Cloning and expression analysis of a HSP70 gene from Korean rockfish (Sebastes schlegeli)

Integrated metabolomic and transcriptomic responses to heat stress in a high-altitude fish, Triplophysa siluroides

Species in Triplophysa display strong adaptability to the extreme environment of the plateau, thus offering an ideal model to study the molecular mechanism of fish adaptation to environmental stress. In the present study, we conducted integrated analysis of the transcriptome and metabolism of liver tissue in Triplophysa siluroides under heat stress (28 °C) and control (10 °C) conditions to identify heat stress-induced genes, metabolites and pathways. RNA-Seq identified 2373 differentially expressed genes, which consisted of 1360 upregulated genes and 1013 downregulated genes, in the heat stress group vs. the control group. Genes in the heat shock protein (Hsp) family, including Hsp40, Hsp70, Hsp90 and other Hsps, were strongly upregulated by heat stress. Pathway enrichment analysis revealed that the PI3K/AKT/mTOR and protein processing in the endoplasmic reticulum (ER) pathways were significantly affected by heat stress. Metabolism sequencing identified a total of 155 differentially abundant metabolites, including 118 significantly upregulated metabolites and 37 downregulated metabolites. Combined analysis of the transcriptome and metabolism results showed that ubiquitin-dependent proteolysis and purine metabolism pathways were enhanced in response to acute heat stress to protect cells from damage under stress conditions. The results of this study may contribute to our understanding of the underlying molecular mechanism of the heat stress response in cold-water fish.

Molecular mechanisms of physiological change under acute total dissolved gas supersaturation stress in yellow catfish (Pelteobagrus fulvidraco)

During the dam discharging period, the strong aeration of high-speed water leads to the supersaturation of total dissolved gas (TDG) in the downstream water, which causes gas bubble disease (GBD) in fish and threatens their survival. TDG supersaturation has now become an ecological and environmental issue of global concern; however, the molecular mechanism underlying the physiological effect of TDG supersaturation on fish is poorly known. Here, we comprehensively investigated the effect of TDG supersaturation on Pelteobagrus fulvidraco at the histopathological, biochemical, transcriptomic, and metabolomic levels. After exposure to 116% TDG, P. fulvidraco exhibited classic GBD symptoms and pathological changes in gills. The level of superoxide dismutase was highly significantly decreased. Transcriptomic results revealed that heat shock proteins (HSPs) and a large number of genes involved in immunity were increased by TDG stress. A key environmental sensor PI3K/Akt/mTOR pathway was significantly stimulated for defence against stress. Integrated transcriptomic and metabolomic analyses revealed that key metabolites and genes were upregulated in the triacylglycerol synthesis pathway and that amino acid levels decreased, which might be associated with TDG supersaturation stress. The present study demonstrated that TDG supersaturation could cause severe physiological damage in fish. HSP genes, immune functions, and energy metabolic pathways were enhanced to counteract the adverse effects.

Identification of mRNA-miRNA-lncRNA regulatory network associated with the immune response to Aeromonas salmonicides infection in the black rockfish (Sebastes schlegelii)

