Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts

Comprehensive genome-wide identification and functional characterization of mapk gene family in northern snakeheads (Channa argus)

The mitogen-activated protein kinase (MAPK) signaling cascade, integral to cellular regulation, orchestrates cell growth, differentiation, stress response, and inflammatory reactions to adapt to challenging environments. The northern snakeheads (Channa argus), a valuable freshwater species known for its hypoxia tolerance, rapid growth, and high nutritional value, lacks comprehensive research on its mapk gene family. In this study, we identified 16 mapk genes in northern snakeheads, among which mapk8, mapk12 and mapk14 have duplicate copies. Phylogenetic analysis confirmed the evolutionary conservation of this gene family. Structural and motif analyses further underscored the conserved nature of these genes. Expression pattern analysis under abiotic and biotic stress conditions showed significant differences expression of mapks in the gills and suprabranchial organ (SBO) after air exposure, as well as in the brain following cold stress, highlighting the extensive role of mapks in stress regulation. It was worth noting that the significant expression differences of mapks were also observed in the spleen after N. seriolae infection, implicating that these genes may be involved in the regulation of innate immune responses. Additionally, analysis of protein-protein interaction (PPI) networks suggested that the co-activation of multiple MAPK signaling pathways may play a key role in regulating an organism's response to biotic and abiotic stresses. This study provides a detailed description of the mapk gene family in the northern snakeheads and elucidates its biological functions under various stress conditions, offering valuable insights into the regulatory mechanisms of the mapk gene family.

Regulation mechanism of oxidative status, immunity and apoptosis induced by hypoxia and heat exposure via PI3K/Akt signaling pathway in Megalobrama amblycephala

Megalobrama amblycephala, a main herbivorous fish with notable economic benefits in China, often faces serious challenges to its survival and growth due to hypoxia and heat caused by factors such as global warming and intensive aquaculture. To evaluate the combined effects of these stressors, we performed a two-factor crossover test to assess the impacts of simultaneous exposure to hypoxia (2 mg/L) and heat (35 °C) on oxidative stress, immunity and apoptosis in M. amblycephala. These results showed that hypoxia and heat exposure significantly enhanced the expression of oxygen-sensing and heat shock protein (HSP) genes, hypoxia inducible factor 1α (Hif-1α), HIF-prolyl hydroxylase-2 (phd2) and factor inhibiting Hif-1 (fih-1), as well as hsp70 and hsp90α. Furthermore, M. amblycephala suffering from hypoxia and heat exposure exhibited several changes in liver tissues, with the most severe lesions and up-regulation of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) observed in those subjected to simultaneous exposure. Moreover, the combined hypoxia and heat exposure initially triggered an increase in the activities of total antioxidant capacity (T-AOC), superoxide dismutase (SOD) and catalase (CAT), and glutathione (GSH) contents, followed by a reduction, and the accumulation of malondialdehyde (MDA), which induced oxidative stress. This was accompanied by an increase and subsequent reduction in the contents of alkaline phosphatase (AKP), acid phosphatase (ACP), complement component 3 (C3) and C4, immunoglobulin M (IgM), and interferon-γ (IFN-γ) leading to immunosuppression. Additionally, hypoxia and heat exposure up-regulated the expression of antioxidant enzyme genes (nrf2, cu/zn-sod, mn-sod cat, ho-1, pi3k and gpx-1a), inflammatory genes (interleukin il-1β, il-8 and tnf-α), immunity effectors (igm and lyz), as well as apoptosis genes (casp3, casp8, casp9 and p53) and activated p-Akt/Akt, suggesting apoptosis may be linked with oxidative stress and inflammation and mediated through the PI3K/Akt signaling pathway. In short, the combined hypoxia and heat exposure disrupted homoeostasis in M. amblycephala, with a more pronounced detrimental effect than exposure to either stressor alone These results will contribute to understanding the mechanism of combined exposure to hypoxia and heat in fish and provide a fundamental base for fisheries management.

The hypoxia response pathway in the Antarctic fish Notothenia coriiceps is functional despite a poly Q/E insertion mutation in HIF-1α

Antarctic notothenioid fishes, inhabiting the oxygen-rich Southern Ocean, possess a polyglutamine and glutamic acid (poly Q/E) insertion mutation in the master transcriptional regulator of oxygen homeostasis, hypoxia- inducible factor-1α (HIF-1α). To determine if this mutation impairs the ability of HIF-1 to regulate gene expression in response to hypoxia, we exposed Notothenia coriiceps, with a poly Q/E insertion mutation in HIF-1α that is 9 amino acids long, to hypoxia (2.3 mg L-1 O2) or normoxia (10 mg L -1 O2) for 12 h. Heart ventricles, brain, liver, and gill tissue were harvested and changes in gene expression quantified using RNA sequencing. Levels of glycogen and lactate were also quantified to determine if anaerobic metabolism increases in response to hypoxia. Exposure to hypoxia resulted in 818 unique differentially expressed genes (DEGs) in liver tissue of N. coriiceps. Many hypoxic genes were induced, including ones involved in the MAP kinase and FoxO pathways, glycolytic metabolism, and vascular remodeling. In contrast, there were fewer than 104 unique DEGs in each of the other tissues sampled. Lactate levels significantly increased in liver in response to hypoxia, indicating that anaerobic metabolism increases in response to hypoxia in this tissue. Overall, our results indicate that the hypoxia response pathway is functional in N. coriiceps despite a poly Q/E mutation in HIF-1α, and confirm that Antarctic fishes are capable of altering gene expression in response to hypoxia.

Transcriptomic atlas for hypoxia and following re-oxygenation in Ancherythroculter nigrocauda heart and brain tissues: insights into gene expression, alternative splicing, and signaling pathways

Hypoxia is a mounting problem that affects the world's freshwaters, with severe consequence for many species, including death and large economical loss. The hypoxia problem has increased recently due to the combined effects of water eutrophication and global warming. In this study, we investigated the transcriptome atlas for the bony fish Ancherythroculter nigrocauda under hypoxia for 1.5, 3, and 4.5 h and its recovery to normal oxygen levels in heart and brain tissues. We sequenced 21 samples for brain and heart tissues (a total of 42 samples) plus three control samples and obtained an average of 32.40 million raw reads per sample, and 95.24% mapping rate of the filtered clean reads. This robust transcriptome dataset facilitated the discovery of 52,428 new transcripts and 6,609 novel genes. In the heart tissue, the KEGG enrichment analysis showed that genes linked to the Vascular smooth muscle contraction and MAPK and VEGF signaling pathways were notably altered under hypoxia. Re-oxygenation introduced changes in genes associated with abiotic stimulus response and stress regulation. In the heart tissue, weighted gene co-expression network analysis pinpointed a module enriched in insulin receptor pathways that was correlated with hypoxia. Conversely, in the brain tissue, the response to hypoxia was characterized by alterations in the PPAR signaling pathway, and re-oxygenation influenced the mTOR and FoxO signaling pathways. Alternative splicing analysis identified an average of 27,226 and 28,290 events in the heart and brain tissues, respectively, with differential events between control and hypoxia-stressed groups. This study offers a holistic view of transcriptomic adaptations in A. nigrocauda heart and brain tissues under oxygen stress and emphasizes the role of gene expression and alternative splicing in the response mechanisms.

Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration

Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics' results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.

Living in a hypoxic world: A review of the impacts of hypoxia on aquaculture

Hypoxia is a harmful result of anthropogenic climate change. With the expansion of global low-oxygen zones (LOZs), many organisms have faced unprecedented challenges affecting their survival and reproduction. Extensive research has indicated that oxygen limitation has drastic effects on aquatic animals, including on their development, morphology, behavior, reproduction, and physiological metabolism. In this review, the global distribution and formation of LOZs were analyzed, and the impacts of hypoxia on aquatic animals and the molecular responses of aquatic animals to hypoxia were then summarized. The commonalities and specificities of the response to hypoxia in aquatic animals in different LOZs were discussed lastly. In general, this review will deepen the knowledge of the impacts of hypoxia on aquaculture and provide more information and research directions for the development of fishery resource protection strategies.

Hepatic transcriptomic analysis reveals that Hif1α/ldha signal is involved in the regulation of hypoxia stress in black rockfish Sebastes schlegelii

Hypoxia has become a common problem for aquatic organisms due to the interaction of global climate change and human activity. Black rockfish inhabits rocky reefs in waters of Japan, Korea and China, whereas the limited hypoxia tolerance leads to mass mortality and great economic loss. In this study, high-throughput RNA-seq for transcriptomic analysis was used to investigate the hepatic response in black rockfish under hypoxia (critical oxygen tension, Pcrit; loss of equilibrium, LOE) and reoxygenation (recover normal dissolved oxygen 24 h, R24) to explore the mechanisms underlying hypoxia tolerance and adaptation. A total of 573,040,410 clean reads and 299 differentially expressed genes (DEGs) in total were obtained during hypoxia and reoxygenation. GO annotation and Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that the DEGs are mainly enriched in the biochemical metabolic pathways and HIF-1 signaling pathways. Transcriptomic analysis also identified 18 DEGs associated with HIF-1 signaling pathway (hif1α, tf, epo, hmox, gult1, mknk2, ldha, pfkfb3, hkdc, aldoa) and biological process (hif2α, apoeb, bcl6, mr1, errfi1, slc38a4, igfbp1a, ap4m1) as further validated by quantitative real-time PCR. Moreover, hif1α was positively or negatively correlated with glucose (ldha, pfkfb3, hkdc, aldoa) and lipid (apoeb) metabolism-related genes. The mRNA level of hif1α was significantly up-regulated under acute hypoxia stress and obtained the higher values than hif2α. Meanwhile, hif1α recognized the hypoxia response element located in the promoter of ldha and directly bound to the promoter to transactivate ldha expression. These results indicated that black rockfish may mainly utilize glycolysis to maintain homeostasis, and hif1α facilities hypoxia tolerance by modulating ldha expression.

