Assigning Function to Yeast Proteins by Integration of Technologies

Molecular Cell, Vol 12, 1353-1365, December 2003

Tony R. Hazbun^1,2, Lars Malmström³, Scott Anderson⁴, Beth J. Graczyk³, Bethany Fox³, Michael Riffle³, Bryan A. Sundin³, J. Derringer Aranda², W. Hayes McDonald⁴, Chui-hwei Chun³, Brian E. Snydsman³, Phillip Bradley³, Eric G. D. Muller³, Stanley Fields^1,2, David Baker^1,3, John R. Yates III⁴ and Trisha N. Davis^3*

¹Howard Hughes Medical Institute, ²Departments of Genome Sciences and Medicine, ³Department of Biochemistry, University of Washington, Seattle, WA, ⁴Department of Cell Biology, Scripps Research Institute, La Jolla, CA

Abstract:

Interpreting genome sequences requires the functional analysis of thousands of predicted proteins, many of which are uncharacterized and without obvious homologues. To assess whether the roles of large sets of uncharacterized genes can be assigned by targeted application of a suite of technologies, we used four complementary protein-based methods to analyze a set of 100 uncharacterized but essential open reading frames (ORFs) of the yeast Saccharomyces cerevisiae. These proteins were subjected to affinity purification and mass spectrometry analysis to identify co-purifying proteins; two-hybrid analysis to identify interacting proteins; fluorescence microscopy to localize the proteins; and structure prediction methodology to predict structural domains or identify remote homologies. Integration of the data assigned function to 48 ORFs using at least two of the Gene Ontology (GO) categories of biological process, molecular function, and cellular component; 77 ORFs were annotated by at least one method. This combination of technologies, coupled with annotation using GO, is a powerful approach to classify genes.

How To Use This Site:

This site provides the ability to search for all of the data we found for a particular ORF or gene. To search, simply type in the name of the ORF or gene in the search box near the top of every page. This search is not limited to the 100 essential uncharacterized ORFs we studied. You are able to view and download all of our mass spectrometry, fluorescence microscopy, yeast two-hybrid and protein structure prediction data for any ORF for which we have experimental data.

In addition, we provide three tables to summarize our findings for the 100 essential uncharacterized ORFs.

• The COMPLEXES table lists the complexes we identified by mass spectrometry. Each complex is also annotated with a Gene Ontology (GO) term for biological process.
• The GO LIST gives the GO terms we have assigned to each of the uncharacterized ORFs for biological process, cellular component and molecular function.
• The STATUS LIST shows which technologies have contributed experimental data for each of the 100 essential uncharacterized ORFs. If a technology failed to yield experimental data, the reason is also given in this table.

Finally, the About YRC page will give you a brief description of the Yeast Resource Center, and provide a link to our official web site.

Supplementary Tables:

• Table S1. Summary and convergence of data obtained from the four technologies.
• Table S2. Assignment of GO terms for all the members of the YDR288w and YML023c DNA repair complexes.