ArticleEukaryotic cell2006
Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae.
Article in Eukaryotic cell, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 98 citations in OpenAlex.
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- Set4 regulates stress response genes and coordinates histone deacetylases within yeast subtelomeres.Life science alliance · 2021Article
- Mitochondrial Retrograde Signaling Contributes to Metabolic Differentiation in Yeast Colonies.International journal of molecular sciences · 2021Article
- MutSα mismatch repair protein stability is governed by subunit interaction, acetylation, and ubiquitination.G3 (Bethesda, Md.) · 2021Article
- Microbial diversity from the continental shelf regions of the Eastern Arabian Sea: A metagenomic approach.Saudi journal of biological sciences · 2020Article
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- SET domains and stress: uncovering new functions for yeast Set4.Current genetics · 2019Review
- Structure Characterization and Action Mechanism of an Antiaging New Compound fromOxidative medicine and cellular longevity · 2019Article
- Set4 is a chromatin-associated protein, promotes survival during oxidative stress, and regulates stress response genes in yeast.The Journal of biological chemistry · 2018Article
- Oxygen-responsive transcriptional regulation of lipid homeostasis in fungi: Implications for anti-fungal drug development.Seminars in cell & developmental biology · 2018Review
- Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response.Journal of visualized experiments : JoVE · 2017Article
- From Lipid Homeostasis to Differentiation: Old and New Functions of the Zinc Cluster Proteins Ecm22, Upc2, Sut1 and Sut2.International journal of molecular sciences · 2017Review
- Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response.G3 (Bethesda, Md.) · 2017Article
- How do yeast sense mitochondrial dysfunction?Microbial cell (Graz, Austria) · 2016Review
- Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.BMC systems biology · 2015Article
- Loss of the thioredoxin reductase Trr1 suppresses the genomic instability of peroxiredoxin tsa1 mutants.PloS one · 2014Article
- Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution.PLoS genetics · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
We conducted a comprehensive genomic analysis of the temporal response of yeast to anaerobiosis (six generations) and subsequent aerobic recovery ( approximately 2 generations) to reveal metabolic-state (galactose versus glucose)-dependent differences in gene network activity and function. Analysis of variance showed that far fewer genes responded (raw P value of <or=10(-8)) to the O(2) shifts in glucose (1,603 genes) than in galactose (2,388 genes). Gene network analysis reveals that this difference is due largely to the failure of "stress"-activated networks controlled by Msn2/4, Fhl1, MCB, SCB, PAC, and RRPE to transiently respond to the shift to anaerobiosis in glucose as they did in galactose. After approximately 1 generation of anaerobiosis, the response was similar in both media, beginning with the deactivation of Hap1 and Hap2/3/4/5 networks involved in mitochondrial functions and the concomitant derepression of Rox1-regulated networks for carbohydrate catabolism and redox regulation and ending (>or=2 generations) with the activation of Upc2- and Mot3-regulated networks involved in sterol and cell wall homeostasis. The response to reoxygenation was rapid (<5 min) and similar in both media, dominated by Yap1 networks involved in oxidative stress/redox regulation and the concomitant activation of heme-regulated ones. Our analyses revealed extensive networks of genes subject to combinatorial regulation by both heme-dependent (e.g., Hap1, Hap2/3/4/5, Rox1, Mot3, and Upc2) and heme-independent (e.g., Yap1, Skn7, and Puf3) factors under these conditions. We also uncover novel functions for several cis-regulatory sites and trans-acting factors and define functional regulons involved in the physiological acclimatization to changes in oxygen availability.
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