Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in Saccharomyces cerevisiae

Lai, Liang-Chuan; Kosorukoff, Alexander L.; Burke, Patricia V.; Kwast, Kurt E.

doi:10.1128/ec.00107-06

Cited by 97Fungal and yeast genetics researchRedox biology and oxidative stressBacterial Genetics and Biotechnology

Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in Saccharomyces cerevisiae

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Lai, Liang-Chuan, Kosorukoff, Alexander L., Burke, Patricia V., Kwast, Kurt E.·2006·Eukaryotic Cell

DOI 10.1128/ec.00107-06PMC PMC1563586

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Abstract

ABSTRACT We conducted a comprehensive genomic analysis of the temporal response of yeast to anaerobiosis (six generations) and subsequent aerobic recovery (≈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 ≤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 ≈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 (≥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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Some of the genes that are most strongly induced upon reoxygenation are involved in the two first modules of ergosterol synthesis.
“In accordance with this hypothesis, some of the genes that are most strongly induced upon reoxygenation are involved in the two first modules of ergosterol synthesis [103].”
From Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae (2020) · cites this paper as [103]
Several genome-wide expression studies under low oxygen conditions have reflected that the pattern of expression differs among ERG genes, although some general trends can be extracted.
“Several genome-wide expression studies based on microarray and RNA-Seq analyses under low oxygen conditions have reflected that the pattern of expression differs among ERG genes, although some general trends can be extracted [94,96,98,100,101,102,103].”
From Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae (2020) · cites this paper as [103]

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Authors: Lai, L.-C., Kosorukoff, A. L., Burke, P. V., & Kwast, K. E.
Affiliations: Department of Molecular and Integrative Physiology
University of Illinois Urbana-Champaign (US)
Corresponding author: Kwast, Kurt E.
ORCID: Lai, Liang-Chuan
Venue: Eukaryotic Cell
Publisher: American Society for Microbiology
Published: 2006-09
Volume: 5
Issue: 9
Pages: 1468-1489
ISSN: 1535-9778 (ISSN-L)
1535-9786
DOI: 10.1128/ec.00107-06
PMC: PMC1563586
OpenAlex: W2162295516
Cited by: 97
References: 113
Citations by year: 2026: 3 · 2025: 2 · 2024: 1 · 2022: 1 · 2021: 6 · 2020: 3 · 2019: 1 · 2018: 3 · 2017: 7 · 2016: 4 · 2015: 1 · 2014: 8 · 2013: 5 · 2012: 9
FWCI: 4.03
Type: journal article
Language: en
Open access: diamond
doi.org
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Eukaryotic Cell (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Institute of General Medical Sciences (R01GM059826)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Redox biology and oxidative stress
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords: anaerobic conditions, reoxygenation, Saccharomyces cerevisiae, transcriptome dynamics, oxygen availability, YAP, HAP1, roX1, UPC2, Skn7, heme regulation, redox regulation, oxidative stress, carbohydrate catabolism, metabolic status
MeSH terms: Anaerobiosis, Galactose, Glucose, Oxygen, Saccharomyces cerevisiae, Down-Regulation, Up-Regulation, Gene Expression Regulation, Fungal, Cluster Analysis, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling

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Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in Saccharomyces cerevisiae

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