Identification and functional characterization of hypoxia-inducible factor 2alpha from the estuarine teleost, Fundulus heteroclitus: interaction of HIF-2alpha with two ARNT2 splice variants

Hypoxia-inducible factor 1 alpha protein increases without changes in mRNA during acute hypoxic exposure of the Gulf killifish, Fundulus grandis

The hypoxia inducible factor 1 (HIF1) is a central regulator of the molecular responses of animals to low oxygen. While the hypoxia-responsiveness of HIF1 is generally attributed to the stabilization of the alpha protein subunit (HIF1α) at low oxygen, several studies on fish report increased tissue levels of HIF1A mRNA during hypoxia, suggesting transcriptional regulation. In the current study, HIF1α protein and HIF1A mRNA were determined in parallel in tissues of Gulf killifish, Fundulus grandis, exposed to short-term hypoxia (24 h at 1 mg O2 l-1). HIF1α protein was higher in brain, ovary, and skeletal muscle from fish exposed to hypoxia compared with normoxic controls by 6 h, and it remained elevated in brain and ovary at 24 h. In contrast, HIF1A mRNA levels were unaffected by hypoxia in any tissue. Moreover, HIF1α protein and HIF1A mRNA levels in the same tissues were not correlated with one another during either normoxia or hypoxia. Hence, an increase in HIF1α protein does not depend upon an increase in HIF1A mRNA during acute exposure to low oxygen in this species. The results support the widely accepted mechanism of post-translational protein stabilization, rather than new transcription, during the initial response of fish to hypoxia.

Role of HIF in fish inflammation

The hypoxia-inducing factor (HIF) is a central transcription factor in cellular oxygen sensing and regulation. It is common that the inflammation always appears in many diseases, like infectious diseases in fishes, and the inflammation is often accompanied by hypoxia, as a hallmark of inflammation. Besides coordinating cellular responses to low oxygen, HIF-mediated hypoxia signaling pathway is also crucial for immune responses such as the regulations of innate immune cell phenotype and function, as well as metabolic reprogramming under the inflammation. However, the understanding of the molecular mechanisms by which HIFs regulate the inflammatory response in fish is still very limited. Here, we review the characteristics of HIF as well as its roles in innate immune cells and the infections caused by bacteria and viruses. The regulatory effects of HIF on the metabolic reprogramming of innate immune cells are also discussed and the future research directions are outlooked. This paper will serve as a reference for elucidating the molecular mechanism of HIF regulating inflammation and identifying treatment strategies to target HIF for fish disease.

Genomic analysis of hypoxia inducible factor alpha in ray-finned fishes reveals missing Ohnologs and evidence of widespread positive selection

As aquatic hypoxia worsens on a global scale, fishes will become increasingly challenged by low oxygen, and understanding the molecular basis of their response to hypoxia may help to better define the capacity of fishes to cope with this challenge. The hypoxia inducible factor (HIF) plays a critical role in the molecular response to hypoxia by activating the transcription of genes that serve to improve oxygen delivery to the tissues or enhance the capacity of tissues to function at low oxygen. The current study examines the molecular evolution of genes encoding the oxygen-dependent HIFα subunit (HIFA) in the ray-finned fishes (Actinopterygii). Genomic analyses demonstrate that several lineages retain four paralogs of HIFA predicted from two rounds of genome duplication at the base of vertebrate evolution, broaden the known distribution of teleost-specific HIFA paralogs, and provide evidence for salmonid-specific HIFA duplicates. Evolution of the HIFA gene family is characterized by widespread episodic positive selection at amino acid sites that potentially mediate protein stability, protein-protein interactions, and transcriptional regulation. HIFA transcript abundance depends upon paralog, tissue, and fish lineage. A phylogenetically-informed gene nomenclature is proposed along with avenues for future research on this critical family of transcription factors.

Aryl hydrocarbon receptor nuclear translocators (ARNT1, ARNT2, and ARNT3) of white sturgeon (Acipenser transmontanus): Sequences, tissue-specific expressions, and response to β-naphthoflavone

Sturgeons (Acipenseridae) are ancient fishes that have tissue-specific profiles of transcriptional responses to dioxin-like compounds (DLCs) that are unique from those generally measured in teleost fishes. Because DLCs exert their critical toxicities through activation of the aryl hydrocarbon receptor (AHR), this transcription factor has been the subject of intensive study. However, less attention has focused on the aryl hydrocarbon receptor nuclear translocator (ARNT), which is the dimerization partner of the AHR and required for AHR-mediated transcription. The present study sequenced ARNT1, ARNT2, and ARNT3 in a representative species of sturgeon, the white sturgeon (Acipenser transmontanus), and quantified tissue-specific basal transcript abundance for each ARNT and the response following exposure to the model agonist of the AHR, β-naphthoflavone. In common with other proteins in sturgeons, the amino acid sequences of ARNTs are more similar to those of tetrapods than are ARNTs of other fishes. Transcripts of ARNT1, ARNT2, and ARNT3 were detected in all tissues investigated. Expression of ARNTs are tightly regulated in vertebrates, but β-naphthoflavone caused down-regulation in liver and up-regulation in gill, while an upward trend was measured in intestine. ARNTs are dimeric partners for multiple proteins, including the hypoxia inducible factor 1α (HIF1α), which mediates response to hypoxia. A downward trend in abundance of HIF1α transcript was measured in liver of white sturgeon exposed to β-naphthoflavone. Altered expression of ARNTs and HIF1α caused by activation of the AHR might affect the ability of certain tissues in sturgeons to respond to hypoxia when co-exposed to DLCs or other agonists.