In aquaculture, Aeromonas salmonicides (A. salmonicida) is a main fish pathogen because of its nearly worldwide distribution, and broad host range. Recently, an increasing number of evidences have uncovered the roles of mRNA-miRNA-lncRNA network in fish diseases. In current study, RNA-seq was conducted in the black rockfish spleen following A. salmonicida infection at 0 h (Sp0 or control) and three different post-infection time-points (2 h: Sp2, 12 h: Sp12 and 24 h: Sp24, respectively) to comprehensively identify differentially expressed (DE) mRNAs, miRNAs and lncRNAs. Enrichment analysis and protein-protein interaction (PPI) analysis of DE mRNAs were performed. Then, expression and correlation analysis for mRNAs and their upstream miRNAs and lncRNAs were conducted. Finally, a total of 1364 mRNAs, 17 miRNAs and 1584 lncRNAs exhibited significantly differential expressions during bacterial infection in the black rockfish spleen. Functional enrichment analysis suggested that they were significantly enriched in several immune-related pathways, including Amino sugar and nucleotide sugar metabolism, Cell adhesion molecules (CAMs), Neuroactive ligand-receptor interaction, Nicotinate and nicotinamide metabolism, Pentose and glucuronate interconversions, Phagosome, Proteasome, etc. Subsequently, 1091 lncRNA-miRNA-mRNA pathways (323 in Sp2, 609 in Sp12 and 207 in Sp24) were constructed including 400 lncRNAs, 69 miRNAs, and 70 mRNAs. Meanwhile, NLRC3/novel-264/LNC_00116154 pathway demonstrated important immune modulating function in the black rockfish against A. salmonicida infection. Finally, the novel mRNA-miRNA-lncRNA sub-networks were established, among which all mRNAs and ncRNAs possessed significant predictive values for further studies for immune responses in the black rockfish.

Expression analysis of the heat shock protein genes and cellular reaction in dojo loach (Misgurnus anguillicaudatus) under the different pathogenic invasion

As molecular chaperones, heat shock proteins (HSPs) play essential roles in cells in response to stress conditions. Recent studies about immune functions of HSPs in fish have also been reported. In this study, based on the reported cDNA sequences of the four HSP genes, HSP70, HSC70, HSP90α and HSP90β, the temporal expression patterns of the four genes during embryonic development of dojo loach(Misgurnus anguillicaudatus) was assayed with qRT-PCR. All of the four genes were ubiquitously expressed in all detected embryonic developmental stages. Among of them, HSP70, HSC70 and HSP90β were highly expressed in the organ formation stage, while HSP90α was the highest expressed in myotome formation stage. Further, the immune responses of the four HSP genes were assayed when loach were infected with three different pathogens, bacterium (Flavobacterium cloumnare G4), parasite (Ichthyophthirius multifiliis) and fungus (Saprolegnia). All of the four genes were differentially expressed in four tissues such as skin, gills, spleen and kidney in response to the pathogenic invasion, but both HSP70 and HSP90α expressions were dramatically up-regulated. Further, the cellular responses of the loach skinand gill tissues were observed, in which the number of the skin goblet cells were significantly increased, and the gill lamellae became shorter and wider after infected. Thus, our work indicated that the HSPs may directly or indirectly involved in immune defense in fish, at least in the loach.

Physicochemical changes in liver and Hsc70 expression in pikeperch Sander lucioperca under heat stress

The pikeperch Sander lucioperca is an economically important freshwater species that is currently threatened by higher summer temperatures caused by global warming. To clarify the physiological state of pikeperch reared under relatively high temperatures and to acquire valuable biomarkers to monitor heat stress in this species, 100 fish were subjected to five different temperature treatments, ranging from 23 °C (control) to 36 °C. The physiological and biochemical indexes of liver and blood were determined, and heat-shock cognate 70 kDa protein (Hsc70) mRNA expression profiles were analyzed. The results showed that the activities of superoxide dismutase, catalase, and glutathione peroxidase in heat-stressed pikeperch first increased and then decreased, exhibiting peaks at 34 °C, 28 °C, and 28 °C, respectively. The level of thiobarbituric acid-reactive substances (TBARS) in all experimental groups was significantly higher than that of the control. The numbers of red blood cells, the packed-cell volume, and the contents of hemoglobin were significantly higher in the 34 °C and 36 °C treatment groups. Under heat stress, the albumin, cholesterol, and triglycerides contents decreased with increasing temperatures. Real-time fluorescence-based quantitative RT-PCR showed that Hsc70 mRNA levels increased in all eight of the tested tissues under heat stress. Expression reached maximum levels at 34 °C in the muscle, heart and gill tissues, and at 36 °C in the other five tissues. These results demonstrate that several physiological and biochemical phenotypes, such as oxidative stress, antioxidant enzymes and molecular chaperones, could be important biomarkers of heat stress in pikeperch, and are potentially valuable to uncover the mechanisms of heat-stress responses in fish.

Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis

Background

The factors determining sex in teleosts are diverse. Great efforts have been made to characterize the underlying genetic network in various species. However, only seven master sex-determining genes have been identified in teleosts. While the function of a few genes involved in sex determination and differentiation has been studied, we are far from fully understanding how genes interact to coordinate in this process.

Results

To enable systematic insights into fish sexual differentiation, we generated a dynamic co-expression network from tilapia gonadal transcriptomes at 5, 20, 30, 40, 90, and 180 dah (days after hatching), plus 45 and 90 dat (days after treatment) and linked gene expression profiles to both development and sexual differentiation. Transcriptomic profiles of female and male gonads at 5 and 20 dah exhibited high similarities except for a small number of genes that were involved in sex determination, while drastic changes were observed from 90 to 180 dah, with a group of differently expressed genes which were involved in gonadal differentiation and gametogenesis. Weighted gene correlation network analysis identified changes in the expression of Borealin, Gtsf1, tesk1, Zar1, Cdn15, and Rpl that were correlated with the expression of genes previously known to be involved in sex differentiation, such as Foxl2, Cyp19a1a, Gsdf, Dmrt1, and Amh.

Conclusions

Global gonadal gene expression kinetics during sex determination and differentiation have been extensively profiled in tilapia. These findings provide insights into the genetic framework underlying sex determination and sexual differentiation, and expand our current understanding of developmental pathways during teleost sex determination.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4756-0) contains supplementary material, which is available to authorized users.

Impact of hypoxia stress on the physiological responses of sea cucumber Apostichopus japonicus: respiration, digestion, immunity and oxidative damage

Hypoxia is one of the most frequently occurring stressors confronted by industrial cultures of sea cucumber and can cause large economic losses and resource degradation. However, its responsive mechanisms are still lacking. In this paper, the physiological responses of Apostichopus japonicus to oxygen deficiency was illustrated, including induced oxidative response and immune defense and changed digestive enzymes activities. Significantly increased activities of alpha-amylase (AMS), acid phosphatase (ACP), lactate dehydrogenase, catalase, peroxidase, succinate dehydrogenase and higher content of malondialdehyde, and decreased activities of lipase and trypsin (TRY) were observed after hypoxia exposure (dissolved oxygen [DO] 2 mg/L). Expressions of key genes showed that AMS, peptidase, ACP, alkaline phosphatase, lysozyme, heat shock protein 70 and glutathione peroxidase were increased and TRY was decreased under hypoxia. With the decline of the DO level, the decreased tendency of oxygen consumption rates was different in varied weight groups. Moreover, respiratory trees were observed degraded under long-term hypoxia stress, thus leading a negative effect of respiration. These results could help to develop a better understanding of the responsive mechanism of sea cucumber under hypoxia stress and provide a theoretical basis for the prevention of hypoxia risk.

Antimicrobial peptides within the Yellowtail Kingfish (Seriola lalandi)

