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ZHANG Yuxin, DING Ming, LIU Jun. Research progress of proximity labeling technology based on biotin ligase in proteomics[J]. Journal of China Pharmaceutical University, 2022, 53(1): 18-24. DOI: 10.11665/j.issn.1000-5048.20220103
Citation: ZHANG Yuxin, DING Ming, LIU Jun. Research progress of proximity labeling technology based on biotin ligase in proteomics[J]. Journal of China Pharmaceutical University, 2022, 53(1): 18-24. DOI: 10.11665/j.issn.1000-5048.20220103
shu

Research progress of proximity labeling technology based on biotin ligase in proteomics

  • 1.

    Center for New Drug Screening, China Pharmaceutical University, Nanjing 210009

  • 2.

    School of Life Science & Technology, China Pharmaceutical University, Nanjing 210009, China

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  • Received Date: June 10, 2021
  • Revised Date: November 06, 2021
    Graphical Abstract
    • Abstract
  • Proximity-dependent biotinylation (PDB) uses biotin ligase fused to the protein of interest to biotinylate adjacent proteins, purify them with streptavidin beads, and then identify the biotinylated protein by mass spectrometry.This technology can be used to detect transient and/or low affinity interactions, provide a chance to learn more about membrane-less organelles and other subcellular structures that cannot be easily isolated or purified, and fill the gap in traditional methods.This article summarizes the technological development and application of PDB in recent years.
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    • References (51)
  • [1]
    . Curr Opin Chem Biol，2019，48：44-54.
    [2]
    Liu Q，Zheng J，Sun W，et al. A proximity-tagging system to identify membrane protein-protein interactions［J］. Nat Methods，2018，15（9）：715-722.
    [3]
    Kido K，Yamanaka S，Nakano S，et al. AirID，a novel proximity biotinylation enzyme，for analysis of protein-protein interactions［J］. Elife，2020，9： e54983.
    [4]
    Ramanathan M，Majzoub K，Rao DS，et al. RNA-protein interaction detection in living cells［J］. Nat Methods，2018，15（3）：207-212.
    [5]
    Zhang Z，Sun W，Shi T，et al. Capturing RNA-protein interaction via CRUIS［J］. Nucleic Acids Res，2020，48（9）：e52.
    [6]
    Roux KJ，Kim DI，Burke B，et al. BioID： a screen for protein-protein interactions［J］. Curr Protoc Protein Sci，2018，91：19.23.1-19.23.15.
    [7]
    Roux KJ，Kim DI，Raida M，et al. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells［J］. J Cell Biol，2012，196（6）：801-810.
    [8]
    Kim DI，Birendra KC，Zhu W，et al. Probing nuclear pore complex architecture with proximity-dependent biotinylation［J］. Proc Natl Acad Sci U S A，2014，111（24）：E2453-2461.
    [9]
    Khan M，Youn JY，Gingras AC，et al. In planta proximity dependent biotin identification （BioID）［J］. Sci Rep，2018，8（1）：9212.
    [10]
    Conlan B，Stoll T，Gorman JJ，et al. Development of a rapid in planta BioID system as a probe for plasma membrane-associated immunity proteins［J］. Front Plant Sci，2018，9：1882.
    [11]
    Morriswood B，Havlicek K，Demmel L，et al. Novel bilobe components in Trypanosoma brucei identified using proximity-dependent biotinylation［J］. Eukaryot Cell，2013，12（2）：356-367.
    [12]
    Nadipuram SM，Kim EW，Vashisht AA，et al. In vivo biotinylation of the Toxoplasma parasitophorous vacuole reveals novel dense granule proteins important for parasite growth and pathogenesis［J］. mBio，2016，7（4）： e00808-16.
    [13]
    Meyer I，Peter T，Batsios P，et al. CP39，CP75 and CP91 are major structural components of the Dictyostelium centrosome''s core structure［J］. Eur J Cell Biol，2017，96（2）：119-130.
    [14]
    Feng W，Liu C，Spinozzi S，et al. Identifying the cardiac dyad proteome in vivo by a BioID2 knock-in strategy［J］. Circulation，2020，141（11）：940-942.
    [15]
    Opitz N，Schmitt K，Hofer-Pretz V，et al. Capturing the Asc1p/Receptor for activated C kinase 1 （RACK1） microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast［J］. Mol Cell Proteomics，2017，16（12）：2199-2218.
    [16]
    Xiong Z，Lo HP，McMahon KA，et al. In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish［J］. Elife，2021，10：e64631.
    [17]
    Branon TC，Bosch JA，Sanchez AD，et al. Efficient proximity labeling in living cells and organisms with TurboID［J］. Nat Biotechnol，2018，36（9）：880-887.
    [18]
    Chojnowski A，Sobota RM，Ong PF，et al. 2C-BioID：an advanced two component BioID system for precision mapping of protein interactomes［J］. iScience，2018，10：40-52.
    [19]
    Schopp IM，Amaya Ramirez CC，Debeljak J，et al. Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes［J］. Nat Commun，2017，8：15690.
    [20]
    De Munter S，Gornemann J，Derua R，et al. Split-BioID：a proximity biotinylation assay for dimerization-dependent protein interactions［J］. FEBS Lett，2017，591（2）：415-424.
    [21]
    Schopp IM，Bethune J. Split-BioID — proteomic analysis of context-specific protein complexes in their native cellular environment［J］. J Vis Exp，2018（134）：57479.
    [22]
