The function of many of the uncharacterized open reading frames discovered by genomic sequencing can be determined at the level of expressed gene products, the proteome. However, identifying the cognate gene from minute amounts of protein has been one of the major problems in molecular biology. Using yeast as an example, we demonstrate here that mass spectrometric protein identification is a general solution to this problem given a completely sequenced genome. As a first screen, our strategy uses automated laser desorption ionization mass spectrometry of the peptide mixtures produced by in-gel tryptic digestion of a protein. Up to 90% of proteins are identified by searching sequence data bases by lists of peptide masses obtained with high accuracy. The remaining proteins are identified by partially sequencing several peptides of the unseparated mixture by nanoelectrospray tandem mass spectrometry followed by data base searching with multiple peptide sequence tags. In blind trials, the method led to unambiguous identification in all cases. In the largest individual protein identification project to date, a total of 150 gel spots-many of them at subpicomole amounts-were successfully analyzed, greatly enlarging a yeast two-dimensional gel data base. More than 32 proteins were novel and matched to previously uncharacterized open reading frames in the yeast genome. This study establishes that mass spectrometry provides the required throughput, the certainty of identification, and the general applicability to serve as the method of choice to connect genome and proteome.

The changes in gene expression underlying the yeast adaptive stress response to H 2 O 2 were analyzed by comparative two-dimensional gel electrophoresis of total cell proteins. The synthesis of at least 115 proteins is stimulated by H 2 O 2 , whereas 52 other proteins are repressed by this treatment. We have identified 71 of the stimulated and 44 of the repressed targets. The kinetics and dose-response parameters of the H 2 O 2 genomic response were also analyzed. Identification of these proteins and their mapping into specific cellular processes give a distinct picture of the way in which yeast cells adapt to oxidative stress. Aerobic organisms have to maintain a reduced cellular redox environment in the face of the prooxidative conditions characteristic of aerobic life. The incomplete reduction of oxygen to water during respiration leads to the formation of redox-active oxygen intermediates (ROI) 1 such as the superoxide anion radical (O 2 Ϫ ), hydrogen peroxide (H 2 O 2 ), and the hydroxyl radical (OH ⅐ ) (for review, see Refs. 1-3). ROI are also produced during the ␤-oxidation of fatty acids, and upon exposure to radiation, light, metals, and redox active drugs. Oxidative stress results from abnormally high levels of ROI which perturb the cell redox status and leads to damage to lipids, proteins, DNA, and eventually cell death. Living organisms constantly sense and adapt to such redox perturbations by the induction of batteries of genes or stimulons whose products act to maintain the cellular redox environment (4 (9,10). Yeast has the same defense mechanisms as higher eukaryotes (for review, see Refs. 11 and 12) and offers the power of genome-wide experimental approaches owing to the availability of the complete sequence of its genome. It therefore represents an ideal eukaryotic model in which to study the cellular redox control and ROI metabolism. We recently established a general method to identify yeast proteins based on two-dimensional gel electrophoresis (13). We used this genome-wide experimental approach to characterize proteins whose expression is altered upon exposure to low doses of H 2 O 2 . Such an oxidative stress challenge results in a dramatic genomic response involving at least 167 proteins. Identification of these proteins and their mapping into cellular processes give a global view of the ubiquitous cellular changes elicited by H 2 O 2 and provides the framework for understanding the mechanisms of cellular redox homeostasis and H 2 O 2 metabolism. ura3-52 lys2-801 amber ade2-101 ochre trp1-⌬1 leu2-⌬1) was used for the analysis of the H 2 O 2 response. The strain S288C (15) was used for protein spot identification. Strains were grown at 30°C in a medium containing 0.67% yeast nitrogen base without amino acids (Difco), 2% glucose, buffered to pH 5.8 with 1% succinate and 0.6% NaOH. For YPH98, uracil, adenine, lysine, tryptophan and leucine (30 mg/liter) were added to the culture medium. MATERIALS AND METHODS Strains and Growth Conditions-The yeast strain YPH98 (14) (MATaIdentification of P...

The multicopy suppressors of the snf1 defect, Msn2p and Msn4p transcription factors (Msn2/4p), activate genes through the stress-responsive cis element (CCCCT) in response to various stresses. This cis element is also the target for repression by the cyclic AMP (cAMP)-signaling pathway. We analyzed the two-dimensional gel electrophoresis pattern of protein synthesis of themsn2 msn4 double mutant and compared it with that of the wild-type strain during exponential growth phase and at the diauxic transition. Thirty-nine gene products (including those ofALD3, GDH3, GLK1, GPP2,HSP104, HXK1, PGM2,SOD2, SSA3, SSA4, TKL2,TPS1, and YBR149W) are dependent upon Msn2/4p for their induction at the diauxic transition. The expression of all these genes is repressed by cAMP. Thirty other genes identified during this study are still inducible in the mutant. A subset of these genes were found to be superinduced at the diauxic transition, and others were subject to cAMP repression (including ACH1,ADH2, ALD6, ATP2, GPD1,ICL1, and KGD2). We conclude from this analysis that Msn2/4p control a large number of genes induced at the diauxic transition but that other, as-yet-uncharacterized regulators, also contribute to this response. In addition, we show here that cAMP repression applies to both Msn2/4p-dependent and -independent control of gene expression at the diauxic shift. Furthermore, the fact that all the Msn2/4p gene targets are subject to cAMP repression suggests that these regulators could be targets for the cAMP-signaling pathway.

In yeast, the transition between the fermentative and the oxidative metabolism, called the diauxic shift, is associated with major changes in gene expression and protein synthesis. The zinc cluster protein Cat8p is required for the derepression of nine genes under nonfermentative growth conditions (ACS1, FBP1, ICL1, IDP2, JEN1, MLS1, PCK1, SFC1, and SIP4). To investigate whether the transcriptional control mediated by Cat8p can be extended to other genes and whether this control is the main control for the changes in the synthesis of the respective proteins during the adaptation to growth on ethanol, we analyzed the transcriptome and the proteome of a cat8⌬ strain during the diauxic shift. In this report, we demonstrate that, in addition to the nine genes known as Cat8p-dependent, there are 25 other genes or open reading frames whose expression at the diauxic shift is altered in the absence of Cat8p. For all of the genes characterized here, the Cat8p-dependent control results in a parallel alteration in mRNA and protein synthesis. It appears that the biochemical functions of the proteins encoded by Cat8p-dependent genes are essentially related to the first steps of ethanol utilization, the glyoxylate cycle, and gluconeogenesis. Interestingly, no function involved in the tricarboxylic cycle and the oxidative phosphorylation seems to be controlled by Cat8p.