Hypoxia alters the expression of hif-1a mRNA and downstream HIF-1 response genes in embryonic and larval lake whitefish (Coregonus clupeaformis)

Lake whitefish (Coregonus clupeaformis) embryos and larvae were exposed to hypoxia at different developmental ages to determine when the cellular response to hypoxia could be initiated. mRNA levels of hypoxia-inducible factor 1α (hif-1α), hsp70, and several HIF-1 target genes were quantified in embryos at 21, 38, 63, 83- and 103-days post fertilisation (dpf) and in larvae at 1, 2, 3- and 4-weeks post hatch (wph) following a 6-hour hypoxia exposure. hsp70 mRNA levels were increased in response to hypoxia at all embryonic ages. By comparison, the first observed change in hif-1α mRNA in response to hypoxia was at 38 dpf, where it was down-regulated from high basal levels, with this response persisting through to 83 dpf. Interestingly, this decrease in hif-1α mRNA coincided with increases in the mRNA levels of the HIF-1 target genes: vegfa (vascular endothelial growth factor A), igfbp1 (insulin-like growth factor binding protein 1), ldha (lactate dehydrogenase a), gapdh (glyceraldehyde-3-phosphate dehydrogenase) and epo (erythropoietin) at select ages. Collectively, this suggests a possible HIF-1-mediated response to hypoxia despite a decrease in hif-1α mRNA. Coinciding with a decrease in basal levels, increases in hif-1α were measured in response to hypoxia at 103 dpf and in larval fish at 1, 2 and 3 wph but there were no consistent increases in HIF-1 target genes at these ages. Overall, our findings indicate that lake whitefish can mount a response to hypoxia early in embryogenesis which may mitigate some of the damaging effects of exposure to low oxygen levels at these critical life history stages.

Sequence and functional characterization of hypoxia-inducible factors, HIF1α, HIF2αa, and HIF3α, from the estuarine fish, Fundulus heteroclitus

The hypoxia-inducible factor (HIF) family of transcription factors plays central roles in the development, physiology, pathology, and environmental adaptation of animals. Because many aquatic habitats are characterized by episodes of low dissolved oxygen, fish represent ideal models to study the roles of HIF in the response to aquatic hypoxia. The estuarine fish Fundulus heteroclitus is found in habitats prone to hypoxia. It responds to low oxygen via behavioral, physiological, and molecular changes, and one member of the HIF family, HIF2α, has been previously described. Herein, cDNA sequencing, phylogenetic analyses, and genomic approaches were used to determine other members of the HIFα family from F. heteroclitus and their relationships to HIFα subunits from other vertebrates. In vitro and cellular approaches demonstrated that full-length forms of HIF1α, HIF2α, and HIF3α independently formed complexes with the β-subunit, aryl hydrocarbon receptor nuclear translocator, to bind to hypoxia response elements and activate reporter gene expression. Quantitative PCR showed that HIFα mRNA abundance varied among organs of normoxic fish in an isoform-specific fashion. Analysis of the F. heteroclitus genome revealed a locus encoding a second HIF2α-HIF2αb-a predicted protein lacking oxygen sensing and transactivation domains. Finally, sequence analyses demonstrated polymorphism in the coding sequence of each F. heteroclitus HIFα subunit, suggesting that genetic variation in these transcription factors may play a role in the variation in hypoxia responses among individuals or populations.

The Effect of Hypoxia and Hyperoxia on Growth and Expression of Hypoxia-Related Genes and Proteins in Spotted Gar Lepisosteus oculatus Larvae and Juveniles

We studied the molecular responses to different water oxygen levels in gills and swim bladder of spotted gar (Lepisosteus oculatus), a bimodal breather. Fish at swim-up stage were exposed for 71 days to normoxic, hypoxic, and hyperoxic water conditions. Then, all aquaria were switched to normoxic conditions for recovery until the end of the experiment (120 days). Fish were sampled at the beginning of the experiment, and then at 71 days of exposure and at 8 days of recovery. We first cloned three hypoxia-related genes, hypoxia-inducible factor 2α (HIF-2α), Na(+) /H(+) exchanger 1 (NHE-1), and NHE-3, and uploaded their cDNA sequences in the GeneBank database. We then used One Step Taqman® real-time PCR to quantify the mRNA copies of target genes in gills and swim bladder of fish exposed to different water O2 levels. We also determined the protein expression of HIF-2α and neuronal nitric oxide synthase (nNOS) in the swim bladder by using confocal immunofluorescence. Hypoxic stress for 71 days significantly increased the mRNA copies of HIF-2α and NHE-1 in gills and swim bladder, whereas normoxic recovery for 8 days decreased the HIF-2α mRNA copies to control values in both tissues. We did not found significant changes in mRNA copies of the NHE-3 gene in either gills or swim bladder in response to hypoxia and hyperoxia. Unlike in normoxic swim bladder, double immunohistochemical staining in hypoxic and hyperoxic swim bladder using nNOS/HIF-2α showed extensive bundles of HIF-2α-positive nerve fibers in the trabecular musculature associated with a few varicose nNOS immunoreactive nerve terminals.

