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Transcriptional profiles of yeast on acetate exposed to pure nitrogen or carbon monoxide

ABSTRACT: Oxygen lack of various severity can force many organisms to enter into recoverable hypometabolic states. To better understand how organisms cope with oxygen deprivation, our lab had previously shown that when challenged with anoxia, both the nematode Caenorhabditis elegans and embryos of the zebrafish Danio rerio enter into suspended animation, where all life processes that can be observed by light microscopy reversibly halt, pending restoration of oxygen. Here, we show that both sporulating and vegetative cells of the budding yeast Saccharomyces cerevisiae also enter into a similar state of suspended animation when made anoxic on a non-fermentable carbon source. Transcriptional profiling using cDNA microarrays shows upregulation of aerobic metabolism genes in carbon monoxide (CO)-induced anoxia, but not nitrogen (N2) gas-induced anoxia, consistent with the known oxygen-mimetic effects of CO. Our results lead us to propose a model for oxygen-regulated gene expression in yeast where two oxygen-sensitive mechanisms operate simultaneously, such that treatment with N2 results in both mechanisms signaling a lack of oxygen, while treatment with CO results in one sensing mechanism signaling a lack of oxygen, while the other signals an abundance of oxygen.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE12004 | GEO | 2008/07/08

SECONDARY ACCESSION(S): PRJNA113273

REPOSITORIES: GEO

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Transcriptional profiles of yeast on acetate exposed to pure nitrogen or carbon monoxide

Project description:Oxygen lack of various severity can force many organisms to enter into recoverable hypometabolic states. To better understand how organisms cope with oxygen deprivation, our lab had previously shown that when challenged with anoxia, both the nematode Caenorhabditis elegans and embryos of the zebrafish Danio rerio enter into suspended animation, where all life processes that can be observed by light microscopy reversibly halt, pending restoration of oxygen. Here, we show that both sporulating and vegetative cells of the budding yeast Saccharomyces cerevisiae also enter into a similar state of suspended animation when made anoxic on a non-fermentable carbon source. Transcriptional profiling using cDNA microarrays shows upregulation of aerobic metabolism genes in carbon monoxide (CO)-induced anoxia, but not nitrogen (N2) gas-induced anoxia, consistent with the known oxygen-mimetic effects of CO. Our results lead us to propose a model for oxygen-regulated gene expression in yeast where two oxygen-sensitive mechanisms operate simultaneously, such that treatment with N2 results in both mechanisms signaling a lack of oxygen, while treatment with CO results in one sensing mechanism signaling a lack of oxygen, while the other signals an abundance of oxygen. Cells were pregrown on glucose media. Cells were then plated onto nylon membranes on acetate solid media and made anoxic using either pure nitrogen or carbon monoxide. Cells were collected at 15, 30, 45, 60, 120 minutes and 24 hours after initiation of gas exposure. Reference samples were derived from cells on acetate in room air for corresponding time point. Six CO-treated samples were compared to room air references and six nitrogen-treated samples were similarly compared to room air references.

2008-07-08 | E-GEOD-12004 | biostudies-arrayexpress

A single cell altas of mouse embryonic diapause and peri-implantation development

Project description:Here, we molecularly defined embryonic diapause at single-cell resolution, revealing hidden transcriptional dynamics while seemingly the embryo resides in a state of suspended animation. Alongside, we found that the dormant pluripotent cells are “aware” of their microenvironment which sustains their viability via Yap-mediated mechanotransduction.

