Protein interaction maps for model organisms

Nature Reviews Molecular Cell Biology

Volumn 2, Issue 1, 2001, Pages 55-62

  Walhout, Albertha J M ^a   Vidal, Marc ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEOME;

ANIMAL; BIOLOGICAL MODEL; HUMAN; MACROMOLECULE; PHYSIOLOGY; REVIEW; TWO HYBRID SYSTEM;

ANIMALS; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, BIOLOGICAL; PROTEINS; PROTEOME; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 0035222942     PISSN: 14710072     EISSN: None     Source Type: Journal    
DOI: 10.1038/35048107     Document Type: Article

References (78)

1. Blattner, F. R. et al. The complete genome sequence of Escherichia coli K12. Science 277, 1453-1474 (1997).
2. Goffeau, A. et al. The yeast genome directory. Nature 387, S1-S105 (1997).
3. The C. elegans sequencing consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018 (1998).
4. Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
5. Pennisi, E. Finally, the book of life and instructions for navigating it. Science 288, 2304-2307 (2000).
6. Ewing, B. & Green, P. Analysis of expressed sequence tags indicates 35,000 human genes. Nature Genet. 25, 232-234 (2000).
7. Roest-Crollius, H. et al. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nature Genet. 25, 235-238 (2000).
8. Liang, F. et al. Gene index analysis of the human genome estimates approximately 120,000 genes. Nature Genet. 25, 239-240 (2000).
9. Chervitz, S. A. et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282, 2022-2027 (1998).
10. Rubin, G. M. et al. Comparative genomics of the eukaryotes. Science 287, 2204-2215 (2000). References 9 and 10 are an excellent source for comparative genomics in worms, yeast and flies.
11. Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
12. Lockhart, D. J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675-1680 (1996).
13. Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610-614 (1996).
14. White, K. P., Rifkin, S. A., Hurban, P. & Hogness, D. S. Microarray analysis of Drosophila development during metamorphosis. Science 286, 2179-2184 (1999).
15. Reinke, V. et al. A global profile of germline gene expression in C. elegans. Mol. Cell 6, 605-616 (2000).
16. Hill, A. A., Hunter, C. P., Tsung, B. T., Tucker-Kellogg, G. & Brown, E. L. Genomic analysis of gene expression in C. elegans. Science 290, 809-812 (2000).
17. Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
18. Ross-Macdonald, P. et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413-418 (1999).
19. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998).
20. Fraser, A. G. et al. Functional genomics analysis of C. elegans chromosome I by systematic RNA interference. Nature 408, 325-330 (2000).
21. Gonczy, P. et al. Functional genomics analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331-336 (2000).
22. Lynch, A. S., Briggs, D. & Hope, I. A. Developmental expression pattern screen for genes predicted in the C. elegans genome sequencing project. Nature Genet. 11, 309-313 (1995).
23. Ding, D. Q. et al. Large-scale screening of intracellular protein localization in living fission yeast cells by the use of a GFP-fusion domain DNA library. Genes Cells 5, 169-190 (2000).
24. Jansen, G. et al. The complete family of genes encoding G proteins of Caenorhabditis elegans. Nature Genet. 21, 414-419 (1999).
25. Bartel, P. L. Roecklein, J. A., SenGupta, D. & Fields, S. A protein linkage map of Escherichia coli bacteriophage T7. Nature Genet. 12, 72-77 (1996).
26. Lander, E. S. The new genomics: global views of biology. Science 274, 536-539 (1996).
27. Walhout, A. J. M., Endoh, H., Thierry-Mieg, N., Wong, W. & Vidal, M. A model of elegance. Am. J. Hum. Genet. 63, 955-961 (1998).
