Proteomic analysis of saccharomyces cerevisiae KAY446 under very high gravity conditions

PROTEOMIC ANALYSIS OF SACCHAROMYCES CEREVISIAE KAY446 UNDER VERY HIGH GRAVITY CONDITIONS Trong Khoa PHAM (ME) Thesis submitted for the degree of Doctor of Philosophy (PhD) to The University of Sheffield, Sheffield, UK On completion of research in the Biological and Environmental Systems Group within the Department of Chemical and Process Engineering May, 2008 This copy of the thesis has been submitted with the condition that anyone who consults it is understood to recognise that the copyright rests with its author No quotation and information derived from this thesis may be published without prior written consent to the author or the University (as may be appropriate) i This thesis is dedicated to my parents, my wife and my daughter ii Declaration This is to declare that I am the sole author of this thesis with work performed and completed in The University of Sheffield, UK, except where acknowledgements are made This work has not been submitted for any other degrees Trong Khoa PHAM (Candidate) iii Acknowledgments I would like to express my sincere appreciations and acknowledgments to all the people who have been helping me to contribute this thesis I have really been surrounded by many nice people! • My deepest appreciation to my supervisor Prof Phillip C Wright for his excellent supervision, invaluable guidance, encouragement and inspiration • I would like to express my gratitude to Dr (Shirly) Poh Kuan Chong, Dr Chee Sian Gan for their teaching during the early years of my research, for their collaborator work, as well as for their endless help when I needed them • I thank Dr Bram Snijders, and Dr Martin Barrios-Llerena for their technical advice Many thanks to Mark Scaife for his advice and discussions • I would like to acknowledge Prof Katherine Smart (from Division of Food Sciences, University of Nottingham) and Dr Mark Dickman (from Department of Chemical and Process Engineering, University of Sheffield) for being my external and internal examiner, as well as a special thanks to Dr Mark Dickman for his technical advice • I also gratefully acknowledge the Ministry of Education and Training of Vietnam for financial support • I thank to Miss Thi Hong Nhan Le who bring a home atmosphere to me and my family iv • Last but not least, I would like to thank my family: my parents, Mr Hau Phuc Pham and Mrs Hoa Thi Trinh who put their hope into my name “Trong Khoa”, for giving me the life, for educating me, for unconditional support and encouragement My wife, Kim-Quyen T Huynh, for her sacrifice, patience, understanding and encouragement for all three years My daughter, Bao-Nhi H Pham, for her excellent performance in my spirit v List of Publications Parts of the work in this thesis have been published as below: (J – Journal paper, O – Oral presentation, P – Poster presentation) (J1) P.K Chong, C.S Gan, T.K Pham, and P.C Wright, “Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) reproducibility: Implication of multiple injections”, Journal of Proteome Research, (5), 2006, 1232-1240 (J2) T.K Pham, P.K Chong, C.S Gan, and P.C Wright, “Proteomic analysis of Saccharomyces cerevisiae under high gravity fermentation conditions”, Journal of Proteome Research, (12), 2006, 3411-3419 (J3) C.S Gan, P.K Chong, T.K Pham, and P.C Wright, “Technical, experimental, and biological variations in Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)”, Journal of Proteome Research, (2), 2007, 821-827 (J4) T.K Pham and P.C Wright, “Review: Proteomic analysis of Saccharomyces cerevisiae”, Expert Review of Proteomics, 2007, 4(6), 793-813 (J5) T.K Pham and P.C Wright, “Proteomic analysis of calcium alginate immobilized Saccharomyces cerevisiae under high gravity fermentation condition”, Journal of Proteome Research, (2), 2008, 515-525 (J6) T.K Pham and P.C Wright, “The proteomic response of Saccharomyces cerevisiae in very high glucose conditions with amino acid supplementation”, Journal of Proteome Research, (11), 2008, 4766-4774 vi (J7) T.K Pham and P.C Wright, “Proteomic analysis of Saccharomyces cerevisiae during continuous fermentation under VHG conditions: Regulation of proteomics versus oscillation of fermentation process”, In preparation (J8) T.K Pham and V.M Le-Van, “Fermentation for ethanol production using immobilized yeast cells in alginate gel” Proceeding of the 8th ASEAN Food Conference, Nov 2003, Hanoi-Vietnam (J9) T.K Pham and V M Le-Van, “Using Saccharomyces cerevisiae immobilized in calcium alginate gel for ethanol fermentation”, Proceeding of the 8th Conference on Science and Technology, Apr 2002, HoChiMinh-Vietnam (O1) P.K Chong, C.S Gan, T.K Pham and P.C Wright, “Application and reliability of isobaric mass tagging technology in proteomics”, 232nd ACS National Meating, San Francisco, CA, Sep 10-14th, 2006 (O2) P.K Chong, C.G Gan, T.K Pham and P.C Wright, “Assessing iTRAQ’s reliability, quantitative proteomics, Applications in Biology and Medicine, Sheffield, Oct 2006 (P1) T.K Pham and P.C Wright, “Proteomic analysis of Saccharomyces cerevisiae under high gravity conditions”, 3rd Joint BSPR/EBI Meeting, Cambridge, UK, Jul 12-14th, 2006 vii Table of Contents Declaration iii Acknowledgments iv List of publications vi Table of contents viii List of tables xiv List of figures xvi Abbreviations xxii Abstract xxv Chapter 26 1.1 Introduction 27 1.2 Aims of this thesis 28 1.3 Thesis overview 28 Chapter 31 2.1 Abstract 32 2.2 Literature review of Saccharomyces cerevisiae proteomic analysis 32 2.2.1 The importance of proteomic investigations in Saccharomyces cerevisiae 32 2.2.2 Proteomics as a tool for the identification and quantitation of S cerevisiae proteins 34 2.2.3 The identification and quantitation of S cerevisiae proteins in proteomics experiments 43 2.2.4 Proteomics