Phylogeny and expression patterns of two apolipoprotein E genes in the flatfish Senegalese sole

Apolipoprotein Eb (On-ApoEb) protects Oreochromis niloticus against Streptococcus agalactiae infection

Apolipoprotein E (ApoE), a critical targeting protein, has been found to play an essential role in the protection against infection and inflammation. However, the immune functions of ApoE against bacterial infection in fish have not been investigated. In this study, a full-length cDNA for ApoE, named On-ApoEb was cloned from Oreochromis niloticus. The predicted cDNA sequence was 831bp in length and coded for a protein of 276 amino acid residues, which shared 63.87%-98.55% identity with ApoEb from other fishes, and about 22% identity with ApoEb from mammals. On-ApoEb from O. niloticus was highly expressed in the liver and could be activated in the tissues (liver, spleen, brain, and intestine) after infection with Streptococcus agalactiae. Moreover, the results revealed that On-ApoEb could decrease the expression levels of pro-inflammatory factors, immune-related pathways, and apoptosis, while increasing the expression levels of anti-inflammatory factors. Furthermore, On-ApoEb was noted to improve the survival rate and reduce the bacterial load in the liver and spleen. These results suggested that On-ApoEb was connected with immune response and had anti-inflammation and anti-apoptosis activities.

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.

Combined effects of arsenic and 2,2-dichloroacetamide on different cell populations of zebrafish liver

Arsenic (As) and disinfection by-products are important health risk factors in the water environment. However, their combined effects on different cell populations in the liver are not well known. Here, zebrafish were exposed to 100 μg/L As, 300 μg/L 2,2-dichloroacetamide (DCAcAm), and their combination for 23 days. Then transcriptome profiles of cell populations in zebrafish liver were analyzed by single-cell RNA sequencing (scRNA-seq). A total of 13,563 cells were obtained, which were identified as hepatocytes, hepatic duct cells, endothelial cells and macrophages. Hepatocytes were the main target cell subtype of As and DCAcAm exposures. DCAcAm exposure induced higher toxicity in male hepatocytes, which specifically changed amino acid metabolism, response to hormone and cofactor metabolism. However, As exposure caused higher toxicity in female hepatocytes, which altered lipid metabolism, carbon metabolism, and peroxisome. Combined exposure to As and DCAcAm decreased toxicities in hepatocytes compared to each one alone. Female hepatocytes had higher tolerance to co-exposure of As and DCAcAm than male hepatocytes. Further, combined exposure to As and DCAcAm induced functional changes in macrophages similar to As alone groups, which mainly altered the transfer of sterol and cholesterol. Hepatic duct cells and endothelial cells were not influenced by exposures to As and DCAcAm. This study for the first time highlights the cell-specific combined responses of As and DCAcAm in zebrafish liver, which provide useful information for their health risk assessment in a co-exposure environment.

A zebrafish pparγ gene deletion reveals a protein kinase network associated with defective lipid metabolism

Peroxisome proliferator-activated receptor γ (Pparγ) is a master regulator of adipogenesis. Chronic pathologies such as obesity, cardiovascular diseases, and diabetes involve the dysfunction of this transcription factor. Here, we generated a zebrafish mutant in pparγ (KO) with CRISPR/Cas9 technology and revealed its regulatory network. We uncovered the hepatic phenotypes of these male and female KO, and then the male wild-type zebrafish (WT) and KO were fed with a high-fat (HF) or standard diet (SD). We next conducted an integrated analyze of the proteomics and phosphoproteomics profiles. Compared with WT, the KO showed remarkable hyalinization and congestion lesions in the liver of males. Strikingly, pparγ deletion protected against the influence of high-fat diet feeding on lipid deposition in zebrafish. Some protein kinases critical for lipid metabolism, including serine/threonine-protein kinase TOR (mTOR), ribosomal protein S6 kinase (Rps6kb1b), and mitogen-activated protein kinase 14A (Mapk14a), were identified to be highly phosphorylated in KO based on differential proteome and phosphoproteome analysis. Our study supplies a pparγ deletion animal model and provides a comprehensive description of pparγ-induced expression level alterations of proteins and their phosphorylation, which are vital to understand the defective lipid metabolism risks posed to human health.

