Table 1 Comparison of previous proteomic studies of protein expression in yeast cells grown in various conditions
Study | Francesca et al. [10] | de Groot et al. [11] | Usaite et al. [12] | Costenoble et al. [13] | Kolkman et al. [14] | Pham et al. [15] |
|---|---|---|---|---|---|---|
Primary Objectives | Comparison of steady state protein levels in cells growth in synthetic medium containing 0.5%, 2%, and 20% glucose to 0.8 O.D./ml | Proteomic differences in anaerobic versus aerobic growth | Comparison of steady state levels of proteins in strains deficient in SNF1/SNF4 involved in glucose repression. | Comparison of steady state levels of proteins in cells grown in glucose, galactose or ethanol. | Comparison of steady state levels of protein expression under chemostat cultures limited for either glucose or ethanol. | Comparison of steady state levels of proteins in cells grown in 120 g/L (normal) to 210 g/L and 300 g/L (high) glucose for 68 hours. |
Analytical Platform employed | 2D-GE; Relative spot volume quantification; MALDI-TOF | Stable-isotope labeling with 14 N and 15 N in cultures grown in anaerobic versus aerobic conditions; 1D-PAGE; RFLC; nanoflow-LC-ESI-MS/ MS | Stable isotope labeling with 14 N and15N in wild-type, Δsnf1, Δsnf4, and Δsnf1Δsnf4 strains; MudPIT; ESI; LTQ-Orbitrap | Targeted proteomics approach based on selected reaction monitoring (SRM) and proteotypic peptides (PTPs); ion trap MS with nanoelectrospray ion source | 2D-GE; Relative spot quantification; MALDI-MS and Nano-ESI-LC-MS/MS | iTRAQ; nano-LC-ESI-MS/MS |
Total number of peptides/proteins identifications/ quantification | 156 protein spots changing significantly; 21 differentially expressed proteins identified by MS analysis | 1499 identified; 474 quantified proteins; 249 proteins showed differential expression levels | 2388 proteins were relatively quantified; 350 showed differential expression levels | The 228 proteins of the central carbon and amino-acid metabolic network in S. cerevisiae | 400 protein spots were detected on each 2D gel; 44 spots were relatively quantified and identified | 413 proteins were identified from 3 replicates; 237 showed differential expression between conditions |
Relevance to our study | Gluconeogenic enzymes were not identified. | 1. Steady state levels of glycolytic enzymes were higher in cells grown in anaerobic condition. | Steady state levels of gluconeogenic enzymes Mls1p, Icl1p, Mdh2p were higher in the Δsnf1Δsnf4 strain than the Δsnf1 strain. | 1. Steady state levels of gluconeogenic enzymes were higher in cells grown in ethanol than in cells grown in glucose. | 1. Steady state levels of glycolytic enzymes were higher in cultures grown in glucose than cells grown in ethanol. | 1. Levels of most glycolytic enzymes were higher in 300 g/L glucose than in normal glucose. |
| Â | Â | 2. Poor correlation of protein ratios and mRNA ratios for enzymes in glycolysis/ gluconeogenesis. | Â | 2. Steady state levels of glycolytic enzymes were higher in cells grown in glucose than in cells grown in ethanol. | 2. Gluconeogenic enzymes such as Mls1p, Pck1p, Mdh2p, and Icl1p were expressed only in ethanol. Fbp1p was not identified. | 2. Levels of Hsp12p, Hsp26p, and other heat shock proteins were lower in cells grown in high glucose than in cells grown in normal glucose. |