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• W2179959243 abstract "Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history. Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history. Genome-wide analysis of multiple organisms is one of the most useful approaches to uncover both the conservation and divergence of biological processes with respect to evolutionary history. Transcriptomic studies using DNA microarrays or deep-sequencing techniques have not only characterized the expression profiles of cell-type and -state specific genes involved in many biological processes, the have also revealed the expression patterns of genes involved in a variety among different species (1.Romero I.G. Ruvinsky I. Gilad Y. Comparative studies of gene expression and the evolution of gene regulation.Nat. Rev. Genet. 2012; 13: 505-516Crossref PubMed Scopus (279) Google Scholar). Proteomic analysis, for which mass spectrometry is one of the most powerful and widely used analytical techniques (2.Ahrens C.H. Brunner E. Qeli E. Basler K. Aebersold R. Generating and navigating proteome maps using mass spectrometry.Nat. Rev. Mol. Cell Biol. 2010; 11: 789-801Crossref PubMed Scopus (133) Google Scholar), can provide much more direct evidence of both conservation and divergence of expression profiles across multiple species. Interspecies comparative proteomic studies with mass spectrometry have been hitherto carried out in primates (3.Fu N. Drinnenberg I. Kelso J. Wu J.R. Pääbo S. Zeng R. Khaitovich P. Comparison of protein and mRNA expression evolution in humans and chimpanzees.PLoS ONE. 2007; 2: e216Crossref PubMed Scopus (60) Google Scholar, 4.Khan Z. Ford M.J. Cusanovich D.A. Mitrano A. Pritchard J.K. Gilad Y. Primate transcript and protein expression levels evolve under compensatory selection pressures.Science. 2013; 342: 1100-1104Crossref PubMed Scopus (155) Google Scholar), yeasts (5.Schmidt M.W. Houseman A. Ivanov A.R. Wolf D.A. Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe.Mol. Syst Biol. 2007; 3: 79Crossref PubMed Scopus (99) Google Scholar), and a variety of other model organisms (6.Schrimpf S.P. Weiss M. Reiter L. Ahrens C.H. Jovanovic M. Malmström J. Brunner E. Mohanty S. Lercher M.J. Hunziker P.E. Aebersold R. von Mering C. Hengartner M.O. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.PLos Biol. 2009; 7: e48Crossref PubMed Scopus (184) Google Scholar, 7.Weiss M. Schrimpf S. Hengartner M.O. Lercher M.J. von Mering C. Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome.Proteomics. 2010; 10: 1297-1306Crossref PubMed Scopus (52) Google Scholar, 8.Laurent J.M. Vogel C. Kwon T. Craig S.A. Boutz D.R. Huse H.K. Nozue K. Walia H. Whiteley M. Ronald P.C. Marcotte E.M. Protein abundances are more conserved than mRNA abundances across diverse taxa.Proteomics. 2010; 10: 4209-4212Crossref PubMed Scopus (101) Google Scholar, 9.Vogel C. Marcotte E.M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses.Nat. Rev. Genet. 2012; 13: 227-232Crossref PubMed Scopus (2486) Google Scholar). Abundance of the core proteome, for which orthologs have been identified in all organisms investigated, are well conserved across a wide range model organisms, including yeasts, plants, worms, flies, and humans (7.Weiss M. Schrimpf S. Hengartner M.O. Lercher M.J. von Mering C. Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome.Proteomics. 2010; 10: 1297-1306Crossref PubMed Scopus (52) Google Scholar). The profiles of orthologous protein abundance appear to be more conserved than profiles of transcript abundance in chimpanzees and humans (4.Khan Z. Ford M.J. Cusanovich D.A. Mitrano A. Pritchard J.K. Gilad Y. Primate transcript and protein expression levels evolve under compensatory selection pressures.Science. 2013; 342: 1100-1104Crossref PubMed Scopus (155) Google Scholar), worms and flies (6.Schrimpf S.P. Weiss M. Reiter L. Ahrens C.H. Jovanovic M. Malmström J. Brunner E. Mohanty S. Lercher M.J. Hunziker P.E. Aebersold R. von Mering C. Hengartner M.O. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes.PLos Biol. 2009; 7: e48Crossref PubMed Scopus (184) Google Scholar), and many other prokaryotes and eukaryotes (8.Laurent J.M. Vogel C. Kwon T. Craig S.A. Boutz D.R. Huse H.K. Nozue K. Walia H. Whiteley M. Ronald P.C. Marcotte E.M. Protein abundances are more conserved than mRNA abundances across diverse taxa.Proteomics. 2010; 10: 4209-4212Crossref PubMed Scopus (101) Google Scholar), suggesting that there is more selection pressure on protein expression than transcript expression. The degree to which protein abundance is conserved in fission yeast and budding yeasts is dependent on functional classes of orthologs (5.Schmidt M.W. Houseman A. Ivanov A.R. Wolf D.A. Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe.Mol. Syst Biol. 2007; 3: 79Crossref PubMed Scopus (99) Google Scholar). However, with one exception (4.Khan Z. Ford M.J. Cusanovich D.A. Mitrano A. Pritchard J.K. Gilad Y. Primate transcript and protein expression levels evolve under compensatory selection pressures.Science. 2013; 342: 1100-1104Crossref PubMed Scopus (155) Google Scholar), previous comparative analyses relied on independent analytical platforms and data derived from nonstandardized growth conditions, thus limiting direct comparisons. Aside from studies demonstrating conservation of proteome, the extent to which abundance of orthologous proteins is conserved across different species under various environmental conditions and what biological functions and processes are relevant to specific characteristics of individual organisms have yet to be thoroughly addressed. Saccharomyces cerevisiae was the first eukaryotic organism for which the genome was completely sequenced (10.Goffeau A. Barrell B.G. Bussey H. Davis R.W. Dujon B. Feldmann H. Galibert F. Hoheisel J.D. Jacq C. Johnston M. Louis E.J. Mewes H.W. Murakami Y. Philippsen P. Tettelin H. Oliver S.G. Life with 6000 genes.Science. 1996; 274: 546-567Crossref PubMed Scopus (3231) Google Scholar), making it an ideal model organism for various types of proteomic studies. S. cerevisiae and very closely related species included in the Saccharomyces sensu stricto group (11.Rainieri S. Zambonelli C. Kaneko Y. Saccharomyces sensu stricto: systematics, genetic diversity and evolution.J. Biosci. Bioeng. 2003; 96: 1-9Crossref PubMed Google Scholar)—known as Crabtree-positive yeasts—can grow under both aerobic and anaerobic conditions and can efficiently convert glucose to ethanol anaerobically during energy production even in the presence of oxygen, when aerobic respiration is repressed by glucose (glucose repression) (12.Klein C.J. Olsson L. Nielsen J. Glucose control in Saccharomyces cerevisiae: the role of Mig1 in metabolic functions.Microbiology. 1998; 144: 13-24Crossref PubMed Scopus (158) Google Scholar, 13.Johnston M. Feasting, fasting and fermenting. Glucose sensing in yeast and other cells.Trends Genet. 1999; 15: 29-33Abstract Full Text Full Text PDF PubMed Scopus (318) Google Scholar, 14.Geladé R. Van de Velde S. Van Dijck P. Thevelein J.M. Multi-level response of the yeast genome to glucose.Genome Biol. 2003; 4: 233Crossref PubMed Scopus (51) Google Scholar, 15.Schüller H.J. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae.Curr. Genet. 2003; 43: 139-160Crossref PubMed Scopus (349) Google Scholar). When glucose is exhausted or when yeasts are grown on nonfermentative carbon sources such as glycerol or ethanol, glucose repression is released leading to activation of gluconeogenesis and oxidative energy production through the tricarboxylic acid (TCA) 1The abbreviations used are:TCA cycletricarboxylic acid cycleORFopen reading framePSMpeptide spectra matchBLASTBasic Local Alignment Search ToolGOgene ontology. cycle and oxidative phosphorylation (12.Klein C.J. Olsson L. Nielsen J. Glucose control in Saccharomyces cerevisiae: the role of Mig1 in metabolic functions.Microbiology. 1998; 144: 13-24Crossref PubMed Scopus (158) Google Scholar, 13.Johnston M. Feasting, fasting and fermenting. Glucose sensing in yeast and other cells.Trends Genet. 1999; 15: 29-33Abstract Full Text Full Text PDF PubMed Scopus (318) Google Scholar, 14.Geladé R. Van de Velde S. Van Dijck P. Thevelein J.M. Multi-level response of the yeast genome to glucose.Genome Biol. 2003; 4: 233Crossref PubMed Scopus (51) Google Scholar, 15.Schüller H.J. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae.Curr. Genet. 2003; 43: 139-160Crossref PubMed Scopus (349) Google Scholar). In contrast, most other Saccharomycetaceae yeast species—known as Crabtree-negative yeasts—require oxygen for growth and aerobically utilize carbon sources, including glucose, for energy production via catabolism through the TCA cycle and ultimately oxidative phosphorylation (16.Pronk J.T. Yde Steensma H. Van Dijken J.P. Pyruvate metabolism in Saccharomyces cerevisiae.Yeast. 