A number of Seriola species are currently farmed or being investigated as future aquaculture species in countries around the world. However they face a number of issues and limitations which will need to be overcome to ensure future stability and growth, one of which are disease outbreaks. Despite this, very little has been done to understand the immune system of Seriola species and very few immune genes have been characterised. Antimicrobial peptides (AMP) are naturally occurring low molecular weight polypeptides that play a major role in an organism's immune system and act effectively as a first line of defence. This investigation isolates the full length cDNA sequences of two AMP's, piscidin and hepcidin from the yellowtail kingfish (Seriola lalandi). The full-length cDNA of the piscidin gene encodes a 65 amino acid prepropeptide, containing a 25-residue peptide, predicted to form an amphipathic helix-loop-helix structure. Phylogenetic analysis using fish piscidin sequences, showed that this AMP is only found in bony fish within the Acanthomorpha clade and that a possible three groups within the piscidin family exists, with S. lalandi belonging to a particular group. The full-length cDNA of the hepcidin gene encodes a 90 amino acid preprohepcidin, which contains a typical RX(R/K)R motif for cleavage of the mature peptide which comprises of eight conserved cysteine residues. Phylogenetic analysis of known vertebrate hepcidin antimicrobial peptide (HAMP) sequences, shows sequences from the Neoteleostei clade of bony fish form two very separate groups, HAMP1 and HAMP2, with the S. lalandi hepcidin gene grouped with the HAMP1 sequences. HAMP2 sequences are found to have multiple copies within fish and genome analysis showed very clearly that these two groups of genes are located on separate regions on the genome, with the multiple HAMP2 copies formed from tandem gene duplications. Lastly, using qPCR the expression of the S. lalandi piscidin gene within healthy fish was highest within, spleen and gills and lowest in liver, whereas hepcidin was highest in the liver with little or no expression in the spleen and gills.

Differential expression of survival proteins during decreased intracellular oxygen tension in brain endothelial cells of grey mullets

The brain requires constant oxygen supply to perform its biological functions essential for survival. Because of low oxygen capacity and poor oxygen diffusibility of water, many fish species have evolved various adaptive mechanisms to cope with depleted oxygen. Endothelial cells (EC) are the primary components responsible for controlled environment of brain. Brain homeostasis largely depends on integrity of the EC. To elucidate their adaptive strategy, EC were isolated from the fish brain of Kovalam-control site and Ennore estuary-test/field hypoxic site and were subjected to low oxygen tension in laboratory. Cell viability, 4-hydroxynonenal (4HNE) and total antioxidant capacity (TAC) were analyzed to ascertain stress. Hypoxic insult, cytoprotective role of HSPs and apoptotic effect were analyzed by assessing hypoxia-inducible-factor-α (HIF1α), heat-shock-protein-70 (HSP70), heme-oxygenase 1 (HO-1), and apoptosis signal regulating kinase-1 (ASK1). This study evidenced that HSP70 and HO-1 are the key stress proteins, confer high tolerance to decreased oxygen tension mediated stress.

Physiological responses and changes in gene expression in the large yellow croaker Larimichthys crocea following exposure to hypoxia

Organisms at all levels of evolutionary complexity react to hypoxic stress. To clarify the effects of acute hypoxia on physiological and biochemical responses of Larimichthys crocea, we measured the activity levels of the antioxidant enzymes superoxide dismutase and catalase, hemoglobin concentration, functional indices of the liver (aspartate transaminase, alanine transaminase), heart (phosphocreatine kinase), and immune system (alkaline phosphatase), as well as mRNA expression levels of the immunity-related genes Hsp70 and HIF-1α at different time points of hypoxic. In addition, liver, gill, and kidney samples were histologically analyzed. We found that hemoglobin concentration and all enzyme activities increased during hypoxia, although these effects were transient and most indices returned to basal levels thereafter. The extent of the increase in the parameter values was inversely proportional to the dissolved oxygen content. Hsp70 and HIF-1α mRNA expression levels increased significantly in the blood, liver, gills, and kidneys following exposure to hypoxia, which may play an important role in protecting fish against oxidative damage. However, we found histological evidence of hypoxia-induced injuries to the gills, liver, and kidneys, which are involved in breathing, detoxification, and osmotic balance maintenance, respectively. Thus, despite the upregulation of defensive mechanisms, acute hypoxia still caused irreversible damage of organs. In conclusion, we observed that, in response to acute hypoxic stress, L. crocea enhances immune defensive function and antioxidant capacity. A better understanding of the regulation of the molecular anti-hypoxia mechanisms can help speeding up the selective breeding of hypoxia-tolerant L. crocea.

