Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus.

To study adaptive evolution in defined environments, we performed evolution experiments with Saccharomyces cerevisiae (yeast) in nitrogen-limited chemostat cultures. We used DNA microarrays to identify copy-number variation associated with adaptation and observed frequent amplifications and deletions at the GAP1 locus. GAP1 encodes the general amino acid permease, which transports amino acids across the plasma membrane.

Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level.

Exist several studies on the correlation between proteome and transcriptome and these studies have shown that generally there is only a weak positive correlation between these two omes, which means that post-transcriptional events play an important role in determining the protein levels in the cell. In this study we combined proteome and transcriptome data from six different published dataset to identify patterns that can provide new insight into the reasons for these deviations. By using a categorization method and integrating genome-scale information we found that the relation between protein and mRNA is related to the gene function.

Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator.

Highly conserved among eukaryotic cells, the AMP-activated kinase (AMPK) is a central regulator of carbon metabolism. To map the complete network of interactions around AMPK in yeast (Snf1) and to evaluate the role of its regulatory subunit Snf4, we measured global mRNA, protein and metabolite levels in wild type, Deltasnf1, Deltasnf4, and Deltasnf1Deltasnf4 knockout strains. Using four newly developed computational tools, including novel DOGMA sub-network analysis, we showed the benefits of three-level ome-data integration to uncover the global Snf1 kinase role in yeast.

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design.

Background: Characterization of cellular growth is central to understanding living systems. Here, we applied a three-factor design to study the relationship between specific growth rate and genome-wide gene expression in 36 steady-state chemostat cultures of Saccharomyces cerevisiae. The three factors we considered were specific growth rate, nutrient limitation, and oxygen availability.

Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods.

The quantitative proteomic analysis of complex protein mixtures is emerging as a technically challenging but viable systems-level approach for studying cellular function. This study presents a large-scale comparative analysis of protein abundances from yeast protein lysates derived from both wild-type yeast and yeast strains lacking key components of the Snf1 kinase complex. Four different strains were grown under well-controlled chemostat conditions.

Physiological characterization of glucose repression in the strains with SNF1 and SNF4 genes deleted.

We investigated the effect of Snf1 kinase and its regulatory subunit Snf4 on the regulation of glucose and galactose metabolism in the yeast Saccharomyces cerevisiae by physiologically characterizing Deltasnf1, Deltasnf4 and Deltasnf1Deltasnf4 in CEN.PK background in glucose and glucose-galactose-mixture batch cultivations. The main result of this study showed that delayed induction of galactose catabolism was SNF1 or SNF4 gene deletion specific.

Global aggregation of newly translated proteins in an Escherichia coli strain deficient of the chaperonin GroEL.

In a newly isolated temperature-sensitive lethal Escherichia coli mutant affecting the chaperonin GroEL, we observed wholesale aggregation of newly translated proteins. After temperature shift, transcription, translation, and growth slowed over two to three generations, accompanied by filamentation and accretion (in approximately 2% of cells) of paracrystalline arrays containing mutant chaperonin complex. A biochemically isolated inclusion body fraction contained the collective of abundant proteins of the bacterial cytoplasm as determined by SDS/PAGE and proteolysis/MS analyses.

Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation.

The yeast Saccharomyces cerevisiae encounters a range of nitrogen sources at various concentrations in its environment. The impact of these two parameters on transcription and metabolism was studied by growing S. cerevisiae in chemostat cultures with l-glutamine, l-alanine, or l-ammonium in limitation and by growing cells in an excess of ammonium.