in the study of S cerevisiae networks 57 2.2.5 Proteomic analysis of S cerevisiae protein modifications 62 2.2.6 Discussion 65 viii 2.2.7 The outlook of S cerevisiae proteomics analysis 68 2.3 Bioethanol fermentation process and methods to improve this process 71 2.3.1 Bioethanol fermentation process 71 2.3.2 Methods (techniques) to improve bioethanol fermentation 78 Chapter 82 3.1 Abstract 83 3.2 Introduction 83 3.3 Materials and Methods 85 3.3.1 Sample preparation 85 3.3.2 Protein preparation 86 3.3.3 Experimental design 86 3.3.4 Isobaric peptide labeling 87 3.3.5 Strong cation exchange fractionation 88 3.3.6 Mass spectrometric analysis 88 3.3.7 Data analysis 89 3.4 Results and discussion 90 3.4.1 Multiple injections 90 3.4.2 Technical variation 97 3.5 Conclusions 99 Chapter 100 4.1 Abstract 101 4.2 Introduction 101 4.3 Materials and methods 104 4.3.1 Fermentation conditions 104 4.3.2 Measurements of fermentation parameters 105 4.3.3 Cell extraction, labeling, mass spectrometry and data analysis 105 4.4 Results and discussion 106 4.4.1 Ethanol fermentation as a function of glucose concentration 106 ix 4.4.2 Relative protein expression under different glucose concentrations 108 4.4.3 The glycolysis pathway 110 4.4.4 Storage carbohydrates 114 4.4.5 The requirement for redox balance led to secondary products generation 115 4.4.6 Tricarboxylic acid cycle (TCA cycle) 118 4.4.7 Amino acids metabolism 118 4.4.8 Proteins involved in eIF (eukaryotic initiation factor), and heat-shock proteins 120 4.5 Conclusions 123 Chapter 125 5.1 Abstract 126 5.2 Introduction 126 5.3 Materials and methods 129 5.3.1 Growth conditions 129 5.3.2 Measurements of fermentation parameters 130 5.3.3 Cell viability determination 130 5.3.4 Dry weight determination 130 5.3.5 Glycogen and trehalose determination 130 5.3.6 Intracellular amino acids determination 131 5.3.7 Labeling, mass spectrometry and data analysis 132 5.4 Results and discussion 133 5.4.1 The cell growth during lag phase under stress condition 133 5.4.2 The fluctuations in intracellular amino acids concentrations 134 5.4.3 The identification and classification of detected proteins 142 5.4.4 The expression of proteins related to the biosynthesis of amino acids 149 5.4.5 Response of heat-shock proteins to VHG conditions with amino acid supplementation 152 x Accession gi|6324121 gi|6322225 gi|6325221 gi|6321430 gi|6322889 gi|6321192 gi|6322815 gi|6324321 gi|6324993 gi|6319806 gi|6323474 gi|6319936 gi|6320304 gi|6323562 gi|6321412 gi|6320119 gi|6320137 gi|6322666 gi|6321456 gi|6320157 gi|6323138 gi|6321772 gi|6323299 gi|6322271 gi|6323399 gi|6322639 gi|6323681 gi|6325058 gi|6322605 gi|6321997 gi|6323746 gi|6321498 gi|6323104 gi|6319407 Protein Name Ynl208wp saccharopine dehydrogenase; Lys1p plasma membrane ATPase; Pma2p plasma membrane H+-ATPase; Pma1p component of CCR4 transcriptional complex; Caf4p Ygl245wp Uridinephosphoglucose pyrophosphorylase; Ugp1p sit4 suppressor, dnaJ homolog; Sis1p mitochondrial and cytoplasmic fumarase (fumarate hydralase); Fum1p protein disulfide isomerase; Pdi1p Ribosomal protein S1A (rp10A); Rps1ap nuclear protein that negatively regulates basal transcription; Cdc39p member of conserved eukaryotic 143-3 gene family; Bmh2p cyclophilin-3 (cyclosporin-sensitive proline rotamase-3); Cpr3p tryptophan synthetase; Trp5p RNA helicase; Sub2p Mitochondrial form of NADP-specific isocitrate dehydrogenase; Idp1p pentafunctional enzyme consisting of the following domains : acetyl transferase, enoyl reductase, de gamma-aminobutyrate (GABA) transaminase (4-aminobutyrate aminotransferase); Uga1p Ydl046wp alkyl hydroperoxide reductase; Ahp1p Ribosomal protein S20; Rps20p Ylr270wp Ribosomal protein S22A (S24A) (rp50) (YS22); Rps22ap Ribosomal protein S22B (S24B) (rp50) (YS22); Rps22bp ubiquitin activating enzyme, similar to Uba2p; Uba1p copper chaperone for superoxide dismutase Sod1p; Lys7p Ribosomal protein L7B (L6B) (rp11) (YL8); Rpl7bp Ribosomal protein S4A (YS6) (rp5) (S7A); Rps4ap Ribosomal protein S4B (YS6) (rp5) (S7B); Rps4bp Ymr099cp 5'-phosphoribosylformyl glycinamidine synthetase; Ade6p Ribosomal protein L10; Ubiquinolcytochrome C reductase complex subunit VI requiring protein; Rpl10p similar to thiol-specific antioxidant enzymes such as Ratio EF Ratio EF Ratio EF 115:114 115:114 116:114 116:114 117:114 117:114 1.6933 5.5197 1.9988 1.9424 1.7798 1.8117 0.7047 5.9533 0.7562 5.631 0.7932 4.6804 0.9309 6.2037 0.7532 1.8492 0.7394 1.9241 0.9309 6.2037 0.7532 1.8492 0.7394 1.9241 0.4525 6.214 0.3632 2.0407 0.7357 10.5888 3.798 6.3001 4.845 5.9014 3.7115 5.1023 1.4238 6.4418 1.3041 11.62 1.1315 3.908 1.5386 6.7202 1.5119 3.7454 1.6702 1.6316 1.949 7.399 2.14 4.1289 1.2709 2.7221 0.2545 7.7667 1.075 1.9072 2.0927 1.1817 1.4377 7.8675 1.2758 1.7083 2.5389 3.7425 0.6302 8.3464 0.5958 872.1031 0.5489 20.1057 0.4324 10.0114 0.3927 7.5203 0.7123 3.8005 1.2624 10.4631 1.4505 6.9805 1.2073 6.912 2.5973 2.856 10.6218 2.0246 10.666 2.6504 5.1885 26.4129 1.521 1.5372 4.0881 12.1907 1.245 11.0751 1.3686 8.8521 0.8516 9.4014 3.2237 11.6737 4.9644 20.2927 2.3878 14.0925 0.672 12.8603 0.6458 12.3448 0.8911 3.9596 1.29 0.7119 0.7135 0.6231 13.347 0.9876 13.3714 0.4809 13.6012 2.239 15.0831 0.7359 13.7991 17.5652 3.8925 1.5421 0.7559 0.6259 4.8731 1.0562 13.4519 13.7139 1.7497 1.3495 1.7394 16.3928 1.5562 1.4932 8.6746 1.5597 1.7394 16.3928 1.5562 1.4932 8.6746 1.5597 1.5657 17.6714 1.2633 85.7366 0.9852 66.7385 2.5603 20.4027 2.6922 9.219 2.47 8.2461 3.2657 21.2977 3.0329 2.4902 1.5613 1.551 3.8869 23.1417 1.9038 56.9039 2.4522 30.0363 3.8869 23.1417 1.9038 56.9039 2.4522 30.0363 1.1502 32.6969 0.8846 1176.3292 0.9648 3.7009 1.5898 34.8956 1.4286 10.6246 0.1924 40.3816 2.5939 2185.2009 6.3423 1373.3862 1.8191 51.9675 2.2175 31.8076 33.0466 1.0438 1.9836 26.1879 326 Accession Protein Name Ratio EF Ratio EF Ratio EF 115:114 115:114 116:114 116:114 117:114 117:114 rehydrin/peroxiredoxin; Ybl064cp gi|6322097 Homo-isocitrate dehydrogenase; Lys12p gi|6324899 gamma-glutamyl phosphate reductase; Pro2p gi|6319602 56 kD synthase subunit of trehalose-6phosphate synthase/phosphatase complex; Tps1p gi|6323332 Ylr301wp gi|6325220 regulator of pol II transcribed genes; Egd1p gi|6323179 gene product has affinity for quadruplex nucleic acids; Stm1p gi|6322831 contains four beta-transducin repeats; Mak11p gi|6322668 Ribosomal protein L17A (L20A) (YL17); Rpl17ap gi|6322284 Ribosomal protein L17B (L20B) (YL17); Rpl17bp gi|6322599 Homoserine dehydrogenase (Lhomoserine:NADP oxidoreductase); Hom6p gi|6319426 44 kDa core protein of yeast coenzyme QH2 cytochrome c reductase; Cor1p gi|6319378 Ribosomal protein L32; Rpl32p gi|6325449 40 kDa ubiquinol cytochrome-c reductase core protein 2; Qcr2p gi|6320839 mannose-6-phosphate isomerase; Pmi40p gi|6325403 asparagine synthetase; Asn1p gi|6324273 Outer mitochondrial membrane porin (voltage-dependent anion channel, or VDAC); Por1p gi|6320260 The gene product has been detected among the proteins secreted by regenerating protoplasts; Pst1p 0.6319 55.4799 0.6217 2.2815 0.7683 2.4447 0.223 56.0373 0.8535 1.5146 1.7254 23.7812 0.3132 57.8658 1.3278 6.2553 2.5111 3.1124 1.894 61.1464 1.8658 318.4872 1.587 423.3688 0.7339 66.1948 1.1119 4.5279 1.3259 1.8415 0.6973 68.1046 1.5113 1.2778 2.1145 1.1627 1.1655 83.0233 0.7073 53.608 0.955 1.0889 3.475 106.205 1.3908 47.9716 4.7391 91.9143 3.475 106.205 1.3908 47.9716 4.7391 91.9143 1.5099 122.6248 1.9652 24.7576 1.882 21.2015 4.0696 169.6916 1.3132 12.0954 3.9831 295.1297 1.6647 184.2814 1.7304 248.7705 0.9426 161.4493 0.503 377.1131 1.0579 1.7976 1.0126 1.25 0.2518 438.7135 0.529 2.3528 0.9009 1.9962 0.1296 469.1502 0.5266 1.2826 0.6302 1.6317 3.0523 555.7373 4.6381 212.8475 1.7024 45.9521 0.8238 598.4929 0.3155 15.0631 61.6972 0.3576 327 Appendix G The ATP data used for the study in Chapter A The ATP standard curve: Relative light intensity (proton count) 300000 y = 3E+06x + 5058 R = 0.9814 250000 200000 150000 100000 50000 0 0.02 0.04 0.06 ATP concentration (μM) 0.08 0.1 Figure The standard ATP calibration curve B Data from ATP assays used to calculate ATP and ADP concentrations (in Table 7.4): Data used to calculate ATP and ADP concentrations in Table 7.4 is shown in Table below: Table Data for calculation of ATP and ADP concentrations (based on enzyme assay and then measured light intensity) Relative light intensity Time ATP(a) ATP+ADP(b) 120 122609 181360 132 140945 187030 144 67554 129372 156 87818 124657 Note: (a) intensity from ATP assay for ATP concentration only (b) intensity from ATP assay with ADP that was converted to ATP (see section 7.3.3 for detail and example in Section ii) below for details) 328 C Methods to calculate ATP and ADP concentrations: The calculation of ATP and ADP concentrations in Figure 7.4 was carried out as below (via examples): i) ATP concentration calculation: An example of calculation of ATP concentration is described below: The ATP data at 120 h was used to illustrate the calculation • From the relative light intensity measured from assay (Table 1, column 2), the relative light intensity of ATP emitted from the assay at 120 h was 122609.26 Therefore, refer to the equation in the standard calibration curve in Figure above (Appendix G, Section A), the concentration of ATP is: 122609 − 5058 = 0.03918 ( μM ) = 39.18 × 10 −9 3000000 • (M ) Sample was diluted 10000 times for the assay, therefore, the ATP concentration before diluted was: 39.18 ¯ 10-9 ¯ 10000 = 39.18¯ 10-5 • (M) Since 10 mL of culture was harvested and extracted using ethanol, then sample was dried using nitrogen before resuspended in mL of deionized water (see section 7.3.3 for details), the mole of ATP was: 39.18 × 10 −5 × × 10 −3 = 39.18 × 10 −8 • (mole) Therefore, the mass of ATP (in 10 mL culture) was: 39.18 × 10 −8 × 507.2 = 19.872 × 10 −5 (g) Where: 507.2 (g) was molecular mass of ATP 329 • Since 10 mL of culture was harvested, and moreover cell dry weight at 120 h was 5.23 g/L (refer to Figure 7.3 for detail), the cell dry weight corresponding to 10 mL was: 10 ¯ 10-3 ¯ 5.23 = 52.3¯ 10-3 • Therefore, the concentration of ATP (based on cell dry weight) was: 19.872 × 10 −5 = 0.38 × 10 − −3 52.3 × 10 • (g) ( g / g dry weight ) = 3.8 (mg / g dry weight ) And then this value was performed in Table 7.4 (column 2) The ATP concentrations for other sampling times were calculated in the same way with this example, and then the results were performed in Table 7.4 (column 2) for discussion ii) ADP concentration calculation: The calculation of ADP concentration was performed in the same way with the calculation of ATP concentration However, ADP was converted to ATP for the assay, therefore, there was a notice that the amount ATP in this case was combined by initial ATP (that was calculated in Section i) above) and the ATP that was produced from the reaction to convert ADP to ATP (see section 7.3.3 for details) The value in the column in Table (Appendix G) was used to calculate ADP concentrations An example of calculation of ADP concentration is described below: The ADP (and ATP) data at 120 h was used to illustrate the calculation • From intensity value in the column in Table (Appendix G), the concentration of total ATP was: 181359.55 − 5058 = 0.05877 ( μM ) = 58.77 × 10 −9 3000000 (M ) 330 • Sample was diluted 10000 times for the assay, therefore, the ATP concentration before diluted was: 58.77 ¯ 10-9 ¯ 10000 = 58.77¯ 10-5 • (M) Since 10 mL of culture was harvested and extracted using ethanol, then solution was dried using nitrogen before resuspended in mL of deionized water (see section 7.3.3 for detail), the mole of total ATP was: 58.77 × 10 −5 × × 10 −3 = 58.77 × 10 −8 • (mole) Since the total amount