Comparative Analysis of Heart Regeneration: Searching for the Key to Heal the Heart-Part II: Molecular Mechanisms of Cardiac Regeneration

Cardiovascular diseases are the leading cause of death worldwide, among which ischemic heart disease is the most representative. Myocardial infarction results from occlusion of a coronary artery, which leads to an insufficient blood supply to the myocardium. As it is well known, the massive loss of cardiomyocytes cannot be solved due the limited regenerative ability of the adult mammalian hearts. In contrast, some lower vertebrate species can regenerate the heart after an injury; their study has disclosed some of the involved cell types, molecular mechanisms and signaling pathways during the regenerative process. In this 'two parts' review, we discuss the current state-of-the-art of the main response to achieve heart regeneration, where several processes are involved and essential for cardiac regeneration.

Effects of hypoxia and reoxygenation on oxidative stress, histological structure, and apoptosis in a new hypoxia-tolerant variety of blunt snout bream (Megalobrama amblycephala)

A new hypoxia-tolerant variety of blunt snout bream was obtained by successive breeding of the wild population, which markedly improved hypoxia tolerance. In this study, the hypoxia-tolerant variety was exposed to hypoxia (2.0 mg O₂·L^-1) for 4, 7 days. The contents of blood biochemical indicators including the number of red blood cells (RBC), total cholesterol (T-CHO), total protein (TP), triglyceride (TG), glucose (GLU), and lactic acid (LD) increased significantly (P < 0.05) under hypoxia. The glycogen content in the liver and muscle decreased significantly (P < 0.05) and the LD content in the brain, muscle and liver increased significantly (P < 0.05) under hypoxia. The levels of oxidative stress-related indicators i.e., superoxide dismutase (SOD), malondialdehyde (MDA), glutathione (GSH), catalase (CAT), and total antioxidant capacity (T-AOC) also changed significantly (P < 0.05) in the heart, liver, and intestine of the new variety under hypoxia. Additionally, hypoxia has caused injuries to the heart, liver, and intestine, but it shows amazing repair ability during reoxygenation. The apoptotic cells and apoptosis rate in the heart, liver, and intestine increased under hypoxia. Under hypoxia, the expression of the B-cell lymphomas 2 (Bcl-2) gene in the heart, liver, and intestine was significantly (P < 0.05) down-regulated, while the expression of the BCL2-associated agonist of cell death (Bad) gene was significantly (P < 0.05) up-regulated. These results are of great significance for enriching the basic data of blunt snout bream new variety in response to hypoxia and promoting the healthy development of its culture industry.

Detection of hypoxia in the pulmonary tissues of Xenopus laevis over repeated dives

The oxygen environment in African clawed frogs (Xenopus laevis) continuously changes during their development, which involves a rapid increase in the body size, metamorphosis, and transition to adulthood. Nevertheless, there are limited reports on experimental models that are available for studying fluctuations in the oxygen environment in X. laevis. Thus, this study aimed to develop an experimental model on intermittent hypoxia in X. laevis and evaluate hypoxia and oxidative stress in the same. X. laevis were submerged in water with a dissolved oxygen concentration of 2 mg/L for 30 min; they were then removed from the water and allowed to freely absorb oxygen for 5 min. Immunostaining of pimonidazole-containing frozen tissue sections of the lung and liver using anti-pimonidazole antibodies as the hypoxia probes revealed that more than 95% of the submerged X. laevis cells were pimonidazole positive, providing direct evidence of tissue hypoxia. When the amount of oxidative stress in the lungs and liver was evaluated in terms of the amount of lipid peroxides, the diving group showed a 2.08-fold and 3.20-fold increase over the normal group, respectively. Following hypoxia exposure, the dry-to-wet weight ratios of the lung tissues was 1.27 times higher (p < .05), while the liver tissues was 1.06 times higher (although not significant). Thus, the degree of damage depended on the tissues affected. In the future, we believe that this model will be a promising option for analyzing the physiological responses of X. laevis to hypoxia and oxidative stress.

Quantitative Proteomics and Network Analysis of Differentially Expressed Proteins in Proteomes of Icefish Muscle Mitochondria Compared with Closely Related Red-Blooded Species

Simple Summary

Antarctic icefish are unusual in that they are the only vertebrates that survive without the protein haemoglobin. One way to try and understand the biological processes that support this anomaly is to record how proteins are regulated in these animals and to compare what we find to closely related Antarctic fish that do still retain haemoglobin. The part of the cell that most clearly utilises oxygen, which is normally transported by haemoglobin, is the mitochondrion. Therefore, we chose to catalogue all the proteins and their relative quantities in the mitochondria (pl.) from two different muscle types in two species of icefish and two species of red-blooded notothenioids. We used an approach called mass spectrometry to reveal relative amounts of the proteins from the muscles of each fish. We present analysis that shows how the connections and relative quantities of proteins differ between these species.

Abstract

Antarctic icefish are extraordinary in their ability to thrive without haemoglobin. We wanted to understand how the mitochondrial proteome has adapted to the loss of this protein. Metabolic pathways that utilise oxygen are most likely to be rearranged in these species. Here, we have defined the mitochondrial proteomes of both the red and white muscle of two different icefish species (Champsocephalus gunnari and Chionodraco rastrospinosus) and compared these with two related red-blooded Notothenioids (Notothenia rossii, Trematomus bernacchii). Liquid Chromatography-Mass spectrometry (LC-MS/MS) was used to generate and examine the proteomic profiles of the two groups. We recorded a total of 91 differentially expressed proteins in the icefish red muscle mitochondria and 89 in the white muscle mitochondria when compared with the red-blooded related species. The icefish have a relatively higher abundance of proteins involved with Complex V of oxidative phosphorylation, RNA metabolism, and homeostasis, and fewer proteins for striated muscle contraction, haem, iron, creatine, and carbohydrate metabolism. Enrichment analyses showed that many important pathways were different in both red muscle and white muscle, including the citric acid cycle, ribosome machinery and fatty acid degradation. Life in the Antarctic waters poses extra challenges to the organisms that reside within them. Icefish have successfully inhabited this environment and we surmise that species without haemoglobin uniquely maintain their physiology. Our study highlights the mitochondrial protein pathway differences between similar fish species according to their specific tissue oxygenation idiosyncrasies.

A Combined Human in Silico and CRISPR/Cas9-Mediated in Vivo Zebrafish Based Approach to Provide Phenotypic Data for Supporting Early Target Validation

The clinical heterogeneity of heart failure has challenged our understanding of the underlying genetic mechanisms of this disease. In this respect, large-scale patient DNA sequencing studies have become an invaluable strategy for identifying potential genetic contributing factors. The complex aetiology of heart failure, however, also means that in vivo models are vital to understand the links between genetic perturbations and functional impacts as part of the process for validating potential new drug targets. Traditional approaches (e.g., genetically-modified mice) are optimal for assessing small numbers of genes, but less practical when multiple genes are identified. The zebrafish, in contrast, offers great potential for higher throughput in vivo gene functional assessment to aid target prioritisation, by providing more confidence in target relevance and facilitating gene selection for definitive loss of function studies undertaken in mice. Here we used whole-exome sequencing and bioinformatics on human patient data to identify 3 genes (API5, HSPB7, and LMO2) suggestively associated with heart failure that were also predicted to play a broader role in disease aetiology. The role of these genes in cardiovascular system development and function was then further investigated using in vivo CRISPR/Cas9-mediated gene mutation analysis in zebrafish. We observed multiple impacts in F0 knockout zebrafish embryos (crispants) following effective somatic mutation, including changes in ventricle size, pericardial oedema, and chamber malformation. In the case of lmo2, there was also a significant impact on cardiovascular function as well as an expected reduction in erythropoiesis. The data generated from both the human in silico and zebrafish in vivo assessments undertaken supports further investigation of the potential roles of API5, HSPB7, and LMO2 in human cardiovascular disease. The data presented also supports the use of human in silico genetic variant analysis, in combination with zebrafish crispant phenotyping, as a powerful approach for assessing gene function as part of an integrated multi-level drug target validation strategy.

