MS [J]. Electrophoresis,2007, 28(12):2095-2099.
[22]Sauer, G., Korner, R., Hanisch, A., et al. Proteome analysis of the human mitotic spindle [J]. Mol Cell Proteomics,2005,4(1):35-43.
[23]Lawlor, K., Nazarian, A., Lacomis, L., et al. Pathway-Based Biomarker Search by High-Throughput Proteomics Profiling of Secretomes [J]. J Proteome Res,2009.
[24]Pahlich, S., Zakaryan, R. P., Gehring, H. Protein arginine methylation:Cellular functions and methods of analysis [J]. Biochim Biophys Acta,2006,1764(12):1890-1903.
[25]Ren, H., Tai, S. K., Khuri, F., et al. Farnesyltransferase inhibitor SCH66336 induces rapid phosphorylation of eukaryotic translation elongation factor 2 in head and neck squamous cell carcinoma cells [J]. Cancer Res,2005,65(13):5841-5847.
[26]Rietschel, B., Arrey, T. N., Meyer, B., et al. Elastase digests:new ammunition for shotgun membrane proteomics [J]. Mol Cell Proteomics,2009,8(5):1029-1043.
[27]Brame, C. J., Boutaud, O., Davies, S. S., et al. Modification of proteins by isoketal-containing oxidized phospholipids [J]. J Biol Chem,2004,279(14):13447-13451.
[28]Mi, J., Kirchner, E., Cristobal, S. Quantitative proteomic comparison of mouse peroxisomes from liver and kidney [J]. Proteomics,2007,7(11):1916-1928.
[29]Buggiotti, L., Primmer, C. R., Kouvonen, P., et al. Identification of differentially expressed proteins in Ficedula flycatchers [J]. Proteomics,2008,8(10):2150-2153.
[30]Xu, S., Ye, M., Xu, D., et al. Matrix with high salt tolerance for the analysis of peptide and protein samples by desorption/ionization time-of-flight mass spectrometry [J]. Anal Chem,2006,78(8):2593-2599.
[31]Williams, T. L., Andrzejewski, D., Lay, J. O., et al. Experimental factors affecting the quality and reproducibility of MALDI TOF mass spectra obtained from whole bacteria cells [J]. J Am Soc Mass Spectrom,2003,14(4):342-351.
[32]Zheng, J., Li, N., Ridyard, M., et al. Simple and robust two-layer matrix/sample preparation method for MALDI MS/MS analysis of peptides [J]. J Proteome Res,2005, 4(5):1709-1716.
[33]Mohring, T., Kellmann, M., Jurgens, M., et al. Top-down identification of endogenous peptides up to 9 kDa in cerebrospinal fluid and brain tissue by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry [J]. J Mass Spectrom,2005,40(2):214-226.
[34]Jakubiec, A., Tournier, V., Drugeon, G., et al. Phosphorylation of viral RNA-dependent RNA polymerase and its role in replication of a plus-strand RNA virus [J]. J Biol Chem,2006,281(30):21236-21249.
[35]Lin, C. Y., Wang, V., Shui, H. A., et al. A comprehensive evaluation of imidazole-zinc reverse stain for current proteomic researches [J]. Proteomics,2009,9(3):696-709.
[36]Lee, C., Levin, A., Branton, D. Copper staining:a five-minute protein stain for sodium dodecyl sulfate-polyacrylamide gels [J]. Anal Biochem,1987,166(2):308-312.
[1]Hershko A., Ciechanover A. The ubiquitin system[J]. Annu Rev Biochem,1998,67: 425-479.
[2]Voges D., Zwickl P., Baumeister W. The 26S proteasome:A molecular machine designed for controlled proteolysis[J]. Annu Rev Biochem,1999,68:1015-1068.
[3]Beers E. P., Callis J. Utility of polyhistidine-tagged ubiquitin in the purification of ubiquitin-protein conjugates and as an affinity ligand for the purification of ubiquitin-specific hydrolases[J]. J Biol Chem,1993,268:21645-21649.
