title: Global gene expression in recombinant and non-recombinant yeast Saccharomyces cerevisiae in three different metabolic states.
abstract: Global gene expression of two strains of Saccharomyces cerevisiae, one recombinant (P+), accumulating large amounts of an intracellular protein Superoxide Dismutase (SOD) and one non-recombinant (P-) which does not contain the recombinant plasmid, were compared in batch culture during diauxic growth when cells were growing exponentially on glucose, when they were growing exponentially on ethanol, and in the early stationary phase when glycerol was being utilized. When comparing the gene expression for P- (and P+) during growth on ethanol to that on glucose (Eth/Gluc), overexpression is related to an increase in consumption of glycerol, activation of the TCA cycle, degradation of glycogen and metabolism of ethanol. Furthermore, 97.6% of genes (80 genes) involved in the central metabolic pathway are overexpressed. This is similar to that observed by DeRisi et al. [DeRisi, J.L., Iyer, V.R. & Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686.] but very different from was observed for Metabolic Flux Analysis (MFA), where the specific growth rate is lowered to ca. 40%, the fluxes in the TCA cycle are reduced to ca. 40% (to 30% in P+), glycolysis is reduced to virtually 0 and protein synthesis to ca. 50% (to 40% in P+). Clearly it is not possible to correlate in a simple or direct way, quantitative mRNA expression levels with cell function which is shown by the Metabolic Flux Analysis (MFA). When comparing the two strains in the 3 growth stages, 4 genes were found to be under or overexpressed in all cases. The products of all of these genes are expressed at the plasma membrane or cell wall of the yeast. While comparing the strains (P+/P-) when growing on glucose, ethanol and in the early stationary phase, many of the genes of the central metabolic pathways are underexpressed in P+, which is similar to the behaviour of the metabolic fluxes of both strains (MFA). Comparing the gene expression for P- (and to some extent P+) during the early stationary phase to growth on ethanol (Stat/Eth), underexpression is generalized. This shows that the switch in metabolism between ethanol and early stationary phases has an almost instantaneous effect on gene expression but a much more retarded effect on metabolic fluxes and that the "early stationary" phase represents a "late ethanol" phase from the metabolic analysis point of view since ethanol is still present and being consumed although at a much slower rate.
authors.affiliation: Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, Institute for Cell Dynamics and Biotechnology: A Centre for Systems Biology, University of Chile, Beauchef 861, Santiago, Chile; Department of Marine Biotechnology, Faculty of Marine Sciences and Natural Resources, University of Valparaiso, Viña del Mar, Chile.
authors.forename: H
authors.initials: H
authors.lastname: Díaz
authors.affiliation: Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, Institute for Cell Dynamics and Biotechnology: A Centre for Systems Biology, University of Chile, Beauchef 861, Santiago, Chile.
authors.forename: B A
authors.initials: BA
authors.lastname: Andrews
authors.affiliation: Faculty of Life Sciences, The University of Manchester, Manchester, M13 9PT, United Kingdom.
authors.forename: A
authors.initials: A
authors.lastname: Hayes
authors.affiliation: Systems Biology, Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
authors.forename: J
authors.initials: J
authors.lastname: Castrillo
authors.affiliation: Systems Biology, Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
authors.forename: S G
authors.initials: SG
authors.lastname: Oliver
authors.affiliation: Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, Institute for Cell Dynamics and Biotechnology: A Centre for Systems Biology, University of Chile, Beauchef 861, Santiago, Chile. Electronic address: juasenjo@ing.uchile.cl.
authors.forename: J A
authors.initials: JA
authors.lastname: Asenjo
mesh_terms: D005285:Fermentation; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis; D011995:Recombination, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic