生物技术通报 ›› 2015, Vol. 31 ›› Issue (1): 11-20.doi: 10.13560/j.cnki.biotech.bull.1985.2015.01.002
李杨 李栋
收稿日期:
2014-06-09
出版日期:
2015-01-09
发布日期:
2015-01-10
作者简介:
李杨,硕士研究生,研究方向:泛素连接酶底物的生物信息学;E-mail:liyang_bprc@163.com
基金资助:
Li Yang, Li Dong
Received:
2014-06-09
Published:
2015-01-09
Online:
2015-01-10
摘要: 泛素是一种包含76个氨基酸的小分子蛋白。泛素共价结合到底物的过程称为泛素化修饰。泛素化修饰过程是一个由级联的泛素激活酶、泛素结合酶和泛素连接酶所介导的复杂过程,泛素化修饰具有高效、ATP依赖、高度特异的特点。泛素化修饰与细胞周期调控、细胞凋亡、转录调控、DNA损伤修复等一系列生物学过程密切相关。在泛素化修饰过程中,泛素连接酶对底物的识别,是决定泛素化修饰特异性的关键环节。泛素连接酶底物识别的相关机制研究不断被报道,鉴定泛素连接酶底物的高通量方法也在不断的改进和发展。随着实验研究的不断深入,实验数据的不断产出,利用生物信息学进行泛素连接酶底物的研究也开始受到关注。对泛素连接酶识别底物的相关机制、高通量泛素连接酶底物的鉴定方法、泛素连接酶底物的生物信息学研究和生物信息学在泛素连接酶底物研究中的发展方向进行讨论。
李杨,李栋. 泛素连接酶-底物选择关系的研究进展[J]. 生物技术通报, 2015, 31(1): 11-20.
Li Yang, Li Dong. Research Advances in the Selective Relationship Between Ubiquitin Ligases and Substrates[J]. Biotechnology Bulletin, 2015, 31(1): 11-20.
[1] Goldstein G, Scheid M, Hammerling U, et al. Isolation of a polypep-tide that has lymphocyte-differentiating properties and is probably represented universally in living cells[J]. Proceedings of the National Academy of Sciences, 1975, 72(1):11-15. [2] Pickart CM, Eddins MJ. Ubiquitin:structures, functions, mechanis-ms[J]. Biochimica et Biophysica Acta(BBA)-Molecular Cell Research, 2004, 1695(1-3):55-72. [3] Komander D, Rape M. The ubiquitin code[J]. Annual Review of Biochemistry, 2012, 81:203-229. [4] Komander D. The emerging complexity of protein ubiquitination[J]. Biochemical Society Transactions, 2009, 37(Pt 5):937-953. [5] Miranda M, Sorkin A. Regulation of receptors and transporters by ubiquitination:new insights into surprisingly similar mechanis-ms[J]. Molecular Interventions, 2007, 7(3):157-167. [6] Ikeda F, Dikic I. Atypical ubiquitin chains:new molecular signals[J]. EMBO Reports, 2008, 9(6):536-542. [7] Ciechanover A, Ben-Saadon R. N-terminal ubiquitination:more protein substrates join in[J]. Trends in Cell Biol, 2004, 14:103-106. [8] Deshaies RJ, Joazeiro CAP. RING domain E3 ubiquitin ligases[J]. Annual Review of Biochemistry, 2009, 78:399-434. [9] Michelle C, Vourc’h P, Mignon L, et al. What was the set of ubiqui-tin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor?[J]. J Mol Evol, 2009, 68(6):616-628. [10] Moynagh PN. The roles of Pellino E3 ubiquitin ligases in immuni-ty[J]. Nature Reviews Immunology, 2014, 14(2):122-131. [11] Wrighton KH. DNA damage response:a ligase makes sense of DNA damage[J]. Nature Reviews Molecular Cell Biology, 2014, 15(2):76-77. [12] Guo X, Baillo A, Dutta SM, et al. HTLV-1 Tax binds to and stabilizes the SUMO-targeted ubiquitin ligase RNF4 during DNA damage response[J]. Retrovirology, 2014, 11(Suppl 1):98. [13] Zhang S, Zhou Y, Sarkeshik A, et al. Identification of RNF8 as a ubiquitin ligase involved in targeting the p12 subunit of DNA polymerase δ for degradation in response to DNA damage[J]. Journal of Biological Chemistry, 2014, 288(5):2941-2950. [14] Inuzuka H, Shaik S, Onoyama I, et al. SCFFBW7 regulates cellular apoptosis by targeting MCL1 for ubiquitylation and destruction[J]. Nature, 2011, 471(7336):104-109. [15] Santra MK, Wajapeyee N, Green MR. F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage[J]. Nature, 