| 1. |
- Fazio, Allessandro, et al.
(författare)
-
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design
- 2008
-
Ingår i: BMC Genomics. ; 9:341
-
Tidskriftsartikel (refereegranskat)abstract
- 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 chemostate cultures of Saccharomyces cerevisiae. The three factors we considered were specific growth rate, nutrient limitation, and oxygen availability.Results: We identified 268 growth rate dependent genes, independent of nutrient limitation and oxygen availability. The transcriptional response was used to identify key areas in metabolism around which mRNA expression changes are significantly associated. Among key metabolic pathways, this analysis revealed de novo synthesis of pyrimidine ribonucleotides and ATP producing and consuming reactions at fast cellular growth. By scoring the significance of overlap between growth rate dependent genes and known transcription factor target sets, transcription factors that coordinate balanced growth were also identified. Our analysis shows that Fhl I, Rap I, and Sfp I, regulating protein biosynthesis, have significantly enriched target sets for genes up-regulated with increasing growth rate. Cell cycle regulators, such as Ace2 and Swi6, and stress response regulators, such as Yap I, were also shown to have significantly enriched target sets.Conclusion: Our work, which is the first genome-wide gene expression study to investigate specific growth rate and consider the impact of oxygen availability, provides a more conservative estimate of growth rate dependent genes than previously reported. We also provide a global view of how a small set of transcription factors, 13 in total, contribute to control of cellular growth rate. We anticipate that multi-factorial designs will play an increasing role in elucidating cellular regulation.
|
|
| 2. |
- Usaite, Renata, et al.
(författare)
-
Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose Repression Saccharomyces cerevisiae Strains: The comparison of two Quantitative Methods
- 2008
-
Ingår i: Journal of Proteome Research. - 1535-3907 .- 1535-3893. ; 266:7, s. 266-275
-
Tidskriftsartikel (refereegranskat)abstract
- 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. Multidimensional protein identification technology followed by quantitation using either spectral counting or stable isotope labeling approaches was used to identify relative changes in the protein expression levels between the strains. A total of 2388 proteins were relatively quantified, and more than 350 proteins were found to have significantly different expression levels between the two strains of comparison when using the stable isotope labeling strategy. The stable isotope labeling based quantitative approach was found to be highly reproducible among biological replicates when complex protein mixtures containing small expression changes were analyzed. Where poor correlation between stable isotope labeling and spectral counting was found, the major reason behind the discrepancy was the lack of reproducible sampling for proteins with low spectral counts. The functional categorization of the relative protein expression differences that occur in Snf1-deficient strains uncovers a wide range of biological processes regulated by this important cellular kinase.
|
|
| 3. |
- Usaite, Renata, et al.
(författare)
-
Physiological characterization of glucose repression in the strains with SNF1 and SNF4 genes deleted
- 2008
-
Ingår i: Journal of Biotechnology. - 1873-4863 .- 0168-1656. ; :133, s. 73-81
-
Tidskriftsartikel (refereegranskat)abstract
- 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 ∆snf1, ∆snf4 and ∆snf1∆snf4 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. In comparison to the reference strain, growth delay on galactose was found to last 2.4 times (7 h), 3.1 times (10.5 h) and 9.6 times (43 h) longer for the ∆snf4, ∆snf1 and ∆snf1∆snf4 strains, respectively. The maximum specific growth rates on galactose were determined to be two to three times lower for the recombinant strains compared to the reference strain (0.13 h-1) and were found to be 0.07, 0.08 and 0.04 h-1 for the ∆snf1, ∆snf4 and ∆snf1∆snf4 strains, respectively. The study showed that Snf1 kinase was not solely responsible for the depression of galactose metabolism.
|
|
| 4. |
- Usaite, Renata, et al.
(författare)
-
Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator
- 2009
-
Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292. ; 5:319, s. 1-12
-
Tidskriftsartikel (refereegranskat)abstract
- Highly conserved among eukaryotic cells, ghe 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, ∆snf1, ∆snf4, and ∆snf1∆snf4 knockout strains. Using four newly developed computional 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. We for the first time identified Snf1's global regulation on gene and protein expression levels, and showed that yeast Snf1 has a far more extensive function in controlling energy metabolism that reported earlier. Additionally, we identified complementary roles of Snf1 and Snf4. Similar to the function of AMPK in humans, our findings showed that Snf1 is a low-energy checkpoint and that yeast can be used more extensively as a model system for studying the molecular mechanisms underlying the global regulation of AMPK in mammals, failure of which leads to metabolic diseases.
|
|