The Inhibitory Effect of Selected D2 Dopaminergic Receptor Agonists on VEGF-Dependent Neovascularization in Zebrafish Larvae: Potential New Therapy in Ophthalmic Diseases

Pathological angiogenesis is correlated with many ophthalmic diseases. The most common are exudative age-related macular degeneration and proliferative diabetic retinopathy. The current treatment for these diseases is based on regularly administered anti-VEGF antibodies injections. In the study, we investigated selected D₂ dopaminergic receptor agonists, namely bromocriptine, cabergoline and pergolide, on hypoxia-induced neovascularization. We used the zebrafish laboratory model, specifically three-day post fertilization (dpf) Tg(fli-1: EGFP) zebrafish larvae. To induce abnormal angiogenesis of hyaloid-retinal vessels (HRVs) and intersegmental vessels (ISVs), the larvae were treated with cobalt chloride (II) (CoCl₂) (a hypoxia-inducing agent) from 24 h post fertilization. The inhibitory role of D₂ dopaminergic receptor agonists was investigated using confocal microscopy and qPCR. Additionally, the results were compared to those obtained in the group treated with CoCl₂ followed by bevacizumab, the well-known antiangiogenic agent. Confocal microscopy analyses revealed severe deformation of vessels in the CoCl₂ treated group, while co-incubation with bromocriptine, cabergoline, pergolide and bevacizumab, respectively, significantly inhibited abnormalities of angiogenesis. The qPCR analyses supported the protective role of the chosen dopaminergic agonists by demonstrating their influence on CoCl₂-derived upregulation of vegfaa expression. The present results suggest that the D₂ receptor agonists can be considered as a new direction in research for antiangiogenic therapy.

Genetics Responses to Hypoxia and Reoxygenation Stress in Larimichthys crocea Revealed via Transcriptome Analysis and Weighted Gene Co-Expression Network

Simple Summary

Hypoxia, which occurs frequently in aquaculture, can cause serious harm to all aspects of the growth, reproduction and metabolism of cultured fish. Due to the intolerance of Larimichthys crocea to hypoxia, Larimichthys crocea often floats head or even dies under hypoxic environment. However, the molecular mechanism of hypoxia tolerance in Larimichthys crocea has not been fully described. Therefore, the aim of this study was to explore the hub regulatory genes under hypoxic stress environment by transcriptome analysis of three key tissues (liver, blood and gill) in Larimichthys crocea. We identified a number of important genes that exercise different regulatory functions. Overall, this study will provide important clues to the molecular mechanisms of hypoxia tolerance in Larimichthys crocea.

Abstract

The large yellow croaker (Larimichthys crocea) is an important marine economic fish in China; however, its intolerance to hypoxia causes widespread mortality. To understand the molecular mechanisms underlying hypoxia tolerance in L. crocea, the transcriptome gene expression profiling of three different tissues (blood, gills, and liver) of L. crocea exposed to hypoxia and reoxygenation stress were performed. In parallel, the gene relationships were investigated based on weighted gene co-expression network analysis (WGCNA). Accordingly, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that several pathways (e.g., energy metabolism, signal transduction, oxygen transport, and osmotic regulation) may be involved in the response of L. crocea to hypoxia and reoxygenation stress. In addition, also, four key modules (darkorange, magenta, saddlebrown, and darkolivegreen) that were highly relevant to the samples were identified by WGCNA. Furthermore, some hub genes within the association module, including RPS16, EDRF1, KCNK5, SNAT2, PFKL, GSK-3β, and PIK3CD, were found. This is the first study to report the co-expression patterns of a gene network after hypoxia stress in marine fish. The results provide new clues for further research on the molecular mechanisms underlying hypoxia tolerance in L. crocea.

Effects of moderate exercise on hepatic amino acid and fatty acid composition, liver transcriptome, and intestinal microbiota in channel catfish (Ictalurus punctatus)

Previous research on swimming exercise in fish has focused on muscle building and quality of flesh. However, the effects of hepatic amino acid and fatty acid composition, liver gene expression profile, and intestinal microbiota are poorly understood. In this study, channel catfish (Ictalurus punctatus) were subjected to a 4-week swimming exercise, and liver transcriptome and intestinal microbiota analyses were performed to broaden our understanding of fish under exercise. When compared to non-exercised channel catfish (N-EXF), exercised channel catfish (EXF) had improved arachidonic acid (C20:4n6; ARA), docosahexaenoic acid (C22:6n3; DHA), aspartic acid (Asp) and glycine (Gly). The liver transcriptome analysis revealed 2912 differentially expressed genes and numerous enriched signaling pathways including those involved in nutrient synthesis, such as biosynthesis of unsaturated fatty acids and amino acids; glucose metabolism, such as glycolysis/gluconeogenesis, insulin signaling, and AMPK signaling pathways; and oxygen transport, such as HIF-1, PI3K-Akt, and MAPK signaling pathways. In addition, bacterial 16S rRNA gene sequencing data revealed that long-term exercise increased bacterial diversity and richness, and changed the intestinal microbial composition in channel catfish. In summary, this study provides insights into hepatic metabolic pathways, candidate genes, and intestinal microbiota underlying the long-term exercised channel catfish.

Comparative analyses of liver transcriptomes reveal the effect of exercise on growth-, glucose metabolism-, and oxygen transport-related genes and signaling pathways in grass carp (Ctenopharyngodon idella)

Grass carp is one of the most common farmed fish and its growth rate has been the focus of various studies. However, the impact of long-term exercise on growth rate of juvenile grass carp has not been clearly established. In this study, a four-month exercise trial and liver transcriptome analysis were performed to investigate changes in growth, liver molecular regulatory network and key genes in grass carp. When compared to the non-exercised grass carp (N-EXF), the exercised grass carp (EXF) showed a significant improvement in growth. Liver transcriptome analysis revealed 1714 significantly up-regulated and 1672 significantly down-regulated genes. These genes were enriched in various signaling pathways. These pathways included: those associated with growth, such as the PI3K-Akt and mTOR signaling pathways; those associated with glucose metabolism, such as glycolysis/gluconeogenesis, insulin and AMPK signaling pathways as well as those associated with oxygen transport, such as HIF-1, PI3K-Akt, PPAR and MAPK signaling pathways. In addition, growth-associated genes, such as ghr, igf1 and igf1r; glucose metabolism-associated genes, such as ins and insr as well as oxygen transport-associated genes, such as vhl, pdha and epo were identified. In conclusion, long-term moderate exercise improved the growth rate of grass carp. Our findings elucidate on changes in the liver molecular regulatory network and functional genes that occur during moderate exercise in fish.

The evolutionary and physiological significance of the Hif pathway in teleost fishes

The hypoxia-inducible factor (HIF) pathway is a key regulator of cellular O2 homeostasis and an important orchestrator of the physiological responses to hypoxia (low O2) in vertebrates. Fish can be exposed to significant and frequent changes in environmental O2, and increases in Hif-α (the hypoxia-sensitive subunit of the transcription factor Hif) have been documented in a number of species as a result of a decrease in O2. Here, we discuss the impact of the Hif pathway on the hypoxic response and the contribution to hypoxia tolerance, particularly in fishes of the cyprinid lineage, which includes the zebrafish (Danio rerio). The cyprinids are of specific interest because, unlike in most other fishes, duplicated paralogs of the Hif-α isoforms arising from a teleost-specific genome duplication event have been retained. Positive selection has acted on the duplicated paralogs of the Hif-α isoforms in some cyprinid sub-families, pointing to adaptive evolutionary change in the paralogs. Thus, cyprinids are valuable models for exploring the evolutionary significance and physiological impact of the Hif pathway on the hypoxic response. Knockout in zebrafish of either paralog of Hif-1α greatly reduces hypoxia tolerance, indicating the importance of both paralogs to the hypoxic response. Here, with an emphasis on the cardiorespiratory system, we focus on the role of Hif-1α in the hypoxic ventilatory response and the regulation of cardiac function. We explore the effects of the duration of the hypoxic exposure (acute, sustained or intermittent) on the impact of Hif-1α on cardiorespiratory function and compare relevant data with those from mammalian systems.

Physiological responses and molecular strategies in heart of silver carp (Hypophthalmichthys molitrix) under hypoxia and reoxygenation

A sufficient oxygen concentration is essential for fish growth, reproduction, and metabolism. Silver carp (Hypophthalmichthys molitrix) is sometimes challenged by hypoxia during intensive aquaculture or because of environmental changes. However, the response to hypoxic stress in the heart of silver carp remains relatively unknown. In the present study, we reported the effects of hypoxia on histological structures, enzyme activities, and gene expression in the heart of silver carp. Hematoxylin and eosin (H&E) staining of heart sections showed that the myocardial fibers gradually became disordered, swollen, and even ruptured during hypoxic treatment. These phenotypes were also supported by increased activities of injury-related enzymes. Moreover, the transcriptome was analyzed to determine the molecular strategies of hypoxia adaptation in the heart. PI3K-Akt signaling pathway, FoxO signaling pathway, and JAK-STAT signaling pathway were the most prominent pathways activated by hypoxia. Twenty significantly differentially expressed genes were selected to create a network diagram related to cell proliferation, carbohydrate metabolism, oxidative stress, and angiogenesis. Additionally, reoxygenation could ameliorate cardiac injury and eliminate the effects of hypoxia on gene expression. This was the first comparative transcriptomic study to explore the molecular mechanism of the response to hypoxia and reoxygenation in the heart of silver carp. Our results provide a theoretical basis for cultivating hypoxia-tolerant carp varieties in the future.

Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

Background

Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia). During grow out, fish were sampled five times to determine individual body weight (BW) gains. We applied a genome-wide association study to identify SNPs and genes associated with the hypoxic and normoxic environments in the 16th generation of a Genetically Improved Farmed Tilapia population.

Results

In the hypoxic environment, 36 SNPs associated with at least one of the five body weight measurements (BW1 till BW5), of which six, located between 19.48 Mb and 21.04 Mb on Linkage group (LG) 8, were significant for body weight in the early growth stage (BW1 to BW2). Further significant associations were found for BW in the later growth stage (BW3 to BW5), located on LG1 and LG8. Analysis of genes within the candidate genomic region suggested that MAPK and VEGF signalling were significantly involved in the later growth stage under the hypoxic environment. Well-known hypoxia-regulated genes such as igf1rb, rora, efna3 and aurk were also associated with growth in the later stage in the hypoxic environment. Conversely, 13 linkage groups containing 29 unique significant and suggestive SNPs were found across the whole growth period under the normoxic environment. A meta-analysis showed that 33 SNPs were significantly associated with BW across the two environments, indicating a shared effect independent of hypoxic or normoxic environment. Functional pathways were involved in nervous system development and organ growth in the early stage, and oocyte maturation in the later stage.

Conclusions

There are clear genotype-growth associations in both normoxic and hypoxic environments, although genome architecture involved changed over the growing period, indicating a transition in metabolism along the way. The involvement of pathways important in hypoxia especially at the later growth stage indicates a genotype-by-environment interaction, in which MAPK and VEGF signalling are important components.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07486-5.

Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)

Climate models predict an increase in extent, frequency, and duration of marine hypoxia events in the twenty first century. A better understanding of organismal responses to hypoxia in individual species is a crucial step for predicting ecosystem responses. We experimentally subjected a common invertebrate, the bearded fireworm (Hermodice carunculata) to two levels of chronic hypoxia and, in a separate experiment, to intermittent hypoxia. We found components of the conserved hypoxia-inducible factor (HIF) pathway and show a modulated response to hypoxia depending on the severity of hypoxic stress: under mild hypoxia, only the HIF-1α subunit is upregulated, while expression of the other subunit, aryl hydrocarbon nuclear translator, only increases significantly at more severe hypoxia levels. The chronic trials revealed down-regulation of genes related to cell adhesion, transport, development and heme-binding, and up-regulation of genes related to glycolysis, oxygen binding, cell differentiation, digestive and reproductive function. The intermittent hypoxia trials revealed an upregulation of heme transporter activity during hypoxia, and our time series analysis characterized nine clusters of genes with similar expression patterns. Our findings suggest that H. carunculata is likely to tolerate, and be resilient to, predicted future hypoxia conditions.

Contrasting strategies of hypoxic cardiac performance and metabolism in cichlids and armoured catfish

The heart of tropical fishes is a particularly useful model system in which to investigate mechanisms of hypoxic tolerance. Here we focus on insights gained from two groups of fishes, cichlids and armoured catfishes. Cichlids respond to hypoxia by entering a sustained hypometabolism with decreased heart performance to match whole animal circulatory needs. Heart rate is decreased along with protein turnover to reduce adenosine triphosphate demand. This occurs despite the inherent capacity for high levels of cardiac power development. Although highly hypoxic tolerant at the whole animal level, the heart of cichlids does not have high constitutive activities of glycolytic enzymes compared to other species. Information is conflicting with respect to changes in glycolytic gene expression and enzyme activity following hypoxic exposure with some studies showing increases and others decreases. In contrast to cichlids, species of armoured catfish, that are routinely exposed to water of low oxygen content, do not display hypoxic bradycardia. Under hypoxia there are early changes in glucose trafficking suggestive of activation of glycolysis before lactate accumulation. Thereafter, heart glycogen is mobilized and lactate accumulates in both heart and blood, in some species to very high levels. Heart performance under hypoxia is enhanced by defense of intracellular pH. A functional sarcoplasmic reticulum and binding of hexokinase to the outer mitochondrial membrane may also play a role in cardioprotection. Maintenance of heart performance under hypoxia may relate to a tradeoff between air breathing via a modified stomach and circulatory demands for digestion.

Comparative transcriptome and methylome analysis of the hindbrain in olive flounder (Paralichthys olivaceus) considering individual behavior-type and oxygen metabolism

In previous studies we employed multiple behavior assays, including propensity to feed, simulated trawl capture and escape response, to prove the presence of bold and shy personality (BP,SP) in olive flounder (Paralichthys olivaceus). However, the molecular mechanism of the different personality has not been elucidated. In this study, firstly, we found that the SP flounder had lower red blood cell count (RBC) and haemoglobin concentration (HBG) than BP flounder. Secondly, the transcriptomic profiles of the hindbrain in flounder with distinct personality were compared. A total of 144 differently expressed genes (DEGs) were identified, including 70 up-regulated and 74 down-regulated genes in SP flounder compared with BP flounder. Genes involved in hypoxia stress were detected in SP flounder, accompanied with down-regulation of ribosomal RNA synthesis. In addition, genes related with calcium signaling pathway, including endothelin, b-Fos, c-Fos and c-Jun were up-regulated in SP flounder. Furthermore, personality-related genes including UI, CCK, c-Fos showed significantly higher level in SP flounder than in BP flounder. GO enrichment analysis indicated that the GO categories "the tight junction pathway" and "lipid transport or localization pathway" were enriched in SP flounder, suggesting that the central nervous system homeostasis would be compromised. Thirdly, using a simple and scalable DNA methylation profiling method (MethylRAD), which allows for methylation analysis for DEGs in RNA-seq, we found that only part of gene expression was negatively associated with promoter methylation. Altogether, our study will not only lay a foundation for further studies on animal personality but also facilitate the selective breeding of olive flounder in aquaculture.

Transcriptome analysis reveals molecular strategies in gills and heart of large yellow croaker (Larimichthys crocea) under hypoxia stress

The gills and heart are two major targets of hypoxia in fish. However, the molecular responses in fish gills and heart to hypoxia challenge remain unclear. Here, RNA-Seq technology was used to study the gene expression profiles in gills and heart of large yellow croaker (Larimichthys crocea) at 6, 24, and 48 h after hypoxia stress. A total of 1,546 and 2,746 differentially expressed genes (DEGs) were identified in gills and heart, respectively. Expression changes of nine genes in each tissue were further validated by the qPCR. Based on KEGG and Gene ontology enrichments, we found that various innate immunity-related genes, such as complement components (C1qs, C2, C3, C6, and C7), chemokines (CCL3, CCL17, CCL19, CCL25, and CXCL8_L3), chemokine receptors (CCR9, CXCR1, and CXCR3), and nitric oxide synthase (NOS), were significantly down-regulated in gills and/or heart, suggesting that innate immune processes mediated by these genes may be inhibited by hypoxia. The genes involved in both glycolysis pathway (LDHA) and tricarboxylic acid cycle (IDH2 and OGDH) were up-regulated in gills and heart of hypoxic large yellow croakers, possibly because gill and heart tissues need enough energy to accelerate gas exchange and blood circulation. Hypoxia also affected the ion transport in gills of large yellow croaker, through down-regulating the expression levels of numerous classical ion transporters, including HVCN1, SLC20A2, SLC4A4, RHBG, RHCG, and SCN4A, suggesting an energy conservation strategy to hypoxia stress. All these results indicate that the immune processes, glycolytic pathways, and ion transport were significantly altered in gills and/or heart of large yellow croaker under hypoxia, possibly contributing to maintain cellular energy balance during hypoxia. Our data, therefore, afford new information to understand the tissue-specific molecular responses of bony fish to hypoxia stress.

Cardiac Transcriptomics Reveals That MAPK Pathway Plays an Important Role in Hypoxia Tolerance in Bighead Carp (Hypophthalmichthys nobilis)

As aquatic animals, fishes often encounter various situations of low oxygen, and they have evolved the ability to respond to hypoxia stress. Studies of physiological and molecular responses to hypoxia stress are essential to clarify genetic mechanisms underlying hypoxia tolerance in fish. In this study, we performed acute hypoxia treatment in juvenile bighead carp (Hypophthalmicthys nobilis) by decreasing water O₂ from 6.5 mg/L to 0.5 mg/L in three hours. This hypoxia stress resulted in a significant increase in blood lactate and serum glucose. Comparisons of heart transcriptome among hypoxia tolerant (HT), hypoxia sensitive (HS), and normoxia control (NC) groups showed that 820, 273, and 301 differentially expressed genes (DEGs) were identified in HS vs. HT, NC vs. HS, and NC vs. HT (false discovery rate (FDR) < 0.01, Fold Change> 2), respectively. KEGG pathway enrichment showed that DEGs between HS and HT groups were mainly involved in mitogen-activated protein kinase (MAPK) signaling, insulin signaling, apoptosis, tight junction and adrenergic signaling in cardiomyocytes pathways, and DEGs in MAPK signaling pathway played a key role in cardiac tolerance to hypoxia. Combined with the results of our previous cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis of hypoxia stress in this species, such genes as stbp2, ttn, mapk, kcnh, and tnfrsf were identified in both studies, representing the significance of these DEGs in hypoxia tolerance in bighead carp. These results provide insights into the understanding of genetic modulations for fish heart coping with hypoxia stress and generate basic resources for future breeding studies of hypoxia resistance in bighead carp.