    Kwak C，Shin S，Park JS，et al. Contact-ID，a tool for profiling organelle contact sites，reveals regulatory proteins of mitochondrial-associated membrane formation［J］. Proc Natl Acad Sci U S A，2020，117（22）：12109-12120.
    [23]
    Kim DI，Jensen SC，Noble KA，et al. An improved smaller biotin ligase for BioID proximity labeling［J］. Mol Biol Cell，2016，27（8）：1188-1196.
    [24]
    Soullam B，Worman HJ. Signals and structural features involved in integral membrane protein targeting to the inner nuclear membrane［J］. J Cell Biol，1995，130（1）：15-27.
    [25]
    Chojnowski A，Werner H，Cook M，et al. Protein-protein interaction mapping by 2C-BioID［J］. Curr Protoc Cell Biol，2019，84（1）：e96.
    [26]
    Cho KF，Branon TC，Rajeev S，et al. Split-TurboID enables contact-dependent proximity labeling in cells［J］. Proc Natl Acad Sci U S A，2020，117（22）：12143-12154.
    [27]
    May DG，Scott KL，Campos AR，et al. Comparative application of BioID and TurboID for protein-proximity biotinylation［J］. Cells，2020，9（5）：1070.
    [28]
    Zhou Y，Zou P. The evolving capabilities of enzyme-mediated proximity labeling［J］. Curr Opin Chem Biol，2021，60：30-38.
    [29]
    Loh KH，Stawski PS，Draycott AS，et al. Proteomic analysis of unbounded cellular compartments：synaptic clefts［J］. Cell，2016，166（5）：1295-1307.
    [30]
    Comartin D，Gupta GD，Fussner E，et al. CEP120 and SPICE1 cooperate with CPAP in centriole elongation［J］. Curr Biol，2013，23（14）：1360-1366.
    [31]
    Gupta GD，Coyaud E，Goncalves J，et al. A dynamic protein interaction landscape of the human centrosome-cilium interface［J］. Cell，2015，163（6）：1484-1499.
    [32]
    Youn JY，Dunham WH，Hong SJ，et al. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies［J］. Mol Cell，2018，69（3）：517-532.
    [33]
    Parker R，Partridge T，Wormald C，et al. Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells［J］. Cell Rep，2021，35（8）：109179.
    [34]
    V''Kovski P，Steiner S，Thiel V. Methods in Molecular Biology ［M］.2203. New York：Springer，2020：187-204.
    [35]
    Coyaud E，Ranadheera C，Cheng D，et al. Global interactomics uncovers extensive organellar targeting by Zika virus［J］. Mol Cell Proteomics，2018，17（11）：2242-2255.
    [36]
    Nkosi D，Sun L，Duke LC，et al. Epstein-Barr virus LMP1 promotes Syntenin-1- and Hrs-induced extracellular vesicle formation for its own secretion to increase cell proliferation and migration［J］. mBio，2020，11（3）：e00589-20.
    [37]
    Rudolph F，Fink C，Huttemeister J，et al. Deconstructing sarcomeric structure-function relations in titin-BioID knock-in mice［J］. Nat Commun，2020，11（1）：3133.
    [38]
    Uezu A，Kanak DJ，Bradshaw TW，et al. Identification of an elaborate complex mediating postsynaptic inhibition［J］. Science，2016，353（6304）：1123-1129.
    [39]
    Kovalski JR，Bhaduri A，Zehnder AM，et al. The functional proximal proteome of oncogenic Ras includes mTORC2［J］. Mol Cell，2019，73（4）：830-844.
    [40]
    Le Sage V，Cinti A，Valiente-Echeverría F，et al. Proteomic analysis of HIV-1 Gag interacting partners using proximity-dependent biotinylation［J］. Virol J，2015，12：138.
    [41]
    Yeung B，Khanal P，Mehta V，et al. Identification of Cdk1-LATS-Pin1 as a novel signaling axis in anti-tubulin drug response of cancer cells［J］. Mol Cancer Res，2018，16（6）：1035-1045.
    [42]
    Rayner SL，Morsch M，Molloy MP，et al. Using proteomics to identify ubiquitin ligase-substrate pairs：how novel methods may unveil therapeutic targets for neurodegenerative diseases［J］. Cell Mol Life Sci，2019，76（13）：2499-2510.
    [43]
    Coyaud E，Mis M，Laurent EM，et al. BioID-based identification of Skp Cullin F-box （SCF）β-TrCP1/2 E3 ligase substrates［J］. Mol Cell Proteomics，2015，14（7）：1781-1795.
    [44]
    Wu G，Lin Q，Lim TK，et al. The interactome of Singapore grouper iridovirus protein ICP18 as revealed by proximity-dependent BioID approach［J］. Virus Res，2021，291：198218.
    [45]
    Das PP，Macharia MW，Lin Q，et al. In planta proximity-dependent biotin identification （BioID） identifies a TMV replication co-chaperone NbSGT1 in the vicinity of 126kDa replicase［J］. J Proteomics，2019，204：103402.
    [46]
    Zhang YL，Li YY，Yang XX，et al. TurboID-based proximity labeling for in planta identification of protein-protein interaction networks［J］. J Vis Exp，2020（159）：e60728.
    [47]
    Trinkle-Mulcahy L. Recent advances in proximity-based labeling methods for interactome mapping［J］. F1000Res，2019，8：F1000 Faculty Rev-135.
    [48]
    Kim DI，Roux KJ. Filling the void：proximity-based labeling of proteins in living cells［J］. Trends Cell Biol，2016，26（11）：804-817.
    [49]
    Liu X，Salokas K，Tamene F，et al. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations［J］. Nat Commun，2018，9（1）：1188.
    [50]
    Motani K，Kosako H. BioID screening of biotinylation sites using the avidin-like protein Tamavidin 2-REV identifies global interactors of stimulator of interferon genes （STING） ［J］. J Biol Chem，2020，295（32）：11174-11183.
    [51]
    Lee SY，Seo JK，Rhee HW. Methods in Molecular Biology ［M］.2008. New York：Springer，2019，97-105.
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