In this study, we examined yeast proteins by two-dimensional (2D) gel electrophoresis and gathered quantitative information from about 1,400 spots. We found that there is an enormous range of protein abundance and, for identified spots, a good correlation between protein abundance, mRNA abundance, and codon bias. For each molecule of well-translated mRNA, there were about 4,000 molecules of protein. The relative abundance of proteins was measured in glucose and ethanol media. Protein turnover was examined and found to be insignificant for abundant proteins. Some phosphoproteins were identified. The behavior of proteins in differential centrifugation experiments was examined. Such experiments with 2D gels can give a global view of the yeast proteome.The sequence of the yeast genome has been determined (9). More recently, the number of mRNA molecules for each expressed gene has been measured (27,30). The next logical level of analysis is that of the expressed set of proteins. We have begun to analyze the yeast proteome by using two-dimensional (2D) gels.2D gel electrophoresis separates proteins according to isoelectric point in one dimension and molecular weight in the other dimension (21), allowing resolution of thousands of proteins on a single gel. Although modern imaging and computing techniques can extract quantitative data for each of the spots in a 2D gel, there are only a few cases in which quantitative data have been gathered from 2D gels. 2D gel electrophoresis is almost unique in its ability to examine biological responses over thousands of proteins simultaneously and should therefore allow us a relatively comprehensive view of cellular metabolism.We and others have worked toward assembling a yeast protein database consisting of a collection of identified spots in 2D gels and of data on each of these spots under various conditions (2,7,8,10,23,25). These data could then be used in analyzing a protein or a metabolic process. Saccharomyces cerevisiae is a good organism for this approach since it has a well-understood physiology as well as a large number of mutants, and its genome has been sequenced. Given the sequence and the relative lack of introns in S. cerevisiae, it is easy to predict the sequence of the primary protein product of most genes. This aids tremendously in identifying these proteins on 2D gels.There are three pillars on which such a database rests: (i) visualization of many protein spots simultaneously, (ii) quantification of the protein in each spot, and (iii) identification of the gene product for each spot. Our first efforts at visualization and identification for S. cerevisiae have been described elsewhere (7,8). Here we describe quantitative data for these proteins under a variety of experimental conditions. ade2-1 his3-11,15 leu2-3, 112 trp1-1 ura3-1 can1-100) was used (26). ϪMet YNB (yeast nitrogen base) medium was 1.7 g of YNB (Difco) per liter, 5 g of ammonium sulfate per liter, and adenine, uracil, and all amino acids except methionine; ϪMet ϪCys YNB medium was the same but wi...

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The calcium channel blockers, verapamil and diltiazem, inhibit phytohemagglutinin (PHA)-induced mitogenesis at concentrations that block the T lymphocyte K channel currents. K channel blockers also inhibit the allogeneic mixed lymphocyte response in a dose-dependent manner with the same potency sequence as for block of K currents. K channel blockers inhibit PHA-stimulated mitogenesis only if added during the first 20-30 h after PHA addition, but not later, indicating a requirement for functional K channels during this period. We investigated the effect of K channel blockers on various aspects of protein synthesis for two reasons: first, protein synthesis appears to be necessary for the events leading to DNA synthesis, and second, the increase in the protein synthetic rate commences during the first 24-48 h after PHA addition. PHA-induced total protein synthesis was reduced to the level in unstimulated T lymphocytes by K channel blockers in a dose-dependent manner with the same potency sequence as for the block of K currents and inhibition of [3H]thymidine incorporation. Two-dimensional gel electrophoresis demonstrated that although the synthesis of the majority of proteins was reduced by K channel blockers to the level in unstimulated T cells, some proteins continued to be synthesized at an enhanced rate compared with resting cells. Two proteins, S and T, detected by two-dimensional gel electrophoresis in unstimulated T lymphocytes, appeared to be reduced in intensity in gels of PHA-treated T lymphocytes, in contrast to the increased synthesis of the remaining proteins. 4-Aminopyridine (4-AP), at concentrations that inhibit protein synthesis, prevented the apparent PHA-induced reduction of proteins S and T. These proteins may play a role in maintaining the T lymphocyte in a resting state and may be related to the translation inhibitory factors reported to be present at a higher specific activity in quiescent T lymphocytes than in PHA-activated T cells. The expression of the IL-2 receptor (Tac) during T lymphocyte activation was not altered by K channel blockers, whereas the production of interleukin 2 (IL-2) was reduced to the level in unstimulated T lymphocytes. Exogenous IL-2 partially relieved the inhibition of mitogenesis by low, but not by high, concentrations of 4-AP. These experiments clarify the role of K channels in T lymphocyte activation and suggest that functional K channels are required either for protein synthesis or for events leading to protein synthesis.

