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Cited by 1,884Advanced Biosensing Techniques and ApplicationsAdvanced Proteomics Techniques and ApplicationsFungal and yeast genetics research

Global Analysis of Protein Activities Using Proteome Chips

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Zhu, Heng, Bilgin, Metin, Bangham, Rhonda, Hall, David, Casamayor, Antonio, Bertone, Paul, Lan, Ning, Jansen, Ronald +7 more·2001·Science
DOI 10.1126/science.1062191
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Abstract

To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. We identified many new calmodulin- and phospholipid-interacting proteins; a common potential binding motif was identified for many of the calmodulin-binding proteins. Thus, microarrays of an entire eukaryotic proteome can be prepared and screened for diverse biochemical activities. The microarrays can also be used to screen protein-drug interactions and to detect posttranslational modifications.

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  1. S. Fields, Y. Kohara, D. J. Lockhart, Proc. Natl. Acad. Sci. U.S.A. 96, 8825 (1999);
  2. A. Goffeau et al., Science 274, 563 (1996).
  3. P. Ross-Macdonald et al., Nature 402, 413 (1999);
  4. J. L., DeRisi, V. R. Iyer, P. O. Brown, Science 278, 680 (1997);
  5. E. A. Winzeler et al., Science 285, 901 (1999);
  6. P. Uetz et al., Nature 403, 623 (2000);
  7. T. Ito et al., Proc. Natl. Acad. Sci. U.S.A. 97, 1143 (2000).
  8. H. Zhu, M. Snyder, Curr. Opin. Chem. Biol. 5, 40 (2001).
  9. M. R. Martzen et al., Science 286, 1153 (1999).
  10. H. Zhu et al., Nature Genet. 26, 283 (2000).
  11. G. MacBeath, S. L. Schreiber, Science 289, 1760 (2000).
  12. A. Caveman, J. Cell Sci. 113, 3543 (2000).
  13. P. Arenkov et al., Anal. Biochem. 278, 123 (2000).
  14. D. A. Mitchell, T. K. Marshall, R. J. Deschenes, Yeast 9, 715 (1993). The expression vector pEGH was created by inserting an RGS-HisX6 epitope tag between the GST gene and the polycloning site of pEG(KG). The yeast ORFs were cloned using the strategy described previously (5), except every step was done in a 96-well format. Plasmid DNAs confirmed by DNA sequencing were reintroduced into both yeast (Y258) and E. coli (DH5α). The library contains 5800 unique ORFs.
  15. For details of 96-well format protein purification protocol, a full list of results from all the experiments, and the design of the positive identification algorithms, please visit our public web site (http://bioinfo.mbb.yale.edu/proteinchip) and supplementary material at Science Online (www.sciencemag.org/cgi/content/full/1062191/DC1).
  16. S. S. Hook, A. R. Means, Annu. Rev. Pharmacol. Toxicol. 41, 471 (2001).
  17. M. S. Cyert, R. Kunisawa, D. Kaim, J. Thorner, Proc. Natl. Acad. Sci. U.S.A. 88, 7376 (1991).
  18. D. A. Stirling, K. A. Welch, M. J. Stark, EMBO J. 13, 4329 (1994).
  19. F. Bohl, C. Kruse, EMBO J. 19, 5514 (2000);
  20. E. Bertrand et al., Mol. Cell 2, 437 (1998).
  21. D. C. Winter, E. Y. Choe, R. Li, Proc. Natl. Acad. Sci. U.S.A. 96, 7288 (1999).
  22. C. Schaerer-Brodbeck, H. Riezman, Mol. Biol. Cell 11, 1113 (2000).
  23. K. Homma, J. Saito, R. Ikebe, M. Ikebe, J. Biol. Chem. 275, 34766 (2000).
  24. J. Menendez, J. Delgado, C. Gancedo, Yeast 14, 647 (1998).
  25. G. Odorizzi, M. Babst, S. D. Emr, Trends Biochem. Sci. 25, 229 (2000);
  26. D. A. Fruman et al., Annu. Rev. Biochem. 67, 481 (1998);
  27. T. F. Martin, Annu. Rev. Cell Dev. Biol. 14, 231 (2000);
  28. S. Wera, J. C. T. Bergsma, FEMS Yeast Res. 1406, 1 (2001).
  29. Positives were identified using a combination of the GenePix software which computes a local intensity / www.sciencexpress.org / 26 July 2001 / Page 4/ 10.1126/science.1062191 background for each spot and a series of algorithms we developed. Details can be found at http://bioinfo.mbb.yale.edu/proteinchip and at www.sciencemag.org/cgi/content/full/1062191/DC1. · DOI
  30. M. C. Costanzo et al., Nucleic Acids Res. 29, 75 (2001).
  31. M. Gerstein, Proteins 33, 518 (1998).
  32. K. Ansari et al., J. Biol. Chem. 274, 30052 (1999).
  33. Y. Barral, M. Parra, S. Bidlingmaier, M. Snyder, Genes Dev. 13, 176 (1999).
  34. Y. Li, T. Kane, C. Tipper, P. Spatrick, D. D. Jenness, Mol. Cell Biol. 19, 3588 (1999).
  35. I. Arnold et al., J. Biol. Chem. 274, 36 (1999).
  36. S. Chu et al., Science 282, 699 (1998).
  37. A. Casamayor et al., Curr. Biol. 9, 186 (1999);
  38. R. Guerra, M. L. Bianconi, Biosci. Rep. 20, 41 (2000).
  39. M. Pardo et al., Yeast 15, 459 (1999).

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Authors
Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, R. A., Gerstein, M., & Snyder, M.
Affiliations
  • Department of Molecular, Cellular, and Developmental Biology and
  • Yale University (US)
  • North Carolina State University (US)
Corresponding author
Snyder, Michael
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2001-09-14
Volume
293
Issue
5537
Pages
2101-2105
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.1062191
OpenAlex
W4233751197
Cited by
1,884
References
37
Citations by year
2026: 9 · 2025: 16 · 2024: 20 · 2023: 23 · 2022: 37 · 2021: 35 · 2020: 34 · 2019: 33 · 2018: 39 · 2017: 49 · 2016: 56 · 2015: 62 · 2014: 61 · 2013: 60 · 2012: 97
FWCI
47.46
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Keywords
proteome microarray, yeast proteome, protein-protein interaction, phospholipid binding, calmodulin-binding proteins, calmodulin binding motif, drug-protein interactions, post-translational modification
MeSH terms
Amino Acid Sequence, Calmodulin, Calmodulin-Binding Proteins, Cell Membrane, Cloning, Molecular, Fungal Proteins, Glucose, Liposomes, Membrane Proteins, Molecular Sequence Data, Phosphatidylcholines, Phosphatidylinositols, Phospholipids, Protein Binding, Recombinant Fusion Proteins, Saccharomyces cerevisiae, Signal Transduction, Open Reading Frames, Peptide Library, Streptavidin, Proteome, Amino Acid Motifs

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