1996; 12: 1607-1633Crossref PubMed Scopus (597) Google Scholar, 17.Piškur J. Langkjær R.B. Yeast genome sequencing: the power of comparative genomics.Mol. Microbiol. 2004; 53: 381-389Crossref PubMed Scopus (87) Google Scholar, 18.Piškur J. Rozpedowska E. Polakova S. Merico A. Compagno C. How did Saccharomyces evolve to become a good brewer?.Trends Genet. 2006; 22: 183-186Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar). In recent decades, the genomes of many yeast species in the Saccharomycetaceae family have been sequenced (19.Kellis M. Patterson N. Endrizzi M. Birren B. Lander E.S. Sequencing and comparison of yeast species to identify genes and regulatory elements.Nature. 2003; 423: 241-254Crossref PubMed Scopus (1428) Google Scholar, 20.Dietrich F.S. Voegeli S. Brachat S. Lerch A. Gates K. Steiner S. Mohr C. Pöhlmann R. Luedi P. Choi S. Wing R.A. Flavier A. Gaffney T.D. Philippsen P. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome.Science. 2004; 304: 304-307Crossref PubMed Scopus (516) Google Scholar, 21.Kellis M. Birren B.W. Lander E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.Nature. 2004; 428: 617-624Crossref PubMed Scopus (1136) Google Scholar, 22.Dujon B. Sherman D. Fischer G. Durrens P. Casaregola S. Lafontaine I. De Montigny J. Marck C. Neuvéglise C. Talla E. Goffard N. Frangeul L. Aigle M. Anthouard V. Babour A. Barbe V. Barnay S. Blanchin S. Beckerich J.M. Beyne E. Bleykasten C. Boisramé A. Boyer J. Cattolico L. Confanioleri F. De Daruvar A. Despons L. Fabre E. Fairhead C. Ferry-Dumazet H. Groppi A. Hantraye F. Hennequin C. Jauniaux N. Joyet P. Kachouri R. Kerrest A. Koszul R. Lemaire M. Lesur I. Ma L. Muller H. Nicaud J.M. Nikolski M. Oztas S. Ozier-Kalogeropoulos O. Pellenz S. Potier S. Richard G.F. Straub M.L. Suleau A. Swennen D. Tekaia F. Wésolowski-Louvel M. Westhof E. Wirth B. Zeniou-Meyer M. Zivanovic I. Bolotin-Fukuhara M. Thierry A. Bouchier C. Caudron B. Scarpelli C. Gaillardin C. Weissenbach J. Wincker P. Souciet J.L. Genome evolution in yeasts.Nature. 2004; 430: 35-44Crossref PubMed Scopus (1254) Google Scholar, 23.Sherman D.J. Martin T. Nikolski M. Cayla C. Souciet J.L. Durrens P. Génolevures, Consortium Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.Nucleic Acids Res. 2009; 37: D550-554Crossref PubMed Scopus (95) Google Scholar, 24.Martin T. Sherman D.J. Durrens P. The Génolevures database.C R Biol. 2011; 334: 585-589Crossref PubMed Scopus (9) Google Scholar), enabling comparative proteomics across multiple yeast species toward our understanding the proteome profiles involved in differences in metabolic processes. tricarboxylic acid cycle open reading frame peptide spectra match Basic Local Alignment Search Tool gene ontology. Additional intriguing differences between Saccharomyces sensu stricto group and Crabtree-negative Saccharomycetaceae yeasts are with respect to genomic architecture. A number of duplicate genes arose in Saccharomyces yeasts through whole-genome duplication, prior to which two yeast clades diverged about 100 million years ago (17.Piškur J. Langkjær R.B. Yeast genome sequencing: the power of comparative genomics.Mol. Microbiol. 2004; 53: 381-389Crossref PubMed Scopus (87) Google Scholar, 20.Dietrich F.S. Voegeli S. Brachat S. Lerch A. Gates K. Steiner S. Mohr C. Pöhlmann R. Luedi P. Choi S. Wing R.A. Flavier A. Gaffney T.D. Philippsen P. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome.Science. 2004; 304: 304-307Crossref PubMed Scopus (516) Google Scholar, 21.Kellis M. Birren B.W. Lander E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.Nature. 2004; 428: 617-624Crossref PubMed Scopus (1136) Google Scholar, 22.Dujon B. Sherman D. Fischer G. Durrens P. Casaregola S. Lafontaine I. De Montigny J. Marck C. Neuvéglise C. Talla E. Goffard N. Frangeul L. Aigle M. Anthouard V. Babour A. Barbe V. Barnay S. Blanchin S. Beckerich J.M. Beyne E. Bleykasten C. Boisramé A. Boyer J. Cattolico L. Confanioleri F. De Daruvar A. Despons L. Fabre E. Fairhead C. Ferry-Dumazet H. Groppi A. Hantraye F. Hennequin C. Jauniaux N. Joyet P. Kachouri R. Kerrest A. Koszul R. Lemaire M. Lesur I. Ma L. Muller H. Nicaud J.M. Nikolski M. Oztas S. Ozier-Kalogeropoulos O. Pellenz S. Potier S. Richard G.F. Straub M.L. Suleau A. Swennen D. Tekaia F. Wésolowski-Louvel M. Westhof E. Wirth B. Zeniou-Meyer M. Zivanovic I. Bolotin-Fukuhara M. Thierry A. Bouchier C. Caudron B. Scarpelli C. Gaillardin C. Weissenbach J. Wincker P. Souciet J.L. 