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

Tian, Changxu; Lin, Xinghua; Saetan, Wanida; Huang, Yang; Shi, Hongjuan; Jiang, Dongneng; Chen, Huapu; Deng, Si‐Ping; Wu, Tian-li; Zhang, Yulei; Li, Guangli; Zhu, Chunhua

doi:10.1016/j.cbd.2020.100715

Cited by 15 publications

(5 citation statements)

References 44 publications

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“…Even less is known about transcriptional responses to hypoxia in aquatic organisms. Data of this type have just started to accumulate, through both transcriptome‐wide studies (Feng et al, 2021; Flight et al, 2011; Hu et al, 2021; Jie et al, 2021; Kim et al, 2021; Mu et al, 2020; Tian et al, 2020; Xu, Fu, et al, 2021; Xu, Miao, et al, 2021; Zhou et al, 2020) and targeted qPCR‐based studies focused on anaerobic metabolism‐related genes (Aksakal & Ekinci, 2021; Amorim et al, 2021; Cota‐Ruiz et al, 2015; Reyes‐Ramos et al, 2018). These studies reveal that signals of some of the hypoxia‐inducible pathways described above are detectable in fish and invertebrates and that several downstream pathways showing response include anaerobic glycolysis, gluconeogenesis, and immune responses.…”

Section: Introductionmentioning

confidence: 99%

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

Ekwudo

Malek

Anderson

et al. 2022

Ecology and Evolution

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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.

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Section: Introductionmentioning

confidence: 99%

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

Ekwudo

Malek

Anderson

et al. 2022

Ecology and Evolution

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“…This study verified the expression patterns of the OR gene family in S. sihama under hypoxic stress in the gill, heart and liver tissues. The hypoxia transcription sequencing databases (RNA-seq) of S. sihama were obtained from Saetan et al [ 38 , 39 ] and Tian et al [ 40 ]. Gene expression level under hypoxic stress was calculated by the FPKM (fragments per kilobase of transcript per million fragments mapped) method.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama)

Lin

Zhang

et al. 2023

Animals

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Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts.

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“…Genes involved in fatty acid synthesis were also found to be downregulated during hypoxic exposure, and the upregulation of apoptosis-related genes was detected [21]. In contrast, a study by Tian et al (2020) pointed out the important role of inhibition of translation and protein synthesis processes in fish adaptation to hypoxic environments [22]. Studies have also reported the effects of acute hypoxia on muscle function and immune-related enzyme activities in Siberian sturgeon (Acipenser baerii), as well as the regulation of antioxidant capacity and anaerobic metabolism in response to hypoxic stress [23].…”

Section: Introductionmentioning

confidence: 94%

Liver Transcriptome Shows Differences between Acute Hypoxia-Tolerant and Intolerant Individuals of Greater Amberjack (Seriola dumerili)

Li,

Yang,

Wang

et al. 2023

Animals

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Acute hypoxia is a common abiotic stress in commercial aquaculture and has significant effects on fish physiology and metabolism. Due to its large size and rapid growth, the greater amberjack (Seriola dumerili) is an economically important fish with high farming value. This species is intolerant to hypoxia, which makes it susceptible to mass mortality and hinders the progress of amberjack cultivation. Based on a comparative analysis of the liver transcriptome between acute hypoxia-tolerant (HT) and -intolerant (HS) groups, this study first explored the molecular mechanisms of acute hypoxia in greater amberjack. By simulating the acute hypoxic environment and using RNA sequencing (RNA-Seq), the differences in liver transcriptional changes between the acute hypoxia-tolerant (HT) and hypoxia-intolerant (HS) groups of greater amberjack were probed. Based on differential expression analysis, 829 differentially expressed genes (DEGs) were screened in both groups. Relative to the HS group, 374 DEGs were upregulated and 455 were downregulated in the HT group. Compared with the HS group, genes such as slc2a5 and prkaa2 related to promoting sugar transport and inhibiting lipid syntheses were upregulated, while genes that inhibit gluconeogenesis and promote lipid syntheses, such as pgp and aacs, were downregulated. The expression of odc1 was significantly and relatively downregulated in the HT group, which would lead to the inhibition of intracellular antioxidant activity and decreased scavenging of ROS. The NF-kB pathway was also promoted to some extent in individuals in the HT group relative to the HS group to resist apoptosis. In addition, the relative downregulation of apoptosis and autophagy-related genes, such as endog, hm13, and casp6, was also detected in the HT group. The present findings first reported the regulation mechanism by which liver tissue coped with the acute hypoxia stress in greater amberjack, which will provide important technical support for preventing acute hypoxia-induced death in advance and reducing economic losses.

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

Cited by 15 publications

References 44 publications

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

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

Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama)

Liver Transcriptome Shows Differences between Acute Hypoxia-Tolerant and Intolerant Individuals of Greater Amberjack (Seriola dumerili)

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