Yeast Biological Networks Unfold the Interplay of Antioxidants, Genome and Phenotype, and Reveal a Novel Regulator of the Oxidative Stress Response

Abstract

BackgroundIdentifying causative biological networks associated with relevant phenotypes is essential in the field of systems biology. We used ferulic acid (FA) as a model antioxidant to characterize the global expression programs triggered by this small molecule and decipher the transcriptional network controlling the phenotypic adaptation of the yeast Saccharomyces cerevisiae.Methodology/Principal FindingsBy employing a strict cut off value during gene expression data analysis, 106 genes were found to be involved in the cell response to FA, independent of aerobic or anaerobic conditions. Network analysis of the system guided us to a key target node, the FMP43 protein, that when deleted resulted in marked acceleration of cellular growth (∼15% in both minimal and rich media). To extend our findings to human cells and identify proteins that could serve as drug targets, we replaced the yeast FMP43 protein with its human ortholog BRP44 in the genetic background of the yeast strain Δfmp43. The conservation of the two proteins was phenotypically evident, with BRP44 restoring the normal specific growth rate of the wild type. We also applied homology modeling to predict the 3D structure of the FMP43 and BRP44 proteins. The binding sites in the homology models of FMP43 and BRP44 were computationally predicted, and further docking studies were performed using FA as the ligand. The docking studies demonstrated the affinity of FA towards both FMP43 and BRP44.ConclusionsThis study proposes a hypothesis on the mechanisms yeast employs to respond to antioxidant molecules, while demonstrating how phenome and metabolome yeast data can serve as biomarkers for nutraceutical discovery and development. Additionally, we provide evidence for a putative therapeutic target, revealed by replacing the FMP43 protein with its human ortholog BRP44, a brain protein, and functionally characterizing the relevant mutant strain.

Transcriptional profiling in Saccharomyces cerevisiae relevant for predicting alachlor mechanisms of toxicity

“…They include GRE2 , reported to be induced by H 2 O 2 or when yeast switch to respiratory metabolism 31, AAD4 and AAD6 that were also induced by oxidative stress mediated by GSH antagonists 32, and a number of genes encoding antioxidant enzymes belonging to the GSH/glutaredoxin and thioredoxin systems, which are required for regulation of redox homeostasis in S. cerevisiae . The latter include the following gene products: Gtt2p, involved in glutaredoxin‐mediated antioxidant activity 30; Gto2p and Gto3p, two homologous thiol transferases (glutaredoxins) proposed to help maintain an adequate redox state of proteins 33; Prx1p and Tsa2p, a mitochondrial peroxiredoxin and a stress‐inducible cytoplasmic thioredoxin peroxidase, respectively, that cooperate with each other in detoxifying peroxides and protecting cells against oxidative and nitrosative stress and GSH depletion 34; Gpx2, a thioredoxin‐dependent phospholipid hydroperoxide peroxidase; and Fmp43p, an ortholog of mammalian brain protein BRP44 recently proposed as being involved in oxidative stress response 15. These transcriptional responses appear to be compatible with the notion that alachlor‐stressed cells may experience a nonphysiological reducing level in the cytoplasmic environment attributable, for instance, to the depletion of endogenous GSH, presumably related to alachlor detoxification reactions 4, 29, although a change in the redox status presumably associated with modifications in energy metabolism also may occur in the alachlor‐stressed cells.…”

“…This microbial model is a promising test organism 11 with a number of advantages: it is easy to manipulate, has a fully sequenced genome (Saccharomyces Genome Database, http://www.yeastgenome.org); and a vast amount of genomics knowledge and resources (the Comprehensive Yeast Genome Database, http://mips.helmholtz‐muenchen.de/genre/proj/yeast/); and shares strong conservation of metabolic and regulatory mechanisms with lower or higher eukaryotes. In particular, a number of results from toxicological studies in this simple eukaryotic model may be relevant for more complex as well as experimentally and genomically less accessible eukaryotes of terrestrial and aquatic ecosystems 10–16. To our knowledge, the global transcriptional response of S. cerevisiae to a chloroacetanilide herbicide has not been analyzed thus far.…”

Prognostic role of mitochondrial pyruvate carrier in isocitrate dehydrogenase–mutant glioma

“…2 Alternatively, MPC2 may participate independently in other biological processes, as suggested recently. 28…”

Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis

“…The lowest carbon yield among these pathways was 62 %, which was calculated for six oxaloacetate-consuming pathways for the production of f6p, g6p, and e4p. This is mainly because of the low degree of reduction (defined as the number of equivalents of available electrons per gram atom C in a compound representing its redox level [ 23 ]) of oxaloacetate, which is only 10 (2.5 per carbon atom). By contrast, the degree of reduction of g6p is 24 (4 per carbon atom) and thus the maximal carbon yield determined by the degree of reduction balance (actually a simplified representation of elemental balance) is 62 % (2.5/4), the same as the pathway yield.…”