结直肠癌组织中泛素化修饰蛋白的蛋白质组学分析
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摘要
蛋白质泛素化修饰在结直肠癌的发生、发展和转移等过程中,发挥着重要作用。本研究提取结直肠癌组织中总蛋白,经胰酶水解得到多肽混合物,利用免疫沉淀技术对其中含-GG标签的肽段富集纯化,最后利用液相色谱-质谱联用技术对富集肽段进行分析,经数据库检索鉴定蛋白。结果表明,在结直肠癌组织中,鉴定得到归属为328种蛋白的2036个肽段。其中,含-GG标签的修饰肽段数为1497个,归属287种蛋白。在鉴定得到的含有-GG标签的肽段中,除了大部分含有1个-GG标签的肽段外,还包括31个含有2个-GG标签的肽段以及3个含有3个-GG标签的肽段。在鉴定得到的泛素化修饰的蛋白中,发现许多与结直肠癌密切相关的蛋白,包括胸腺素α原(Prothymosin alpha)、转化酸性含卷曲螺旋蛋白3(Transforming acidic coiled-coil-containing protein 3)、中性氨基酸转运蛋白B(0)(Neutral amino acid transporter B(0))等。对所鉴定的泛素化修饰蛋白的生物信息学分析表明,结直肠癌组织中泛素化修饰蛋白涵盖了多种基本的生物学过程和分子功能,在细胞内的各个亚细胞器及胞外基质成分中均有分布。本研究对结直肠癌组织中的泛素修饰蛋白的种类、分布等情况提供了一种特异、有效的研究方法,研究结果为深入研究结直肠癌中泛素化修饰调控分子机制提供了基础数据。
Protein ubiquitination modification plays an important role in the occurrence,development and metastasis of colorectal cancer. In this work,the total protein extracted from colorectal cancer tissues was hydrolyzed by trypsin to obtain a peptide mixture. Then the peptide mixture containing-GG tag was enriched and purified by immunoprecipitation technique. Finally, the enriched peptides were analyzed by liquid chromatography-mass spectrometry (LC-MS) and the proteins were identified by database search. The results showed that 2036 peptides belonging to 328 proteins were identified in colorectal cancer tissues. Among them,1497 were the modified peptides containing-GG tag,which were derived from 287 proteins. Apart from most of the peptides containing one-GG tag,31 peptides containing two-GG tags and 3 peptides containing three-GG tags were identified. Among the identified ubiquitinated proteins,many proteins were found to be closely associated with colorectal cancer,including Prothymosin alpha,Transforming acidic coiled-coil-containing protein 3,Neutral amino acid transporter B (0). Bioinformatics analysis of the identified ubiquitinated proteins showed that ubiquitinated proteins in colorectal cancer tissues were enriched in a variety of basic biological processes and molecular functions,and were distributed in various subcellular organelles and extracellular matrix components. This study provided a specific and effective method for studying the types and distribution of ubiquitinated proteins in colorectal cancer tissues. The results could be used as primary data for further studying the molecular mechanism of ubiquitination regulation in colorectal cancer.
Protein ubiquitination modification plays an important role in the occurrence,development and metastasis of colorectal cancer. In this work,the total protein extracted from colorectal cancer tissues was hydrolyzed by trypsin to obtain a peptide mixture. Then the peptide mixture containing-GG tag was enriched and purified by immunoprecipitation technique. Finally, the enriched peptides were analyzed by liquid chromatography-mass spectrometry (LC-MS) and the proteins were identified by database search. The results showed that 2036 peptides belonging to 328 proteins were identified in colorectal cancer tissues. Among them,1497 were the modified peptides containing-GG tag,which were derived from 287 proteins. Apart from most of the peptides containing one-GG tag,31 peptides containing two-GG tags and 3 peptides containing three-GG tags were identified. Among the identified ubiquitinated proteins,many proteins were found to be closely associated with colorectal cancer,including Prothymosin alpha,Transforming acidic coiled-coil-containing protein 3,Neutral amino acid transporter B (0). Bioinformatics analysis of the identified ubiquitinated proteins showed that ubiquitinated proteins in colorectal cancer tissues were enriched in a variety of basic biological processes and molecular functions,and were distributed in various subcellular organelles and extracellular matrix components. This study provided a specific and effective method for studying the types and distribution of ubiquitinated proteins in colorectal cancer tissues. The results could be used as primary data for further studying the molecular mechanism of ubiquitination regulation in colorectal cancer.
引文
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2 Sethi M K,Fanayan S.Int.J.Mol.Sci.,2015,16(12):29278-29304
3 Chen Z,Zhou Y,Zhang Z,Song J.Brief Bioinform.,2015,16(4):640-657
4 Popovic D,Vucic D,Dikic I.Nat.Med.,2014,20(11):1242-1253
5 Callis J.Arabidopsis Book,2014,12:e0174
6 Fraile J M,Quesada V,Rodríguez D,Freije J M,López-Otín C.Oncogene,2012,31(19):2373-2388
7 Mansour M A.Int.J.Biochem.Cell.Biol.,2018,101:80-93
8 Ma Y,Zhao M,Zhong J,Shi L,Luo Q,Liu J,Wang J,Yuan X,Huang C.J.Cell.Biochem.,2010,110(6):1512-1519
9 Grossegesse M,Doellinger J,Fritsch A,Laue M,Piesker J,Schaade L,Nitsche A.Sci.Rep.,2018,8(1):1807
10 Chu X L,Feng M G,Ying S H.Curr.Genet.,2016,62(1):191-201
11 Xie X,Kang H,Liu W,Wang G L.J.Proteome Res.,2015,14(5):2017-2025
12 Coghlin C,Murray G I.Proteomics Clin.Appl.,2015,9(1-2):64-71
13 Yang Z,Liu J,Shi Q,Chao Y,Di Y,Sun J,Zhang J,Huang L,Guo H,He C.Oncotargets Ther.,2018,11:4159-4166
14 Mi H,Huang X,Muruganujan A,Tang H,Mills C,Kang D,Thomas P D.Nucleic Acids Res.,2017,45(D1):D183-D189
15 Huang D W,Sherman B T,Lempicki R A.Nat.Protoc.,2009,4(1):44-57
16 Zhang M,Cui F,Lu S,Lu H,Jiang T,Chen J,Zhang X,Jin Y,Peng Z,Tang H.Int.J.Clin.Exp.Pathol.,2014,7(8):4867-4876
17 Yun M,Rong J,Lin Z R,He Y L,Zhang J X,Peng Z W,Tang L Q,Zeng M S,Zhong Q,Ye S.Oncol.Rep.,2015,34(3):1397-1405
18 Cheng S,Douglas-Jones A,Yang X,Mansel R E,Jiang W G.Cancer Genomics Proteomics,2010,7(2):67-73
19 Ma H,Wu Z,Peng J,Li Y,Huang H,Liao Y,Zhou M,Sun L,Huang N,Shi M,Bin J,Liao Y,Rao J,Wang L,Liao W.Int.J.Cancer,2018,142(12):2578-2588
20 Rocha M R,Barcellos-de-Souza P,Sousa-Squiavinato A C M,Fernandes P V,de Oliveira I M,Boroni M,Morgado-Diaz J A.Sci.Rep.,2018,8(1):11285
21 Tan X,He X,Jiang Z,Wang X,Ma L,Liu L,Wang X,Fan Z,Su D.Mol.Cell.Biochem.,2015,408(1-2):205-213
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