Molecular characterization of p38 MAPK and tissue-specific expression under cadmium stress in red swamp crayfish (Procambarus clarkii)

Keeping harmful pollutants out of some crucial tissues as much as possible is a key trait for the organism to survive in adverse conditions, such as in heavy-metal contaminated aquatic environments. In the current study, it was hypothesized that the p38 Mitogen-activated Protein Kinase (MAPK) controls the distribution of cadmium (Cd) in red swamp crayfish (Procambarus clarkii) by regulating the accumulation of Cd in different tissues under Cd-stressed conditions. To test this hypothesis, this study analyzed the p38 MAPK gene and compared the differential expression levels in the heart, antennal gland, gill, hepatopancreas, and muscles. Differences in expression levels of p38 MAPK gene between different tissues were conducted under controlled Cd exposure. This study found that the expression of p38 MAPK is tissue-specific in all tested samples under non-stressed condition. Under Cd-stressed condition and with the prolongation of Cd exposure time, the content of Cd in all examined tissues of P. clarkii has substantially increased compared to the control, although the Cd contents in the heart, antennal gland, and muscle remained relatively lower than those observed in the hepatopancreas. Consequently, the levels of p38 MAPK in the heart, antennal gland, and muscle were higher than the level in the hepatopancreas. These results indicate that p38 MAPK regulates the distribution and accumulation of Cd in different tissues of P. clarkii under Cd-stressed condition. Furthermore, the results suggested that the higher expression of p38 MAPK played a crucial role in keeping Cd out of the tissues in the Cd-rich aquatic environment to maintain the normal physiological function of the red swamp crayfish, a process necessary for survival and growth.

Acute hypoxia changes the mode of glucose and lipid utilization in the liver of the largemouth bass (Micropterus salmoides)

Dissolved oxygen (DO) undountedly affects fish distribution, metabolism, and evern survival. Intensive aquaculture and environmental changes will inevitably lead to hypoxic stress for largemouth bass (Micropterus salmoides). The different metabolic responses and mechanism still remains relatively unknown during acute hypoxia exposure. In this study, largemouth bass were subjected to hypoxic stress (3.0 ± 0.2 mg/L and 1.2 ± 0.2 mg/L) for 24 h and 12 h reoxygenation to systemically evaluate indicators of glucose and lipid metabolism. A regulatory network was constructed using RNA-seq to further elucidate the transcriptional regulation of glucose and lipid metabolism. During hypoxia for 4 h, the liver glycogen, glucose and pyruvic acid contents significantly decreased, whereas plasma glucose content and liver lactic acid content increased significantly. The accumulation of liver triglycerides and non-esterified fatty acids was enhanced during hypoxia for 8 h. The activity of key enzymes revealed the different metabolic responses to hypoxia exposure for 4 h, including the enhancement of glycolysis, and inhibition of gluconeogenesis. Furthermore, hypoxia exposure for 8 h increased lipid mobilization, and inhibited the β-oxidation. In addition, an integrated regulatory network of 9 major pathways involved in the response to hypoxia exposure was constructed, including HIF signaling pathway, VEGF signaling pathway, AMPK signaling pathway, insulin signaling pathway and PPAR signaling pathway; glycolysis/gluconeogenesis, pyruvate metabolism, fatty acid degradation and fatty acid biosynthesis. Additionally, reoxygenation inhibited glycolysis, and promoted gluconeogenesis and lipid oxidation, but energy deficits persisted. In short, although the mobilization and activation of fatty acid in liver were enhanced in the early stage of hypoxia, glycolysis was the main energy source under acute hypoxia. The extent and duration of hypoxia determine the degree of change in energy metabolism.

Transcriptome and physiology analysis identify key metabolic changes in the liver of the large yellow croaker (Larimichthys crocea) in response to acute hypoxia

The large yellow croaker (Larimichthys crocea) is one of the most important marine economic fish in the southeast coast of China. However, hypoxia stress become a major obstacle to the benign development of L. crocea industry. To understand the energy metabolism mechanism adapted to hypoxia, we analyzed the transcriptome and physiology of L. crocea liver in response to hypoxia stress for different durations. We obtained 243,756,080 clean reads, of which 83.38% were successfully mapped to the reference genome of L. crocea. The heat map analysis showed that genes encoding enzymes involved in glycolysis/gluconeogenesis were significantly upregulated at various time points. Moreover, genes encoding enzymes related to the citrate cycle, oxidative phosphorylation, and amino acid metabolism were significantly downregulated at 6 and 24 h, but upregulated at 48 and 96 h. The change of liver in physiology processes, including respiratory metabolism, and activities of the carbohydrate metabolism enzymes showed a similar trend. The results revealed that the respiratory metabolism of L. crocea was mainly anaerobic within 24 h of hypoxia stress, and aerobic metabolism was dominant after 24 h. Carbohydrate metabolism plays a crucial role in energy supply and amino acid metabolism is an important supporting character to cope with acute hypoxia stress. There was no significant change in lipid utilization under short-term acute stress. This study increases our understanding of the energy metabolism mechanism of the hypoxia response in fish and provides a useful resource for L. crocea genetics and breeding.

Short-term cyclical stretch phosphorylates p38 and ERK1/2 MAPKs in cultured fibroblasts from the hearts of rainbow trout, Oncorhynchus mykiss

The form and function of the rainbow trout heart can remodel in response to various stressors including changes in environmental temperature and anemia. Previous studies have hypothesized that changes in biomechanical forces experienced by the trout myocardium as result of such physiological stressors could play a role in triggering the remodeling response. However, there has been no work examining the influence of biomechanical forces on the trout myocardium or of the cellular signals that would translate such a stimuli into a biological response. In this study, we test the hypothesis that the application of biomechanical forces to trout cardiac fibroblasts activate the cell signaling pathways associated with cardiac remodeling. This was done by cyclically stretching cardiac fibroblasts to 10% equibiaxial deformation at 0.33 Hz and quantifying the activation of the p38-JNK-ERK mitogen activated protein kinase (MAPK) pathway. After 20 min, p38 MAPK phosphorylation was elevated by 4.2-fold compared to control cells (P<0.05) and after 24 h of stretch, p38 MAPK phosphorylation remained elevated and extracellular-regulated kinase 1/2 was phosphorylated by 2.4-fold compared to control (P<0.05). Together, these results indicate that mechanotransductive pathways are active in cardiac fibroblasts, and lead to the activation of cell signaling pathways involved in cardiac remodeling.

Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart

While the heart regenerates poorly in mammals, efficient heart regeneration occurs in zebrafish. Studies in zebrafish have resulted in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. To identify which processes occur in proliferating cardiomyocytes we have used a single-cell RNA-sequencing approach. We uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the nonproliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover, these cells have reduced expression of mitochondrial genes and reduced mitochondrial activity, while glycolysis gene expression and glucose uptake are increased, indicative for metabolic reprogramming. Furthermore, we find that the metabolic reprogramming of border zone cardiomyocytes is induced by Nrg1/ErbB2 signaling and is important for their proliferation. This mechanism is conserved in murine hearts in which cardiomyocyte proliferation is induced by activating ErbB2 signaling. Together these results demonstrate that glycolysis regulates cardiomyocyte proliferation during heart regeneration.

Heart attacks are a common cause of death in the Western world. During a heart attack, oxygen levels in the affected part of the heart decrease, which causes heart muscle cells to die. In humans the dead cells are replaced by a permanent scar that stabilizes the injury but does not completely heal it. As a result, individuals have a lower quality of life after a heart attack and are more likely to die from a subsequent attack.

Unlike humans, zebrafish are able to regenerate their hearts after injury: heart muscle cells close to a wound divide to produce new cells that slowly replace the scar tissue and restore normal function to the area. It remains unclear, however, what stimulates the heart muscle cells of zebrafish to start dividing. To address this question, Honkoop, de Bakker et al. used a technique called single-cell sequencing to study heart muscle cells in wounded zebrafish hearts.

The experiments identified a group of heart muscle cells close to the site of the wound that multiplied to repair the damage. This group of cells had altered their metabolism compared to other heart muscle cells so that they relied on a pathway called glycolysis to produce the energy and building blocks they needed to proliferate. Blocking glycolysis impaired the ability of the heart muscle cells to divide, indicating that this switch is necessary for the heart to regenerate. Further experiments showed that a signaling cascade, which includes the molecules Nrg1 and ErbB2, induces heart muscle cells in both zebrafish and mouse hearts to switch to glycolysis and undergo division.