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae

Senegalese sole is an economically important flatfish species in aquaculture and an attractive model to decipher the molecular mechanisms governing the severe transformations occurring during metamorphosis, where retinoic acid seems to play a key role in tissue remodeling. In this study, a robust sole transcriptome was envisaged by reducing the number of assembled libraries (27 out of 111 available), fine-tuning a new automated and reproducible set of workflows for de novo assembling based on several assemblers, and removing low confidence transcripts after mapping onto a sole female genome draft. From a total of 96 resulting assemblies, two "raw" transcriptomes, one containing only Illumina reads and another with Illumina and GS-FLX reads, were selected to provide SOLSEv5.0, the most informative transcriptome with low redundancy and devoid of most single-exon transcripts. It included both Illumina and GS-FLX reads and consisted of 51,348 transcripts of which 22,684 code for 17,429 different proteins described in databases, where 9527 were predicted as complete proteins. SOLSEv5.0 was used as reference for the study of retinoic acid (RA) signalling in sole larvae using drug treatments (DEAB, a RA synthesis blocker, and TTNPB, a RA-receptor agonist) for 24 and 48 h. Differential expression and functional interpretation were facilitated by an updated version of DEGenes Hunter. Acute exposure of both drugs triggered an intense, specific and transient response at 24 h but with hardly observable differences after 48 h at least in the DEAB treatments. Activation of RA signalling by TTNPB specifically increased the expression of genes in pathways related to RA degradation, retinol storage, carotenoid metabolism, homeostatic response and visual cycle, and also modified the expression of transcripts related to morphogenesis and collagen fibril organisation. In contrast, DEAB mainly decreased genes related to retinal production, impairing phototransduction signalling in the retina. A total of 755 transcripts mainly related to lipid metabolism, lipid transport and lipid homeostasis were altered in response to both treatments, indicating non-specific drug responses associated with intestinal absorption. These results indicate that a new assembling and transcript sieving were both necessary to provide a reliable transcriptome to identify the many aspects of RA action during sole development that are of relevance for sole aquaculture.

Assessment of Growth, Lipid Metabolism and Gene Expression Responses in Senegalese Sole Larvae Fed With Low Dietary Phospholipid Levels

Phospholipids (PL) are essential molecules for larval growth and development. In this study, growth, lipid metabolism and gene expression responses associated with different dietary PL levels in pelagic sole larvae were evaluated. In a first trial, the long-term effects on growth and survival of two experimental microdiets (MD) containing high (High-PL) or low (Low-PL) PL levels were tested and compared to a diet based on live prey (rotifers). The MD were supplied from 3 to 10 days post-hatch (dph) and Artemia from day 8 to 29 dph. High-PL fed larvae had higher dry mass (1.2-fold) than Low-PL fed larvae at 8 dph and both MD were smaller (2.9-fold) than larvae fed live preys. However, a compensatory growth (33% between 8 and 20 dph) occurred when MD were substituted by Artemia and by the end of the trial no significant differences in mass or survival occurred between the dietary treatments. In a second trial, growth, lipid metabolism and gene expression profiles of larvae fed with MD up to 8 dph were analyzed. Growth data confirmed that mass of larvae fed with High-PL was higher (1.3-fold) than the those fed Low-PL and they had lower levels of triacylglycerol (2.8-fold), cholesterol (1.2-fold) and cetoleic acid (1.7-fold). Histological analysis indicated an excess of lipid vacuoles in larvae fed with Low-PL and the expression analysis revealed a coordinated response to enhance lipid mobilization since the expression of genes involved in PL intermediate synthesis, PL remodeling as well as eight apolipoprotein was up-regulated. The down-regulation of apolipoprotein apob2 in larvae fed with Low-PL indicated a specific regulation by PL levels. The present work provides insight into the responses associated with dietary PL in early fish larvae, which will be of use for future studies aimed as designing effective larval sole diets.

Apolipoprotein E in lipoprotein metabolism, health and cardiovascular disease

Apolipoprotein E (apoE), a 34 kDa circulating glycoprotein of 299 amino acids, predominantly synthesised in the liver, associates with triglyceride-rich lipoproteins to mediate the clearance of their remnants after enzymatic lipolysis in the circulation. Its synthesis in macrophages initiates the formation of high density-like lipoproteins to effect reverse cholesterol transport to the liver. In the nervous system apoE forms similar lipoproteins which perform the function of distributing lipids amongst cells. ApoE accounts for much of the variation in plasma lipoproteins by three common variants (isoforms) that influence low-density lipoprotein concentration and the risk of atherosclerosis. ApoE2 generally is most favourable and apoE4 least favourable for cardiovascular and neurological health. The apoE variants relate to different amino acids at positions 112 and 158: cysteine in both for apoE2, arginine at both sites for apoE4, and respectively cysteine and arginine for apoE3 that is viewed as the wild type. Paradoxically, under metabolic stress, homozygosity for apoE2 may result in dysbetalipoproteinaemia in adults owing to impaired binding of remnant lipoproteins to the LDL receptor and related proteins as well as heparan sulphate proteoglycans. This highly atherogenic condition is also seen with other mutations in apoE, but with autosomal dominant inheritance. Mutations in apoE may also cause lipoprotein glomerulopathy. In the central nervous system apoE binds amyloid β-protein and tau protein and fragments may incur cellular damage. ApoE4 is a strong risk factor for the development of Alzheimer's disease. ApoE has several other physiological effects that may influence health and disease, including supply of docosahexaenoic acid for the brain and modulating immune and inflammatory responses. Genotyping of apoE may have application in disorders of lipoprotein metabolism as well as glomerulopathy and may be relevant to personalised medicine in understanding cardiovascular risk, and the outcome of nutritional and therapeutic interventions. Quantitation of apoE will probably not be clinically useful. ApoE is also of interest as it may generate peptides with biological function and could be employed in nanoparticles that may allow crossing of the blood-brain barrier. Therapeutic options may emerge from these newer insights.