Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 39, 2015, Pages 12093-12098

  Chen, Chiao Lin ^a   Hu, Yanhui ^a   Udeshi, Namrata D ^b   Lau, Thomas Y ^b   Wirtz Peitz, Frederik ^a   He, Li ^a   Ting, Alice Y ^b,c   Carr, Steven A ^b   Perrimon, Norbert ^a,d  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

APEX; Drosophila; Proteomics

Indexed keywords

ASCORBATE PEROXIDASE; MITOCHONDRIAL PROTEIN; PROTEOME;

ANIMAL TISSUE; ARTICLE; BIOTINYLATION; CELL COMPARTMENTALIZATION; CELL ORGANELLE; CELL SPECIFICITY; CONTROLLED STUDY; DROSOPHILA; ENZYME ENGINEERING; ENZYME MECHANISM; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; ANIMAL; BIOLOGY; GENETIC ENGINEERING; GENETICS; METABOLISM; PROCEDURES; PROTEIN DATABASE; STAINING;

ANIMALS; ASCORBATE PEROXIDASES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DROSOPHILA; GENETIC ENGINEERING; PROTEOMICS; STAINING AND LABELING;

EID: 84942852102     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1515623112     Document Type: Article

References (32)

1. Rhee HW, et al. (2013) Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 339(6125): 1328-1331.
2. Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118(2): 401-415.
3. Kalderon D, Roberts BL, Richardson WD, Smith AE (1984) A short amino acid sequence able to specify nuclear location. Cell 39(3 Pt 2): 499-509.
4. Wen W, Meinkoth JL, Tsien RY, Taylor SS (1995) Identification of a signal for rapid export of proteins from the nucleus. Cell 82(3): 463-473.
5. Rizzuto R, Brini M, Pizzo P, Murgia M, Pozzan T (1995) Chimeric green fluorescent protein as a tool for visualizing subcellular organelles in living cells. Curr Biol 5(6): 635-642.
6. McQuibban GA, Lee JR, Zheng L, Juusola M, Freeman M (2006) Normal mitochondrial dynamics requires rhomboid-7 and affects Drosophila lifespan and neuronal function. Curr Biol 16(10): 982-989.
7. Martell JD, et al. (2012) Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nat Biotechnol 30(11): 1143-1148.
8. Ross PL, et al. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12): 1154-1169.
9. DeSouza L, et al. (2005) Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J Proteome Res 4(2): 377-386.
10. Wiese S, Reidegeld KA, Meyer HE, Warscheid B (2007) Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research. Proteomics 7(3): 340-350.
11. Mertins P, et al. (2012) iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol Cell Proteomics 11(6): M111.014423.
12. Vinayagam A, et al. (2013) Protein complex-based analysis framework for high-throughput data sets. Sci Signal 6(264): rs5.
13. Guruharsha KG, et al. (2011) A protein complex network of Drosophila melanogaster. Cell 147(3): 690-703.
14. Soltys BJ, Gupta RS (1999) Mitochondrial-matrix proteins at unexpected locations: Are they exported? Trends Biochem Sci 24(5): 174-177.
15. Stadler C, et al. (2013) Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. Nat Methods 10(4): 315-323.
16. Yin S, et al. (2013) Quantitative evaluation of the mitochondrial proteomes of Drosophila melanogaster adapted to extreme oxygen conditions. PLoS One 8(9): e74011.
17. Lotz C, et al. (2014) Characterization, design, and function of the mitochondrial proteome: From organs to organisms. J Proteome Res 13(2): 433-446.
18. Smith AC, Blackshaw JA, Robinson AJ (2012) MitoMiner: A data warehouse for mitochondrial proteomics data. Nucleic Acids Res 40(Database issue): D1160-D1167.
19. Sardiello M, Licciulli F, Catalano D, Attimonelli M, Caggese C (2003) MitoDrome: A database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion. Nucleic Acids Res 31(1): 322-324.
20. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using Target P, SignalP and related tools. Nat Protoc 2(4): 953-971.
21. Hu Y, et al. (2011) An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics 12: 357.
22. Rand DM, Haney RA, Fry AJ (2004) Cytonuclear coevolution: The genomics of cooperation. Trends Ecol Evol 19(12): 645-653.
23. Priyadarsini KI (2010) Radiation Chemistry Applied to Antioxidant Research. Recent Trends in Radiation Chemistry, eds Wishart JF, Madhava Rao (World Scientific, Singapore), pp 577-596.
24. Mortensen A, Skibsted LH (1997) Importance of carotenoid structure in radical-scavenging reactions. J Agric Food Chem 45(8): 2970-2977.
25. Bendayan M (2001) Worth its weight in gold. Science 291(5507): 1363-1365.
26. Mayer G, Bendayan M (1997) Biotinyl-tyramide: A novel approach for electron microscopic immunocytochemistry. J Histochem Cytochem 45(11): 1449-1454.
27. Ranganayakulu G, Schulz RA, Olson EN (1996) Wingless signaling induces nautilus expression in the ventral mesoderm of the Drosophila embryo. Dev Biol 176(1): 143-148.
28. Hinz U, Giebel B, Campos-Ortega JA (1994) The basic-helix-loop-helix domain of Drosophila lethal of Scute protein is sufficient for proneural function and activates neurogenic genes. Cell 76(1): 77-87.
29. Speicher SA, Thomas U, Hinz U, Knust E (1994) The Serrate locus of Drosophila and its role in morphogenesis of the wing imaginal discs: Control of cell proliferation. Development 120(3): 535-544.
30. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2(8): 1896-1906.
31. Pagliarini DJ, et al. (2008) A mitochondrial protein compendium elucidates complex I disease biology. Cell 134(1): 112-123.
32. Berezikov E, et al. (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res 21(2): 203-215.