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Next Generation Sequencing identifies O2-responsive genes in the human pathogenic fungus Aspergillus fumigatus

ABSTRACT: Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation. As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation ≈ 260 µmol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (≈ 13 µmol l-1).

ORGANISM(S): Aspergillus fumigatus

PROVIDER: GSE55943 | GEO | 2014/07/25

SECONDARY ACCESSION(S): PRJNA241401

REPOSITORIES: GEO

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Next Generation Sequencing identifies O2-responsive genes in the human pathogenic fungus Aspergillus fumigatus

Project description:Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation. As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation M-bM-^IM-^H 260 M-BM-5mol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (M-bM-^IM-^H 13 M-BM-5mol l-1). Dynamics of low and high O2 responses of A. fumigatus cultivated in an O2-controlled fermenter

2014-07-25 | E-GEOD-55943 | biostudies-arrayexpress

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2019-01-07 | PXD009626 | Pride

Gene expression profile of HIF-1Î± silenced or non-silenced human DCs stimulated with A. fumigatus under normoxic or hypoxic conditions

Project description:DCs play a central role for the immune response against the mold Aspergillus fumigatus. Hypoxic microenvironments occur during infection with A. fumigatus. Hypoxia and signaling via hypoxia inducible factor 1Î± may modulate the response of DCs; however, the role in fungal infections is unclear. We used microarrays to determine the influence of hypoxia and HIF-1Î± signaling on the immune response of human DCs towards A. fumigatus. HIF-1Î± silenced or non-silenced, human monocyte-derived DCs were cultivated for 6 h in normoxia or hypoxia (1 % O2) without stimulation or stimulated with inactivated germ tubes of A. fumigatus. Three independent experiments with DCs derived from different blood donors were performed. RNA was extracted and hybridized on Affymetrix microarrays.

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Isolation of a novel heterodimeric PSII complex involved in PSII repair

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Project description:Hypoxia (i.e., low oxygen (O2) levels) is a common environmental challenge for several aquatic species, including fish and invertebrates. To survive or escape these conditions, these animals have developed novel biological mechanisms, some regulated by neuropeptides. By utilizing mass spectrometry, this study aims to provide a global perspective of neuropeptides in the blue crab, Callinectes sapidus, and their changes over time (0, 1, 4, and 8 hours) due to severe hypoxia (~10% O2 water saturation) stress using a 4-plex dimethyl labeling strategy to increase throughput. Using both electrospray ionization and matrix-assisted laser desorption/ionization provided complementary coverage– 88 neuropeptides were identified with only five overlapping between the two ionization techniques. Interesting trends include (1) an overall decrease in expression due to hypoxia exposure, (2) a return to basal levels after 4 or 8 hours of exposure following an initial response, (3) changes only after 4+ hours exposure, and (4) an oscillating pattern. Overall, this study boosts the power of multiplexed quantitation to understand the large-scale changes due to severe hypoxia stress over time.

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Multifaceted activity of cytokinin at distinct phases of leaf development shapes its size and structure in Arabidopsis thaliana

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2015-09-04 | E-GEOD-72691 | biostudies-arrayexpress

Long-term adaptation to hypoxic conditions - Febit transcriptome analysis

Project description:Aspergillus fumigatus is an opportunistic, airborne pathogen causing invasive aspergillosis in immunocompromised patients. During the infection process A. fumigatus is challenged by hypoxic microenvironments occurring in inflammatory, necrotic tissue. To gain further insights into the adaptation mechanism, A. fumigatus was cultivated in an oxygen-controlled chemostat under hypoxic and normoxic conditions. Transcriptome analysis revealed significant increases in transcripts associated with cell wall polysaccharide metabolism, amino acid and metal ion transport, nitrogen metabolism and glycolysis. A concomitant reduction in transcript levels was observed with cellular trafficking and G-protein coupled signaling. To learn more about the functional roles of hypoxia-induced transcripts we deleted A. fumigatus genes putatively involved in reactive nitrogen species detoxification (fhpA), NAD+ regeneration (frdA, osmA) nitrogen metabolism (niaD, niiA) and respiration (rcfB). We show that the NO-detoxifying flavohemoprotein fhpA is strongly induced by hypoxia independent of the nitrogen source, but is dispensable for hypoxic survival. By deleting the nitrate reductase gene niaD, the nitrite reductase gene niiA and the two fumarate reductases genes frdA and osmA, we found that alternative electron acceptors such as nitrate and fumarate do not have a significant impact on growth of A. fumigatus during hypoxia, but that functional mitochondrial respiratory chain complexes are essential under these conditions. Inhibition studies indicated that primarily complex III and IV play a crucial role in the hypoxic growth of A. fumigatus.

2014-07-01 | E-MTAB-2699 | biostudies-arrayexpress

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Project description:Sulfolobus solfataricus P2 was grown aerobically, with O2 concentrations ranging from 1.5 to 26 % (v/v; gas phase). To gain some insight in control of the respiratory system, transcriptomes of the strain cultivated in different O2 concentrations (1.5 % vs 21 %, 1.5 % vs 26 %) were compared using a DNA microarray approach.

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