Transcriptome analysis of liver provides insight into metabolic and translation changes under hypoxia and reoxygenation stress in silver sillago (Sillago sihama)

Transcriptional and physiological profiles reveal the respiratory, antioxidant and metabolic adaption to intermittent hypoxia in the clam Tegillarca granosa

Tegillarca granosa can survive intermittent hypoxia for a long-term. We used the clam T. granosa as model to investigate the respiratory, antioxidant and metabolic responses to consecutive hypoxia-reoxygenation (H/R) stress at both physiological and transcriptional levels. The results showed that the clams were able to rapidly regulate oxygen consumption and ammonia excretion during H/R stress, and alleviate oxidative stress during the second-time challenge. The clams also efficiently balanced energy metabolism through the rapid conversion and decomposition of glycogen. According to the transcriptome profile, KEGG pathways of starch and sucrose metabolism, ECM-receptor interaction, and protein processing in endoplasmic reticulum were significantly enriched in H group (the second-time 24 h hypoxia exposure), while pathways associated with lipid metabolism were significantly enriched in h group (the first-time 24 h hypoxia exposure). DEGs including hspa5, birc2/3, and map3k5 might play important roles in alleviating endoplasmic reticulum stress, cpla2 and pla2g16 might mitigate oxidative stress by adjusting the composition of cellular membrane. In conclusions, our findings suggest that rapid adjustment of oxygen consumption, ammonia metabolism, glycogen metabolism, and the ability to adjust the composition of the membrane lipid may be critical for T. granosa in maintaining energy homeostasis and reducing oxidative damage during intermittent H/R exposure. This study preliminarily clarified the response of T. granosa to intermittent hypoxia stress on the physiological and molecular levels, offering insights into the hypoxia-tolerant mechanisms in this species and providing a reference for the following study on the other hypoxic-tolerant species.

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.

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.

The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia

Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Here we report the lifespan effects of chronic, mild, intermittent hypoxia, and short-term survival in acute severe hypoxia in four clones of Daphnia magna originating from either permanent or intermittent habitats. We test the hypothesis that acclimation to chronic mild intermittent hypoxia can extend lifespan through activation of antioxidant and stress-tolerance pathways and increase survival in acute severe hypoxia through activation of oxygen transport and storage proteins and adjustment to carbohydrate metabolism. Unexpectedly, we show that chronic hypoxia extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to acute hypoxia. Exposure to chronic hypoxia did not protect against acute hypoxia; to the contrary, Daphnia from the chronic hypoxia treatment had lower acute hypoxia tolerance than normoxic controls. Few transcripts changed their abundance in response to the chronic hypoxia treatment in any of the clones. After 12 h of acute hypoxia treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in oxygen transport, mitochondrial and respiratory metabolism, and gluconeogenesis, showing upregulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to acute hypoxia than those from permanent habitats, contrary to predictions, there were no significant hypoxia-by-habitat of origin or chronic-by-acute treatment interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through upregulation of cuticular proteins and neurotrophins, respectively.

Physiological Effects and Transcriptomic Analysis of sbGnRH on the Liver in Pompano (Trachinotus ovatus)