2009, 459(7247):722-725. [16] Paolino M, Choidas A, Wallner S, et al. The E3 ligase Cbl-b and TAM receptors regulate cancer metastasis via natural killer cells[J]. Nature, 2014, 507(7493):508-512. [17] Duan S, Cermak L, Pagan JK, et al. FBXO11 targets BCL6 for degradation and is inactivated in diffuse large B-cell lymphomas[J]. Nature, 2012, 481(7379):90-93. [18] Severe N, Dieudonné FX, Marie PJ. E3 ubiquitin ligase-mediated regulation of bone formation and tumorigenesis[J]. Cell Death & Disease, 2013, 4(1):e463. [19] Berkers CR, Ovaa H. Drug discovery and assay development in the ubiquitinproteasome system[J]. Biochemical Society Transactions, 2010, 38(1):14. [20] Yang Y, Ludwig RL, Jensen JP, et al. Small molecule inhibitors of HDM2 ubiquitin ligase activity stabilize and activate p53in cells[J]. Cancer Cell, 2005, 7(6):547-559. [21] Obenauer JC, Cantley LC, Yaffe MB. Scansite 2.0:proteome-wide prediction of cell signaling interactions using short sequence motifs[J]. Nucleic Acids Res, 2003, 31(13):3635-3641. [22] Lindon C, Pines J. Ordered proteolysis in anaphase inactivates Plk1 to contribute to proper mitotic exit in human cells[J]. The Journal of Cell Biology, 2004, 164(2):233-241. [23] Lasorella A, Stegmüller J, Guardavaccaro D, et al. Degradation of Id2 by the anaphase-promoting complex couples cell cycle exit and axonal growth[J]. Nature, 2006, 442(7101):471-474. [24] Pfleger CM, Kirschner MW. The KEN box:an APC recognition signal distinct from the D box targeted by Cdh1[J]. Genes & Development, 2000, 14(6):655-665. [25] Arquint C, Nigg EA. STIL Microcephaly mutations interfere with APC/C-mediated degradation and cause centriole amplification[J]. Current Biology, 2014, 24(4):351-360. [26] Ichim G, Mola M, Finkbeiner MG, et al. The histone acetyltransferase component TRRAP is targeted for destruction during the cell cycle[J]. Oncogene, 2014, 33(2):181-192. [27] Ingham RJ, Gish G, Pawson T. The Nedd4 family of E3 ubiquitin ligases:functional diversity within a common modular architecture[J]. Oncogene, 2004, 23(11):1972-1984. [28] Rotin D, Kumar S. Physiological functions of the HECT family of ubiquitin ligases[J]. Nature Reviews Molecular Cell Biology, 2009, 10(6):398-409. [29] Graham L, Padmanabhan S. NEDD4L in essential hypertension[J]. Journal of Hypertension, 2014, 32(2):230-232. [30] Fei C, He X, Xie S, et al. Smurf1-mediated axin ubiquitination requires Smurf1 C2 domain and is cell-cycle dependent[J]. Journal of Biological Chemistry, 2014, 289(20):14170-14177. [31] Zhi X, Chen C. WWP1:a versatile ubiquitin E3 ligase in signaling and diseases[J]. Cell Mol Life Sci, 2012, 69(9):1425-1434. [32] Kavsak P, Rasmussen RK, Causing CG, et al. Smad7 binds to Smurf2 to form an E3 ubiquitin ligase that targets the TGFβ receptor for degradation[J]. Molecular Cell, 2000, 6(6):1365-1375. [33] Geetha T, Jiang J, Wooten MW. Lysine 63 polyubiquitination of the nerve growth factor receptor TrkA directs internalization and signaling[J]. Molecular Cell, 2005, 20(2):301-312. [34] Laney JD, Hochstrasser M. Substrate targeting in the ubiquitin system[J]. Cell, 1999, 97(4):427-430. [35] An H, Krist DT, Statsyuk AV. Crosstalk between kinases and Nedd4 family ubiquitin ligases[J]. Molecular Biosystems, 2014, 10(7):1643-1657. [36] Zhao Y, Brickner JR, Majid MC, et al. Crosstalk between ubiquitin and other post-translational modifications on chromatin during double-strand break repair[J]. Trends in Cell Biology, 2014, 24(7):426-434. [37] Gill G. SUMO and ubiquitin in the nucleus:different functions, similar mechanisms?