Molecular cloning and expression analysis of five heat shock protein 70 (HSP70) family members in Lateolabrax maculatus with Vibrio harveyi infection

Heat shock proteins 70 (HSP70s) are molecular chaperones that aid in protection against environmental stress. In this study, we cloned and characterized five members of the HSP70 family (designated as HSPa1a, HSC70-1, HSC70-2, HSPa4 and HSPa14) from Lateolabrax maculatus using rapid amplification cDNA ends (RACE). Multiple sequence alignment and structural analysis revealed that all members of the HSP70 family had a conserved domain architecture, with some distinguishing features unique to each HSP70. Quantitative real-time (qPCR) analysis revealed that all members of the HSP70 family were ubiquitously and differentially expressed in all major types of tissues, including testicular tissue. This indicated that HSP70s have vital and conserved biological functions, and may also function in the development of germinal cells. The expression of mRNA of the five HSP70 family members mRNA expression was significantly increased in the head kidney, intestine and gill after Vibrio harveyi challenge, suggesting that HSP70s play an important role in the immune response.

Effect of desiccation on oxidative stress and antioxidant response of the black tiger shrimp Penaeus monodon

In the present study, the oxidative stress and antioxidant response in hepatopancreas of the black tiger shrimp Penaeus monodon under desiccation stress were studied, such as activities of antioxidant enzymes (SOD, CAT, GPx and POD), oxidative damage to lipid and protein which indexed by contents of LPO, MDA, protein carbonyl (PC) and ROS production, and the expression of HSP70 and ferritin gene. The duration of desiccation significantly influenced the shrimp survival, and the mortality rates were 10% and 55.0% after desiccation 0.5 h and 3 h, respectively. Compared with the control group, after exposed to desiccation stress, the content of LPO, MDA, PC and ROS production in hepatopancreas increased significantly. SOD, CAT and POD activity in hepatopancreas increased significantly at 0.5 h, but decreased markedly at 1 h. GPx activity in hepatopancreas increased significantly at 0.5 h and 1 h, then decreased significantly at 3 h. The transcript levels of HSP70 and ferritin gene in hepatopancreas increased significantly at 1 h. HE staining showed that desiccation induced damage symptoms in hepatopancreas of P. monodon. These results revealed that desiccation could induce oxidative stress and antioxidant response via confusion of antioxidant enzymes activity and gene transcript level in hepatopancreas of P. monodon, and the time of shrimp under desiccation should lower than 0.5 h.

Cloning HSP70 and HSP90 genes of kaluga (Huso dauricus) and the effects of temperature and salinity stress on their gene expression

The genes encoding HSP70 and HSP90 proteins were isolated from kaluga by homologous cloning and rapid amplification of complementary DNA (cDNA) ends (RACE). HSP70 (GenBank accession no. KP050541) and HSP90 (GenBank accession no. KP050542) cDNAs were composed of 2275 and 2718 bp and encoded polypeptides of 650 and 725 amino acids, respectively. Basic Local Alignment Search Tool (BLAST) analysis showed that HSP70 and HSP90 of kaluga shared high identities with those of Acipenser ruthenus, Acipenser schrenckii, and Acipenser baerii (98-99 %). Fluorescent real-time RT-PCR under unstressed conditions revealed that HSP70 and HSP90 were expressed in 11 different tissues of kaluga. Messenger RNA (mRNA) expressions of both HSP70 and HSP90 were highest in the intestine and lowest in the muscle. In addition, the patterns of mRNA expression of HSP70 and HSP90 were similar, although the level of expression was more in HSP90 than in HSP70 (P < 0.05).We also analyzed patterns of HSP70 and HSP90 expression in the muscle, gill, and liver of kaluga under different combinations of temperature and salinity stress, including temperatures of 4,10, 25, and 28 °C at 0 ppt salinity, and salinities of 10, 20, 30, and 40 ppt at 16 °C, where 16 °C at 0 ppt (parts per thousand) served as the control. We found that levels of mRNA expression of both HSP70 and HSP90 were highest at 4 °C in the muscle, gill, and liver and changed little with salinity stress. These results increase understanding of the mechanisms of stress response of cold freshwater fish.