Identification and expression analysis of 26 oncogenes of the receptor tyrosine kinase family in channel catfish after bacterial infection and hypoxic stress

Receptor tyrosine kinases (RTKs) are high-affinity cell surface receptors for many polypeptide growth factors, cytokines and hormones. RTKs are not only key regulators of normal cellular processes, but are also involved in the progression of many types of tumors, and responses to various biotic and abiotic stresses. Catfish is a primary aquaculture species in the United States, while its industry is drastically hindered by several major diseases including enteric septicemia of catfish (ESC) that is caused by Edwardsiella ictaluri. Disease outbreaks are often accompanied by hypoxic stress, which affects the performance and survival of fish by reducing disease resistance. In this study, we identified 26 RTK oncogenes in the channel catfish genome, and determined their expression profiles after ESC infection and hypoxic stress. The 26 RTK genes were divided into four subfamilies according to phylogenetic analysis, including TIE (2 genes), ErbB (6 genes), EPH (14 genes), and INSR (4 genes). All identified RTKs possess a similar molecular architecture including ligand-binding domains, a single transmembrane helix and a cytoplasmic region, which suggests that these genes could play conserved biological roles. The expression analysis revealed that eight RTKs were significantly regulated after bacterial infection, with dramatic induction of insulin receptor genes including INSRb, IGF1Ra, and IGF1Rb. Upon hypoxic stress, EPHB3a, EGFR, ErbB4b, and IGF1Rb were expressed at higher levels in the tolerant catfish, while EPHA2a, EPHA2, TIE1 and INSRa were expressed at higher levels in the intolerant catfish. These results suggested the involvement of RTKs in immune responses and hypoxic tolerance.

Analysis of hypoxia-inducible factor alpha polyploidization reveals adaptation to Tibetan Plateau in the evolution of schizothoracine fish

BACKGROUND

Hypoxia-inducible factor (HIF) is a master regulator that mediates major changes in gene expression under hypoxic conditions. Though HIF family has been identified in many organisms, little is known about this family in schizothoracine fish.

RESULTS

Duplicated hif-α (hif-1αA, hif-1αB, hif-2αA, and hif-2αB) genes were identified in schizothoracine fish. All the deduced HIF-α proteins contain the main domains (bHLH-PAS, ODDD, and TAD), also found in humans. Evidence suggests a Cyprinidae-specific deletion, specifically, a conserved proline hydroxylation motif LxxLAP, in the NODD domain of schizothoracine fish HIF-1αA. In addition, a schizothoracine-specific mutation was observed in the CODD domain of the specialized and highly specialized schizothoracine fish HIF-1αB, which is the proline hydroxylation motif mutated into PxxLAP. Standard and stochastic branch-site codon model analysis indicated that only HIF-1αB has undergone positive selection, which may have led to changes in function. To confirm this hypothesis, HIF-αs tagged with Myc were transfected into HEK 293 T cells. Each HIF-1αB was found to significantly upregulate luciferase activity under normoxic and hypoxic conditions, which indicated that the HIF-1αB protein was more stable than other HIF-αs.

CONCLUSIONS

All deduced HIF-α proteins of schizothoracine fish contain important domains, like their mammalian counterparts, and each HIF-α is shorter than that of human. Our experiments reveal that teleost-specific duplicated hif-α genes played different roles under hypoxic conditions, and HIF-1αB may be the most important regulator in the adaptation of schizothoracine fish to the environment of the Tibetan Plateau.

Transcriptional regulation of hypoxia inducible factors alpha (HIF-α) and their inhibiting factor (FIH-1) of channel catfish (Ictalurus punctatus) under hypoxia

Hypoxia inducible factors (HIFs) are considered to be the master switch of oxygen-dependent gene expression with mammalian species. In most cases, regulation of HIF has been believed at posttranslational levels. However, little is known of HIF regulation in channel catfish, a species highly tolerant to low oxygen condition. Here we report the identification and characterization of HIF-1α, HIF-2αa, HIF-2αb, HIF-3α, and FIH-1 genes, and their mRNA expression under hypoxia conditions. The transcripts of the five genes were found to be regulated temporally and spatially after low oxygen challenge, suggesting regulation of HIF-α genes at pre-translational levels. In most tissues, the HIF-α mRNAs were down-regulated 1.5h but up-regulated 5h after hypoxia treatment. Of these HIF-α mRNAs, the expression of HIF-3α mRNA was induced in the most dramatic fashion, both in the speed of induction and the extent of induction, compared to HIF-1α and HIF-2α genes, suggesting its importance in responses to hypoxia.

Molecular characterization and expression analysis of three hypoxia-inducible factor alpha subunits, HIF-1α, -2α and -3α in hypoxia-tolerant Indian catfish, Clarias batrachus [Linnaeus, 1758]

The present study aimed at characterization of three HIF-α subunits, HIF-1α -2α and -3α from hypoxia-tolerant Clarias batrachus, as well as to elucidate their expression pattern under short and long-term hypoxic conditions and identification of biomarker candidate. The complete cDNAs of HIF-1α, -2α and -3α were 2,833, 4,270 and 3,256 bp in length, encoding 774, 818 and 628 amino acid residues, respectively. In C. batrachus, HIF-α subunits were structurally similar in DNA binding, dimerization, degradation and transcriptional activation domains, but differed in their oxygen-dependent degradation domains. Presence of c-Jun N-terminal kinase binding domain in HIF-α subunits was reported here for the first time in fish. In adult C. batrachus, three HIF-α mRNAs were detected in different tissues under normoxic conditions, however HIF-1α was highly expressed in all the tissues studied, in comparison to HIF-2α and -3α. Short-term hypoxia exposure caused significant increase in three HIF-α transcripts in brain, liver and head kidney, while after long-term hypoxia exposure, significant up-regulation of HIF-1α in spleen and -2α in muscle was observed and HIF-3α significantly down-regulated in head kidney. These observations suggest that the differential expression of HIF-α subunits in C. batrachus was hypoxic time period dependent and may play specialized roles in adaptive response to hypoxia. HIF-2α, with its highly elevated expression in muscle tissues, can be a robust biomarker candidate for exposure to hypoxic environment.