[J]. Genes & Development, 2004, 18(17):2046-2059. [38] Kawakami T, Chiba T, Suzuki T, et al. NEDD8 recruits E2-ubiquitin to SCF E3 ligase[J]. The EMBO Journal, 2001, 20(15):4003-4012. [39] Darwanto A, Curtis MP, Schrag M, et al. A modified “cross-talk” between histone H2B Lys-120 ubiquitination and H3 Lys-79 methylation[J]. J Biol Chem, 2010, 285(28):21868-21876. [40] Lee JS, Shukla A, Schneider J, et al. Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS[J]. Cell, 2007, 131(6):1084-1096. [41] Yen HCS, Xu Q, Chou DM, et al. Global protein stability profiling in mammalian cells[J]. Science, 2008, 322(5903):918-923. [42] Yen HCS, Elledge SJ. Identification of SCF ubiquitin ligase substrates by global protein stability profiling[J]. Science, 2008, 322(5903):923-929. [43] Andrews PS, Schneider S, Yang E, et al. Identification of substrates of SMURF1 ubiquitin ligase activity utilizing protein microarrays[J]. Assay and Drug Development Technologies, 2010, 8(4):471-487. [44] Loch CM, Eddins MJ, Strickler JE. Protein microarrays for the identification of praja1 e3 ubiquitin ligase substrates[J]. Cell Biochemistry and Biophysics, 2011, 60(1-2):127-135. [45] Guo Z, Wang X, Li H, et al. Screening E3 substrates using a live phage display library[J]. PloS One, 2013, 8(10):e76622. [46] Yumimoto K, Matsumoto M, Oyamada K, et al. Comprehensive identification of substrates for F-box proteins by differential proteomics analysis[J]. Journal of Proteome Research, 2012, 11(6):3175-3185. [47] Shi Y, Chan DW, Jung SY, et al. A data set of human endogenous protein ubiquitination sites[J]. Molecular & Cellular Proteomics, 2011, 10(5):M110. 002089. [48] Rubel CE, Schisler JC, Hamlett ED, et al. Diggin' on U(biquitin):a novel method for the identification of physiological E3 ubiquitin ligase sustrates[J]. Cell Biochemistry and Biophysics, 2013, 67(1):127-138. [49] Zhuang M, Guan S, Wang H, et al. Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase, the NEDDylator[J]. Molecular Cell, 2013, 49(2):273-282. [50] Han Y, Lee H, Park JC, et al. E3Net:a system for exploring E3-mediated regulatory networks of cellular functions[J]. Molecular & Cellular Proteomics, 2012, 11(4):0111. [51] Du Y, Xu N, Lu M, et al. hUbiquitome:a database of experimen-tally verified ubiquitination cascades in humans[J]. Database, 2011, 2011:bar055. [52] Lee WC, Lee M, Jung JW, et al. SCUD:Saccharomyces cerevisiae ubiquitination database[J]. BMC Genomics, 2008, 9(1):440. [53] Chernorudskiy AL, Garcia A, Eremin EV, et al. UbiProt:a database of ubiquitylated proteins[J]. BMC Bioinformatics, 2007, 8(1):126. [54] Du Z, Zhou X, Li L, et al. PlantsUPS:a database of plants’ Ubiquitin Proteasome System[J]. BMC Genomics, 2009, 10(1):227. [55] Jadhav TS, Wooten MW, Wooten MC. Mining the TRAF6/p62 interactome for a selective ubiquitination motif[J]. BMC Proc, 2011, 5(suppl 2):S4. [56] Liu ZX, Yuan F, Ren J, et al. GPS-ARM:computational analysis of the APC/C recognition motif by predicting D-boxes and KEN-boxes[J]. PloS One, 2012, 7(3):e34370. [57] Xue Y, Zhou F, Zhu M, et al. GPS:a comprehensive www server for phosphorylation sites prediction[J]. Nucleic Acids Research, 2005, 33(suppl 2):W184-W187. [58] Xue Y, Ren J, Gao X, et al. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy[J]. Molecular & Cellular Proteomics, 2008, 7(9):1598-1608. [59] Jansen R, Yu H, Greenbaum D, et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data[J]. Science, 2003, 302(5644):449-453. [60] Rhodes DR, Tomlins SA, Varambally S, et al. Probabilistic model of the human protein-protein interaction network[J]. Nature Biotechnology, 2005, 23(8):951-959. [61] Li D, Liu W, Liu Z, et al. PRINCESS, a protein interaction confidence evaluation system with multiple data sources[J]. Molecular & Cellular Proteomics, 2008, 7(6):1043-1052. [62] Zhang Q C, Petrey D, Deng L, et al. Structure-based prediction of protein-protein interactions on a genome-wide scale[J]. Nature, 2012, 490(7421):556-560. [63] Snel B, Lehmann G, Bork P, et al. STRING:a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene[J]. Nucleic Acids Research, 2000, 28(18):3442-3444. [64] Thierry-Mieg N. A new pooling strategy for high-throughput screening:the Shifted Transversal Design[J]. BMC Bioinforma-tics, 2006, 7(1):28. |
[1] | 张路阳, 韩文龙, 徐晓雯, 姚健, 李芳芳, 田效园, 张智强. 烟草TCP基因家族的鉴定及表达分析[J]. 生物技术通报, 2023, 39(6): 248-258. |
[2] | 李敬蕊, 王育博, 解紫薇, 李畅, 吴晓蕾, 宫彬彬, 高洪波. 甜瓜PIN基因家族的鉴定及高温胁迫表达分析[J]. 生物技术通报, 2023, 39(5): 192-204. |
[3] | 郭三保, 宋美玲, 李灵心, 尧子钊, 桂明明, 黄胜和. 斑地锦查尔酮合酶基因及启动子的克隆与分析[J]. 生物技术通报, 2023, 39(4): 148-156. |
[4] | 王艺清, 王涛, 韦朝领, 戴浩民, 曹士先, 孙威江, 曾雯. 茶树SMAS基因家族的鉴定及互作分析[J]. 生物技术通报, 2023, 39(4): 246-258. |
[5] | 杨岚, 张晨曦, 樊学伟, 王阳光, 王春秀, 李文婷. 鸡 BMP15 基因克隆、表达模式及启动子活性分析[J]. 生物技术通报, 2023, 39(4): 304-312. |
[6] | 陈强, 邹明康, 宋家敏, 张冲, 吴隆坤. 甜瓜LBD基因家族的鉴定和果实发育进程中的表达分析[J]. 生物技术通报, 2023, 39(3): 176-183. |
[7] | 平怀磊, 郭雪, 余潇, 宋静, 杜春, 王娟, 张怀璧. 滇牡丹PdANS的克隆、表达及与花青素含量的相关性[J]. 生物技术通报, 2023, 39(3): 206-217. |
[8] | 邢媛, 宋健, 李俊怡, 郑婷婷, 刘思辰, 乔治军. 谷子AP基因家族鉴定及其对非生物胁迫的响应分析[J]. 生物技术通报, 2023, 39(11): 238-251. |
[9] | 陈楚怡, 杨小梅, 陈胜艳, 陈斌, 岳莉然. ABA和干旱胁迫下菊花脑ZF-HD基因家族的表达分析[J]. 生物技术通报, 2023, 39(11): 270-282. |
[10] | 杨敏, 龙雨青, 曾娟, 曾梅, 周新茹, 王玲, 付学森, 周日宝, 刘湘丹. 灰毡毛忍冬UGTPg17、UGTPg36基因克隆及功能研究[J]. 生物技术通报, 2023, 39(10): 256-267. |
[11] | 郭志浩, 金泽鑫, 刘琦, 高利. 小麦矮腥黑粉菌效应蛋白g11335的生物信息学分析、亚细胞定位及毒性验证[J]. 生物技术通报, 2022, 38(8): 110-117. |
[12] | 于秋琳, 马婧怡, 赵盼, 孙鹏芳, 何玉美, 刘世彪, 郭惠红. 绞股蓝GpMIR156a和GpMIR166b的克隆与功能分析[J]. 生物技术通报, 2022, 38(7): 186-193. |
[13] | 陈佳敏, 刘永杰, 马锦绣, 李丹, 公杰, 赵昌平, 耿洪伟, 高世庆. 小麦组蛋白甲基化酶在杂交种中干旱胁迫表达模式分析[J]. 生物技术通报, 2022, 38(7): 51-61. |
[14] | 王楠, 张瑞, 潘阳阳, 何翃宏, 王靖雷, 崔燕, 余四九. 牦牛TGF-β1基因克隆及在雌性生殖系统主要器官中的表达定位[J]. 生物技术通报, 2022, 38(6): 279-290. |
[15] | 李宇航, 王兴平, 杨箭, 罗仍卓么, 任倩倩, 魏大为, 马云. miR-665在奶牛乳腺上皮细胞炎症中的表达及功能分析[J]. 生物技术通报, 2022, 38(5): 159-168. |
阅读次数 | ||||||||||||||||||||||||||||||||||||||||||||||||||
全文 209
|
|
|||||||||||||||||||||||||||||||||||||||||||||||||
摘要 421
|
|
|||||||||||||||||||||||||||||||||||||||||||||||||