of ATP in this assay = initial ATP calculated from Section i) above + ATP produced from the phosphorylation of ADP Moreover, mole of ATP produced from the phosphorylation of ADP = mole of ADP Therefore, the mole of ADP in 10 mL of culture was: 58.77 ¯ 10-8 – 39.18 ¯ 10-8 = 19.59 ¯ 10-8 • (mole) Therefore, the mass of ADP (in 10 mL culture) was: 19.59 × 10 −8 × 427.3 = 8.37 × 10 −5 (g) Where: 427.3 (g) was molecular weigh of ADP • Since 10 mL of culture was harvested, and moreover cell dry weight at 120 h was 5.23 g/L (refer to Figure 7.3 for detail), the cell dry weight corresponding to 10 mL was: 10 ¯ 10-3 ¯ 5.23 = 52.3¯ 10-3 • (g) Therefore, the concentration of ATP (based on cell dry weight) was: 8.37 × 10 −5 = 0.16 × 10 − −3 52.3 × 10 ( g / g dry weight ) = 1.6 (mg / g dry weight ) 331 • And then this value was performed in Table 7.4 (column 3) The ADP concentrations for other sampling times were calculated in the same way with this example, and then the results were performed in Table 7.4 for discussion 332 Appendix H The lists of proteins and peptides for the study performed in Chapter Due to large number of supporting information for the lists of proteins as well as peptides, the full lists are made in a soft-copy (CD formatted) attached to the back of this thesis, rather than as hard-copy • File name: Appendix H • File type: Microsoft Excel • Description: The full lists of proteins and peptides for the study performed in Chapter The table below is the crucial protein list with ratio and EF (error factor) values Full lists are presented in Appendix H as a soft-copy (CD formatted) Note: 114, 115, 116, and 117 were representatives for samples harvested at 120, 132, 144, and 156 h, respectively The sample harvested at 120 h (114) was used as a control sample for comparisons Accession Protein Name gi|6319857 3-phosphoglycerate kinase; Pgk1p Glyceraldehyde-3-phosphate gi|6322409 dehydrogenase 1; Tdh1p gi|6324703 Yor129cp phosphoribosylamino-imidazolegi|6324702 carboxylase; Ade2p gi|6321693 enolase I; Eno1p gi|6319279 Pyruvate kinase; Cdc19p gi|6321968 enolase; Eno2p gi|6322790 aldolase; Fba1p gi|6323073 pyruvate decarboxylase; Pdc1p topoisomerase II, Top2p localizes to gi|6324241 axial cores in meiosis; Top2p gi|6319546 heat shock protein 26; Hsp26p Mitochondrial matrix protein gi|6322505 involved in protein import; subunit of SceI endonuclease; Ssc1p gi|6322697 Phosphoglycerate mutase; Gpm1p Ratio EF Ratio EF Ratio EF 115:114 115:114 116:114 116:114 117:114 117:114 1.1061 1.037 0.9087 1.0346 0.9091 1.0388 1.641 1.0407 1.0065 1.036 2.032 1.0405 0.5081 3.8347 1.0777 1.4217 0.6744 1.0454 1.1949 6.6142 2.1284 1.434 1.6712 1.0503 1.4064 0.7057 0.6959 0.6916 0.9707 1.0529 1.0567 1.0612 1.063 1.0728 1.1294 0.7921 0.7926 0.6974 1.3032 1.0507 1.0583 1.0679 1.0601 1.0709 1.1941 0.7225 0.7736 0.6506 1.2869 1.0532 1.0641 1.0685 1.069 1.0708 0.9868 2.4012 0.8152 1.8701 0.7794 1.073 3.6086 1.0747 1.2769 1.0707 2.2596 1.0769 0.7881 1.0994 1.0173 1.0858 0.9389 1.0877 0.9994 1.0866 1.033 1.0869 1.0363 1.0879 333 Calcium and phospholipid binding gi|6325209 protein homologous to translation elongation factor 1-gamma (EF-1ga Glyceraldehyde-3-phosphate gi|6321631 dehydrogenase 3; Tdh3p gi|6319809 Glucokinase; Glk1p gi|6320255 triosephosphate isomerase; Tpi1p Glucose-6-phosphate isomerase; gi|6319673 Pgi1p thioredoxin-peroxidase (TPx); reduces H2O2 and alkyl gi|6323613 hydroperoxides with the use of hydrogens provid gi|6321096 12 kDa heat shock protein; Hsp12p alkyl hydroperoxide reductase; gi|6323138 Ahp1p putative S-adenosyl-L-homocysteine gi|6320882 hydrolase; Sah1p YGP1 encodes gp37, a glycoprotein gi|6324169 synthesized in response to nutrient limitation which is homologous Heat shock protein of HSP70 family, gi|6319314 cytoplasmic; Ssa1p gi|6323002 104 kDa heat shock protein; Hsp104p gi|6322564 Cu, Zn superoxide dismutase; Sod1p gi|9755343 Ynr034w-ap translational elongation factor EF-1 gi|6325337 alpha; Tef1p translational elongation factor EF-1 gi|6319594 alpha; Tef2p gi|6320223 Ydr020cp putative dihydroxyacetone kinase; gi|6323570 Dak1p gi|6324793 dipeptidyl aminopeptidase; Ste13p gi|6320079 Ydl124wp translation elongation factor (EFgi|6324707 2); Eft1p translation elongation factor (EFgi|6320593 2); Eft2p (putative) lipid binding protein; gi|6323207 supressor of a cdc25 mutation; Tfs1p Heat shock protein also induced by gi|6324601 canavanine and entry into stationary phase; Sti1p mitochondrial chaperonin, homolog gi|6323288 of E coli groEL protein; Hsp60p gi|6320742 Ydr533cp member of 70 kDa heat shock protein gi|6323004 family; Ssa2p gi|6324486 Alcohol dehydrogenase; Adh1p gi|6321896 a keto-aldose reductase; Gre3p Manganese-containing superoxide gi|6321796 dismutase; Sod2p aromatic amino acid gi|6321236 aminotransferase; Aro8p Hexokinase I (PI) (also called gi|6321168 Hexokinase A); Hxk1p 6-phosphogluconate dehydrogenase; gi|6321977 probable GND gene; Gnd1p gi|6320469 involved in DNA repair; Din7p gi|6320905 DL-glycerol-3-phosphatase; Hor2p gi|6325331 Transketolase 1; Tkl1p 0.8019 1.8202 1.4873 1.2688 1.1697 1.0919 1.0917 1.1654 1.1113 1.0978 1.1817 1.0923 1.2182 0.7276 1.0999 1.1076 0.9602 0.9411 1.1094 1.0909 1.0449 0.9073 1.0938 1.0976 0.9688 1.0977 1.1321 1.0818 1.0106 1.1015 0.6692 1.0967 0.8799 1.0789 0.673 1.1017 0.8268 1.1053 0.6125 1.1023 0.8176 1.1037 1.0319 1.0807 1.1337 1.0937 1.092 1.1044 0.7203 1.175 1.1817 1.1582 0.8818 1.1061 1.3446 1.1439 1.3415 1.1512 1.67 1.1069 1.9407 1.1028 1.6926 1.099 1.8545 1.107 0.8078 0.8582 0.6633 1.1087 1.1192 1.0849 0.9612 1.0443 0.5624 1.1156 1.1057 1.1452 1.0222 1.1725 0.5934 1.1174 1.1217 1.1246 2.2167 1.1607 3.748 1.1228 3.2662 1.1279 2.2167 1.1607 3.748 1.1228 3.2662 1.1279 0.9298 1.3038 0.8629 1.079 0.8991 1.1295 1.358 1.1358 2.1491 1.1523 2.0871 1.1338 0.6903 1.5353 1.4949 1.1599 0.5356 1.1648 1.231 