Combined transcriptomics–metabolomics profiling of the heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus

Esteves, M. Alexandra; Graça, Gonçalo; Peyriga, Lindsay; Torcato, Inês M.; Borges, Nuno; Portais, Jean‐Charles; Santos, Helena

doi:10.1007/s00792-018-1065-0

Cited by 12 publications

(11 citation statements)

References 70 publications

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“…Because of the low adjusted p values and therefore high statistical reproducibility, genes meeting this criteria were considered even if they showed small changes (in terms of the log 2 fold change) between the two conditions. This is in line with previous archaeal studies that have identified and/or observed genes of physiological significance with a focus on a p value cut-off irrespective of the low log 2 fold changes [30,31]. Of the differentially expressed genes, 784 were upregulated (24.7 % of detected genes) and 763 were downregulated (24.0% of detected genes) in Cu-limited cultures.…”

Section: Rna Sequencing Analysissupporting

confidence: 89%

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

et al. 2020

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Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled by downregulation of ammonia oxidation, electron transport, carbon fixation, nucleotide, and lipid biosynthesis pathway genes. Under Cu-limitation, 1547 out of 3180 detected genes were differentially expressed, with 784 genes upregulated and 763 downregulated. The most highly upregulated genes encoded proteins with a possible role in Cu binding and uptake, such as the Cu chelator and transporter CopC/D, disulfide bond oxidoreductase D (dsbD), and multicopper oxidases. While this response differs from the marine strain Nitrosopumilus maritimus, conserved sequence motifs in some of the Cu-responsive genes suggest conserved transcriptional regulation in terrestrial AOA. This study provides possible gene regulation and energy conservation mechanisms linked to Cu bioavailability and presents the first model for Cu uptake by a soil AOA.

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Section: Rna Sequencing Analysissupporting

confidence: 89%

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

et al. 2020

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“…We decided to subject the cells to a rather mild high-temperature stress, in order not to incorporate variations in gene expression due to cell death. This strategy has previously been used for HS-response gene expression studies in S. solfataricus and P. furiosus (Tachdjian & Kelly, 2006;Esteves et al, 2019). According to the above-described growth and cell survival experiments, we considered that a 10°C-HS of 84°C (corresponding to the "85°C//84°C"-temperature profile in Figure 2) was of interest as cells experience a high-temperature stress at this cultivation temperature, reflected by an increased td (Figure 1; Table 1), but not resulting in a loss in cell viability as demonstrated by the spot tests (Figure 3; Supplementary Figure S8).…”

Section: Transcriptional Expression Of Important Hsps Upon Hsmentioning

confidence: 99%

“…This deleterious effect was strongly diminished when subjecting cells to an adaptative pretreatment at 88°C, which could be associated with the upregulation of the thermosome β subunit (Thβ) protein (Trent et al, 1990;Trent et al, 1994). Transcriptomic analyses in Archaeoglobus fulgidus, Pyrococcus furiosus and S. solfataricus revealed that a significant genome-wide transcriptional reprogramming is taking place upon HS, with 14%, 26% and 33%, respectively, of all genes exhibiting differential expression (Rohlin et al, 2005;Tachdjian & Kelly, 2006;Esteves et al, 2019). This is reflective of a large-scale, dynamic process.…”

Section: Introductionmentioning

confidence: 99%

Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius

et al. 2020

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“…Recently, metabolomics has provided new insight into identifying metabolic responses to stress in extremophiles. For instance, the metabolomic analysis suggested that levels of di-myo-inositol phosphate, mannosylglycerate, UDP-N-acetylglucosamine, and UDP-N-acetylgalactosamine were enhanced considerably in Pyrococcus furiosus in response to heat stress [6]. Empirical evidence suggests that metabolites including proline, proline analog, glycine betaine, pinitol, myo-inositol, mannitol, sorbitol, O-methylmucoinositol, and polyamines are essential for halophytes to grow in high saline conditions [7].…”

Section: Introductionmentioning

confidence: 99%

Untargeted Metabolomics Unveil Changes in Autotrophic and Mixotrophic Galdieria sulphuraria Exposed to High-Light Intensity

Liu

Sanchez-Arcos

Pohnert

et al. 2021

IJMS

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The thermoacidophilic red alga Galdieria sulphuraria has been optimizing a photosynthetic system for low-light conditions over billions of years, thriving in hot and acidic endolithic habitats. The growth of G. sulphuraria in the laboratory is very much dependent on light and substrate supply. Here, higher cell densities in G. sulphuraria under high-light conditions were obtained, although reductions in photosynthetic pigments were observed, which indicated this alga might be able to relieve the effects caused by photoinhibition. We further describe an extensive untargeted metabolomics study to reveal metabolic changes in autotrophic and mixotrophic G. sulphuraria grown under high and low light intensities. The up-modulation of bilayer lipids, that help generate better-ordered lipid domains (e.g., ergosterol) and keep optimal membrane thickness and fluidity, were observed under high-light exposure. Moreover, high-light conditions induced changes in amino acids, amines, and amide metabolism. Compared with the autotrophic algae, higher accumulations of osmoprotectant sugars and sugar alcohols were recorded in the mixotrophic G. sulphuraria. This response can be interpreted as a measure to cope with stress due to the high concentration of organic carbon sources. Our results indicate how G. sulphuraria can modulate its metabolome to maintain energetic balance and minimize harmful effects under changing environments.

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Combined transcriptomics–metabolomics profiling of the heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus

Cited by 12 publications

References 70 publications

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius

Untargeted Metabolomics Unveil Changes in Autotrophic and Mixotrophic Galdieria sulphuraria Exposed to High-Light Intensity

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