28. Hengartner, M. O. in C. elegans II (eds Riddle, D. L., Blumenthal, T., Meyer, B. & Priess, J. R.) 383-415 (Cold Spring Hartor Laboratory Press, Cold Spring Harbor, 1997).
29. Yang, X., Chang, H. Y. & Baltimore, D. Essential role of CED-4 oligomerization in CED-3 activation and apoptosis. Science 281, 1355-1357 (1998).
30. Chinnaiyan, A. M., O'Rourke, K., Lane, B. R. & Dixit, V. M. Interaction of CED-4 with CED-3 and CED-9: a molecular framework for cell death. Science 275, 1122-11126 (1997).
31. Choi, K. Y., Satterberg, B., Lyons, D. M. & Elion, E. A. Ste5 tethers multiple protein kinases in the MAP kinase cascade required for mating in S. cerevisiae. Cell 78, 499-512 (1994).
32. Zhu, L., Harlow, E. & Dynlacht, B. D. p107 uses a P21CIP1-related domain to bind cyclin/cdk2 and regulate interactions with E2F. Genes Dev. 9, 1740-1752 (1995).
33. Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294 (1998).
34. Harlow, E., Whyte, P., Franza, B. R. J. & Schley, C. Association of adenovirus early-region 1A proteins with cellular polypeptides. Mol. Cell. Biol. 6, 1579-1589 (1986).
35. Whyte, P. et al. Association between an oncogene and an anti-oncogene: the adenovirus E1A proteins bind to the retinoblastoma gene product. Nature 334, 124-129 (1988).
36. Pandey, A. & Mann, M. Proteomics to study genes and genomes. Nature 405, 837-846 (2000).
37. Yates, J. R. Mass spectrometry. From genomics to proteomics. Trends Genet. 16, 5-8 (2000).
38. Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture and transport mechanism. J. Cell Biol. 148, 635-651 (2000). This paper describes a comprehensive approach for identifying components of a large protein complex and describes validation strategies to strengthen these observations obtained by classical proteomic strategies.
39. Martzen, M. R. et al. A biochemical genomics approach for identifying genes by the activity of their products. Science 286, 1153-1155 (1999). This paper describes a biochemical genomic approach in yeast by identifying enzymes using the yeast proteome fused to glutathione-S-transferase (GST).
40. Burge, C. & Karlin, S. Prediction of complete structures in human genomic DNA. J. Mol. Biol. 268, 78-94 (1997).
41. Birney, E. & Durbin, R. Using GeneWise in the Drosophila annotation experiment. Genome Res. 10, 547-548 (2000).
42. Reese, M. G., Kulp, D., Tammana, H. & Haussler, D. Genie - gene finding in Drosophila melanogaster. Genome Res. 10, 529-538 (2000).
43. Enright, A. J., Iliopoulos, I., Kyrpides, N. C. & Ouzonis, C. A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 85-89 (1999).
44. Marcotte, E. M. et al. Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753 (1999).
45. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. & Eisenberg, D. A combined algorithm for genome-wide prediction of protein function. Nature 402, 83-86 (1999). References 43-45 were among the first to describe in silico reverse proteomic strategies.
46. Xenarios, I. et al. DIP: the database of interacting proteins. Nucleic Adds Res. 28, 289-291 (2000).
47. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96, 4285-4288 (1999).
48. Walhout, A. J. M. et al. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287, 116-122 (2000). This paper describes the first, small-scale, worm protein interaction map using the yeast two-hybrid system.
49. Fields, S. & Song, O. A novel genetic system to detect protein-protein interactions. Nature 340, 245-246 (1989).
50. Finley, R. L. Jr & Brent, R. Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc. Natl Acad. Sci. USA 91, 12980-12984 (1994).
51. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
52. Ito, T. et al. Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between yeast proteins. Proc. Natl Acad. Sci. USA 97, 1143-1147 (2000). References 51 and 52 describe large-scale protein interaction maps for yeast using the yeast two-hybrid system.
