活细胞内亚细胞结构蛋白质组学研究新技术——几种邻近标记策略的应用及比较
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摘要
真核细胞内多种无膜及有膜细胞器为各种生物学过程的发生提供场所.被膜细胞器通过它们之间的膜接触位点所进行的信息交流和物质交换是维持生命活动所必需的.绘制活细胞中细胞器或膜接触位点等处的蛋白质组图谱,将有助于解析这些部位的生物学功能及作用机制,并为研究细胞器相互作用提供基础.但由于无膜细胞器或膜接触位点很难分离纯化,传统的生化方法难以系统解析其中的蛋白质组.最近报道的几种基于酶类的蛋白质邻近标记技术,则为系统分析上述空间受限的蛋白质组这一难题提供了有效的解决方案.通过将能催化产生活性自由基(最常见的是生物素及其衍生物的自由基)的酶连接到目标蛋白上,可对其邻近的蛋白质组进行共价标记,从而使后者的分离和鉴定成为可能,并可以运用于活细胞中的动态标记.我们在此综述了几种最新的邻近标记策略的原理及应用,并对它们的优势与局限性进行了比较,以期为细胞器互作的蛋白质组学研究提供参考.
Membrane-less and membrane-bound organelles provide sites for many crucial biological processes to take place within eukaryotic cells. Signalling and exchange of materials occurring at membrane contact sites(MCSs) among membrane-bound organelles are also vital for cell homeostasis. Proteomic mapping of molecular machineries within membrane-less organelles or MCSs are essential for the understanding all those events within such sites, as well as for the study of organelle interactions. However, the attempts to dissect molecular determinants in these sites using traditional biochemical techniques were far from fruitful. Recent advances in proximity labelling techniques provide an ideal solution for this challenge. Mostly by utilizing different type of biotin ligases which fused to target proteins, proteomes surrounding the target protein(within tens of nanometers)could be tagged(often with biotin or its derivatives). These covalently labelled proteins could then be enriched and identified with mass spectrometry.Here,we reviewed most recent advances in proximity labeling approaches,hoping to provide a general guide for researches focusing on proteomic mapping of molecular machineries within organelles or MCSs.
Membrane-less and membrane-bound organelles provide sites for many crucial biological processes to take place within eukaryotic cells. Signalling and exchange of materials occurring at membrane contact sites(MCSs) among membrane-bound organelles are also vital for cell homeostasis. Proteomic mapping of molecular machineries within membrane-less organelles or MCSs are essential for the understanding all those events within such sites, as well as for the study of organelle interactions. However, the attempts to dissect molecular determinants in these sites using traditional biochemical techniques were far from fruitful. Recent advances in proximity labelling techniques provide an ideal solution for this challenge. Mostly by utilizing different type of biotin ligases which fused to target proteins, proteomes surrounding the target protein(within tens of nanometers)could be tagged(often with biotin or its derivatives). These covalently labelled proteins could then be enriched and identified with mass spectrometry.Here,we reviewed most recent advances in proximity labeling approaches,hoping to provide a general guide for researches focusing on proteomic mapping of molecular machineries within organelles or MCSs.
引文
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[15]Lin Q,Zhou Z,Luo W,et al.Screening of proximal and interacting proteins in rice protoplasts by proximity-dependent biotinylation.Frontiers in Plant Science,2017,8:749
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[17]Gu B,Lambert J P,Cockburn K,et al.AIRE is a critical spindleassociated protein in embryonic stem cells.eLife,2017,6:pii:e28131
[18]Dingar D,Kalkat M,Chan P K,et al.BioID identifies novel cMYC interacting partners in cultured cells and xenograft tumors.Journal of Proteomics,2015,118:95-111
[19]Uezu A,Kanak D J,Bradshaw T W,et al.Identification of an elaborate complex mediating postsynaptic inhibition.Science,2016,353(6304):1123-1129
[20]Jan C H,Williams C C,Weissman J S.Principles of ERcotranslational translocation revealed by proximity-specific ribosome profiling.Science,2014,346(6210):1257521
[21]Comartin D,Gupta G D,Fussner E,et al.CEP120 and SPICE1cooperate with CPAP in centriole elongation.Current Biology:CB,2013,23(14):1360-1366
[22]Cole A,Wang Z,Coyaud E,et al.Inhibition of the mitochondrial protease ClpP as a therapeutic strategy for human acute myeloid leukemia.Cancer Cell,2015,27(6):864-876
[23]Elzi D J,Song M,Hakala K,et al.Proteomic analysis of the EWS-Fli-1 interactome reveals the role of the lysosome in EWS-Fli-1turnover.Journal of Proteome Research,2014,13(8):3783-3791
[24]Guo Z,Neilson L J,Zhong H,et al.E-cadherin interactome complexity and robustness resolved by quantitative proteomics.Science Signaling,2014,7(354):rs7
[25]Steed E,Elbediwy A,Vacca B,et al.MarvelD3 couples tight junctions to the MEKK1-JNK pathway to regulate cell behavior and survival.The Journal of Cell Biology,2014,204(5):821-838
[26]Ueda S,Blee A M,Macway K G,et al.Force dependent biotinylation of myosin IIA by alpha-catenin tagged with a promiscuous biotin ligase.Plos One,2015,10(3):e0122886
