GEO DataSets

(Submitter supplied) Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon Pyrococcus furiosus: Characterization of a Coenzyme A-Dependent NAD(P)H Sulfur Oxidoreductase The hyperthermophilic archaeon Pyrococcus furiosus, uses carbohydrates as a carbon source and produces acetate, CO2 and H2 as end products. When S° is added to a growing culture, within 10 min the rate of H2 production rapidly decreases and H2S is detected. more...

Organism:

Pyrococcus furiosus; Pyrococcus furiosus DSM 3638

Type:

Expression profiling by array

Platform:

GPL4688

18 Samples

Download data: TXT

(Submitter supplied) Glass slide, see protocol above. Protocol: Each of the known 2192 ORFs in P. furiosus were amplified individually by PCR. Primers were selected to produce full-length PCR products. In case of large ORFs >2 kb PCR primers were designed to yield a PCR product around 1 kb. Expected PCR products with high homology to more than one locus were replace by a 50-mer specific oligo. Oligos were purchased from MWG Biotech (High Point, NC) in a 96-well format. more...

Organism:

Pyrococcus furiosus DSM 3638

2 Series

27 Samples

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(Submitter supplied) Oxidative Stress Protection and the Repair Response To Hydrogen Peroxide in the Hyperthermophilic Archaeon Pyrococcus furiosus Pyrococcus furiosus is a shallow marine, anaerobic archaeon that grows optimally at 100°C. Addition of H2O2 (0.5 mM) to a growing culture resulted in cessation of growth with a 2 hour lag before normal growth resumed. Whole genome transcriptional profiling revealed that the main response occurs within 30 min of peroxide addition, with the up-regulation of 62 open reading frames (ORFs), 36 of which are part of 10 potential operons. more...

Organism:

Pyrococcus furiosus DSM 3638

Type:

Expression profiling by array

Platform:

GPL4688

9 Samples

Download data: TXT

(Submitter supplied) The remarkable survival of the hyperthermophilic archaeon Pyrococcus furiosus to ionizing radiation was previously demonstrated. Using a time course study and whole-genome microarray analyses of mRNA transcript levels, the genes and regulatory pathways involved in the repair of lesions produced by ionizing irradiation (oxidative damage and DNA strand breaks) in P. furiosus were investigated. Data analyses showed that radA, encoding the archaeal homolog of the RecA/Rad51 recombinase, was moderately up regulated by irradiation and that a putative DNA-repair gene cluster was specifically induced by exposure to ionizing radiation. more...

Organism:

Pyrococcus furiosus

Type:

Expression profiling by array

Dataset:

GDS2469

Platform:

GPL3926

21 Samples

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Analysis of Pyrococcus furiosus cells exposed to 2.5 kGy of gamma radiation and then incubated at 90º C for up to 4 hours. At this dose, P. furiosus exhibits 75% survival. Results provide insight into the pathways involved in the repair of lesions produced by ionizing irradiation in P. furiosus.

Organism:

Pyrococcus furiosus

Type:

Expression profiling by array, log10 ratio, 2 agent, 6 time sets

Platform:

GPL3926

Series:

GSE5919

21 Samples

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(Submitter supplied) (from abstract): Iron oxidation is a desirable trait of biomining microorganisms, although the mechanism is not well-understood in extreme thermoacidophiles. The complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula DSM 5348 (2.2 Mb, ~2300 ORFs) provides insights into biologically catalyzed metal sulfide oxidation. Comparative genomics was used to identify pathways and proteins (in)directly involved with bioleaching. more...

Organism:

Metallosphaera sedula

Type:

Expression profiling by array

Platform:

GPL6785

1 Sample

Download data: CSV

(Submitter supplied) A DNA microarray was designed and constructed based on at least 2258 protein-coding sequences in the M. sedula genome obtained from the Department on Energy’s Joint Genomes Institute (http://genome.ornl.gov/microbial/msed). OligoArray 2.1 (Rouillard, 2003) was used to generate at least one 60-mer oligonucleotide probe sequence for each open reading frame. The probes were synthesized (Integrated DNA Technologies, IA), re-suspended in 50% DMSO, and printed onto Ultragap microarray slides (Corning, NY) using a QArrayMini arrayer (Genetix, UK). more...

Organism:

Metallosphaera sedula

7 Series

33 Samples

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(Submitter supplied) A strong promoter increases transcription of the genes of interest and enhances the production of various valuable substances. For a hyperthermophilic archaeon Thermococcus onnurineus NA1, which can produce H2 by carbon monoxide oxidation, we searched for a novel endogenous strong promoter by transcriptome analysis using high-throughput RNA sequencing. Based on the relative transcript abundance, we selected one promoter to encode a hypothetical gene, of which homologs were found only in several Thermococcales strains. more...

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

2 Samples

Download data: TXT

(Submitter supplied) The amino acid biosynthetic pathway of invasive pathogenic fungi has been studied as a potential antifungal drug target. Studies of the disruption of genes involved in amino acid biosynthesis have demonstrated the importance of this pathway in the virulence of Cryptococcus neoformans. Here, we identified the MET5 (CNL05500) and MET10 (CNG03990) genes in this pathway, both encoding sulfite reductase, which catalyzes the reduction of sulfite to sulfide. more...

Organism:

Cryptococcus neoformans var. neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28805

4 Samples

Download data: TXT

(Submitter supplied) Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 67µM. more...

Organism:

Thermococcus gammatolerans

Type:

Expression profiling by array

Platform:

GPL6958

24 Samples

Download data: GPR

(Submitter supplied) Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for hydrogen, phosphate, or leucine were compared to determine the regulatory response to hydrogen limitation. This was done by comparing hydrogen limited cultures to both leucine limited and phosphate limited cultures. Slow and rapid growing samples limited for either hydrogen or phosphate were compared to determine the regulatory effects of growth rate. more...

Organism:

Methanococcus maripaludis

Type:

Expression profiling by array

Platform:

GPL2509

68 Samples

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(Submitter supplied) To study mixotrophy, it is desirable to have an organism capable of growth in the presence and absence of both organic and inorganic carbon sources, as well as organic and inorganic energy sources. Metallosphaera sedula is an extremely thermoacidophilic archaeon which has been shown to grow in the presence of inorganic carbon and energy source supplements (autotrophy), organic carbon and energy source supplements (heterotrophy), and in the presence of organic carbon and inorganic energy source supplements. more...

Organism:

Metallosphaera sedula

Type:

Expression profiling by array

Platform:

GPL6785

7 Samples

Download data: CSV

(Submitter supplied) Pyrococcus yayanosii CH1 is the first and only obligate piezophilic hyperthermophilic microorganism discovered so far, that extends the physical and chemical limits of life on Earth and strengthens the idea of the existence of a hyperthermophilic biosphere in the depth of our planet. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses where performed in order to study the mechanisms implemented by the cell to face high hydrostatic pressure variations. more...

Organism:

Pyrococcus yayanosii; Pyrococcus; Pyrococcus furiosus

Type:

Expression profiling by array

Platform:

GPL20888

15 Samples

Download data: TXT