Pompano (Trachinotus ovatus) is one of the important economic marine fishes in the south coast of China. At present, the research on the basic biology of pompano is relatively weak, which has seriously affected the development of this economic important fish. The liver is an important digestive and metabolic organ of fish which plays an important regulatory role in its growth and development. It is necessary to clarify the effects of sea bream gonadotropin releasing hormone (sbGnRH) on liver physiology and metabolic enzyme activity. The effects of sbGnRH peptides (10 ng/gbw) on the physiological and biochemical indices and metabolic enzyme activities of pompano liver were studied. It was found that after injection of 10 ng/gbw sbGnRH peptides, the contents of albumin, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, glucose, creatine kinase, iron, magnesium, aspartate aminotransferase, alanine aminotransferase and creatinine increased, while of cholesterol and calcium contents decreased. The activities of amylase, lipase, pyruvate kinase, acyl CoA oxidase, superoxide dismutase, phospholipid hydroperoxide glutathione peroxidase, catalase, glucose-6-phosphate dehydrogenase, fatty acid synthase and lipoprotein lipase increased, while the activities of malic enzyme, carnitine acyl, carnitine translocation, acetyl CoA carboxylase and malondialdehyde decreased. Three hours after the injection of different concentrations of sbGnRH peptides (0 and 10 ng/gbw), the transcriptome sequences of the two groups of livers were sequenced. After quality control and removal of some low-quality data, clean reads of 21,283,647、19,427,359、21,873,990、21,732,174、23,660,062 and 21,592,338 were obtained respectively. In this study, 99 genes were screened and identified as differentially expressed genes, including 77 up-regulated genes and 22 down-regulated genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses, these pathways and the typical genes involved can be divided into cellular processes, environmental information processing, genetic information processing, diseases, metabolism and organismal systems. The results from this study provide a the oretical basis for studying the effects of sbGnRH on the physiology, biochemistry and metabolic enzyme activities of liver in pompano.

Transcriptomic analysis of pituitary in female and male spotted scat (Scatophagus argus) after 17β-estradiol injection

Spotted scat (Scatophagus argus) is a popular species of marine fish cultured in China. It shows normal sexual growth dimorphism. Female spotted scat grows quicker and bigger than males. Growth and reproduction are the most important traits in aquaculture. In vertebrates, the pituitary gland occupies an important position in the growth and reproduction axis. Estrogen is involved in regulating growth and reproduction in the pituitary gland in an endocrine fashion. Transcriptome sequencing of the pituitary was performed in female and male fish at 6 h after 17β-estradiol injection (4.0 μg E₂/g body weight, BW). Compared with the pituitary of female and male groups, 144 and 64 genes [|log₂^{(fold change)}| ≥ 1.0 and false discovery rate (FDR) < 0.05] were significantly differentially expressed in E₂-injected females and males, respectively (p < 0.05). Of these, 59 and 48 were up-regulated, and 85 and 16 were down-regulated. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses, DEGs were involved in signal pathways, such as growth, reproduction, oocyte meiosis and steroid biosynthesis. Of these, estrogen affected the expression of some sex steroid synthesis and receptor genes in the pituitary gland through feedback, such as hsd17b7, pgr and cyp19a1b, regulating the reproductive activities. Besides, some growth-related genes, such as gap43, junbb, mstn2 and insm1a responded to estrogen. E₂ might affect the expression level of gh mRNA by regulating the expression levels of growth-related genes. Our results provide a theoretical basis for studying the molecular mechanism of growth and reproduction regulation at the pituitary level of spotted scat responded to E₂.

Genome-wide identification and expression profiling of glutathione S-transferase family under hypoxia stress in silver sillago (Sillago sihama)

Glutathione S-transferase (GST) is an important detoxification enzyme in organisms. GSTs play an important role in responding to environmental stresses. This study aimed to identify the GST gene superfamily in silver sillago (Sillago sihama) and analyze its expression pattern under hypoxia stress. A total of 17 GST genes were identified in silver sillago. Phylogenetic analysis showed that the GST gene family contained two subgroups (cytosolic and MAPEGs), and lacked three subgroups (i.e. Pi, Kappa, and MGST2). Phylogenetic and syntenic analysis revealed that GST genes were conserved in evolution. Eight SsGSTs were significantly differentially expressed under hypoxia stress in silver sillago by RNA-seq and qRT-PCR analysis. The expression levels of SsMGST3b, SsGSTO1, SsGSTT1b and SsGSTR2 genes were significantly up-regulated after 4 h of reoxygenation in the gill tissue. In the heart tissue, the expression of SsGSTR3 was significantly up-regulated after 1 h of hypoxia while the expression levels of SsGSTT1b and SsFLAP genes were significantly down-regulated after 4 h of hypoxia. In summary, this study provides for the first time a comprehensive analysis of the GST gene superfamily of silver sillago.