Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis

Abstract

Hypoxia is important in both biomedical and environmental contexts and necessitates rapid adaptive changes in metabolic organization. Mammals, as air breathers, have a limited capacity to withstand sustained exposure to hypoxia. By contrast, some aquatic animals, such as certain fishes, are routinely exposed and resistant to severe environmental hypoxia. Understanding the changes in gene expression in fishes exposed to hypoxic stress could reveal novel mechanisms of tolerance that may shed new light on hypoxia and ischemia in higher vertebrates. Using cDNA microarrays, we have studied gene expression in a hypoxia-tolerant burrow-dwelling goby fish, Gillichthys mirabilis. We show that a coherent picture of a complex transcriptional response can be generated for a nonmodel organism for which sequence data were unavailable. We demonstrate that: (i) although certain shifts in gene expression mirror changes in mammals, novel genes are differentially expressed in fish; and (ii) tissue-specific patterns of expression reflect the different metabolic roles of tissues during hypoxia.

Figure 1

Cluster images of the hypoxic expression profile in (a) liver and (b) muscle-type tissues. Supplemental expression data for liver are also presented: a repeat hypoxia time course on G. mirabilis (72 and 144 h, experiment 2) and acute exposure of G. seta to 5% pO₂ (24 h acute). The expression data for muscle-type tissues are for G. mirabilis. For clarity, just two measurements are shown for genes that were represented by more than one array element. The quantitative changes in gene expression are represented in color: red indicates induced genes, and green indicates repressed genes. Missing data points are represented as gray bars. Expanded annotated figures showing the gene names and associated accession numbers are published as supplemental data on the PNAS web site, www.pnas.org.

Figure 2

Genes selected from data presented in Fig. 1 and grouped into categories on the basis of their probable biological role. (a) ATP metabolism; (b) locomotion and contraction; (c) protein translation; (d) iron metabolism; (e) antigrowth and proliferation; (f) amino acid metabolism; and (g) cryptic role. Note that only a small fraction of the unknown genes discovered in this work are shown. (h) Northern blot analysis confirming the expression of a number of hypoxia-regulated genes in liver of G. mirabilis. The expression of β-actin, shown for reference, does not appear to significantly change in liver.