2024-06-18 | GSE241462 | GEO

Transcription profiling of rainbow trout cells following anoxia exposure

Project description:The rainbow trout, Oncorhynchus mykiss, is relatively sensitive to hypoxia and does not survive deep hypoxia or anoxia. Given this lack of hypoxia-tolerance in the whole animal, the aim of this experiment was to investigate the in vitro responses of cultured rainbow trout cells following anoxia exposure. Rainbow trout hypodermal fibroblast (RTHDF) cells were exposed to anoxia for 12 and 24 h, whilst control cells were held under normoxic conditions for 24 h. Differential gene expression as a consequence of the treatments was analysed using an oligoarray composed of approximately 21,500 BLAST-identified sequences fabricated on the Agilent microarray platform. 57 genes were found to display significant responses to oxygen deprivation and these genes were assigned Gene Ontology terms and IDs. Of the 57 differentially expressed genes, 6 genes associated with carbohydrate metabolism were up-regulated following anoxia, these included phosphoglucomutase (PGM) and glycogen phosphorylase, consistent with glycogen serving as an important energy source during anoxia. Other genes up-regulated in response to anoxia included a number of putative targets of hypoxia inducible factor 1 alpha (HIF1A), namely phosphoglycerate kinase, triosephosphate isomerase and the glucose transporter, GLUT2. Egl9 homolog 3, the proline hydroxylase responsible for HIF1A regulation, was also induced. This analysis indicates that cultured trout cells have the capacity for adaptive gene responses when subjected to oxygen levels that are lethal to the whole organism.

2008-06-11 | E-MAXD-41 | biostudies-arrayexpress

1-deoxydihydroceramide causes anoxic death by impairing chaperonin-mediated protein folding

Project description:Ischemic heart disease and stroke are the most common causes of death world-wide. In both pathologies anoxia, the lack of oxygen, triggers profound metabolic and cellular changes. Sphingolipids have been implicated in anoxia injury, but the pathomechanism is unknown. Here we show that injury is caused by the accumulation of the non-canonical sphingolipid, 1-deoxydihydroceramide (DoxDHCer). We found that anoxia causes an imbalance between serine and alanine resulting in a switch from normal serine-derived sphinganine biosynthesis to non-canonical alanine-derived 1-deoxysphinganine. 1-deoxysphinganine is incorporated into DoxDHCer which impairs actin folding via the cytosolic chaperonin TRiC/CCT, leading to growth arrest in yeast and increased cell death upon ischemia-reperfusion injury in worms and mouse hearts. Prevention of DoxDHCer accumulation in worms and in mouse hearts resulted in decreased anoxia-induced injury. These findings unravel key metabolic changes during oxygen deprivation and point to novel strategies to avoid tissue damage and death.

2019-08-20 | PXD014573 | Pride

Disulphide bond inhibitors in 2 cancer cell lines

Project description:To elucidate which ER cargo maturation processes may be oxygen dependent, we first reasoned that the transcriptional response may be tailored specifically to counteract the mechanism of the imposed stress. Therefore, we compared the transcriptional regulation of the ERome during anoxic conditions to ER stress caused by lack of glycosylation (tunicamycin) or chaperone inactivation by calcium depletion (thapsigargin) In two cancer cell lines (colon carcinoma HCT116, and hepatocellular carcinoma Hep G2) cells were given one of 4 treatments. 24 hours of 0.0% O2 (Anoxia), 1.5 µg/ml tunicamycin or 0.3 µM thapsigargin with a control 21% O2 (Normoxia). Cells were exposed to hypoxia and anoxia in H35 and H85 HypOxystations (Don Whitley Scientific). 3 biological replicates of each experiment were carried out. Total of 24 samples.

2013-11-06 | E-GEOD-41666 | biostudies-arrayexpress

Evolution of diapause in the African killifish by remodeling ancient gene regulatory landscape

Project description:Suspended animation (e.g. hibernation, diapause) allows organisms to survive extreme environments. But the mechanisms underlying the evolution of suspended animation states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every summer. Here, we show that gene duplicates – paralogs – exhibit specialized expression in diapause compared to normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient and are present even in vertebrates that do not exhibit diapause. To determine if evolution of diapause is due to the regulatory landscape rewiring at ancient paralogs, we assessed chromatin accessibility genome-wide in fish species with or without diapause. This analysis revealed an evolutionary recent increase in chromatin accessibility at very ancient paralogs in African turquoise killifish. The increase in chromatin accessibility is linked to the presence of new binding sites for transcription factors, likely due to de novo mutations and transposable element (TE) insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes, and our lipidomics studies uncover a striking difference in lipid species in African turquoise killifish diapause, which could be critical for long-term survival. Together, our results show that diapause likely originated by repurposing pre-existing gene programs via recent changes in the regulatory landscape. This work raises the possibility that suspended animation programs could be reactivated in other species for long-term preservation via transcription factor remodeling and suggests a mechanism for how complex adaptations evolve in nature.

