Protein knockouts in living eukaryotes using degradFP and green fluorescent protein fusion targets

Current Protocols in Protein Science

Volumn , Issue SUPPL.73, 2013, Pages

  Caussinus, Emmanuel ^a   Kanca, Oguz ^a   Affolter, Markus ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Drosophila; F Box; GFP; Nanobodies

Indexed keywords

DEGRADE GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; RNA; UNCLASSIFIED DRUG; NANOBODY;

ARTICLE; EUKARYOTE; GENE FUNCTION; GENE LOSS; GENE MUTATION; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DEPLETION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; RNA INTERFERENCE; ANIMAL; CHEMISTRY; DROSOPHILA; DROSOPHILA MELANOGASTER; F-BOX; GENE INACTIVATION; GENETICS; GFP; METABOLISM; METHODOLOGY; PROTEIN STABILITY;

DROSOPHILA; F-BOX; GFP; NANOBODIES;

ANIMALS; DROSOPHILA MELANOGASTER; GENE KNOCKOUT TECHNIQUES; GREEN FLUORESCENT PROTEINS; PROTEIN STABILITY; RECOMBINANT FUSION PROTEINS;

EID: 84907279793     PISSN: 19343655     EISSN: 19343663     Source Type: Journal    
DOI: 10.1002/0471140864.ps3002s73     Document Type: Article

References (38)

