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Submitted on August 25, 2003
Departments of Physics and Computer Science, Wake Forest University, Winston-Salem, NC 27109-7507
Corresponding Author: fetrowjs{at}wfu.edu
An analysis of the structurally and catalytically diverse serine hydrolase protein family in the Saccharomyces cerevisiae proteome was undertaken using two independent but complementary, large-scale approaches. The first approach is based on computational analysis of serine hydrolase active site structures; the second utilizes the chemical reactivity of the serine hydrolase active site in complex mixtures. These proteomics approaches share the ability to fractionate the complex proteome into functional subsets. Each method identified a significant number of sequences, but fifteen proteins were identified by both methods. Eight of these were unannotated in the Saccharomyces Genome Database (SGD) at the time of this study and are thus novel serine hydrolase identifications. Three of the previously uncharacterized proteins are members of a eukaryotic serine hydrolase family, designated as Fsh (Family of Serine Hydrolase), identified here for the first time. OVCA2, a potential human tumor suppressor, and DYR_SCHPO, a dihydrofolate reductase from S. pombe, are members of this family. Comparing the combined results to results of other proteomic methods showed that only four of the fifteen proteins were identified in a recent large-scale, “shotgun” proteomic analysis and eight were identified using a related, but similar, approach (neither identifies function). Only ten of the fifteen were annotated using alternate motif-based computational tools. The results demonstrate the precision derived from combining complementary, function-based approaches to extract biological information from complex proteomes. The chemical proteomics technology indicates that a functional protein is being expressed in the cell, while the computational proteomics technology adds details about the specific type of function and residue that is likely being labeled. The combination of synergistic methods facilitates analysis, enriches true positive results and increases confidence in novel identifications. This work also highlights the risks inherent in annotation transfer and the use of scoring functions for determination of correct annotations.
Revised on November 18, 2003
Accepted on November 24, 2003
Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast
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