2021-08-05 | ST001898 | MetabolomicsWorkbench

Quantitative proteomic changes during anoxia and reoxygenation in anoxia-tolerant crucian carp

Project description:The freshwater fish crucian carp (Carassius carassius) can survive complete oxygen depletion (anoxia) for several months at low temperatures, achieved by a combination of reduced energy demand and increased glycolysis fueled by large hepatic glycogen stores. In crucian carp, the energy-requiring protein synthesis is controlled in a tissue-specific manner when oxygen levels decrease. During anoxia, translational rates are maintained at almost normoxic levels in brain, while heart and liver translation rates are strongly reduced. However, little is known about how the global proteome of these tissues are affected by oxygen variations. By applying mass spectrometry-based proteomics, 3304 proteins in brain, 3004 proteins in heart and 2516 proteins in liver were detected, of which 66 brain proteins, 243 cardiac proteins and 162 hepatic proteins were differentially expressed during the course of anoxia-reoxygenation compared to normoxic control. The brain proteome showed few differences in response to oxygen variations, indicating that anoxic survival is not regulated through protein expression in this tissue. Cardiac and hepatic adaptions to anoxia included enrichment of mitochondrial proteins involved in aerobic respiration and mitochondrial membrane integrity. We show that enzymes in the electron transport system (ETS) are regulated in a tissue-specific manner since no ETS components were regulated in brain, but were downregulated in heart and upregulated in liver during anoxia and reoxygenation. Furthermore, complement system activation was enriched in heart during anoxia. During reoxygenation, proteins involved in the cristae junction organization were regulated in the heart, possibly explaining how reactive oxygen species can be avoided when oxygen returns in this master of anoxic survival.

2023-01-27 | PXD032830 | Pride

Transcriptome analysis of Paracoccus denitrificans following exposure to hexavalent chromium under aerobic and anoxic conditions

Project description:Suspended cell studies were performed to document whole-genome transcriptional profiles as a function of Cr(VI) reduction under different electron accepting conditions. Cell suspension studies were performed in 250 mL serum bottles for two conditions: 1) under anoxic condition with lactate as carbon source and nitrate as electron acceptor, and 2) under aerobic condition with lactate as carbon source and oxygen as electron acceptor. The initial Cr(VI) and nitrate concentrations were 1000 μg/L and 40 mg N/L, respectively. Samples from both the conditions were collected after 5 hours and the cell pellet was saved at -80°C.

2021-08-11 | GSE181731 | GEO

Transcriptional Response to Dauer-Inducing Ascarosides in Late L1 in C. elegans

Project description:There are two steps in the C. elegans decision to enter the dauer-diapause lifestage. The first is a choice between L2 and L2d and the second is between L3 and dauer. We studied the transcriptional changes when well-fed worms were given a cocktail of dauer-inducing ascarosides in the late L1 phase as opposed to worms that received no such treatment. This study was done in both N2 wild-type worms, and daf-22 worms, which lack an enzyme necessary to produce endogenous ascarosides.

2021-03-30 | GSE171089 | GEO

Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause [ChIP-Seq]

Project description:Exposure of unicellular or multicellular organisms to adverse environmental conditions, including nutrient deprivation, may induce a state of suspended animation or diapause. We here report that broad repression of RNA Pol II-driven gene expression by inhibiting the BET family's bromodomain-containing proteins (BET) triggers diapause in mouse embryonic stem (ES) cells. The diapause ES cells upregulate a functionally linked group of genes encoding negative regulators of MAP kinase signaling (NRMKS), which play a crucial role in ES cell differentiation. The elevated NRMKS expression is a hallmark of cells exposed to distinct diapause-inducing conditions, including mTOR inhibition, and are required for the pluripotency maintenance during diapause. Mechanistically, inhibition of mTORC1/2 leads to rapid decline of the Capicua transcriptional repressor (CIC) at the NRMKS gene promoters, followed by rapid transcriptional NRMKS gene upregulation. The mTOR and BET-dependent transcriptional switch supporting the undifferentiated state of the diapause ES cells suggests a broader usage of this mechanism in maintaining the undifferentiated state of metabolically dormant stem- or stem-like cells in different tissues.

2024-10-08 | GSE269920 | GEO

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