1.1433 0.5791 1.3134 1.1353 1.1392 0.8408 1.119 1.1996 1.1293 0.9645 1.1404 0.8408 1.119 1.1996 1.1293 0.9645 1.1404 1.0631 1.1693 0.7081 1.4286 0.8516 1.1423 1.7322 1.111 1.8432 1.1596 1.7198 1.1445 0.979 1.1424 1.3395 1.1493 1.1824 1.1512 1.6606 1.1233 1.7582 1.1435 2.1119 1.1519 3.3004 1.1058 2.512 1.1126 2.5134 1.1543 3.623 1.8734 1.1316 1.4336 2.241 1.5061 1.1517 1.1875 1.826 1.685 1.155 1.1642 0.6379 1.2159 0.8202 1.1811 0.8519 1.1656 0.4576 1.201 0.78 1.2785 0.6342 1.1703 1.7356 1.1841 1.897 1.177 1.4123 1.1762 0.6365 1.1207 0.8403 1.1467 0.7758 1.1784 0.7931 1.4649 0.5389 1.4149 1.1942 1.1709 1.4105 2.6119 0.9724 1.4704 1.1676 1.2061 1.2256 2.37 0.8368 1.1825 1.1831 1.1846 334 Isopropylmalate isomerase, catalyzes gi|6321429 the second step in the leucine biosynthesis pathway; Leu2p gi|6319483 Inorganic pyrophosphatase; Ipp1p cyclophilin peptidyl-prolyl cis-trans gi|6320359 isomerase; Cph1p vacuolar ATPase V1 domain subunit gi|6324907 E (27 kDa); Vma4p phosphofructokinase beta subunit; gi|6323861 Pfk2p EF-3 (translational elongation factor gi|6323278 3); Yef3p mitochondrial aldehyde gi|6324950 dehydrogenase; Ald4p Transaldolase, enzyme in the pentose gi|6323386 phosphate pathway; Tal1p NAPDH dehydrogenase (old yellow gi|6321973 enzyme), isoform 2; Oye2p chromosome segregation protein; gi|6320460 Chl4p Glutaredoxin (thioltransferase) gi|6320720 (glutathione reductase); Ttr1p HSP70 family member, highly gi|6325151 homologous to Ssa1p and Sse2p; Sse1p high-affinity hexose transporter; gi|6321100 Hxt10p phosphofructokinase alpha subunit; gi|6321679 Pfk1p cytoplasmic member of the HSP70 gi|6319972 family; Ssb1p Hexokinase II (PII) (also called gi|6321184 Hexokinase B); Hxk2p translation initiation factor eIF4A; gi|6322323 Tif2p translation initiation factor eIF4A; gi|6322912 Tif1p gi|6320200 ATP synthase delta subunit; Atp16p glycerol-3-phosphate dehydrogenase; gi|6320181 Gpd1p gi|6321069 Actin; Act1p gi|6325221 plasma membrane ATPase; Pma2p citrate synthase Nuclear encoded gi|6324328 mitochondrial protein.; Cit1p member of 70 kDa heat shock protein gi|6320950 family; Ssa4p gi|6320200 ATP synthase delta subunit; Atp16p gi|6325147 Ypl110cp gi|6323335 Aconitase, mitochondrial; Aco1p gi|6321648 thioredoxin; Trx2p mitochondrial malate dehydrogenase; gi|6322765 Mdh1p gi|6321159 Yfr044cp Homolog to serendipity protein (D gi|6319587 melanogaster); Ysa1p gi|6323590 transcriptional regulator; Gal80p gi|6322746 vacuolar aminopeptidase ysc1; Lap4p gi|6319597 Glycyl-tRNA synthase; Grs1p gi|6320077 microsomal ATPase; Cdc48p heavy chain of cytoplasmic dynein; gi|6322907 Dyn1p 1.1265 1.3363 0.9231 1.2796 1.92 1.1849 0.8147 1.1675 0.9761 1.1737 0.9188 1.1862 0.6878 1.1424 0.6548 1.1558 0.6543 1.1904 1.4166 1.0149 1.393 1.3163 1.3861 1.1907 1.641 1.1669 0.5912 1.1691 0.7142 1.2016 0.6078 1.1827 1.0157 1.1397 0.8782 1.2041 0.6871 1.1485 0.7494 1.1939 0.7281 1.205 1.2043 1.19 1.1329 1.2439 1.2187 1.2099 0.9176 1.1928 1.0439 1.2163 1.1839 1.2099 0.4845 1.1451 0.6117 1.1191 0.2891 1.2112 0.9304 1.3005 0.9426 1.3025 1.0902 1.2116 0.943 1.1769 1.0708 1.2278 1.0347 1.2134 1.4025 1.6738 0.9224 2.1332 1.2769 1.2164 1.8356 1.225 0.6341 1.1668 0.6713 1.2209 1.732 1.2004 1.1551 1.1988 1.7884 1.2225 1.623 1.1811 1.8325 1.2201 1.3972 1.2236 1.2603 1.1545 1.3534 1.2672 1.3695 1.2299 1.2603 1.1545 1.3534 1.2672 1.3695 1.2299 1.6234 1.123 2.132 1.432 1.672 1.231 1.3236 1.1729 1.792 1.2423 2.3424 1.2311 0.7604 3.5212 1.1686 1.1705 1.0939 1.821 1.1774 1.1712 0.8621 2.5212 1.2327 1.233 0.6309 1.2749 0.8213 1.238 0.7956 1.2346 0.8843 1.1616 1.3238 1.2158 1.248 1.2354 0.8843 1.3953 0.7556 0.6975 1.321 1.265 1.2085 1.2018 1.621 1.2067 0.8931 0.602 1.122 1.2833 1.2141 1.2672 1.6816 1.3359 0.8378 0.5833 1.2398 1.2418 1.2427 1.243 0.7977 1.1818 0.7083 1.1984 0.7192 1.2487 0.6527 1.2362 0.8696 1.2126 0.7332 1.2489 1.0113 2.9017 0.9222 3.6822 1.2006 1.2504 1.5596 0.5622 0.8119 1.2966 1.1908 1.2229 1.1898 1.2587 0.898 0.5935 1.0148 1.382 1.2183 1.2076 1.2125 1.2539 0.9186 0.5659 0.8715 1.3945 1.2511 1.2578 1.2589 1.2678 1.2316 1.5091 1.3067 1.1865 1.3474 1.2679 335 gi|6325016 gi|6323011 gi|6320788 gi|6319315 gi|6323821 gi|6325097 gi|6322978 gi|6322581 gi|6319517 gi|6324195 gi|6322468 gi|6322350 gi|6323196 gi|6324321 gi|6323752 gi|6320936 gi|6324951 gi|6319513 gi|6325196 gi|6324129 gi|6321525 gi|6322002 gi|6322770 gi|6319603 gi|6322225 gi|6319370 gi|6321401 gi|6324429 gi|6319307 gi|6323504 gi|6321772 gi|6323387 gi|6322869 gi|6319602 82 kDa heat shock protein; homolog of mammalian Hsp90; Hsp82p Aspartyl-tRNA synthetase, cytosolic; Dps1p Yel047cp Translation elongation factor EF1beta, GDP/GTP exchange factor for Tef1p/Tef2p; Efb1p aldehyde dehydrogenase; Ald3p cytosolic leucyl tRNA synthetase; Cdc60p Cofilin, actin binding and severing protein; Cof1p F(1)F(0)-ATPase complex beta subunit, mitochondrial; Atp2p Ybr043cp Ynl134cp glyceraldehyde 3-phosphate dehydrogenase; Tdh2p Component of Chaperonin Containing T-complex subunit seven; Cct7p Ribosomal protein S31 (S37) (YS24); Rps31p sit4 suppressor, dnaJ homolog; Sis1p Phosphoglucomutase; Pgm2p vitamin B12-(cobalamin)independent isozyme of methionine synthase (also called N5methyltetrahydrof NADP-specific glutamate dehydrogenase; Gdh1p gamma subunit of mitochondrial ATP synthase; Atp3p Cytosolic Aldehyde Dehydrogenase; Ald6p Ynl200cp cytoplasmic catalase T; Ctt1p branched-chain amino acid transaminase, highly similar to mammalian ECA39, which is regulated by the vacuolar ATPase V1 domain subunit C (42 kDa); Vma5p vacuolar ATPase V1 domain subunit B (60 kDa); Vma2p saccharopine dehydrogenase; Lys1p mitochondrial F1F0-ATPase alpha subunit; Atp1p pyrazinamidase and nicotinamidase; Pnc1p 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase); Rib4p cystathionine gamma-lyase; Cys3p Yml131wp Ribosomal protein S20; Rps20p acetohydroxyacid