[4]Peng J., Schwartz D., Elias J.E., et al. A proteomics approach to understanding protein ubiquitination[J]. Nat Biotechnol,2003,21:921-926.
[5]Hitchcock A. L., Auld K., Gygi S.P., et al. A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery[J]. Proc Natl Acad Sci USA,2003,100:12735-12740.
[6]Tsirigotis M., Thurig S., Dube M., et al. Analysis of ubiquitination in vivo using a transgenic mouse model [J]. Biotechniques,2001,31:120-126,128,130.
[7]Kirkpatrick D. S., Weldonl S. F., Tsaprailis G., et al. Liebler and A. Jay Gandolfi, Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin[J]. Proteomics,2005,5:2104-2111.
[8]Ricolleau G., Charbonnel C., Lode L., et al. Surface-enhanced laser desorption/ionization time of flight mass spectrometry protein profiling identifies ubiquitin and ferritin light chain as prognostic biomarkers in node-negative breast cancer tumors[J]. Proteomics,2006,6:1963-1975.
[9]Mayor T., Russell-Lipford J., Graumann J., et al. Analysis of poly-ubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets[J]. Mol Cell Proteomics,2005,4:741-751.
[10]Johnson E. S. Protein modification by sumo[J]. Annu. Rev. Biochem,2004,73: 355-382.
[11]Wohlschlegel J. A., Johnson E. S., Reed S. I., et al. Global analysis of protein sumoylation in Saccharomyces cerevisiae[J]. J Biol Chem,2004,279:45662-45668.
[12]Zhao Y., Kwon S. W., Anselmo A., et al. Broad spectrum identification of cellular small ubiquitin-related modifier (SUMO) substrate proteins[J]. J Biol Chem,2004, 279:20999-21002.
[13]Vertegaal A. C., Ogg S. C., Jaffray E., et al. A proteomic study of SUMO-2 target proteins[J]. J Biol Chem,2004,279:33791-33798.
[14]Rosas-Acosta G., Russell W. K., Deyrieux A., et al. A Universal Strategy for Proteomic Studies of SUMO and Other Ubiquitin-like Modifiers[J]. Mol Cell Proteomics,2005,4:56-72.
[15]Panse V. G., Hardeland U., Werner T., et al. A proteome-wide approach identifies sumoylated substrate proteins in yeast[J]. J Biol Chem,2004,279:41346-41351.
[16]Nalepa G., Rolfe M., Harper J.W. Drug discovery in the ubiquitin-proteasome system[J]. Nat Rev Drug Dis,2006,5:596-613
[17]Zachariae W. Mass spectrometric analysis of the anaphase-promoting complex from yeast:identification of a subunit related to cullins[J]. Science,1998,279:1216-1219.
[18]Yoon H. J. Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes[J]. Curr Biol,2002,12:2048-2054.
[19]Seol J. H., Feldman R. M., Zachariae W., et al. Cdc53/cullin and the essential Hrtl RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34[J]. Genes Dev,1999,13:1614-1626.
[20]Seol J. H., Shevchenko A., Deshaies R. J. Skpl forms multiple protein complexes, including RAVE, a regulator of V-ATPase assembly[J]. Nat Cell Biol,2001,3:384-391.
[21]Peters J. M. The anaphase promoting complex/cyclosome:a machine designed to destroy [J]. Nat Rev Mol Cell Biol,2006,7:644-656.
[22]Reed S. I. The ubiquitin-proteasome pathway in cell cycle control[J]. Results Probl Cell Differ,2006,42:147-81
[23]Lechner E., Achard P., Vansiri A., et al. F-box proteins everywhere[J]. Curr Opin Plant Biol,2006,25. [Epub ahead of print].
[24]Hemelaar J., Galardy P. J., Borodovsky A., et al. Chemistry-based functional proteomics:mechanismbased activity-profiling tools for ubiquitin and ubiquitin-like specific proteases[J]. J Proteome Res,2004,3:268-276.
