PROTEOME STUDIES OF SACCHAROMYCES-CEREVISIAE - IDENTIFICATION AND CHARACTERIZATION OF ABUNDANT PROTEINS

Two-dimensional (2-D) gel electrophoresis can now be coupled with prot ein identification techniques and genome sequence information for dire ct detection, identification, and characterization of large numbers of proteins from microbial organisms. 2-D electrophoresis, and new prote in identification techniques such as amino acid composition, are prote ome research techniques in that they allow direct characterization of many proteins at the same time. Another new tool important for yeast p roteome research is the Yeast Protein Database (YPD), which provides t he sequence-derived protein properties needed for spot identification and tabulations of the currently known properties of the yeast protein s. Studies presented here extend the yeast 2-D protein map to 169 iden tified spots based upon the recent completion of the yeast genome sequ ence, and they show that methods of spot identification based on predi cted isoelectric point, predicted molecular mass, and determination of partial amino acid composition from radiolabeled gels are powerful en ough for the identification of at least 80% of the spots representing abundant proteins. Comparison of proteins predicted by YPD to be detec table on 2-D gels based on calculated molecular mass, isoelectric poin t and codon bias (a predictor of abundance) with proteins identified i n this study suggests that many glycoproteins and integral membrane pr oteins are missing from the 2-D gel patterns. Using the 2-D gel map an d the information available in YDP, 2-D gel experiments were analyzed to characterize the yeast proteins associated with: (i) an environment al change (heat shock), (ii) a temperature-sensitive mutation (the prp 2 mRNA splicing mutant), (iii) a mutation affecting post-translational modification (N-terminal acetylation), and (iv) a purified subcellula r fraction (the ribosomal proteins). The methods used here should allo w future extension of these studies to many more proteins of the yeast proteome.