reductoisomerase; Ilv5p Ykr017cp 56 kD synthase subunit of trehalose6-phosphate synthase/phosphatase complex; Tps1p 1.2049 1.1996 2.1345 1.282 1.7268 1.2733 0.6237 1.3377 0.8539 1.3104 0.7461 1.2737 0.5519 1.3254 0.5942 1.1737 0.5714 1.2791 0.8837 1.3069 1.3793 1.165 1.2205 1.28 2.9961 1.2845 2.5282 1.3181 3.7942 1.2801 0.5581 1.3436 0.9687 1.2795 0.8819 1.2818 0.617 1.2824 1.3196 1.1415 0.9957 1.284 2.4378 1.3287 3.3363 1.2953 2.8448 1.2842 0.4691 0.9211 1.2338 1.2695 0.3795 1.1536 1.3229 1.2789 0.3757 1.2672 1.2901 1.2944 1.7592 1.2214 1.4018 1.1821 2.232 1.2961 2.2262 1.3707 1.2617 1.4389 1.458 1.2973 0.7959 1.3021 1.0068 1.2421 0.9183 1.3082 0.791 2.0802 1.1656 1.2675 1.0176 1.937 1.1038 1.2472 0.8825 1.8573 1.3109 1.3154 0.3272 1.1283 0.4259 1.1477 0.3863 1.3315 0.4755 1.4341 0.972 1.1792 0.7245 1.3319 1.5326 1.4311 1.7298 1.3505 1.8481 1.3462 1.105 1.4692 1.1533 1.3689 1.1139 1.352 1.0354 2.2568 1.2968 1.2833 0.9626 1.9283 1.1855 1.3766 0.9878 2.6385 1.3537 1.3564 0.177 1.3012 0.265 1.2959 0.2413 1.3572 1.3825 1.2885 1.5154 1.3214 1.336 1.3634 1.9032 1.3697 2.1178 1.367 2.0837 1.3684 0.8303 1.5191 0.6721 1.4668 1.7291 1.3694 1.8007 1.3173 2.5441 1.3334 1.9001 1.3697 1.1064 1.4193 1.2675 1.3659 1.3422 1.3844 0.6249 1.3158 1.0474 1.5771 1.2112 1.3899 0.7628 0.5822 3.7708 1.4482 1.2917 1.4448 1.3213 0.7215 3.7149 1.3648 1.0816 1.4371 1.2242 0.6682 3.1799 1.3915 1.3919 1.3924 0.4122 1.4897 0.529 1.4083 0.5288 1.4127 0.939 1.5358 0.6424 1.4117 0.6586 1.4197 1.1247 1.3308 1.2975 1.471 1.2916 1.4265 336 gi|6321931 gi|6322783 gi|6325418 gi|6323172 gi|6323840 gi|6323480 gi|6323568 gi|6322565 gi|6322815 gi|6325229 gi|6319658 gi|6325167 gi|6319407 gi|6324833 gi|6321390 gi|6319593 gi|6320696 gi|6320768 gi|6319714 gi|6322599 gi|6323077 gi|6321653 gi|6319396 gi|6323399 gi|6322271 gi|6321807 gi|6324923 gi|6320432 gi|6320704 gi|6320679 gi|6321798 gi|6320775 gi|6322556 gi|6323537 gi|6320016 gi|6321695 gi|6320235 sporulation-specific wall maturation protein; Sps100p probable nucleoside-diphosphate kinase (EC 2.7.4.6); Ynk1p Glycogen phosphorylase; Gph1p Ylr143wp constitutively expressed heat shock protein; Hsc82p vacuolar ATPase V0 domain subunit d (36 kDa); Vma6p Yml072cp Yjr105wp Uridinephosphoglucose pyrophosphorylase; Ugp1p acetoacetyl CoA thiolase; Erg10p 40S ribosomal gene product S6B (S10B) (rp9) (YS4); Rps6bp Ribosomal protein S6A (S10A) (rp9) (YS4); Rps6ap similar to thiol-specific antioxidant enzymes such as rehydrin/peroxiredoxin; Ybl064cp ATPase; component of the 26S proteasome cap subunit; Rpt4p ATPase; Rpt6p transketolase, homologous to tkl1; Tkl2p similar to rat dynein intermediate chain; Pac11p histone acetyltransferase complex subunit; Hpa3p RNA helicase homolog; Prp5p Homoserine dehydrogenase (Lhomoserine:NADP oxidoreductase); Hom6p Ribosomal protein S0B; Rps0bp Ribosomal protein S0A; Rps0ap heat-inducible cytosolic member of the 70 kDa heat shock protein family; Ssa3p Ribosomal protein S22B (S24B) (rp50) (YS22); Rps22bp Ribosomal protein S22A (S24A) (rp50) (YS22); Rps22ap Asparaginyl-tRNA synthetase; Ded81p pyruvate kinase; Pyk2p adenylate kinase; Adk1p Ydr496cp Ribosomal protein L27B; Rpl27bp Ribosomal protein L27A; Rpl27ap vacuolar protease B; Prb1p Yjr096wp 123 kD regulatory subunit of trehalose-6-phosphate synthase/phosphatase complex; homologous to TPS3 vacuolar ATPase V1 domain subunit A (69 kDa); Tfp1p 6-phosphogluconate dehydrogenase; Gnd2p Pst2p 0.9954 1.5546 0.5179 1.2338 0.608 1.4275 0.6877 1.3399 0.7717 1.4301 0.8286 1.4296 1.6194 1.2795 1.239 1.0974 0.9697 1.5051 1.3944 1.9724 0.9498 1.4538 1.436 1.4564 1.0884 1.8773 2.4424 1.6965 1.9075 1.4625 1.0884 1.123 2.4424 1.253 1.9075 1.4721 0.5307 0.8162 2.3648 1.4061 0.5826 0.9268 2.053 1.3365 0.6608 0.9302 1.4749 1.4765 0.9201 1.2776 1.1463 1.3599 1.2063 1.4788 0.5848 1.9515 0.4649 2.2371 0.5222 1.4997 7.7435 1.8022 8.2095 1.4767 6.7903 1.5019 7.7435 1.8022 8.2095 1.4767 6.7903 1.5019 1.1772 1.2513 1.6268 1.0617 1.3752 1.5144 1.8597 1.6929 2.0762 1.6878 1.9352 1.5203 1.8597 1.6929 2.0762 1.6878 1.9352 1.5203 0.9984 1.569 1.1145 1.5853 1.3766 1.5347 0.597 1.6055 0.7891 1.7435 0.6334 1.5372 1.6367 1.6297 1.5185 1.622 1.8663 1.5417 0.8439 1.5738 1.0646 1.0805 0.8268 1.5427 0.897 1.8789 1.0147 1.6812 0.864 1.5475 6.266 6.266 1.5905 1.5905 6.0928 6.0928 1.5452 1.5452 5.2014 5.2014 1.5544 1.5544 0.2992 32.9199 0.4353 1.2771 0.4458 1.5698 8.1856 5.0095 6.6654 15.7798 4.9199 1.5713 8.1856 5.0095 6.6654 15.7798 4.9199 1.5713 0.6249 2.8584 1.0312 1.6558 0.8096 1.584 1.823 0.6452 0.6497 6.2188 6.2188 0.6081 0.5925 2.1971 1.5406 1.4143 1.8958 1.8958 1.5762 1.5119 0.8339 0.7931 0.6103 6.6628 6.6628 0.7621 0.5685 2.1817 1.6198 1.7968 1.7117 1.7117 2.0288 1.8848 1.3247 0.8508 0.5719 5.6365 5.6365 0.5998 0.8151 1.5865 1.5882 1.599 1.6121 1.6121 1.6245 1.626 1.3967 1.508 1.5356 2.1378 1.5313 1.6474 2.2169 1.6988 2.2558 1.5447 1.9337 1.6637 0.5368 1.6253 0.518 1.4881 0.5133 1.6691 0.6168 1.238 0.5988 1.4796 0.5734 1.6764 337 gi|6321879 Yhr087wp gi|6321619 ribonucleotide reductase; Rnr4p alcohol dehydrogenase isoenzyme gi|6321181 IV; Adh4p Mitochondrial heat shock protein 78 gi|6320464 kDa; Hsp78p gi|6321594 Cystathionine beta-synthase; Cys4p gi|6325292 glutamine synthetase; Gln1p gi|6319819 histidinol dehydrogenase; His4p gi|6325384 Ypr127wp gi|6323464 Ylr432wp ubiquitin activating enzyme, similar gi|6322639 to Uba2p; Uba1p ATP phosphoribosyltransferase; gi|6320896 His1p gi|6321480 Ygr043cp 60S ribosomal protein P0 (A0) gi|6323371 (L10E); Rpp0p putative ATPase, 26S protease gi|6322704 subunit component; Rpt1p Ribosomal protein L3 (rp1) (YL1); gi|6324637 Rpl3p gi|6320576 similar to aldo-keto reductase; Ypr1p carbamoyl-phophate synthetase, gi|6322331 aspartate transcarbamylase, and glutamine amidotransferase; Ura2p gi|6324804 Transcriptional modulator; Wtm1p Ribosomal protein S3 (rp13) (YS3); gi|6324151 Rps3p