These findings indicate that activating glycolysis in heart muscle cells may help to stimulate the heart to regenerate after a heart attack or other injury. The next step following on from this work is to develop methods to activate glycolysis and promote cell division in injured hearts.

Activation of oxygen-responsive pathways is associated with altered protein metabolism in Arctic char exposed to hypoxia

Fish exposed to fluctuating oxygen concentrations often alter their metabolism and/or behaviour to survive. Hypoxia tolerance is typically associated with the ability to reduce energy demand by supressing metabolic processes such as protein synthesis. Arctic char is amongst the most sensitive salmonid to hypoxia, and typically engage in avoidance behaviour when faced with lack of oxygen. We hypothesized that a sensitive species will still have the ability (albeit reduced) to regulate molecular mechanisms during hypoxia. We investigated the tissue-specific response of protein metabolism during hypoxia. Little is known about protein degradation pathways during hypoxia in fish and we predict that protein degradation pathways are differentially regulated and play a role in the hypoxia response. We also studied the regulation of oxygen-responsive cellular signalling pathways [hypoxia inducible factor (HIF), unfolded protein response (UPR) and mTOR pathways] since most of what we know comes from studies on cancerous mammalian cell lines. Arctic char were exposed to cumulative graded hypoxia trials for 3 h at four air saturation levels (100%, 50%, 30% and 15%). The rate of protein synthesis was measured using a flooding dose technique, whereas protein degradation and signalling pathways were assessed by measuring transcripts and phosphorylation of target proteins. Protein synthesis decreased in all tissues measured (liver, muscle, gill, digestive system) except for the heart. Salmonid hearts have preferential access to oxygen through a well-developed coronary artery, therefore the heart is likely to be the last tissue to become hypoxic. Autophagy markers were upregulated in the liver, whereas protein degradation markers were downregulated in the heart during hypoxia. Further work is needed to determine the effects of a decrease in protein degradation on a hypoxic salmonid heart. Our study showed that protein metabolism in Arctic char is altered in a tissue-specific fashion during graded hypoxia, which is in accordance with the responses of the three major hypoxia-sensitive pathways (HIF, UPR and mTOR). The activation pattern of these pathways and the cellular processes that are under their control varies greatly among tissues, sometimes even going in the opposite direction. This study provides new insights on the effects of hypoxia on protein metabolism. Adjustment of these cellular processes is likely to contribute to shifting the fish phenotype into a more hypoxia-tolerant one, if more than one hypoxia event were to occur. Our results warrant studying these adjustments in fish exposed to long-term and diel cycling hypoxia.

Acute Stress and an Electrolyte- Imbalanced Diet, but Not Chronic Hypoxia, Increase Oxidative Stress and Hamper Innate Immune Status in a Rainbow Trout (Oncorhynchus mykiss) Isogenic Line

In aquaculture, fish may be exposed to sub-optimal rearing conditions, which generate a stress response if full adaptation is not displayed. However, our current knowledge of several coexisting factors that may give rise to a stress response is limited, in particular when both chronic and acute stressors are involved. This study investigated changes in metabolic parameters, oxidative stress and innate immune markers in a rainbow trout (Oncorhynchus mykiss) isogenic line exposed to a combination of dietary (electrolyte-imbalanced diet, DEB 700 mEq Kg-1) and environmental (hypoxia, 4.5 mg O2 L-1) challenges and their respective controls (electrolyte-balanced diet, DEB 200 mEq Kg-1 and normoxia, 7.9 or mg O2 L-1) for 49 days. At the end of this period, fish were sampled or subjected to an acute stressor (2 min of handling/confinement) and then sampled. Feeding trout an electrolyte-imbalanced diet produced a reduction in blood pH, as well as increases in cortisol levels, hepato-somatic index (HSI) and total energy content in the liver. The ratio between the lactate dehydrogenase (LDH) and isocitrate dehydrogenase (IDH) activities decreased in the liver of trout fed the DEB 700 diet, but increased in the heart, suggesting a different modulation of metabolic capacity by the dietary challenge. Several markers of oxidative stress in the liver of trout, mainly related to the glutathione antioxidant system, were altered when fed the electrolyte-imbalanced diet. The dietary challenge was also associated with a decrease in the alternative complement pathway activity (ACH50) in plasma, suggesting an impaired innate immune status in that group. Trout subjected to the acute stressor displayed reduced blood pH values, higher plasma cortisol levels as well as increased levels of metabolic markers associated with oxidative stress in the liver. An interaction between diet and acute stressor was detected for oxidative stress markers in the liver of trout, showing that the chronic electrolyte-imbalance impairs the response of rainbow trout to handling/confinement. However, trout reared under chronic hypoxia only displayed changes in parameters related to energy use in both liver and heart. Taken together, these results suggest that trout displays an adaptative response to chronic hypoxia. Conversely, the dietary challenge profoundly affected fish homeostasis, resulting in an impaired physiological response leading to stress, which then placed constraints on a subsequent acute challenge.

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Background

Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.

Results

Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs.

Conclusions

This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.

Physiological Responses to Swimming-Induced Exercise in the Adult Zebrafish Regenerating Heart

Exercise promotes a set of physiological responses known to provide long-term health benefits and it can play an important role in cardioprotection. In the present study, we examined cardiac responses to exercise training in the adult zebrafish and in the context of cardiac regeneration. We found that swimming-induced exercise increased cardiomyocyte proliferation and that this response was also found under regenerating conditions, when exercise was performed either prior to and after ventricular cryoinjury (CI). Exercise prior to CI resulted in a mild improvement in cardiac function and lesion recovery over the non-exercise condition. Transcriptomic profiling of regenerating ventricles in cryoinjured fish subjected to exercise identified genes possibly involved in the cardioprotective effects of exercise and that could represent potential targets for heart regeneration strategies. Taken together, our results suggest that exercise constitutes a physiological stimulus that may help promote cardiomyogenic mechanisms of the vertebrate heart through the induction of cardiomyocyte proliferation. The zebrafish exercise model may be useful for investigating the potential cardioprotective effects of exercise in teleost fish and to contribute to further identify and develop novel avenues in basic research to promote heart regeneration.

The developmental origin of heart size and shape differences in Astyanax mexicanus populations

Regulation of heart size and shape is one of the least understood processes in developmental biology. We have for the first time analysed the hearts of Astyanax mexicanus and identified several differences in heart morphology between the surface (epigean morph) and cave-dwelling (troglomorph) morphs. Examination of the adult revealed that the troglomorph possesses a smaller heart with a rounder ventricle in comparison to the epigean morph. The size differences identified appear to arise early in development, as early as 24 h post-fertilisation (hpf), while shape differences begin to appear at 2 days post-fertilisation. The heart of the first-generation cross between the cave-dwelling and river-dwelling morph shows uncoupling of different phenotypes observed in the parental populations and indicates that the cardiac differences have become embedded in the genome during evolution. The differences in heart morphology are accompanied by functional changes between the two morphs, with the cave-dwelling morph exhibiting a slower heart rate than the river-dwelling morph. The identification of morphological and functional differences in the A. mexicanus heart could allow us to gain more insight into how such parameters are regulated during cardiac development, with potential relevance to cardiac pathologies in humans.

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Differences in heart size, shape and tissue structure between Astyanax populations.

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Furthermore, differences in cardiac melanophore and adipocyte numbers.

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Heart size and shape differences are apparent early in development.

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Surface and Pachón show differences in heart rate during development and adulthood.

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F1 hybrids show uncoupling of features observed in surface and Pachón populations.

Acute hypoxia stress induced abundant differential expression genes and alternative splicing events in heart of tilapia

Hypoxia is one of the critical environmental stressors for fish in aquatic environments. Although accumulating evidences indicate that gene expression is regulated by hypoxia stress in fish, how genes undergoing differential gene expression and/or alternative splicing (AS) in response to hypoxia stress in heart are not well understood. Using RNA-seq, we surveyed and detected 289 differential expressed genes (DEG) and 103 genes that undergo differential usage of exons and splice junctions events (DUES) in heart of a hypoxia tolerant fish, Nile tilapia, Oreochromis niloticus following 12h hypoxic treatment. The spatio-temporal expression analysis validated the significant association of differential exon usages in two randomly selected DUES genes (fam162a and ndrg2) in 5 tissues (heart, liver, brain, gill and spleen) sampled at three time points (6h, 12h, and 24h) under acute hypoxia treatment. Functional analysis significantly associated the differential expressed genes with the categories related to energy conservation, protein synthesis and immune response. Different enrichment categories were found between the DEG and DUES dataset. The Isomerase activity, Oxidoreductase activity, Glycolysis and Oxidative stress process were significantly enriched for the DEG gene dataset, but the Structural constituent of ribosome and Structural molecule activity, Ribosomal protein and RNA binding protein were significantly enriched only for the DUES genes. Our comparative transcriptomic analysis reveals abundant stress responsive genes and their differential regulation function in the heart tissues of Nile tilapia under acute hypoxia stress. Our findings will facilitate future investigation on transcriptome complexity and AS regulation during hypoxia stress in fish.