Molecular characterization and expression analysis of three hypoxia-inducible factor alpha subunits, HIF-1α/2α/3α of the hypoxia-sensitive freshwater species, Chinese sucker

Hypoxia-inducible factors (HIFs) are transcription factors that respond to changes in oxygen tension in the cellular environment. In this study, we identified full-length cDNAs of HIF-1α, HIF-2α and HIF-3α in an endangered hypoxia-sensitive fish species, Chinese sucker. The HIF-1α/2α/3α cDNAs are 3890, 3230 and 3374 bp in length, encoding 780, 782 and 632 amino acid residues, respectively. The real-time PCR results suggested that HIF-1α and HIF-3α mRNAs were highly expressed in liver and gonads, followed by spleen and muscle. Moreover, HIF-1α and HIF-3α transcription factors revealed similar developmental expression patterns, with the lowest expression at 48h post-fertilization, and reaching the highest expression level at 360 h post-fertilization. Short-term hypoxia exposure (2.2, 2.8 and 3.2mg/L dissolved oxygen for 24h) increased mRNA levels of HIF-1α and HIF-3α. HIF-2α mRNA showed similar expression patterns with that of HIF-1α and HIF-3α, however, its expression was extremely low in the spatio-temporal expression patterns and hypoxia treatment. This is the first report describing the potential to identify hypoxia-sensitive/tolerant fishes according to the number of the serine residues of fish oxygen-dependent degradation (ODD) domain. It was suggested that Cyprinomorpha fishes, with less than 40 serine residues in fish ODD domain were hypoxia-sensitive fishes and more than 40 serine residues in this domain were hypoxia-tolerant fishes.

Interactions between hypoxia and sewage-derived contaminants on gene expression in fish embryos

Fish embryos were used to evaluate the interaction among common environmental and chemical stressors found in urban coastal environments, namely hypoxia, aryl hydrocarbon receptor (AhR) agonists, and estrogenic compounds. At the molecular level, the systems responding to these stressors share common response factors, and evidence exists for cross-talk between them. Biomarkers of exposure to these stressors, cytochrome P4501a (Cyp1a), estrogen receptor alpha (ERα), brain cytochrome P450 aromatase (Cyp19a2 or AromB), and hypoxia inducible factor 1 alpha (Hif-1α) mRNA expression were examined using qRT-PCR simultaneously in embryos of two well studied species, the Atlantic killifish, Fundulus heteroclitus, and the zebrafish Danio rerio. Embryos of both species were exposed to the model Cyp1a inducer β-naphthoflavone (BNF) or 17-β estradiol (E2) under either normoxic or hypoxic (5% oxygen atmosphere) conditions and harvested prior to hatch at 9 days post fertilization (dpf) for the killifish, and 48h post fertilization (hpf) for the zebrafish. BNF significantly induced Cyp1a expression in embryos of both species with killifish embryos being more responsive (700-fold>control) than zebrafish embryos (7-100-fold>control). AromB was also significantly influenced by treatment, but to a lesser extent, with mean expression levels increased by less than two-fold over control values in response to E2, and in one case upregulated by BNF. ERα and Hif-1α were constitutively expressed in embryos of both species, but expression was unaffected by exposure to either BNF or E2. Hypoxic conditions downregulated AromB expression strongly in killifish but not in zebrafish embryos. The impact of hypoxia on expression of other genes in either species was inconsistent, although an interactive effect between hypoxia and BNF on several of the genes evaluated was observed. These data are the first to examine expression patterns of these important environmental response genes together in embryos of two important model fish species. The results support the use of Cyp1a expression as a biomarker of AhR agonists in fish embryos, and indicate that AromB may be more responsive than ERα to estrogenic chemicals at this stage in development. Hif-1α expression was not found to be a good biomarker of hypoxic exposure in either killifish or zebrafish embryos. The interaction observed between BNF and co-exposure to hypoxia warrants further investigation. Finally killifish embryos are generally more sensitive than zebrafish embryos at this stage of development supporting their use in environmental assessments.

From oxygen to erythropoietin: relevance of hypoxia for retinal development, health and disease

Photoreceptors and other cells of the retina consume large quantities of energy to efficiently convert light information into a neuronal signal understandable by the brain. The necessary energy is mainly provided by the oxygen-dependent generation of ATP in the numerous mitochondria of retinal cells. To secure the availability of sufficient oxygen for this process, the retina requires constant blood flow through the vasculature of the retina and the choroid. Inefficient supply of oxygen and nutrients, as it may occur in conditions of disturbed hemodynamics or vascular defects, results in tissue ischemia or hypoxia. This has profound consequences on retinal function and cell survival, requiring an adaptational response by cells to cope with the reduced oxygen tension. Central to this response are hypoxia inducible factors, transcription factors that accumulate under hypoxic conditions and drive the expression of a large variety of target genes involved in angiogenesis, cell survival and metabolism. Prominent among these factors are vascular endothelial growth factor and erythropoietin, which may contribute to normal angiogenesis during development, but may also cause neovascularization and vascular leakage under pathologically reduced oxygen levels. Since ischemia and hypoxia may have a role in various retinal diseases such as diabetic retinopathy and retinopathy of prematurity, studying the cellular and molecular response to reduced tissue oxygenation is of high relevance. In addition, the concept of preconditioning with ischemia or hypoxia demonstrates the capacity of the retina to activate endogenous survival mechanisms, which may protect cells against a following noxious insult. Part of these mechanisms is the local production of protective factors such as erythropoietin. Due to its plethora of effects in the retina including neuro- and vaso-protective activities, erythropoietin has gained strong interest as potential therapeutic factor for retinal degenerative diseases.