[27]Van Itallie C M,Aponte A,Tietgens A J,et al.The N and C termini of ZO-1 are surrounded by distinct proteins and functional protein networks.The Journal of Biological Chemistry,2013,288(19):13775-13788
[28]Nishimura T,Padamsi Z,Fakim H,et al.The eIF4E-binding protein 4E-T is a component of the mRNA decay machinery that bridges the 5'and 3'termini of target mRNAs.Cell Reports,2015,11(9):1425-1436
[29]Cheng Y S,Seibert O,Kloting N,et al.PPP2R5C couples hepatic glucose and lipid homeostasis.Plos Genetics,2015,11(10):e1005561
[30]Couzens A L,Knight J D,Kean M J,et al.Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions.Science Signaling,2013,6(302):rs15
[31]Rodriguez-Fraticelli A E,Bagwell J,Bosch-Fortea M,et al.Developmental regulation of apical endocytosis controls epithelial patterning in vertebrate tubular organs.Nature Cell Biology,2015,17(3):241-250
[32]Schumacher M M,Elsabrouty R,Seemann J,et al.The prenyltransferase UBIAD1 is the target of geranylgeraniol in degradation of HMG CoA reductase.e Life,2015,4(DOI:10.7554/eLife.05560)
[33]Zhou Z,Rawnsley D R,Goddard L M,et al.The cerebral cavernous malformation pathway controls cardiac development via regulation of endocardial MEKK3 signaling and KLFexpression.Dev Cell,2015,32(2):168-180
[34]Coyaud E,Mis M,Laurent E M,et al.BioID-based identification of Skp cullin F-box(SCF)beta-TrCP1/2 E3 ligase substrates.Molecular&Cellular Proteomics,2015,14(7):1781-1795
[35]Yeh C,Coyaud E,Bashkurov M,et al.The deubiquitinase USP37regulates chromosome cohesion and mitotic progression.Current Biology,2015,25(17):2290-2299
[36]Kueck T,Foster T L,Weinelt J,et al.Serine phosphorylation of HIV-1 Vpu and its binding to tetherin regulates interaction with clathrin adaptors.Plos pathogens,2015,11(8):e1005141
[37]Le Sage V,Cinti A,Valiente-Echeverria F,et al.Proteomic analysis of HIV-1 Gag interacting partners using proximity-dependent biotinylation.Virology Journal,2015,12:138
[38]Ritchie C,Cylinder I,Platt E J,et al.Analysis of HIV-1 Gag protein interactions via biotin ligase tagging.Journal of Virology,2015,89(7):3988-4001
[39]De Munter S,Gornemann J,Derua R,et al.Split-BioID:a proximity biotinylation assay for dimerization-dependent protein interactions.FEBS Letters,2017,591(2):415-424
[40]Schopp I M,Amaya Ramirez C C,Debeljak J,et al.Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes.Nature Communications,2017,8:15690
[41]Chojnowski A,Sobota R M,Ong P F,et al.2C-BioID:An advanced two component BioID system for precision mapping of protein interactomes.iScience,2018,10:40-52
[42]Branon T C,Bosch J A,Sanchez A D,et al.Efficient proximity labeling in living cells and organisms with TurboID.Nature Biotechnology,2018,36(9):880-887
[43]Ramanathan M,Majzoub K,Rao D S,et al.RNA-protein interaction detection in living cells.Nature Methods,2018,15(3):207-212
[44]Fernandez-Suarez M,Chen T S,Ting A Y.Protein-protein interaction detection in vitro and in cells by proximity biotinylation.Journal of the American Chemical Society,2008,130(29):9251-9253
[45]Lajko M,Haddad A F,Robinson C A,et al.Using proximity biotinylation to detect herpesvirus entry glycoprotein interactions:Limitations for integral membrane glycoproteins.Journal of Virological Methods,2015,221:81-89
[46]Belshan M,Schweitzer C J,Donnellan M R,et al.In vivo biotinylation and capture of HIV-1 matrix and integrase proteins.Journal of Virological Methods,2009,159(2):178-184
[47]Steel E,Murray V L,Liu A P.Multiplex detection of homo-and heterodimerization of g protein-coupled receptors by proximity biotinylation.Plos One,2014,9(4):e93646
[48]Shoaib M,Kulyyassov A,Robin C,et al.PUB-NChIP--"in vivo biotinylation"approach to study chromatin in proximity to a protein of interest.Genome Research,2013,23(2):331-340
[49]Thyagarajan A,Ting A Y.Imaging activity-dependent regulation of neurexin-neuroligin interactions using trans-synaptic enzymatic biotinylation.Cell,2010,143(3):456-469
[50]Kotani N,Gu J,Isaji T,et al.Biochemical visualization of cell surface molecular clustering in living cells.Proc Natl Acad Sci USA,2008,105(21):7405-7409
[51]Honke K,Kotani N.Identification of cell-surface molecular interactions under living conditions by using the enzymemediated activation of radical sources(EMARS)method.Sensors,2012,12(12):16037-16045
[52]Miyagawa-Yamaguchi A,Kotani N,Honke K.Expressed glycosylphosphatidylinositol-anchored horseradish peroxidase identifies co-clustering molecules in individual lipid raft domains.Plos One,2014,9(3):e93054
[53]Yamashita R,Kotani N,Ishiura Y,et al.Spatiotemporallyregulated interaction between beta1 integrin and ErbB4 that is involved in fibronectin-dependent cell migration.Journal of Biochemistry,2011,149(3):347-355
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