Reduced Cardiac Calcineurin Expression Mimics Long-Term Hypoxia-Induced Heart Defects in Drosophila

BACKGROUND

Hypoxia is often associated with cardiopulmonary diseases, which represent some of the leading causes of mortality worldwide. Long-term hypoxia exposures, whether from disease or environmental condition, can cause cardiomyopathy and lead to heart failure. Indeed, hypoxia-induced heart failure is a hallmark feature of chronic mountain sickness in maladapted populations living at high altitude. In a previously established Drosophila heart model for long-term hypoxia exposure, we found that hypoxia caused heart dysfunction. Calcineurin is known to be critical in cardiac hypertrophy under normoxia, but its role in the heart under hypoxia is poorly understood.

METHODS AND RESULTS

In the present study, we explore the function of calcineurin, a gene candidate we found downregulated in the Drosophila heart after lifetime and multigenerational hypoxia exposure. We examined the roles of 2 homologs of Calcineurin A, CanA14F, and Pp2B in the Drosophila cardiac response to long-term hypoxia. We found that knockdown of these calcineurin catalytic subunits caused cardiac restriction under normoxia that are further aggravated under hypoxia. Conversely, cardiac overexpression of Pp2B under hypoxia was lethal, suggesting that a hypertrophic signal in the presence of insufficient oxygen supply is deleterious.

CONCLUSIONS

Our results suggest a key role for calcineurin in cardiac remodeling during long-term hypoxia with implications for diseases of chronic hypoxia, and it likely contributes to mechanisms underlying these disease states.

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.

Acute stress is detrimental to heart regeneration in zebrafish

Psychological stress is one of the factors associated with human cardiovascular disease. Here, we demonstrate that acute perceived stress impairs the natural capacity of heart regeneration in zebrafish. Beside physical and chemical disturbances, intermittent crowding triggered an increase in cortisol secretion and blocked the replacement of fibrotic tissue with new myocardium. Pharmacological simulation of stress by pulse treatment with dexamethasone/adrenaline reproduced the regeneration failure, while inhibition of the stress response with anxiolytic drugs partially rescued the regenerative process. Impaired heart regeneration in stressed animals was associated with a reduced cardiomyocyte proliferation and with the downregulation of several genes, including igfbp1b, a modulator of IGF signalling. Notably, daily stress induced a decrease in Igf1r phosphorylation. As cardiomyocyte proliferation was decreased in response to IGF-1 receptor inhibition, we propose that the stress-induced cardiac regenerative failure is partially caused by the attenuation of IGF signalling. These findings indicate that the natural regenerative ability of the zebrafish heart is vulnerable to the systemic paracrine stress response.

Evolution, comparative biology and ontogeny of vertebrate heart regeneration

There are 64,000 living species of vertebrates on our planet and all of them have a heart. Comparative analyses devoted to understanding the regenerative potential of the myocardium have been performed in a dozen vertebrate species with the aim of developing regenerative therapies for human heart disease. Based on this relatively small selection of animal models, important insights into the evolutionary conservation of regenerative mechanisms have been gained. In this review, we survey cardiac regeneration studies in diverse species to provide an evolutionary context for the lack of regenerative capacity in the adult mammalian heart. Our analyses highlight the importance of cardiac adaptations that have occurred over hundreds of millions of years during the transition from aquatic to terrestrial life, as well as during the transition from the womb to an oxygen-rich environment at birth. We also discuss the evolution and ontogeny of cardiac morphological, physiological and metabolic adaptations in the context of heart regeneration. Taken together, our findings suggest that cardiac regenerative potential correlates with a low-metabolic state, the inability to regulate body temperature, low heart pressure, hypoxia, immature cardiomyocyte structure and an immature immune system. A more complete understanding of the evolutionary context and developmental mechanisms governing cardiac regenerative capacity would provide stronger scientific foundations for the translation of cardiac regeneration therapies into the clinic.

Protective Effects of Otophylloside N on Pentylenetetrazol-Induced Neuronal Injury In vitro and In vivo

Approximately 30% of epileptic patients worldwide are medically unable to control their seizures. In addition, repeated epileptic seizures generally lead to neural damage. Pentylenetetrazol (PTZ) is a clinical circulatory and respiratory stimulant that is experimentally used to mimic epileptic convulsion in epilepsy research. Here, we systematically explore the neuroprotective effects of a pure compound isolated from Cynanchum otophyllum Schneid (Qingyangshen), Otophylloside N (OtoN), against PTZ-induced neuronal injury. We used three models: in vitro primary cortical neurons, in vivo mice, and in vivo zebrafish. Our results revealed that OtoN treatment may attenuate PTZ-induced morphology changes, cell death, LDH efflux in embryonic neuronal cells of C57BL/6J mice, and convulsive behavior in zebrafish. Additionally, our Western blot and RT-PCR results demonstrated that OtoN may attenuate PTZ-induced apoptosis and neuronal activation in neuronal cells, mice, and zebrafish. OtoN may reduce PTZ-induced cleavage of poly ADP-ribose polymerase and upregulation of the Bax/Bcl-2 ratio and decrease the expression level of c-Fos. This study is the first investigation of the neuroprotective effects of OtoN, which might be developed as a novel antiepileptic drug.

Long-term hypoxia exposure alters the cardiorespiratory physiology of steelhead trout (Oncorhynchus mykiss), but does not affect their upper thermal tolerance

It has been suggested that exposure to high temperature or hypoxia may confer tolerance to the other oxygen-limited stressor (i.e., 'cross-tolerance'). Thus, we investigated if chronic hypoxia-acclimation (>3 months at 40% air saturation) improved the steelhead trout's critical thermal maximum (CT_Max), or affected key physiological variables that could impact upper thermal tolerance. Neither CT_Max (24.7 vs. 25.3°C) itself, nor oxygen consumption ( [Formula: see text] ), haematocrit, blood haemoglobin concentration, or heart rate differed between hypoxia- and normoxia-acclimated trout when acutely warmed. However, the cardiac output (Q̇) of hypoxia-acclimated fish plateaued earlier compared to normoxia-acclimated fish due to an inability to maintain stroke volume (S_V), and this resulted in a ~50% lower maximum Q̇. Despite this reduced maximum cardiac function, hypoxia-acclimated trout were able to consume more O₂ per volume of blood pumped as evidenced by the equivalent [Formula: see text] . These results provide additional evidence that long-term hypoxia improves tissue oxygen utilization, and that this compensates for diminished cardiac pumping capacity. The limited S_V in hypoxia-acclimated trout in vivo was not associated with changes in cardiac morphology or in vitro maximum S_V, but the affinity and density of myocardial ß-adrenoreceptors were lower and higher, respectively, than in normoxia-acclimated fish. These data suggest that alterations in ventricular filling dynamics or myocardial contractility constrain cardiac function in hypoxia-acclimated fish at high temperatures. Our results do not support (1) 'cross-tolerance' between high temperature and hypoxia when hypoxia is chronic, or (2) that cardiac function is always the determinant of temperature-induced changes in fish [Formula: see text] , and thus thermal tolerance, as suggested by the oxygen- and capacity-limited thermal tolerance (OCLTT) theory.

Integrated analysis of mRNA-seq and miRNA-seq in the liver of Pelteobagrus vachelli in response to hypoxia

Pelteobagrus vachelli is a well-known commercial species in Asia. However, a sudden lack of oxygen will result in mortality and eventually to pond turnover. Studying the molecular mechanisms of hypoxia adaptation in fishes will not only help us to understand fish speciation and the evolution of the hypoxia-signaling pathway, but will also guide us in the breeding of hypoxia-tolerant fish strains. Despite this, the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in hypoxia responses in fish have remained unexamined. In the present study, we used next-generation sequencing technology to characterise mRNA-seq and miRNA-seq of control- and hypoxia-treated P. vachelli livers to elucidate the molecular mechanisms of hypoxia adaptation. We were able to find miRNA-mRNA pairs using bioinformatics analysis and miRNA prediction algorithms. Furthermore, we compared several key pathways which were identified as involved in the hypoxia response of P. vachelli. Our study is the first report on integrated analysis of mRNA-seq and miRNA-seq in fishes and offers a deeper insight into the molecular mechanisms of hypoxia adaptation. qRT-PCR analysis further confirmed the results of mRNA-Seq and miRNA-Seq analysis. We provide a good case study for analyzing mRNA/miRNA expression and profiling a non-model fish species using next-generation sequencing technology.