The effects of mitochondrial genotype on hypoxic survival and gene expression in a hybrid population of the killifish, Fundulus heteroclitus

The physiological link between oxygen availability and mitochondrial function is well established. However, whether or not fitness variation is associated with mitochondrial genotypes in the field remains a contested topic in evolutionary biology. In this study, we draw on a population of the teleost fish, Fundulus heteroclitus, where functionally distinct subspecies hybridize, likely as a result of past glacial events. We had two specific aims: (i) to determine the effect of mtDNA genotype on survivorship of male and female fish under hypoxic stress and (ii) to determine the effect of hypoxic stress, sex and mtDNA genotype on gene expression. We found an unexpected and highly significant effect of sex on survivorship under hypoxic conditions, but no significant effect of mtDNA genotype. Gene expression analyses revealed hundreds of transcripts differentially regulated by sex and hypoxia. Mitochondrial transcripts and other predicted pathways were among those influenced by hypoxic stress, and a transcript corresponding to the mtDNA control region was the most highly suppressed transcript under the conditions of hypoxia. An RT-PCR experiment on the control region was consistent with microarray results. Effects of mtDNA sequence variation on genome expression were limited; however, a potentially important epistasis between mtDNA sequence and expression of a nuclear-encoded mitochondrial translation protein was discovered. Overall, these results confirm that mitochondrial regulation is a major component of hypoxia tolerance and further suggest that purifying selection has been the predominant selective force on mitochondrial genomes in these two subspecies.

Functional genomics in aquatic toxicology-do not forget the function

Toxicological responses of an organism are disturbances of function. This as a starting point we review and discuss issues that we consider important in applying functional genomics to aquatic toxicology. Functional genomics includes all the steps in gene expression pathway. Thus, ultimately the goal is to relate genome information to protein activity. In ecotoxicogenomics the toxicological responses must further be combined with responses to natural environmental changes. We focus on fish, but also consider commonly used invertebrates, mainly Daphnia. We first go through the toxicologically important features of genomes of aquatic animals, and then review the reference gene approach to quantify transcript amount. Thereafter we emphasize the need to relate the mRNA and protein levels, and protein activity of individual genes. Finally we discuss how functional genomic investigations may be important in resolving current environmental problems and give our views of valuable future research topics.

HIF-2α as a possible therapeutic target of osteoarthritis

OBJECTIVE

Endochondral ossification, a conversion process from nonvascularized and hypoxic cartilage to highly vascularized bone, plays a crucial role in osteoarthritis (OA) development as well as in physiological skeletal growth. We have shown that hypoxia-inducible factor-2α (HIF-2α, encoded by EPAS1) is an extensive regulator of the endochondal ossification process. Here we review the possible signaling network regulating OA development on the axis of HIF-2α.

METHODS

Peer reviewed publications published prior to August 2010 were searched in the Pubmed database. Articles that were relevant to HIF and molecular mechanisms of the endochondral ossification and OA were selected.

RESULTS

As a trigger of OA, mechanical stress may induce the upstream NF-κB signal and HIF-2α expression in joint cartilage of mice and humans, which causes transactivation of endochondral ossification-related molecules with the most potent β-subunit partner aryl hydrocarbon nuclear translocator-like (ARNTL). In contrast to HIF-2α, HIF-1α functions to maintain cartilage via a distinct mechanism, so that the shifting of the HIFs might possibly be involved in an OA pathogenesis.

CONCLUSION

Signals on the HIF-2α axis from NF-κB signaling to the endochondral ossification-related molecules, possibly in combination with HIF-2α and ARNTL, may represent a rational therapeutic target for OA with minimal effects on physiological skeletal homeostasis.

A novel hypoxia-response element in the lactate dehydrogenase-B gene of the killifish Fundulus heteroclitus

Previous studies have suggested that the lactate dehydrogenase-B gene (Ldh-B) of the Atlantic killifish, Fundulus heteroclitus, is a hypoxia-responsive gene. Here, we demonstrate that the F. heteroclitus Ldh-B promoter confers hypoxia-dependence upon reporter gene expression in transiently transfected mammalian (Hep3B) and fish (RTG-2 and RTH-149) cells in culture. Mutation and deletion analyses identified a putative hypoxia-response element (HRE) between 109 and 90 nucleotides upstream of the major start site. This HRE is characterized by the sequence 5'-GATGTG-3' spaced by 8 nucleotides from a perfect inverted repeat, and both sites are necessary for hypoxic induction of reporter gene expression in mammalian and fish cells. This HRE differs from the canonical sequence at one nucleotide position that is invariant among HREs from a wide range of hypoxia-sensitive genes. In fish cells, maximal induction of reporter gene expression driven by this HRE occurred at the lowest oxygen level tested (0.5%), took 48 h to 96 h, and was independent of glucose concentration (between 5.6 and 25 mM). Under all conditions tested, hypoxic induction of gene expression was lower in RTH-149 cells than in RTG-2, suggesting a potential defect in hypoxia signaling in RTH-149 cells. These results demonstrate that the F. heteroclitus Ldh-B promoter contains a novel HRE that is capable of driving reporter gene expression in a sequence-specific and oxygen-, time-, and cell line-dependent manner.