[25]Borodovsky A., Ovaa H., Kolli N., et al. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family[J]. Chem Biol,2002, 9:1149-1159.
[26]Gururaja T., Li W., Noble W. S., et al. Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing[J]. J Proteome Res,2003,2:394-404.
[27]Li T., Evdokimov E., Shen R. F., et al. Sumoylation of heterogeneous nuclear ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins:a proteomic analysis[J]. Proc Natl Acad Sci,2004,101:8551-8556.
[28]Sato K., Hayami R., Wu W., et al. Nucleophosmin/B23 is a candidate substrate for the BRCA1-BARD1 ubiquitin ligase[J]. J Biol Chem,2004,279:30919-30922.
[29]Starita L. M., Machida Y., Sankaran S., et al. BRCA1-dependent ubiquitination of y-tubulin regulates centrosome number[J]. Mol Cell Biol,2004,24:8457-8466.
[30]Chang T. L., Cubillos F. F., Kakhniashvili D. G., et al. Ankyrin is a target of spectrin's E2/E3 ubiquitin-conjugating/ligating activity[J]. Cell Mol Biol,2004, 50:59-66.
[31]Chung T. L., Hsiao H. H., Yeh Y. Y., et al. In vitro modification of human centromere protein CENP-C fragments by small ubiquitinlike modifier (SUMO) protein:definitive identification of the modification sites by tandem mass spectrometry analysis of isopeptides[J]. J Biol Chem,2004,279:39653-39662.
[32]Marotti L. A. Jr., Newitt R., Wang Y., et al. Direct identification of a G protein ubiquitination site by mass spectrometry [J]. Biochem,2002,41:5067-5074.
[33]Moren A., Hellman U., Inada Y., et al. Differential ubiquitination defines the functional status of the tumor suppressor Smad4[J]. J Biol Chem 2003,278:33571-33582.
[34]Lee J. S., Hong U. S., Lee T. H., et al. Mass spectrometry analysis of tumor necrosis factor receptor-associated factor 1 ubiquitinatin mediated by cellular inhibitor of apoptosis 2[J]. Proteomics,2004,4:3376-3382.
[35]Flick K., Ouni I., Wohlschlegel J. A., et al. Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain[J]. Nat Cell Biol, 2004,6:634-641.
[36]Kirkpatrick D. S., Gerber S. A., Gygi S. P. The absolute quantification strategy:a general procedure for the quantification of proteins and post-translational modifications[J]. Methods,2005,35:265-273.
[37]Li M., Brooks C. L., Wu-Baer F., et al. Mono-versus polyubiquitination: differential control of p53 fate by mdm2[J]. Science,2003,302:1972-1975.
[38]Haglund K., Sigismund S., Polo S., et al. Multiple monoubiquitination of RTKs is sufficient for their endocytosis and degradation[J]. Nat Cell Biol,2003,5:461-466.
[39]Coux O., Tanaka K., Goldberg A. L. Structure and functions of the 20S and 26S proteasomes[J]. Ann Rev Biochem,1996,65,801-847.
[40]Voges D., Zwickl P., Baumeister W. The 26S proteasome:a molecular machine
designed for controlled proteolysis[J]. Annu Rev Biochem,1999,68,1015-1068.
[41]Tanaka K. Proteasomes:structure and biology[J]. J Biochem(tokyo),1998,123, 195-204.
[42]Fruh K., Gossen M., Wang K., et al. Displacement of housekeeping proteasome subunits by MHC encoded LMPs:a newly discovered mechanism for modulating the multicatalytic proteinase complex[J]. EMBO J,1994,13:3236-3244
[43]Morel S., Levy F., Burlet-Schiltz O., et al. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells[J]. Immunity,2000,12:107-117
[44]Dahlmann B., Ruppert T., Kuehn L., et al., Different proteasome subtypes in a single tissue exhibit different enzymatic properties [J]. J Mol Biol,2000,303:643-653.