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The major group comprises duplicate gene pairs exhibiting divergent sequences or differentially regulated expression profiles that have resulted in asymmetric evolution to facilitate the acquisition of new functions or the partitioning of ancestral roles into individual genes during differentiation from the ancestral gene (21.Kellis M. Birren B.W. Lander E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.Nature. 2004; 428: 617-624Crossref PubMed Scopus (1136) Google Scholar, 25.Wolfe K.H. Shields D.C. Molecular evidence for an ancient duplication of the entire yeast genome.Nature. 1997; 387: 708-713Crossref PubMed Scopus (1392) Google Scholar, 26.Wolfe K. Evolutionary genomics: yeasts accelerate beyond BLAST.Curr. Biol. 2004; 14: R392-394Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar, 28.Langkjær R.B. Cliften P.F. Johnston M. Piškur J. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes.Nature. 2003; 421: 848-852Crossref PubMed Scopus (118) Google Scholar). Duplicate gene pairs in the minor group that are characterized by conserved sequences and slow evolution rates (21.Kellis M. Birren B.W. Lander E.S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.Nature. 2004; 428: 617-624Crossref PubMed Scopus (1136) Google Scholar, 26.Wolfe K. Evolutionary genomics: yeasts accelerate beyond BLAST.Curr. Biol. 2004; 14: R392-394Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar) and include genes encoding many cytoplasmic ribosomal proteins. The evolutionary role and mechanism of retention of duplicate genes with conserved sequences—that is, increasing protein abundance (gene dosage) (29.Kondrashov F.A. Koonin E.V. 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Comparative analyses of protein abundance across yeast species are expected to provide insights into whether the presence of conserved duplicate genes confers an evolutionary advantage with respect to protein dosage. Thus, yeast species in two clades, Saccharomyces sensu stricto group (Crabtree-positive) and Crabtree-negative yeasts within the Saccharomycetaceae family, are ideal model organisms for use in comparative proteomics, especially in regard to elucidating the significance of global molecular differences involved in distinct metabolic processes and the evolutionary role for duplicate genes. Furthermore, employing closely related unicellular organisms enables the use of identical growth conditions, thereby allowing direct comparisons of the proteome. In this study, we conducted an interspecies comparative proteomic analysis of four closely related yeast species (S. cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) using label-free quantification of protein abundance via mass spectrometry. Yeasts were grown in either glucose- or glycerol-containing medium to reveal differences in the proteome profiles under fermentative and nonfermentative growth conditions, respectively. S. cerevisiae strain S288C was used in this study. Other yeast strains were obtained from National Bio Resource Project (NBRP, Japan; http://www.nbrp.jp/): Saccharomyces paradoxus strain FSP2–3C (NBRP ID, BY20701), S. mikatae strain IFO1815 (NBRP ID, BY20110), Saccharomyces bayanus strain Su1A (NBRP ID, BY20703), Candida glabrata strain YAT3377 (NBRP ID, BY23876), Saccharomyces kluyveri strain SK125 (NBRP ID, BY21541), K. waltii strain IFO1666 (NBRP ID, BY20700), and K. lactis strain PM6–7A (NBRP ID, BY21799). After overnight culture in YPD medium (1% bacto yeast extract, 2% bacto peptone, and 2% glucose) or YPG medium (1% bacto yeast extract, 2% bacto peptone, and 3% glycerol) at 30 °C, yeast cells were inoculated into fresh medium and cultured in YPD or YPG medium at 30 °C in an exponential growth phase. Growth rate was determined by at least triplicate measurements of the optical density at 600 nm at five or more time points during a 6- to 8-hour culture. For protein extraction, yeast cells cultured in YPD medium were harvested at a density of 3∼6 × 107/ml after 4.5 h of culture; yeast cells cultured in YPG medium were harvested at a density of 1∼2 × 107/ml