Regulation of pyruvate dehydrogenase in the common killifish, Fundulus heteroclitus, during hypoxia exposure

We examined the metabolic responses of the hypoxia-tolerant killifish (Fundulus heteroclitus) to 15 h of severe hypoxia and recovery with emphasis on muscle substrate usage and the regulation of the mitochondrial protein pyruvate dehydrogenase (PDH), which controls carbohydrate oxidation. Hypoxia survival involved a transient activation of substrate-level phosphorylation in muscle (decreases in [creatine phospate] and increases in [lactate]) during which time mechanisms to reduce overall ATP consumption were initiated. This metabolic transition did not affect total cellular [ATP], but had an impact on cellular energy status as indicated by large decreases in [ATP]/[ADP(free)] and [ATP]/[AMP(free)] and a significant loss of phosphorylation potential and Gibbs free energy of ATP hydrolysis (DeltafG'). The activity of PDH was rapidly (within 3 h) decreased by approximately 50% upon hypoxia exposure and remained depressed relative to normoxic samples throughout. Inactivation of PDH was primarily mediated via posttranslational modification following the accumulation of acetyl-CoA and subsequent activation of pyruvate dehydrogenase kinase (PDK). Estimated changes in cytoplasmic and mitochondrial [NAD(+)]/[NADH] did not parallel one another, suggesting the mitochondrial NADH shuttles do not function during hypoxia exposure. Large increases in the expression of PDK (PDK isoform 2) were consistent with decreased PDH activity; however, these changes in mRNA were not associated with changes in total PDK-2 protein content assessed using mammalian antibodies. No other changes in the expression of other known hypoxia-responsive genes (e.g., lactate dehydrogenase-A or -B) were observed in either muscle or liver.

Fundulus as the premier teleost model in environmental biology: opportunities for new insights using genomics

A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms.

Hypoxia-inducible factor, gsHIF, of the grass shrimp Palaemonetes pugio: Molecular characterization and response to hypoxia

Hypoxia-inducible factor 1alpha (HIF-1alpha) is a key transcription factor that controls a variety of cellular and systemic homeostatic responses to hypoxic stress. Expression and function of HIF-1alpha have not been studied in crustaceans, which experience wide fluctuations of oxygen tensions in their aquatic environment. Here we show that an HIF-1alpha homolog, gsHIF, is present in the hypoxia-tolerant grass shrimp Palaemonetes pugio. Using RT-PCR and 3' and 5'RACE, we cloned a full-length gsHIF cDNA (3822 bp) with an open reading frame encoding a 1057 amino acid protein. Similar to vertebrate HIF-1alpha, gsHIF has one basic helix-loop-helix (bHLH) domain, two PAS domains, an oxygen-dependent degradation domain (ODD) with two proline hydroxylation motifs, and a C-terminal transactivation domain (C-TAD) with an asparagine hydroxylation motif. In addition to these conserved sequences, gsHIF has a unique 230 amino acid sequence (aa 790-1020) not found in any vertebrate HIF proteins. Phylogenetic analysis indicates that grass shrimp and vertebrate HIFs belong to distinct clades within the HIF protein family. Expression analysis shows that gsHIF is constitutively expressed under normoxic (7.5 ppm DO), moderate (2.5 ppm DO) and severe (1.5 ppm DO) hypoxic conditions. In addition to gsHIF, we cloned a fragment of a second bHLH-PAS transcription factor from the grass shrimp, which had one bHLH and two PAS domains, and an overall 68% amino acid sequence homology with Apis mellifera trachealess protein.

Molecular characterization and tissue distribution of aryl hydrocarbon receptor nuclear translocator isoforms, ARNT1 and ARNT2, and identification of novel splice variants in common cormorant (Phalacrocorax carbo)

High levels of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related planar halogenated aromatic hydrocarbons (PHAHs) are accumulated in fish-eating birds including common cormorant (Phalacrocorax carbo). Most of the biochemical and toxic effects of TCDD are mediated by a basic helix-loop-helix and a conserved region among Per, ARNT, and Sim (bHLH/PAS) proteins, aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT). To study the molecular mechanism of TCDD toxicity in common cormorant as an avian model species, characterization of the AHR/ARNT signaling pathway in this species is necessary. The present study focuses on molecular characterization of ARNT from common cormorant (ccARNT). The cDNA of the ccARNT isoform, ccARNT1 obtained by the screening of hepatic cDNA library contains a 2424-bp open reading frame that encodes 807 amino acids, exhibiting high identities (92%) with chicken ARNT. This isoform contains a unique 22 amino acid residue in 3' end of PAS A domain as is also recognized in chicken ARNT. The ccARNT2 cDNA isolated from brain tissue has a 2151-bp open reading frame. The deduced amino acid sequence of ccARNT2 protein (716 aa) shows a conservation of bHLH and PAS motif in its N-terminal region with high similarities (96% and 78%, respectively) to that of ccARNT1. Using quantitative RT-PCR methods, the tissue distribution profiles of ccARNT1 and ccARNT2 were unveiled. Both ccARNT1 and ccARNT2 mRNAs were ubiquitously expressed in all examined tissues including liver. The expression profile of ccARNT1 was comparable with that of rodent ARNT1, but ccARNT2 was not with rodent ARNT2, implying different roles of ARNT2 between the two species. There was a significant positive correlation between ARNT1 and ARNT2 mRNA expression levels in the liver of wild cormorant population, indicating that their expressions may be enforced by similar transcriptional regulation mechanism. Novel variants of ccARNT1 and ccARNT2 isoforms that were supposed to arise from their splicing process were also identified and their hepatic expression profiles were determined. These results indicate that ccARNT1, ccARNT2 and their splice variants may more intricately regulate the AHR/ARNT signaling pathway and consequently may be responsible for the species diversity of toxic effects and susceptibility to PHAHs.

