A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae


Two large-scale yeast two-hybrid screens were undertaken to identify protein–protein interactions between full-length open reading frames predicted from the Saccharomyces cerevisiae genome sequence. In one approach, we constructed a protein array of about 6,000 yeast transformants, with each transformant expressing one of the open reading frames as a fusion to an activation domain. This array was screened by a simple and automated procedure for 192 yeast proteins, with positive responses identified by their positions in the array. In a second approach, we pooled cells expressing one of about 6,000 activation domain fusions to generate a library. We used a high-throughput screening procedure to screen nearly all of the 6,000 predicted yeast proteins, expressed as Gal4 DNA-binding domain fusion proteins, against the library, and characterized positives by sequence analysis. These approaches resulted in the detection of 957 putative interactions involving 1,004 S. cerevisiae proteins. These data reveal interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes. The results of these screens are shown here.

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Figure 1: The two-hybrid assay carried out by screening a protein array.
Figure 2: Data analysis software.
Figure 3: Expanded pathways shown using the software as described in the text.


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We thank K. Furtak, J. Gilbert, N. Huber, M. Laurino, L. Matthies, A. Perna, C. Pratt and B. Rittman for technical assistance; B. Drees, R. Hughes and S. McCraith for help with some of the experiments; P. Hodges (Proteome) for providing a compilation of protein interactions; and B. Byers, M. Olson, R. Franza, M. Roth, D. Lewin, T. Jarvie and J. Simons for comments on the manuscript. S.F. is supported by grants from the NIH and the Merck Genome Research Institute. P.U. is supported by a fellowship from the Deutscher Akademischer Austauschdienst (DAAD). S.F. is an investigator of the Howard Hughes Medical Institute.

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Correspondence to Stanley Fields.

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Uetz, P., Giot, L., Cagney, G. et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000). https://doi.org/10.1038/35001009

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