Ribosomal protein L19B (YL14) gi|6319444 (L23B) (rpl5L); Rpl19bp Ribosomal protein L19A (L23A) gi|6319559 (rpl5L) (YL14); Rpl19ap 3-hydroxy-3-methylglutaryl gi|6323509 coenzyme A synthase; Hmgsp Histone H2B (HTB1 and HTB2 code gi|6320430 for nearly identical proteins); Htb1p Histone H2B (HTB1 and HTB2 code gi|6319471 for nearly identical proteins); Htb2p alpha subunit of succinyl-CoA ligase; gi|6324716 Lsc1p mannose-1-phosphate gi|6320148 guanyltransferase, GDP-mannose pyrophosphorylase; Psa1p yeast dnaJ homolog (nuclear gi|6324265 envelope protein); heat shock protein; Ydj1p gi|6323985 Ymr323wp gi|6324974 Similar to enolase; Err2p gi|6324969 enolase homolog; Err1p gi|6321231 Spt16p dihydroorotate dehydrogenase; gi|6322633 Ura1p encodes the cytoplasmic trifunctional gi|6321643 enzyme C1-tetrahydrofolate synthase; Ade3p gi|6319391 62-kDa protein; Pet112p Phenylalanyl-tRNA synthetase, alpha gi|6323089 subunit, cytoplasmic; Frs1p gi|6319814 Glutaredoxin; Grx1p HSP70 family member, highly gi|6319646 homologous to Sse1p; Sse2p 1.1288 1.0158 1.6487 3.7883 1.257 1.6047 0.7809 25.0473 1.4522 0.726 1.6822 1.6833 2.8231 1.2902 3.4023 1.8816 1.632 1.7862 1.049 1.6171 1.2772 1.8847 1.2156 1.815 0.5882 0.4435 1.3349 1.7725 1.3889 1.1212 1.5182 1.4174 1.7067 2.1176 0.6309 0.8259 1.627 1.2467 0.9791 1.2268 1.2462 1.9029 1.8774 1.7565 0.689 0.7285 1.386 1.3562 0.9251 1.8312 1.8465 1.8732 1.8849 1.8856 0.9973 2.5161 2.3633 1.4198 1.8802 1.9093 1.1895 1.0045 1.6046 2.1264 2.1393 1.9125 0.7099 2.0849 0.8213 1.7602 0.9704 1.929 4.5759 1.7762 4.4466 1.7996 3.6631 1.959 3.0287 1.8967 4.3158 3.7144 1.6604 1.9795 2.3772 1.8021 2.2026 3.0848 2.1634 1.9891 1.4436 1.7162 1.7582 1.5766 1.6827 2.0181 1.7746 1.416 4.4587 1.9222 2.8252 2.0648 0.9278 1.6942 0.8032 1.9263 0.753 2.067 4.9301 2.2453 4.4177 2.1625 3.1837 2.0878 5.0947 2.1266 5.2194 1.8567 3.8895 2.1186 5.0947 2.1266 5.2194 1.8567 3.8895 2.1186 0.713 1.967 1.0182 1.6133 0.9855 2.1404 0.7494 1.2406 0.7532 2.2899 0.5802 2.1484 0.7494 1.2406 0.7532 2.2899 0.5802 2.1484 1.0791 2.7903 1.1486 2.0608 1.2549 2.1515 1.9263 2.0047 2.9878 2.247 2.6846 2.1867 1.2663 1.3242 1.8979 2.1692 1.6781 2.1993 3.0237 3.0237 3.0237 0.5542 2.1386 2.1386 2.1386 4.3948 2.443 2.443 2.443 1.3663 2.0637 2.0637 2.0637 2.3495 3.5998 3.5998 3.5998 0.9402 2.215 2.215 2.215 2.2566 0.4049 1.7017 0.6197 1.9102 0.5425 2.2936 0.6312 2.1704 0.961 1.8927 0.9128 2.3139 0.8418 1.3165 0.7633 1.0605 0.731 2.3869 0.8134 3.0127 1.2923 3.5312 1.0498 2.4182 1.0446 2.9076 1.0785 5.0197 1.2511 2.4189 0.8311 4.0127 1.0315 2.6687 1.1559 2.7368 338 gi|6324027 gi|6324451 gi|6320560 gi|9755335 gi|6323547 gi|6323667 gi|6323579 gi|6320925 gi|6322116 gi|6322138 gi|6322583 gi|6320269 gi|6324709 gi|6320304 gi|6321569 gi|6324291 gi|6322136 gi|6321855 gi|6324463 gi|6323246 gi|6324109 gi|6324873 gi|6324117 gi|6323737 gi|6323179 gi|6322699 gi|6320215 gi|6319505 gi|6324533 gi|6322476 gi|6323829 gi|6322434 gi|6322171 gi|6321145 gi|6322847 gi|6321786 gi|6324343 gi|6322412 gi|6321753 Ribosomal protein S19B (rp55B) (S16aB) (YS16B); Rps19bp 40S ribosomal protein S19A (S16aA) (rp55A) (YS16A); Rps19ap Thioredoxin reductase; Trr1p aminopeptidase yscII; Ape2p proteasome component Y7; Pre8p Ymr025wp 5' to 3' DNA helicase; Pif1p 3-phosphoglycerate dehydrogenase; Ser3p 3-phosphoglycerate dehydrogenase; Ser33p Mmd1p Ribosomal protein S5 (S2) (rp14) (YS8); Rps5p Ribosomal protein S13 (S27a) (YS15); Rps13p NAD+-dependent isocitrate dehydrogenase; Idh2p member of conserved eukaryotic 143-3 gene family; Bmh2p Ygr130cp alpha-4-beta-4 subunit of mitochondrial isocitrate dehydrogenase 1; Idh1p DL-glycerol-3-phosphatase; Rhr2p Hsp70 Protein; Pdr13p Overexpression causes resistance to Zeocin; Zeo1p cyclophilin related to the mammalian CyP-40; Cpr6p adenylosuccinate synthetase; Ade12p multiprotein bridging factor; Mbf1p Vid27p Ymr090wp gene product has affinity for quadruplex nucleic acids; Stm1p NADH-cytochrome b5 reductase; Mcr1p Ribosomal protein L4B (L2B) (rp2) (YL2); Rpl4bp Ribosomal protein L4A (L2A) (rp2) (YL2); Rpl4ap 40S ribosomal protein S15 (S21) (rp52) (RIG protein); Rps15p dihydroxyacid dehydratase; Ilv3p Sip18p small subunit of ribonucleotide reductase; Rnr2p Ribosomal protein L2B (L5B) (rp8) (YL6); Rpl2bp Ribosomal protein L2A (L5A) (rp8) (YL6); Rpl2ap Ribosomal protein L14A; Rpl14ap Ribosomal protein L14B; Rpl14bp acetyl-CoA carboxylase; Acc1p Yjl049wp Single-strand nucleic acid binding protein; Sbp1p 8.4531 3.6818 7.4563 3.8619 6.4363 2.8139 8.4531 3.6818 7.4563 3.8619 6.4363 2.8139 1.103 1.1393 1.4379 0.6098 1.407 1.4293 1.2232 1.9804 16.2682 1.9793 1.5569 1.6271 1.2706 17.0138 0.9413 4.5759 0.7998 9.8019 1.3374 2.0961 1.4486 0.8803 0.927 0.7022 1.3198 3.1282 3.3239 3.6363 3.7355 3.7496 0.2211 4.1961 0.3358 2.0188 0.2453 4.0688 0.2211 4.1961 0.3358 2.0188 0.2453 4.0688 1.3186 1.7756 1.1346 1.9395 1.0072 4.102 10.6579 3.7747 10.2581 3.5109 7.6514 4.1039 5.94 3.1379 6.495 3.1928 5.3088 4.1514 0.7098 18.3796 0.6191 17.6861 0.7523 4.2037 0.5177 5.1586 0.6498 1.7295 0.5116 4.3866 2.7489 14.5431 1.3483 7.0822 2.1183 4.4433 0.7822 2.9474 0.819 17.3372 0.7375 4.5035 1.9676 1.5399 1.1537 1.3447 2.1417 2.0939 3.4276 2.4545 2.5371 1.892 4.5766 4.8056 0.6829 14.1151 0.7264 5.8504 0.6582 4.8775 0.599 2.8846 0.6256 7.4835 0.5452 5.9966 0.7384 0.9165 0.9913 1.0055 6.1611 2.5043 1.5152 1.2999 1.0078 0.9287 1.084 0.7531 8.2722 1.75 1.5904 4.9225 1.0098 1.025 1.1814 0.9505 6.6012 7.0946 7.1762 9.5331 1.0538 7.8688 1.3621 4.4122 1.1519 10.3131 0.566 2.072 0.6996 6.8813 0.7002 10.896 3.9088 18.8019 3.1068 20.3294 2.7976 18.7224 3.9088 18.8019 3.1068 20.3294 2.7976 18.7224 5.0314 104.5815 4.9842 121.569 4.1188 21.4844 0.4878 0.6365 3.8918 31.0461 0.7217 0.2604 3.5378 11.595 0.6993 0.4599 22.1983 23.5181 0.7386 15.2038 0.6838 29.0328 0.5979 23.577 2.7779 7.3955 2.9928 9.3202 2.0942 24.4369 2.7779 7.3955 2.9928 