Molecular cloning, characterization and expression of two hypoxia-inducible factor alpha subunits, HIF-1alpha and HIF-2alpha, in a hypoxia-tolerant marine teleost, Atlantic croaker (Micropogonias undulatus)

Alteration of gene expression is a crucial component of adaptation by animals to hypoxic conditions and is mediated by specific transcription factors, hypoxia-inducible factors (HIFs), which are composed of alpha and beta subunits. In this study, we report the cloning and characterization of two HIF-alpha subunits, HIF-1alpha and HIF-2alpha, and their expression in various tissues of a hypoxia-tolerant marine teleost, Atlantic croaker (Micropogonias undulatus). The full-length croaker HIF-1alpha (2805 bp) and HIF-2alpha (3205 bp) cDNAs contain open reading frames encoding proteins with 720 and 847 amino acids, respectively, which are highly homologous to the HIF-1alpha and HIF-2alpha proteins of other non-mammalian species. Croaker HIF-1 alpha shares only 43% sequence identity with the croaker HIF-2alpha subunit. However, the basic helix-loop-helix/Per-ARNT-Sim regions appear to be relatively well conserved between the two proteins, with identities of 75-83%. The core oxygen-dependent degradation domain regions in croaker HIFs are well conserved, suggesting a similar mechanism of HIF degradation to that in other vertebrate species. Northern blot analysis showed that croaker HIF-1alpha and HIF-2alpha mRNAs (transcript sizes 3.0-3.8 kb) are highly expressed in the brain, heart, liver, and gonads under hypoxic conditions, whereas muscle tissues show lower levels of expression. Short-term (1.7 mg/L dissolved oxygen, DO for 3 days to 1 week) and long-term (1.7, 2.7 and 3.7 mg/L DO for 3 weeks) hypoxia exposure caused significant increases in HIF-1alpha and HIF-2alpha mRNA expression in croaker ovaries compared to mRNA levels in fish held in normoxic conditions (DO: 6.5 mg/L). However, HIF transcript levels in hypoxia-exposed fish had returned to control values 24 h after the DO in the tanks was restored to normoxic levels. The results suggest that the upregulation of both HIF-1alpha and HIF-2alpha subunits at the transcriptional level is an important component of adaptation of croaker to chronic hypoxia and HIF-alphas are potentially useful molecular indicators of

Cloning and expression analysis of two distinct HIF-alpha isoforms--gcHIF-1alpha and gcHIF-4alpha--from the hypoxia-tolerant grass carp, Ctenopharyngodon idellus

Background

Hypoxia-inducible factors (HIFs) are involved in adaptive and survival responses to hypoxic stress in mammals. In fish, very little is known about the functions of HIFs.

Results

We have cloned and characterized two distinct HIF-alpha cDNAs – gcHIF-1alpha and gcHIF-4alpha – from the hypoxia-tolerant grass carp. The deduced gcHIF-1alpha protein is highly similar to the HIF-1alphas (57–68%) from various vertebrate species, while gcHIF-4alpha is a novel isoform, and shows an equivalent degree of amino acid identity (41–47%) to the HIF-1alpha, HIF-2alpha and HIF-3alpha proteins so far described. Parsimony analysis indicated that gcHIF-4alpha is most closely related to the HIF-3alpha proteins. Northern blot analysis showed that mRNA levels of gcHIF-1alpha and gcHIF-4alpha differ substantially under normoxic and hypoxic conditions, while Western blot studies demonstrated that the endogenous protein levels for both gcHIF-1alpha and gcHIF-4alpha are similarly responsive to hypoxia. Our findings suggest that both gcHIF-1alpha and gcHIF-4alpha are differentially regulated at the transcriptional and translational levels. HRE-luciferase reporter assays show that both proteins function as transcription activators and play distinct roles in modulating the hypoxic response in grass carp.

Conclusion

There are at least two distinct HIF-alpha isoforms – gcHIF-1alpha and gcHIF-4alpha – in the hypoxia-tolerant grass carp, which are differentially expressed and regulated in different fish organs in response to hypoxic stress. Overall, the results suggest that unique molecular mechanisms operate through these two HIF-alpha isoforms, which underpin the hypoxic response in the hypoxia-tolerant grass carp.

Differential display of hepatic mRNA from killifish (Fundulus heteroclitus) inhabiting a Superfund estuary

Fundulus heteroclitus (Atlantic killifish, mummichog) from a highly contaminated site on the Elizabeth River (VA, USA) are resistant to the toxicity of sediment from the site. However, the mechanistic changes that confer resistance to the toxicity are not yet well understood. We utilized differential display to identify mRNAs that are differentially expressed in hepatic tissue of male and female killifish from the Elizabeth River environment, compared to killifish from a non-contaminated reference site, King's Creek (VA, USA). Seventy-four differentially expressed mRNAs were initially identified (including sex and population-specific differences), and 65 of these were isolated and sequenced. A reverse northern blot array constructed of these cDNAs (plus an additional 15 previously sequenced mRNAs of interest) was used to confirm and quantify expression differences. High interindividual variability was observed in mRNA expression, but multiple differentially expressed mRNAs were identified, including 11 population-specific differences occurring in both sexes, 24 population-specific differences occurring in only one sex, and 22 sex-specific differences. Many of these differentially expressed mRNAs were novel, or not previously hypothesized to play a role in response to contaminant exposure. In addition, the results indicate that the effect of contaminated sediment exposure on the expression of a large proportion of the differentially expressed mRNAs was dependent on the sex of the fish.

Oxygen-dependent gene expression in fishes

The role of oxygen in regulating patterns of gene expression in mammalian development, physiology, and pathology has received increasing attention, especially after the discovery of the hypoxia-inducible factor (HIF), a transcription factor that has been likened to a "master switch" in the transcriptional response of mammalian cells and tissues to low oxygen. At present, considerably less is known about the molecular responses of nonmammalian vertebrates and invertebrates to hypoxic exposure. Because many animals live in aquatic habitats that are variable in oxygen tension, it is relevant to study oxygen-dependent gene expression in these animals. The purpose of this review is to discuss hypoxia-induced gene expression in fishes from an evolutionary and ecological context. Recent studies have described homologs of HIF in fish and have begun to evaluate their function. A number of physiological processes are known to be altered by hypoxic exposure of fish, although the evidence linking them to HIF is less well developed. The diversity of fish presents many opportunities to evaluate if inter- and intraspecific variation in HIF structure and function correlate with hypoxia tolerance. Furthermore, as an aquatic group, fish offer the opportunity to examine the interactions between hypoxia and other stressors, including pollutants, common in aquatic environments. It is possible, if not likely, that results obtained by studying the molecular responses of fish to hypoxia will find parallels in the oxygen-dependent responses of mammals, including humans. Moreover, novel responses to hypoxia could be discovered through studies of this diverse and species-rich group.