Centrifugal elutriation was used to separate cells of Saccharomyces cerevisiae in balanced exponential growth according to position in the cell cycle. Macromolecular synthesis was examined. DNA synthesis was found to be periodic, but RNA and protein synthesis showed an exponential increase in rate. Two-dimensional electrophoresis was used to determine the rate of synthesis of individual proteins, with 111 of the more abundant cellular proteins selected for analysis from among thq more than 1000 proteins that migrate in the system. All the extknined proteins showed an exponentially increasing rate of synthesis. The total amount of protein increases continuously throughout the cell cycle in bacteria and yeast (1). However, both periodic and continuous increases in the activities of a variety of enzymes from many species of prokaryotic and eukaryotic organisms have been reported (1-4). Four general patterns of activity increase through the cell cycle have been considered. The patterns of continuous increase can be subdivided into two types: (i) exponential increase and (ii) linear increase with a doubling in the rate at some point during the cell cycle. Additionally, patterns of periodic increase can be subdivided into: (iii) step patterns like that of DNA accumulation and (iv) patterns in which activity reaches a peak followed by inactivation or degradation of the enzyme.Despite the extensive literature on periodic changes in enzymatic activity, speculations on the periodic nature of the synthesis of individual enzymatic proteins have been viewed with skepticism for the following reasons:(i) The various researchers reporting on enzyme accumulation measured enzyme activity and not enzyme synthesis. Mitchison and Creanor (5) reported that there is a delay of 20% of the cell cycle in the yeast Schizosaccharomyces pombe between synthesis of the enzyme precursor and its activation. This indicates that increased enzyme activity is not necessarily synonymous with enzyme synthesis. Furthermore, because the activities of many enzymes are regulated by feedback mechanisms, the periodicity that many researchers reported may be due to periodic changes in the synthesis of regulatory molecules affecting enzyme activity and not enzyme synthesis.(ii) Many studies of periodic synthesis utilized synchronous cultures prepared by induction techniques that involve media changes. These methods might be expected to drastically affect the nature of periodic synthesis of enzymes during at least the first synchronous division cycle. Furthermore, a study in Schizosaccharomyces pombe (6) showed that when total protein was subdivided into small groups on one-dimensional sodium dodecyl sulfate gels, their synthesis was exponential. In addition, in Saccharomyces cerevtsiae, the synthesis of a well-defined class of proteins, the ribosomal proteins, is nonperiodic (ref. 7; unpublished data).In light of these problems, we decided to reexamine enzyme synthesis in S. cerevisiae. Our reexamination is based on two recent technical innovation...

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Two-dimensional (2-D) gel electrophoresis can now be coupled with protein identification techniques and genome sequence information for direct detection, identification, and characterization of large numbers of proteins from microbial organisms. 2-D electrophoresis, and new protein identification techniques such as amino acid composition, are proteome research techniques in that they allow direct characterization of many proteins at the same time. Another new tool important for yeast proteome research is the Yeast Protein Database (YPD), which provides the sequence-derived protein properties needed for spot identification and tabulations of the currently known properties of the yeast proteins. Studies presented here extend the yeast 2-D protein map to 169 identified spots based upon the recent completion of the yeast genome sequence, and they show that methods of spot identification based on predicted isoelectric point, predicted molecular mass, and determination of partial amino acid composition from radiolabeled gels are powerful enough for the identification of at least 80% of the spots representing abundant proteins. Comparison of proteins predicted by YPD to be detectable on 2-D gels based on calculated molecular mass, isoelectric point and codon bias (a predictor of abundance) with proteins identified in this study suggests that many glycoproteins and integral membrane proteins are missing from the 2-D gel patterns. Using the 2-D gel map and the information available in YDP, 2-D gel experiments were analyzed to characterize the yeast proteins associated with: (i) an environmental change (heat shock), (ii) a temperature-sensitive mutation (the prp2 mRNA splicing mutant), (iii) a mutation affecting post-translational modification (N-terminal acetylation), and (iv) a purified subcellular fraction (the ribosomal proteins). The methods used here should allow future extension of these studies to many more proteins of the yeast proteome.

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