Global, Quantitative and Dynamic Mapping of Protein Subcellular Localization

Overview

Journal Elife

Specialty Biology

Date 2016 Jun 10

PMID 27278775

Citations 296

Authors

Daniel N Itzhak

Stefka Tyanova

Jurgen Cox

Georg Hh Borner

Affiliations

Soon will be listed here.

Abstract

Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology.

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References

Plotnikov A, Zehorai E, Procaccia S, Seger R . The MAPK cascades: signaling components, nuclear roles and mechanisms of nuclear translocation. Biochim Biophys Acta. 2010; 1813(9):1619-33. DOI: 10.1016/j.bbamcr.2010.12.012. View

Christoforou A, Mulvey C, Breckels L, Geladaki A, Hurrell T, Hayward P . A draft map of the mouse pluripotent stem cell spatial proteome. Nat Commun. 2016; 7:8992. PMC: 4729960. DOI: 10.1038/ncomms9992. View

Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A . The quantitative proteome of a human cell line. Mol Syst Biol. 2011; 7:549. PMC: 3261713. DOI: 10.1038/msb.2011.82. View

Dunkley T, Watson R, Griffin J, Dupree P, Lilley K . Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics. 2004; 3(11):1128-34. DOI: 10.1074/mcp.T400009-MCP200. View

Deeb S, Tyanova S, Hummel M, Schmidt-Supprian M, Cox J, Mann M . Machine Learning-based Classification of Diffuse Large B-cell Lymphoma Patients by Their Protein Expression Profiles. Mol Cell Proteomics. 2015; 14(11):2947-60. PMC: 4638038. DOI: 10.1074/mcp.M115.050245. View

Larance M, Lamond A . Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol. 2015; 16(5):269-80. DOI: 10.1038/nrm3970. View

Calvo S, Clauser K, Mootha V . MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res. 2015; 44(D1):D1251-7. PMC: 4702768. DOI: 10.1093/nar/gkv1003. View

Uhlen M, Fagerberg L, Hallstrom B, Lindskog C, Oksvold P, Mardinoglu A . Proteomics. Tissue-based map of the human proteome. Science. 2015; 347(6220):1260419. DOI: 10.1126/science.1260419. View

Huh W, Falvo J, Gerke L, Carroll A, Howson R, Weissman J . Global analysis of protein localization in budding yeast. Nature. 2003; 425(6959):686-91. DOI: 10.1038/nature02026. View

10.

Cox J, Hein M, Luber C, Paron I, Nagaraj N, Mann M . Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014; 13(9):2513-26. PMC: 4159666. DOI: 10.1074/mcp.M113.031591. View

11.

Scheltema R, Hauschild J, Lange O, Hornburg D, Denisov E, Damoc E . The Q Exactive HF, a Benchtop mass spectrometer with a pre-filter, high-performance quadrupole and an ultra-high-field Orbitrap analyzer. Mol Cell Proteomics. 2014; 13(12):3698-708. PMC: 4256516. DOI: 10.1074/mcp.M114.043489. View

12.

Humphrey S, Azimifar S, Mann M . High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics. Nat Biotechnol. 2015; 33(9):990-5. DOI: 10.1038/nbt.3327. View

13.

Marx V . Mapping proteins with spatial proteomics. Nat Methods. 2015; 12(9):815-9. DOI: 10.1038/nmeth.3555. View

14.

Kulak N, Pichler G, Paron I, Nagaraj N, Mann M . Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods. 2014; 11(3):319-24. DOI: 10.1038/nmeth.2834. View

15.

Raguz J, Wagner S, Dikic I, Hoeller D . Suppressor of T-cell receptor signalling 1 and 2 differentially regulate endocytosis and signalling of receptor tyrosine kinases. FEBS Lett. 2007; 581(24):4767-72. DOI: 10.1016/j.febslet.2007.08.077. View

16.

Fisher H, COOPER T . Electron microscope studies of the microvilli of HeLa cells. J Cell Biol. 1967; 34(2):569-76. PMC: 2107303. DOI: 10.1083/jcb.34.2.569. View

17.

Zanivan S, Krueger M, Mann M . In vivo quantitative proteomics: the SILAC mouse. Methods Mol Biol. 2011; 757:435-50. DOI: 10.1007/978-1-61779-166-6_25. View

18.

Ong S, Blagoev B, Kratchmarova I, Kristensen D, Steen H, Pandey A . Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics. 2002; 1(5):376-86. DOI: 10.1074/mcp.m200025-mcp200. View

19.

Borner G, Hein M, Hirst J, Edgar J, Mann M, Robinson M . Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. Mol Biol Cell. 2014; 25(20):3178-94. PMC: 4196868. DOI: 10.1091/mbc.E14-07-1198. View

20.

Andersen J, Wilkinson C, Mayor T, Mortensen P, Nigg E, Mann M . Proteomic characterization of the human centrosome by protein correlation profiling. Nature. 2003; 426(6966):570-4. DOI: 10.1038/nature02166. View