Hypoxia-inducible factor 3 biology: complexities and emerging themes

The hypoxia-inducible factor (HIF) family has three distinct members in most vertebrates. All three HIFs consist of a unique and oxygen-labile α-subunit and a common and stable β-subunit. While HIF-1 and HIF-2 function as master regulators of the transcriptional response to hypoxia, much less is known about HIF-3. The HIF-3α gene gives rise to multiple HIF-3α variants due to the utilization of different promoters, different transcription initiation sites, and alternative splicing. These HIF-3α variants are expressed in different tissues, at different developmental stages, and are differentially regulated by hypoxia and other factors. Recent studies suggest that different HIF-3α variants have different and even opposite functions. There is strong evidence that full-length HIF-3α protein functions as an oxygen-regulated transcription activator and that it activates a unique transcriptional program in response to hypoxia. Many HIF-3α target genes have been identified. While some short HIF-3α variants act as dominant-negative regulators of HIF-1/2α actions, other HIF-3α variants can inhibit HIF-1/2α actions by competing for the common HIF-β. There are also a number of HIF-3α variants yet to be explored. Future studies of these naturally occurring HIF-3α variants will provide new and important insights into HIF biology and may lead to the development of new therapeutic strategies.

Cognitive appraisal of aversive stimulus differs between individuals with contrasting stress coping styles; evidences from selected rainbow trout (Oncorhynchus mykiss) strains

In animals, personality variations in response to stress and energy demands have been established. Cognitive processing of negative stimuli correlates with stress response patterns. Still, the relative contribution of cognitive appraisal or physiological demands to the behavioural output needs to be clarified. In this study we utilized reactive (high-responsive, HR) and proactive (low-responsive, LR) rainbow trout strains to investigate how contrasting reactions to hypoxia are related to individual variation in metabolism and/or cognition. The HR-LR strains did not differ in standard metabolic rate or hypoxia tolerance. HR trout displayed more pronounced avoidance to a signal cue after being conditioned with hypoxia, suggesting that they experienced this stimulus more aversive than LR trout. Together with differences in forebrain c-fos activation patterns in dorsomedial pallium, these results suggest cognitive differences between the strains. These results demonstrate that differences in personality/stress coping style can be related to contrasts in cognition, which are independent of metabolic differences.

Cardiac responses to hypoxia and reoxygenation in Drosophila

An adequate supply of oxygen is important for the survival of all tissues, but it is especially critical for tissues with high-energy demands, such as the heart. Insufficient tissue oxygenation occurs under a variety of conditions, including high altitude, embryonic and fetal development, inflammation, and thrombotic diseases, often affecting multiple organ systems. Responses and adaptations of the heart to hypoxia are of particular relevance in human cardiovascular and pulmonary diseases, in which the effects of hypoxic exposure can range in severity from transient to long-lasting. This study uses the genetic model system Drosophila to investigate cardiac responses to acute (30 min), sustained (18 h), and chronic (3 wk) hypoxia with reoxygenation. Whereas hearts from wild-type flies recovered quickly after acute hypoxia, exposure to sustained or chronic hypoxia significantly compromised heart function upon reoxygenation. Hearts from flies with mutations in sima, the Drosophila homolog of the hypoxia-inducible factor alpha subunit (HIF-α), exhibited exaggerated reductions in cardiac output in response to hypoxia. Heart function in hypoxia-selected flies, selected over many generations for survival in a low-oxygen environment, revealed reduced cardiac output in terms of decreased heart rate and fractional shortening compared with their normoxia controls. Hypoxia-selected flies also had smaller hearts, myofibrillar disorganization, and increased extracellular collagen deposition, consistent with the observed reductions in contractility. This study indicates that longer-duration hypoxic insults exert deleterious effects on heart function that are mediated, in part, by sima and advances Drosophila models for the genetic analysis of cardiac-specific responses to hypoxia and reoxygenation.

Transcriptional events co-regulated by hypoxia and cold stresses in Zebrafish larvae

BACKGROUND

Hypoxia and temperature stress are two major adverse environmental conditions often encountered by fishes. The interaction between hypoxia and temperature stresses has been well documented and oxygen is considered to be the limiting factor for the thermal tolerance of fish. Although both high and low temperature stresses can impair the cardiovascular function and the cross-resistance between hypoxia and heat stress has been found, it is not clear whether hypoxia acclimation can protect fish from cold injury.

RESULTS

Pre-acclimation of 96-hpf zebrafish larvae to mild hypoxia (5% O2) significantly improved their resistance to lethal hypoxia (2.5% O2) and increased the survival rate of zebrafish larvae after lethal cold (10°C) exposure. However, pre-acclimation of 96-hpf larvae to cold (18°C) decreased their tolerance to lethal hypoxia although their ability to endure lethal cold increased. RNA-seq analysis identified 132 up-regulated and 41 down-regulated genes upon mild hypoxia exposure. Gene ontology enrichment analyses revealed that genes up-regulated by hypoxia are primarily involved in oxygen transport, oxidation-reduction process, hemoglobin biosynthetic process, erythrocyte development and cellular iron ion homeostasis. Hypoxia-inhibited genes are enriched in inorganic anion transport, sodium ion transport, very long-chain fatty acid biosynthetic process and cytidine deamination. A comparison with the dataset of cold-regulated gene expression identified 23 genes co-induced by hypoxia and cold and these genes are mainly associated with oxidation-reduction process, oxygen transport, hemopoiesis, hemoglobin biosynthetic process and cellular iron ion homeostasis. The alleviation of lipid peroxidation damage by both cold- and hypoxia-acclimation upon lethal cold stress suggests the association of these genes with cold resistance. Furthermore, the alternative promoter of hmbsb gene specifically activated by hypoxia and cold was identified and confirmed.

CONCLUSIONS

Acclimation responses to mild hypoxia and cold stress were found in zebrafish larvae and pre-acclimation to hypoxia significantly improved the tolerance of larvae to lethal cold stress. RNA-seq and bioinformatics analyses revealed the biological processes associated with hypoxia acclimation. Transcriptional events co-induced by hypoxia and cold may represent the molecular basis underlying the protection of hypoxia-acclimation against cold injury.

Oxygen- and temperature-dependent expression of survival protein kinases in crucian carp (Carassius carassius) heart and brain

Living without oxygen is limited to very few vertebrates, one species being the fresh water fish crucian carp (Carassius carassius), which can survive months of anoxia at low temperatures. Mammalian heart and brain are particularly intolerant to oxygen deprivation, yet these organs can be conditioned to display increased resistance, possibly due to activation of several protein kinases. We hypothesized increased phosphorylation status of these kinases in hypoxic and anoxic crucian carp heart and brain. Moreover, we wanted to investigate whether the kinases showing the strongest phosphorylation during hypoxia/anoxia, ERK 1/2, p38-MAPK, JNK, PKCε, and PKCδ, also had increased expression and phosphorylation at cold temperatures, to better cope with the anoxic periods during winter. We found small differences in the phosphorylation status of ERK 1/2, p38-MAPK, JNK, PKCε, and PKCδ during 10 days of severe hypoxia in both heart and brain (0.3 mg O₂/l) and varying responses to reoxygenation. In contrast, 7 days of anoxia (<0.01 mg O₂/l) markedly increased phosphorylation of ERK 1/2, p38-MAPK, JNK in the heart, and p38-MAPK and PKCε in the brain. Similarly, varying acclimation temperature between 4, 10 and 20°C induced large changes in phosphorylation status. Total protein expression in heart and brain neither changed during different oxygen regimes nor with different acclimation temperatures, except for ERK 1/2, which slightly decreased in the heart at 4°C compared with 20°C. A phylogenetic analysis confirmed that these protein kinases are evolutionarily conserved across a wide range of vertebrate species. Our findings indicate important roles of several protein kinases during oxygen deprivation.

Evolution of the oxygen sensitivity of cytochrome c oxidase subunit 4

Vertebrates possess two paralogs of cytochrome c oxidase (COX) subunit 4: a ubiquitous COX4-1 and a hypoxia-linked COX4-2. Mammalian COX4-2 is thought to have a role in relation to fine-tuning metabolism in low oxygen levels, conferred through both structural differences in the subunit protein structure and regulatory differences in the gene. We sought to elucidate the pervasiveness of this feature across vertebrates. The ratio of COX4-2/4-1 mRNA is generally low in mammals, but this ratio was higher in fish and reptiles, particularly turtles. The COX4-2 gene appeared unresponsive to low oxygen in nonmammalian models (zebrafish, goldfish, tilapia, anoles, and turtles) and fish cell lines. Reporter genes constructed from the amphibian and reptile homologues of the mammalian oxygen-responsive elements and hypoxia-responsive elements did not respond to low oxygen. Unlike the rodent ortholog, the promoter of goldfish COX4-2 did not respond to hypoxia or anoxia. The protein sequences of the COX4-2 peptide showed that the disulfide bridge seen in human and rodent orthologs would be precluded in other mammalian lineages and lower vertebrates, all of which lack the requisite pair of cysteines. The coordinating ligands of the ATP-binding site are largely conserved across mammals and reptiles, but in Xenopus and fish, sequence variations may disrupt the ability of the protein to bind ATP at this site. Collectively, these results suggest that many of the genetic and structural features of COX4-2 that impart responsiveness and benefits in hypoxia may be restricted to the Euarchontoglires lineage that includes primates, lagomorphs, and rodents.