[45]Merforth S., Kuehn L., Osmers A., et al. Alteration of 20S proteasome-subtypes and proteasome activator PA28 in skeletal muscle of rat after induction of diabetes mellitus[J]. Int J Biochem Cell Biol,2003,35:740-748.
[46]Froment C., Uttenweiler-Joseph S., ousquet-Dubouch M. P., et al. A quantitative proteomic approach using two-dimensional gel electrophoresis and isotope-coded affinity tag labeling for studying human 20S proteasome heterogeneity[J]. Proteomics, 2005,5:2351-2363
[47]Tokunaga F., Aruga R., Iwanaga S., et al. The NH2-terminal residues of rat liver proteasome (multicatalytic proteinase complex) subunits, C2,. C3 and C8, are N-acetylated[J]. FEBS Lett,1990,263:373-375.
[48]Kimura J., Takaoka M., Tanaka S., et al., N -Acetylation and Proteolytic Activity of the Yeast 20 S Proteasome[J]. J Biol Chem,2000,275:4635-4639.
[49]Mason G. G. F., Hendil K. B., Rivett A. J. Phosphorylation of proteasomes in mammalian cells:identification of two phosphorylated subunits and the effect of phosphorylation on activity[J]. Eur J Biochem,1996,238:453-462.
[50]Bose S., Stratford F. L. L., Broadfoot K. I., et al. Phosphorylation of 20S proteasome alpha subunit C8[J]. Biochem. J.2004,378:177-184.
[51]Schmid H. P., Vallon R., Tomek W., et al. Glycosylation and deglycosylation of proteasomes (prosomes) from calf-liver cells:high abundance of neuraminic acid[J]. Biochimie,1993,75:905-910.
[52]Sumegi M., Hunyadi-Gulyas e., Medzihradszky K. F., et al.26S proteasome subunits are O-linked N-acetylglucosamine-modified in Drosophila melanogaster[J]. Biochem Biophys Res Commun,2003,312:1284-1289.
[53]Schmidt F., Dahlmann B., Janek K., et al. Comprehensive quantitative proteome analysis of 20S proteasome subtypes from rat liver by isotope coded affinity tag and 2-D gel-based approaches[J]. Proteomics,2006,6:4622-4632.
[54]Claverol S., Burlet-Schiltz O., Girbal-Neuhauser E., et al. Structural Dissection of Human 20 S Proteasome Using Proteomic Approaches [J]. Mol. Cell. Proteomics, 1:567-578.
[55]Huang L., Burlingame A. L. Comprehensive mass spectrometric analysis of the 20S proteasome complex[J]. Methods Enzymol,2005,405:187-236.
[56]Sone T., Saeki Y., Toh-e A., et al. Semlp is a Novel Subunit of the 26S Proteasome from Saccharomyces cerevisiae[J]. J Bio Chem,2004,279:28807-28816.
[57]Verma R., Chen S., Feldman R. Proteasomal Proteomics:Identification of Nucleotidesensitive Proteasome-interacting Proteins by Mass Spectrometric Analysis of Affinity-purified Proteasomes[J]. Mol Biol Cell,2000,11:3425-3439.
[58]Guerrero C., Tagwerker C., Kaiser P., Huang L. An Integrated Mass Spectrometry-Based Proteomics Approach-QTAX to Decipher the 26S Proteasome Interacting Network[J]. Mol Cell Proteomics,2006,5:366-378.
[59]Hannich J. T. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae[J]. J Biol Chem 2005,280:4102-4110.
[60]Wykoff D. D., O'Shea E. K. Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome[J]. Mol Cell Proteomics,2005,4: 73-83.
[61]Zhou W., Ryan J. J., Zhou H. Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses[J]. J Biol Chem,2004,279:32262-32268.
[62]Denison C., Rudner A. D., Gerber S. A., et al. A Proteomic strategy for gaining insights into protein sumoylation in yeast[J]. Mol Cell Proteomics,2005,4:246-254.