Global gene expression analysis was carried out with Blastocladiella emersonii cells subjected to oxygen deprivation (hypoxia) using cDNA microarrays. In experiments of gradual hypoxia (gradual decrease in dissolved oxygen) and direct hypoxia (direct decrease in dissolved oxygen), about 650 differentially expressed genes were observed. A total of 534 genes were affected directly or indirectly by oxygen availability, as they showed recovery to normal expression levels or a tendency to recover when cells were reoxygenated. In addition to modulating many genes with no putative assigned function, B. emersonii cells respond to hypoxia by readjusting the expression levels of genes responsible for energy production and consumption. At least transcriptionally, this fungus seems to favor anaerobic metabolism through the upregulation of genes encoding glycolytic enzymes and lactate dehydrogenase and the downregulation of most genes coding for tricarboxylic acid (TCA) cycle enzymes. Furthermore, genes involved in energy-costly processes, like protein synthesis, amino acid biosynthesis, protein folding, and transport, had their expression profiles predominantly downregulated during oxygen deprivation, indicating an energy-saving effort. Data also revealed similarities between the transcriptional profiles of cells under hypoxia and under iron(II) deprivation, suggesting that Fe 2؉ ion could have a role in oxygen sensing and/or response to hypoxia in B. emersonii. Additionally, treatment of fungal cells prior to hypoxia with the antibiotic geldanamycin, which negatively affects the stability of mammalian hypoxia transcription factor HIF-1␣, caused a significant decrease in the levels of certain upregulated hypoxic genes.Oxygen is essential for the survival of most eukaryotic organisms due to its crucial role in important biochemical and physiological processes, including energy production (in the form of ATP) from glucose by aerobic metabolism. In nature, oxygen deprivation challenges can occur with a significantly high frequency, depending on the organism lifestyle. Accordingly, organisms have evolved a complex set of cellular and molecular adaptive responses activated by decreases in oxygen availability (hypoxia or anoxia). These responses are adaptive because they can lead to changes in the physiological and metabolic status of the cells, which will allow them to cope with the stress associated with oxygen limitation and ultimately enhance cellular survival. Especially in aquatic habitats, hypoxia can be an important evolutionary driving force, resulting in both convergent and divergent physiological strategies for survival under low-oxygen conditions.The unicellular eukaryote Saccharomyces cerevisiae has been used as a model system to understand many basic cellular functions and biochemical processes in eukaryotic systems. Hypoxia response studies are not an exception. Yeast responds to changes in O 2 availability by altering the expression of a number of oxygen-responsive genes, consisting of hypoxic genes that are trans...