after 8 h of culture. Cell density was determined using a Burker-Turk hemocytometer with at least triplicate measurements for yeast cells fixed in 5% formaldehyde. Protein extractions for mass spectrometric analyses for each strain and growth condition were performed in biological duplicate experiments (experiments 1 and 2), in which proteins were extracted from independent culture of yeast cells. Yeast cells were collected by centrifugation at 2300 × g at 4 °C and then lysed by incubation in 1% β-mercaptoethanol and 0.26 N NaOH for 10 min at 4 °C, followed by addition of trichloroacetic acid (TCA) to a final concentration of 6.1%. After 30 min of incubation at 4 °C, proteins and cell debris were collected by centrifugation at 20,400 × g for 5 min at 4 °C. The resulting pellet was washed with ice-cold acetone and allowed to dry at room temperature for 30 min. Proteins were extracted from the pellet by the addition of dissolving buffer (0.1 m Tris-HCl (pH 8.5), 1% SDS, and 50 mm DTT), followed by sonication for 10 min and subsequent incubation at 95 °C for 10 min. After vortexing for 30 min to thoroughly dissolve extracted proteins, cell debris was removed by centrifugation at 20,400 × g for 5 min at room temperature. The concentration of protein in the resulting supernatant was determined by Bradford assay (Bio Rad, Hercules, CA) using bovine serum albumin as a standard. A total of 120 μg of proteins was digested using trypsin, and the resulting peptides were fractionated by gel-free isoelectric focusing. The protein solution was diluted to 200 μl by addition of 0.1 m Tris-HCl buffer (pH 8.5). Proteins were precipitated by methanol/chloroform precipitation method as described below. After the sequential addition of 600 μl of methanol, 150 μl of chloroform and 450 μl of distilled water and vortexing at each addition, the solution was then centrifuged at 13,000 × g for 5 min at 4 °C. The top aqueous layer was removed and 500 μl of methanol was added and the sample was vortexed. After centrifugation at 20,400 × g for 10 min at 4 °C, the precipitated proteins were dried for 2 min using a SpeedVac system (EYELA, Japan). Proteins were then re-dissolved by addition of 30 μl of 0.1 m Tris-HCl buffer (pH 8.5) containing 8 m urea and vortexing for 1 h. For cysteine reduction, DTT (final concentration, 5 mm) was added and the sample was incubated for 1 h at 37 °C, after which cysteine alkylation was performed by addition of iodoacetamide (final concentration, 10 mm) and incubated for 1 h at room temperature with in the dark. Next, 30 μl of 0.1 m Tris-HCl buffer (pH 8.5) and 60 μl of distilled water were added to reduce the urea concentration to 2 m, and then sequencing-grade modified trypsin (Promega, Wisconsin, WI) was added at a substrate to enzyme ratio of 20:1 and the sample was incubated for 15–18 h at 37 °C. A total of 100 μg of the yeast tryptic peptide mixture was separated into 24 fractions using a model 3100 OFFGEL fractionator of isoelectric focusing system (Agilent technologies, Santa Clara, CA) according to the manufacturer's protocol. Briefly, the sample of tryptic peptides dissolved in 0.05 m Tris-HCl buffer (pH 8.5) containing 2 m urea was diluted 36-fold with peptide OFFGEL stock solution (Agilent technologies), and the sample was loaded into the wells (∼4 μg/well) of a 3100 OFFGEL High-Res kit, pH 3–10 (Agilent technologies), followed by overnight electrophoresis at a current of 50 μA. Separation was completed upon reaching 50 kV-h. The fractionated peptides contained in each well were collected and stored at −80 °C until analyzed by mass spectrometry. Tryptic peptides were analyzed by data-dependent liquid chromatography-tandem mass spectrometry (LC-MS/MS) using a Dina nano LC system (KYA technologies, Tokyo, Japan) and an LTQ-Orbitrap XL mass spectrometer (Thermo Fisher Scientific, Waltham, MA), as follows. The peptide mixture was loa" @default.
• W2179959243 created "2016-06-24" @default.
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• W2179959243 date "2016-01-01" @default.
• W2179959243 modified "2023-10-05" @default.
• W2179959243 title "Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication" @default.
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• W2179959243 doi "https://doi.org/10.1074/mcp.m115.051854" @default.
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