53. Fromont-Racine, M., Rain, J. C. & Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet. 16, 277-282 (1997).
54. Fromont-Racine, M. et al. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17, 95-110 (2000).
55. Flores, A. et al. A protein-protein interaction map of yeast RNA polymerase III. Proc. Natl Acad. USA 96, 7815-7820 (1999).
56. Walhout, A. J. M., Boulton, S. J. & Vidal, M. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17, 88-94 (2000).
57. Garrels, J. I. YPD - A database for the proteins of Saccharomyces cerevisiae. Nucleic Acids Res. 24, 46-49 (1996).
58. Ferguson, E. L. & Horvitz, H. R. The multivulva phenotype of certain Caenorhabditis elegans mutants results from defects in two functionally redundant pathways. Genetics 123, 109-121 (1989).
59. Solari, F. & Ahringer, J. NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans. Curr. Biol. 10, 223-226 (2000).
60. Hsieh, J. et al. The RING finger/B-box factor TAM-1 and a retinoblastoma-like protein UN-35 modulate context-dependent gene silencing in Caenorhabditis elegans. Genes Dev. 13, 2958-2970 (1999).
61. Thomas, J. H. & Horvitz, H. R. The C. elegans gene lin-36 acts cell autonomously in the lin-35 Rb pathway. Development 126, 3449-3459 (1999).
62. Xue, Y. et al. NURD, a novel complex with both ATP-dependent chromatin-remodeling and histone deacetylase activities. Mol. Cell 2, 851-861 (1998).
63. Wittinghofer, A. & Nassar, N. How Ras-related proteins talk to their effectors. Trends Biochem. Sci. 21, 488-491 (1996).
64. Tan, P. B. & Kim, S. K. Signaling specificity: the RTK/RAS/MAP kinase pathway in metazoans. Trends Genet. 15, 145-149 (1999).
65. Greenwald, I. LIN-12/Notch signaling: lessons from worms and flies. Genes Dev. 12, 1751-1762 (1998).
66. Petcherski, A. G. & Kimble, J. LAG-3 is a putative transcriptional activator in the C. elegans Notch pathway. Nature 405, 364-368 (2000).
67. Damelin, M. & Silver, P. A. Mapping interactions between nuclear transport factors in living cells reveals pathways through the nuclear pore complex. Mol. Cell 5, 133-140 (2000). This paper describes the use of fluorescence resonance energy transfer (FRET) for protein interaction mapping in vivo in yeast.
68. Kaech, S. M., Whitfield, C. W. & Kim, S. K. The LIN-2/LIN-7/LIN-10 complex mediates basolateral membrane localization of the C. elegans EGF receptor LET-23 in vulval epithelial cells. Cell 94, 761-771 (1998).
69. Vidal, M., Brachmann, R., Fattaey, A., Harlow, E. & Boeke, J. D. Reverse two-hybrid and one-hybrid systems to detect dissocation of protein-protein and DNA-protein interactions. Proc. Natl Acad. Sci. USA 93, 10315-10320 (1996).
70. 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).
71. Vidal, M. & Endoh, H. Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol. 17, 374-381 (1999).
72. Walhout, A. J. M. et al. GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328, 575-592 (2000).
73. Zozulya, S., Lioubin, M., Hill, R. J., Abram, C. & Gishizky. M. L. Mapping signal transduction pathways by phage display. Nature Biotechnol. 17, 1193-1198 (1999).
74. Pelletier, J. N., Arndt, K. M., Pluckthun, A. & Michnick, S. W. An in vivo library-versus-library selection of optimized protein-protein interactions. Nature Biotechnol. 17, 683-690 (1999).
75. Walhout, A. J. M. & Vidal, M. A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome Res. 9, 1128-1134 (1999).
76. Aronheim, A., Zandi, E., Hennemann, H., Elledge, S. J. & Karin, M. Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions. Mol. Cell. Biol. 17, 3094-3102 (1997).
77. Sternberg, P. W. & Han, M. Genetics of RAS signalling in C. elegans. Trends Genet. 14, 466-472 (1998).
78. Lu, X. & Horvitz, H. R. lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48. Cell 95, 981-991 (1998).