'Edgetic' perturbation of a C. elegans BCL2 ortholog

Nature Methods

Volumn 6, Issue 11, 2009, Pages 843-849

  Dreze, Matija ^a,b   Charloteaux, Benoit ^a,c   Milstein, Stuart ^a,d   Vidalain, Pierre Olivier ^a,e   Yildirim, Muhammed A ^a   Zhong, Quan ^a   Svrzikapa, Nenad ^a,d   Romero, Viviana ^a   Laloux, Géraldine ^a,b   Brasseur, Robert ^c   Vandenhaute, Jean ^b   Boxem, Mike ^a,f   Cusick, Michael E ^a   Hill, David E ^a   Vidal, Marc ^a  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b UNIVERSITY OF NAMUR   (Belgium)

^c UNIVERSITY OF LIÈGE   (Belgium)

^d ALNYLAM PHARMACEUTICALS   (United States)

^e CNRS   (France)

^f UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; CELL PROTEIN; PROTEIN BCL 2; PROTEIN CED 9; UNCLASSIFIED DRUG;

ALLELE; APOPTOSIS; ARTICLE; CAENORHABDITIS ELEGANS; CENTROSOME; CONTROLLED STUDY; EDGETIC ALLELE; GENE FUNCTION; GENE INTERACTION; GENOTYPE PHENOTYPE CORRELATION; KNOCKOUT GENE; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; TWO HYBRID SYSTEM;

ALLELES; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CALCIUM-BINDING PROTEINS; GENES, HELMINTH; GENOTYPE; MODELS, MOLECULAR; PHENOTYPE; PROTEIN INTERACTION MAPPING; PROTO-ONCOGENE PROTEINS C-BCL-2; REPRESSOR PROTEINS; TWO-HYBRID SYSTEM TECHNIQUES;

CAENORHABDITIS ELEGANS;

EID: 70350721508     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1394     Document Type: Article

References (44)