9.3202 2.0942 24.4369 5.3461 5.3461 0.898 0.3757 20.1846 20.1846 8.0931 24.7589 6.0603 6.0603 0.9911 0.4297 36.2528 36.2528 54.3667 39.6085 4.464 4.464 0.8721 0.3269 32.7587 32.7587 33.5665 34.0481 1.5363 13.3473 3.3733 10.0691 2.9158 39.8474 339 gi|6323087 gi|6325006 gi|6323848 gi|6323054 gi|6322698 gi|6319931 gi|6324945 gi|6322831 gi|6320658 gi|6323615 gi|6321315 gi|6321335 gi|6320781 gi|6320625 gi|6321487 serine hydroxymethyltransferase; Shm2p Ribosomal protein L36B (L39) (YL39); Rpl36bp Ribosomal protein L36A (L39) (YL39); Rpl36ap Sed5p is a t-SNARE (soluble NSF attachment protein receptor) required in ER to Golgi transport.; Sed Ykl151cp Actin binding protein; Abp1p 40S ribosomal protein S12; Rps12p contains four beta-transducin repeats; Mak11p Ribosomal protein S18A; Rps18ap Ribosomal protein S18B; Rps18bp Ribosomal protein S2 (S4) (rp12) (YS5); Rps2p Ribosomal protein L28 (L29) (rp44) (YL24); Rpl28p Ribosomal protein L12A (L15A) (YL23); Rpl12ap Ribosomal protein L12B (L15B) (YL23); Rpl12bp Ygr050cp 3.6316 67.4684 4.2006 11.1774 4.3654 44.0636 5.3923 1.2545 6.018 8.6569 4.4305 48.6513 5.3923 1.2545 6.018 8.6569 4.4305 48.6513 0.8721 2.0311 1.1241 249.4613 1.1025 89.6812 0.5719 116.6811 0.6204 650.4467 0.8411 184.1222 1.5146 169.0269 2.7009 30.9681 1.5482 621.0313 7.0069 873.7128 5.896 201.2165 5.2152 1192.354 0.552 1590.582 0.4322 443.1712 0.4935 3116.996 4.6152 199736.3 5.0693 67297.16 4.5818 16494.54 4.6152 199736.3 5.0693 67297.16 4.5818 16494.54 2.2729 125828.1 2.6868 2630.403 2.2048 16864.98 5.6932 52759.75 6.4775 65939.23 4.7281 17930.48 1.7432 856.5343 1.4954 641.2964 1.232 77579.28 1.7432 856.5343 1.4954 641.2964 1.232 77579.28 0.7844 4779.788 0.5645 23516.43 0.4366 107430.6 340 [...]... analysis of S cerevisiae are reviewed Furthermore, the bioethanol fermentation using S cerevisiae as well as current issuses to improve ethanol fermentation are also surveyed here 2.2 2.2.1 Literature review of Saccharomyces cerevisiae proteomic analysis The importance of proteomic investigations in Saccharomyces cerevisiae The proteomic analysis of S cerevisiae is the next step in the analysis of biological... terms of proteomics, an understanding of S cerevisiae in responding to this stress conditions (because of VHG conditions) has not yet been reported, and the proteomes of brewing yeast have still largely unknown [3] Therefore, in this thesis, proteomic analyses of S cerevisiae were performed to understand how the wild-type S cerevisiae KAY446 strain adapts to stress conditions generated by the VHG conditions. .. this thesis, S cerevisiae KAY446 was used for ethanol fermentation under very high gravity (VHG) conditions This strain showed an ability to ferment under these conditions since an average ethanol concentration of 117.5 g/L was determined for continuous fermentation In terms of deeper biological aspects, a proteomic analysis of S cerevisiae was also performed to gain an understanding of this micro-organism... bioprocess 30 Chapter 2 Review: Proteomic Analysis of Saccharomyces cerevisiae and Bioethanol Fermentation The contents of this chapter were published in Expert Review of Proteomics, 2007, 4(6), 793-813 31 2.1 Abstract Nowadays, proteomics is recognised as one of the fastest growing tools in many areas of research This is especially true for the study of Saccharomyces cerevisiae, as it is considered as a... changes of S cerevisiae (under different conditions) as well as measurements of metabolites Finally, the enhanced ethanol fermentation under VHG conditions was achieved by applying media and process condition changes to overcome issues that were highlighted from an analysis of the proteomic data Thus this thesis demonstrates that proteomics can be used to improve a bioprocess 30 Chapter 2 Review: Proteomic. .. relationship of DNA, RNA, and protein in terms of “-omics” The Figure also illustrates the main functions of proteomics in the study of S cerevisiae 33 Figure 2.2 The identification and quantitation methods which have been applied to the proteomic analysis of S cerevisiae 35 Figure 2.3 An overview of the workflows involved in the various labeling methods 36 Figure 2.4 Structure of reagents... relationship of DNA, RNA, and protein in terms of “-omics” The Figure also illustrates the main functions of proteomics in the study of S cerevisiae 33 Briefly, the main aims of proteomics in studying S cerevisiae include (see Figure 2.1): (i) identification of proteins as well as comparison of protein expression changes in response to different states or environment changes; then, (ii) characterization of cellular... biological systems of this domain, after genomics and transcriptomics The global analysis of proteins is now receiving significant attention over that of genes, since the expression of proteins directly provides an understanding of function and regulation of cells in response to their environments In comparison to gene expression analysis at the mRNA level, proteomic expression analysis provides deeper... different domains of life including S cerevisiae (eukaryotes), S solfataricus (archaea) and Synechocystis sp (bacteria) The evaluation of this technique is also included 28 • Chapter 4: An understanding of S cerevisiae proteomes under elevated glucose concentrations is presented in this chapter This is first time a global proteome analysis of S cerevisiae using iTRAQ has been carried out to understand the... understand the responses of yeast to osmotic stress condition (high concentrations of glucose) • Chapter 5: This chapter investigates the benefits of amino acid supplementation in VHG media for ethanol fermentation Proteomic analysis of S cerevisiae was performed during the lag and early exponential phase to illustrate the benefits of amino acids addition • Chapter 6: The application of two techniques, immobilized