1. Asakawa, K. and Kawakami, K. 2009. The tol2-mediated Gal4-UAS method for gene and enhancer trapping in zebrafish. Methods 49:275-281.
2. Ashburner, M. 1990. Drosophila: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
3. Banaszynski, L.A., Chen, L.C., Maynard-Smith, L.A., Ooi, A.G. and Wandless, T.J. 2006. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules. Cell 126:995-1004.
4. Berdougo, E., Terret, M.E., and Jallepalli, P.V. 2009. Functional dissection of mitotic regulators through gene targeting in human somatic cells. Methods Mol. Biol. 545:21-37.
5. Brand, A.H. and Perrimon, N. 1993. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401-415.
6. Buszczak, M., Paterno, S., Lighthouse, D., Bachman, J., Planck, J., Owen, S., Skora, A.D., Nystul, T.G., Ohlstein, B., Allen, A., Wilhelm, J.E., Murphy, T.D., Levis, R.W., Matunis, E., Srivali, N., Hoskins, R.A., and Spradling, A.C. 2007. The carnegie protein trap library: A versatile tool for Drosophila developmental studies. Genetics 175:1505-1531.
7. Carette, J.E., Guimaraes, C.P., Varadarajan M., Park, A.S., Wuethrich, I., Godarova, A., Kotecki, M., Cochran, B.H., Spooner, E., Ploegh, H.L., and Brummelkamp, T.R. 2009. Haploid genetic screens in human cells identify host factors used by pathogens. Science 326:1231-1235.
8. Caussinus, E., Kanca, O., and Affolter, M. 2011. Fluorescent fusion protein knockout mediated by anti-GFP nanobody. Nat. Struct. Mol. Biol. 19:117-121.
9. Ciechanover, A. 1998. The ubiquitin-proteasome pathway: On protein death and cell life. EMBO J. 17:7151-7160.
10. Dohmen, R.J., Wu, P., and Varshavsky, A. 1994. Heat-inducible degron: A method for constructing temperature-sensitive mutants. Science 263:1273-1276.
11. Ekker, S.C. 2000. Morphants: A new systematic vertebrate functional genomics approach. Yeast 17:302-306.
12. Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., and Mello, C.C. 1998. Potent and specific genetic interference by doublestranded RNA in C. elegans. Nature 391:806-811.
13. Greenspan, R.J. 2004. Fly pushing: the theory and practice of Drosophila genetics second edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
14. Harder, B., Schomburg, A., Pflanz, R., Küstner, K., Gerlach, N., and Schuh, R. 2008. Tev proteasemediated cleavage in Drosophila as a tool to analyze protein functions in living organisms. Biotechniques 44:765-772.
15. Hartenstein, V. 1993. Atlas of Drosophila Development. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
16. Haruki,H., Nishikawa, J., and Laemmli, U.K. 2008. The anchor-away technique: Rapid, conditional establishment of yeast mutant phenotypes. Mol. Cell 31:925-932.
17. Inoue, T., Heo, W.D., Grimley, J.S., Wandless, T.J. and Meyer, T. 2005. An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways. Nat. Methods 2:415-418.
18. Jiang, J. and Struhl, G. 1998. Regulation of the hedgehog and wingless signalling pathways by the F-box/WD40-repeat protein Slimb. Nature 391:493-496.
19. Kawakami, K., Abe, G., Asada, T., Asakawa, K., Fukuda, R., Ito, A., Lal, P., Mouri, N.,Muto, A., Suster, M.L., Takakubo, H., Urasaki, A., Wada, H., and Yoshida M. 2010. Ztrap: Zebrafish gene trap and enhancer trap database. BMC Dev. Biol. 10:105.
20. Kelso R.J., Buszczak, M., Quiñones, A.T., Castiblanco, C., Mazzalupo, S., and Cooley, L. 2004. Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster. Nucleic Acids Res. 32:D418-D420.
21. Mavrakis, M., Rikhy, R., Lilly, M. and Lippincott-Schwartz, J. 2008. Fluorescence imaging techniques for studying Drosophila embryo development. Curr. Protoc. Cell Biol. 39:4.18.1-4.18.43.
22. McGuire, S.E., Le, P.T., Osborn, A.J., Matsumoto, K., and Davis, R.L. 2003. Spatiotemporal rescue of memory dysfunction in Drosophila. Science 302:1765-1768.
23. Morin, X., Daneman, R., Zavortink, M., and Chia, W. 2001. A protein trap strategy to detect gfptagged proteins expressed from their endogenous loci in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 98:15050-15055.
24. Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T., and Kanemaki, M. 2009. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 6:917-922.
25. Pauli, A., Althoff, F., Oliveira, R.A., Heidmann, S., Schuldiner, O., Lehner, C.F., Dickson, B.J., and Nasmyth, K. 2008. Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons. Dev. Cell 14:239-251.
26. Pastrana, E. 2012. Degrading proteins with intracellular antibodies. Nat. Methods 9:228.
27. Pina,C. and Pignoni, F. 2012. Tubby-RFP balancers for developmental analysis: FM7c 2xTb-RFP, CyO 2xTb-RFP, and TM3 2xTb-RFP. Genesis 50:119-123.
28. Quiñones-Coello, A.T., Petrella, L.N., Ayers, K., Melillo, A., Mazzalupo, S., Hudson, A.M., Wang, S., Castiblanco, C., Buszczak, M., Hoskins, R.A., and Cooley, L. 2007. Exploring strategies for protein trapping in Drosophila. Genetics 175:1089-1104.
29. Rothbauer, U., Zolghadr, K., Muyldermans, S., Schepers, A., Cardoso, M.C., and Leonhardt, H. 2008. A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins. Mol. Cell Proteomics 7:282-289.
30. Royou, A., Field, C., Sisson, J.C., Sullivan,W., and Karess, R. 2004. Reassessing the role and dynamics of nonmuscle myosin II during furrow formation in early Drosophila embryos. Mol. Biol. Cell 15:838-850.
31. Saerens, D., Pellis, M., Loris, R., Pardon, E., Dumoulin, M., Matagne, A., Wyns, L., Muyldermans, S., and Conrath, K. 2005. Identification of a universal vhh framework to graft non-canonical antigen-binding loops of camel single-domain antibodies. J. Mol. Biol. 352:597-607.
32. Sakamoto, K.M., Kim, K.B., Kumagai, A., Mercurio, F., Crews, C.M., and Deshaies, R.J. 2001. Protacs: Chimeric molecules that target proteins to the SKP1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl. Acad. Sci. U.S.A. 98:8554-8559.
33. Schornack, S., Fuchs, R., Huitema, E., Rothbauer, U., Lipka,V., and Kamoun, S. 2009. Protein mislocalization in plant cells using a GFP-binding chromobody. Plant J. 60:744-754.
34. Tabata, T., Eaton, S., and Kornberg, T.B. 1992. The Drosophila hedgehog gene is expressed specifically in posterior compartment cells and is a target of engrailed regulation. Genes Dev. 6:2635-2645.
35. Taxis, C., Stier, G., Spadaccini, R., and Knop, M. 2009. Efficient protein depletion by genetically controlled deprotection of a dormant N-degron. Mol. Syst. Biol. 5:267.
36. Varshavsky, A. 2012. The ubiquitin system, an immense realm. Ann. Rev. Biochem. 81: 167-176.
37. Zhang, J., Zheng, N., and Zhou, P. 2003. Exploring the functional complexity of cellular proteins by protein knockout. Proc. Natl. Acad. Sci. U.S.A. 100:14127-14132.
38. Zhou, P., Bogacki, R., Mcreynolds, L., and Howley, P.M. 2000. Harnessing the ubiquitination machinery to target the degradation of specific cellular proteins. Mol. Cell 6:751-756.