1. Barabási, A.L. & Oltvai, Z.N. Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
2. Vidal, M. Interactome modeling. FEBS Lett. 579, 1834-1838 (2005).
3. Shih, H.M. et al. A positive genetic selection for disrupting protein-protein interactions: Identification of CREB mutations that prevent association with the coactivator CBP. Proc. Natl. Acad. Sci. USA 93, 13896-13901 (1996).
4. Leanna, C.A. & Hannink, M. The reverse two-hybrid system: A genetic scheme for selection against specific protein/protein interactions. Nucleic Acids Res. 24, 3341-3347 (1996).
5. Vidal, M., Braun, P., Chen, E., Boeke, J.D. & Harlow, E. Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system. Proc. Natl. Acad. Sci. USA 93, 10321-10326 (1996).
6. Vidal, M., Brachmann, R.K., Fattaey, A., Harlow, E. & Boeke, J.D. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA 93, 10315-10320 (1996).
7. Endoh, H. et al. Integrated version of reverse two-hybrid system for the postproteomic era. Methods Enzymol. 350, 525-545 (2002).
8. Gray, P.N., Busser, K.J. & Chappell, T.G. A novel approach for generating full-length, high coverage allele libraries for the analysis of protein interactions. Mol. Cell. Proteomics 6, 514-526 (2007).
9. Kritikou, E.A. et al. C. elegans GLA-3 is a novel component of the MAP kinase MPK-1 signaling pathway required for germ cell survival. Genes Dev. 20, 2279-2292 (2006).
10. Inouye, C., Dhillon, N., Durfee, T., Zambryski, P.C. & Thorner, J. Mutational analysis of STE5 in the yeast Saccharomyces cerevisiae: application of a differential interaction trap assay for examining protein-protein interactions. Genetics 147, 479-492 (1997).
11. Serebriiskii, I., Khazak, V. & Golemis, E.A. A two-hybrid dual bait system to discriminate specificity of protein interactions. J. Biol. Chem. 274, 17080-17087 (1999).
12. Hengartner, M.O., Ellis, R.E. & Horvitz, H.R. Caenorhabditis elegans gene ced-9 protects cells from programmed cell death. Nature 356, 494-499 (1992).
13. Yang, X., Chang, H.Y. & Baltimore, D. Essential role of CED-4 oligomerization in CED-3 activation and apoptosis. Science 281 1355-1357 (1998).
14. Conradt, B. & Horvitz, H.R. The C. elegans protein EGL-1 is required for programmed cell death and interacts with the Bcl-2-like protein CED-9. Cell 93, 519-529 (1998).
15. del Peso, L., Gonzalez, V.M. & Nunez, G. Caenorhabditis elegans EGL-1 disrupts the interaction of CED-9 with CED-4 and promotes CED-3 activation. J. Biol. Chem. 273, 33495-33500 (1998).
16. Yan, N. et al. Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans. Nature 437, 831-837 (2005).
17. Hengartner, M.O. & Horvitz, H.R. Activation of C. elegans cell death protein CED-9 by an amino-acid substitution in a domain conserved in Bcl-2. Nature 369, 318-320 (1994).
18. Yan, N. et al. Structural, biochemical, and functional analyses of CED-9 recognition by the proapoptotic proteins EGL-1 and CED-4. Mol. Cell 15, 999-1006 (2004).
19. Woo, J.S. et al. Unique structural features of a BCL-2 family protein CED-9 and biophysical characterization of CED-9/EGL-1 interactions. Cell Death Differ. 10, 1310-1319 (2003).
20. Walhout, A.J. et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287 116-122 (2000).
21. Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004).
22. Spector, M.S., Desnoyers, S., Hoeppner, D.J. & Hengartner, M.O. Interaction between the C. elegans cell-death regulators CED-9 and CED-4. Nature 385, 653-656 (1997).
23. Hamill, D.R., Severson, A.F., Carter, J.C. & Bowerman, B. Centrosome maturation and mitotic spindle assembly in C. elegans require SPD-5, a protein with multiple coiled-coil domains. Dev. Cell 3 673-684 (2002).
24. Boeke, J.D., LaCroute, F. & Fink, G.R. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197, 345-346 (1984).
25. Rual, J.F. et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178 (2005).
26. Lettre, G. et al. Genome-wide RNAi identifies p53-dependent and -independent regulators of germ cell apoptosis in C. elegans. Cell Death Differ. 11, 1198-1203 (2004).
27. Ellis, H.M. & Horvitz, H.R. Genetic control of programmed cell death in the nematode C. elegans. Cell 44, 817-829 (1986).
28. Boag, P.R., Nakamura, A. & Blackwell, T.K. A conserved RNA-protein complex component involved in physiological germline apoptosis regulation in C. elegans. Development 132, 4975-4986 (2005).
29. Jeffery, C.J. Moonlighting proteins-an update. Mol. Biosyst. 5 345-350 (2009).
30. Zhong, Q. et al. Edgetic perturbation models of human genetic disorders. Mol. Syst. Biol. (in the press).
31. Venkatesan, K. et al. An empirical framework for binary interactome mapping. Nat. Methods 6, 83-90 (2009).
32. Walhout, A.J. & Vidal, M. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24, 297-306 (2001).
33. Walhout, A.J. et al. GATEWAY recombinational cloning: Application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328, 575-592 (2000).
34. Reboul, J. et al. C. elegans ORFeome version 1.1: Experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34, 35-41 (2003).
35. Xu, L. et al. BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3. Nature 425 316-321 (2003).
36. Sali, A. & Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815 (1993).
37. Lins, L., Thomas, A. & Brasseur, R. Analysis of accessible surface of residues in proteins. Protein Sci. 12, 1406-1417 (2003).
38. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77 71-94 (1974).
39. Praitis, V., Casey, E., Collar, D. & Austin, J. Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics 157, 1217-1226 (2001).
40. Hofmann, E.R. et al. Caenorhabditis elegans HUS-1 is a DNA damage checkpoint protein required for genome stability and EGL-1-mediated apoptosis. Curr. Biol. 12, 1908-1918 (2002).
41. Rual, J.F. et al. Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 14, 2162-2168 (2004).
42. Timmons, L., Court, D.L. & Fire, A. Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263, 103-112 (2001).
43. Lehner, B., Tischler, J. & Fraser, A.G. RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions. Nat. Protocols 1, 1617-1620 (2006).
44. Gumienny, T.L., Lambie, E., Hartwieg, E., Horvitz, H.R. & Hengartner, M.O. Genetic control of programmed cell death in the Caenorhabditis elegans hermaphrodite germline. Development 126, 1011-1022 (1999).