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. L imitation in availability of oxygen (hypoxia) is a stress important in both biomedical and environmental contexts (1). In humans and other air-breathing vertebrates, hypoxia leads to rapid adaptive changes in metabolic organization, for instance in activation of anaerobic ATP-generating pathways like glycolysis. In mammals, a central role for a specific transcription factor, the hypoxia-inducible factor (HIF)-1␣ has been demonstrated. HIF-1␣ mediates the expression of a series of genes involved in both cellular and systemic responses to hypoxia, leading to enhanced anaerobic metabolism and induced erythropoiesis and angiogenesis (2).The patterns of differential gene expression associated with hypoxic stress in aquatic animals, for instance fishes, remain largely unknown. Understanding the tissue-specific and temporal changes in gene expression in fishes exposed to hypoxia could reveal new mechanisms of hypoxia tolerance and shed light on the evolution of this adaptive response in vertebrates. The long-jaw mudsucker Gillichthys mirabilis is a hypoxia-tolerant species that inhabits estuaries along the coastline of central and southern California, where it lives in burrows that characteristically have low levels of dissolved oxygen (3). Here, we exploit DNA microarray technology to investigate the response of this euryoxic fish to prolonged (up to 6 d) hypoxia. The application of DNA microarrays allows the expression of hundreds to many thousands of genes to be monitored simultaneously, providing a broad and integrated picture of the way an organism responds to a changing environment (4). To date, however, microarray analyses have been applied almost exclusively to model species for which gene sequence data are abundant. We show the utility of microarray approaches for the study of gene expression in a species for which, at the onset of our investigation, sequence data were unavailable. Our study thus provides a road map for exploiting DNA mic...

Identification and characterization of hypoxia-induced genes in Carassius auratus blastulae embryonic cells using suppression subtractive hybridization

“…This is reflected by gene expression changes observed in other fish exposed to hypoxia (Gracey et al, 2001;Ton et al, 2003;David et al, 2005;Ju et al, 2007). In our study, no genes involved in TCA cycle and the electron transfer chain were found to be induced.…”

“…A range of physiological adaptations on transcriptional levels have received considerable attention in fish. cDNA microarray has been used to identify hypoxiainduced genes in tissues from several fish species (Gracey et al, 2001;Gracey and Cossins, 2003;Ton et al, 2003;David et al, 2005;Ju et al;2007). Suppression subtractive hybridization is a powerful approach to identify differentially expressed gene that involved in physiological and pathological processes without bias of the prerequisite knowledge of a specific gene.…”

“…In contrast, genes involved in glycolysis, like phosphoglycerate mutase 1 (PGAM1), 6-phosphofructo-2-kinase (PFK-2), phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase (GPDH) and aldolase C, showed increased expression under hypoxic conditions. These genes have been identified as the target genes of the hypoxia inducible factor 1 (HIF-1) in fish and mammals (Semenza, 2002;Gracey et al, 2001;Ton et al, 2003;David et al, 2005). The results are consistent with the observations on these genes in tissues and cell lines from several fish species (Gracey et al, 2001;Ton et al, 2003;Nikinmaa and Rees, 2005;Olohan et al, 2008).…”

“…These genes have been identified as the target genes of the hypoxia inducible factor 1 (HIF-1) in fish and mammals (Semenza, 2002;Gracey et al, 2001;Ton et al, 2003;David et al, 2005). The results are consistent with the observations on these genes in tissues and cell lines from several fish species (Gracey et al, 2001;Ton et al, 2003;Nikinmaa and Rees, 2005;Olohan et al, 2008). The induction of GPDH, aldolase C, PGAM1, phosphofructokinase and PFK-2 may contribute to the regulation of the glycolytic flux under reduced oxygen tension in CAB cells under hypoxia.…”

“…Since water has a low oxygen capacity and poor oxygen diffusibility, many fish species have evolved behavioral, anatomical, physiological, biochemical and molecular adaptations that enable them to cope with periods of hypoxia (Wu, 2002;Nikinmaa, 2002;Nilsson and Ostlund-Nilsson, 2004). Hypoxia has been revealed to cause significant morphological and gene transcription changes in fish (Gracey et al, 2001;Ton et al, 2003;Sollid et al, 2003Sollid et al, , 2005David et al, 2005). However, the molecular mechanisms of hypoxia tolerance in fish remain largely unknown.…”