The hypoxia-inducible factor and tumor progression along the angiogenic pathway

The hypoxia-inducible factor (HIF) is a transcription factor that plays a key role in the response of cells to oxygen levels. HIF is a heterodimer of alpha- and beta-subunits where the alpha-subunit is translated constitutively but has a very short half-life under normal oxygen concentrations. Negative regulation of the half-life and activity of the alpha-subunit is dependent on its posttranslational hydroxylation by hydroxylases that are dependent on oxygen for activity. Thus under low oxygen (hypoxic) conditions the hydroxylases are inactive and the alpha-subunit is stable and able to interact with the beta-subunit to bind and induce transcription of target genes. Hypoxic conditions are encountered in development and in disease states such as cancer. Tumors that have outstripped their blood supply become hypoxic and express high levels of HIF. HIF in turn targets genes that induce survival, glycolysis, and angiogenesis, a form of neovascularization, which ensures the tumor with a continued supply of oxygen and nutrients for further growth.

Ontogenetic changes and developmental adjustments in lactate dehydrogenase isozymes of an obligate air-breathing fish Channa punctatus during deprivation of air access

In air-breathing snakehead Channa punctatus, Ldh-B is expressed at all ontogenetic and developmental stages, while Ldh-A is expressed temporally in pre-hatchlings 12-13 days ahead of bimodal respiration marked by air-breathing. Remarkable differences are observed in the LDH isozyme expression among various ontogenetic and developmental stages upon denying air access. When denied air access, water-breathing larvae show two distinct characteristics: (i) they survive longer than transitory air-breathers due to independence from air-breathing and (ii) there is more transient induction of Ldh-B than Ldh-A. Transition to bimodal breathing, which occurred post-hatching in 15-day old larvae, is coincidental with inducibility of Ldh-A and concomitant down-regulation of Ldh-B. Heart tissue from air-breathing adults denied air access shows a preferential expression of LDH-A subunit and slight down-regulation of LDH-B. Heterotetramers of A and B subunits participate in adjusting LDH levels among those stages which either precede air-breathing switchover, or are subsequent to this transition. The contribution of heterotetramers depends on the stage-specific levels of LDH homotetramers A(4) or B(4). Scaling of muscle mass during growth, tolerance to extended deprivation of air access and induction of Ldh-A are correlated. Response to restoring air contact indicated that advanced air-breathing stages of C. punctatus possess an inherent capacity to sense surface air. In kinetic properties, LDH isozymes of C. punctatus are teleost-like but species specificity is displayed in oxidative potential by cardiac muscle and in L-lactate reduction by skeletal muscle.

ARNT gene multiplicity in amphibians: characterization of ARNT2 from the frog Xenopus laevis

The aryl hydrocarbon receptor nuclear translocator (ARNT) is a member of the Per-ARNT-Sim (PAS) protein superfamily, transcription factors that mediate the cellular responses to various developmental signals and environmental conditions. A beta-class ("partner") PAS protein, ARNT exhibits the capacity to form transcriptionally active heterodimers with several alpha-class ("sensor") proteins, including the aryl hydrocarbon receptors (AHRs), the hypoxia-inducible factors (HIFs), and the Single minded (Sim) proteins. Two genes encode different forms of ARNT in mammals: ARNT1, which is widely expressed, and ARNT2, which is limited to the brain and kidneys of adults and specific neural and branchial tissues of embryos. In contrast, fish apparently express only a single ARNT gene, although in different species, this may be either ARNT1 or ARNT2. In efforts to understand the evolution of ARNT proteins throughout the vertebrate lineage, we isolated an ARNT cDNA from early life stages of the amphibian Xenopus laevis. The encoded protein binds cognate DNA sequences in concert with mouse AHR. Phylogenetic analysis reveals that this sequence is orthologous to mammalian ARNT2 and paralogous to the recently reported X. laevis ARNT1. ARNT2 mRNA expression begins later than ARNT1 (stage 22 vs. stage 8), suggesting the two proteins play distinct roles during development. Hence, in the expression of two well-conserved ARNT paralogs with distinct expression patterns, X. laevis resembles mammals rather than fish. Diversity in the number and function of PAS proteins, including ARNT, may underlie significant species differences in developmental programming and biochemical response to environmental conditions. The identification of multiple amphibian ARNT paralogs represents an important step in the understanding of evolution and functional variation of ARNT in vertebrates.

Oxygen-dependent cellular functions--why fishes and their aquatic environment are a prime choice of study

Owing to the variability of oxygen tension in aquatic, especially the freshwater environment, oxygen has been a major force in the evolution of fishes. Their long evolutionary history, and the present different oxygen requirements between species, and acclimatory responses to hypoxic and hyperoxic conditions make fishes prime models in the study of oxygen-dependent cellular functions and their regulation. In the present article oxygen-dependent membrane transport, cellular signalling, energy metabolism, gene expression and apoptosis are reviewed with an emphasis on available results on fish. Available data on oxygen sensing are described and examples on the cascade from sensing oxygen to its physiological effects are given. From the data it is clear that hitherto fish have not been utilised in the study of oxygen-dependent cellular regulation as much as their evolutionary history and present oxygen requirements would give possibilities to. Even more generally, oxygen has hitherto seldom been a carefully controlled key variable in experimental cell biology.