In silico characterisation, homology modelling and structure-based functional annotation of blunt snout bream (Megalobrama amblycephala) Hsp70 and Hsc70 proteins

Background

Heat shock proteins play an important role in protection from stress stimuli and metabolic insults in almost all organisms.

Methods

In this study, computational tools were used to deeply analyse the physicochemical characteristics and, using homology modelling, reliably predict the tertiary structure of the blunt snout bream (Ma-) Hsp70 and Hsc70 proteins. Derived three-dimensional models were then used to predict the function of the proteins.

Results

Previously published predictions regarding the protein length, molecular weight, theoretical isoelectric point and total number of positive and negative residues were corroborated. Among the new findings are: the extinction coefficient (33725/33350 and 35090/34840 - Ma-Hsp70/ Ma-Hsc70, respectively), instability index (33.68/35.56 – both stable), aliphatic index (83.44/80.23 – both very stable), half-life estimates (both relatively stable), grand average of hydropathicity (−0.431/-0.473 – both hydrophilic) and amino acid composition (alanine-lysine-glycine/glycine-lysine-aspartic acid were the most abundant, no disulphide bonds, the N-terminal of both proteins was methionine). Homology modelling was performed by SWISS-MODEL program and the proposed model was evaluated as highly reliable based on PROCHECK’s Ramachandran plot, ERRAT, PROVE, Verify 3D, ProQ and ProSA analyses.

Conclusions

The research revealed a high structural similarity to Hsp70 and Hsc70 proteins from several taxonomically distant animal species, corroborating a remarkably high level of evolutionary conservation among the members of this protein family. Functional annotation based on structural similarity provides a reliable additional indirect evidence for a high level of functional conservation of these two genes/proteins in blunt snout bream, but it is not sensitive enough to functionally distinguish the two isoforms.

HIFs genes expression and hematology indices responses to different oxygen treatments in an ovoviviparous teleost species Sebastes schlegelii

Hypoxia-inducible factors (HIFs) are transcription factors considered as a respond factor to oxygen tension. By using quantitative real-time PCR, expression files of HIF-1α and HIF-2α mRNA were detected in the Korean rockfish ovary, liver, gill and spleen after 30 min and 60 min acute hypoxia exposure. Meanwhile, the cortisol levels, white blood cells and several serum biochemical values of Korean rockfish under different oxygen concentration treatments were also detected. All the results might be helpful for further understanding of the potential effect of hypoxia in ovoviviparous fish.

Two HSPs gene from juvenile Amur sturgeon (Acipenser schrenckii): cloning, characterization and expression pattern to crowding and hypoxia stress

In this study, the cDNA sequences of HSP70 and HSP90 were isolated from the special chondr-ganoid scale, Amur sturgeon, for the first time. Homology analysis indicated that amino acid sequences of HSP70 and HSP90 shared high identity with other species (82.68-99.07 and 90.19-98.07%, respectively). The tissue expression analysis showed that the asHSP70 and asHSP90 mRNA were ubiquitously expressed in all the examined tissues under unstressed condition. The expression pattern of HSP70 and HSP90 under chronic (crowding) and acute (hypoxia) stress was examined by q-PCR in liver, spleen and kidney. Results showed that stocking density could significantly influence the expression of HSP70 at day 20 and/or day 40. In contrast to stocking density, levels of HSP70 transcripts indicated a remarkable increase in all examined tissues after hypoxia stress. HSP90 levels in liver and spleen increased significantly in high stocking density. By comparison, significant increase of asHSP90 in kidney was only found in high stocking density at day 40. Similar to HSP70, the levels of HSP90 transcripts showed significant increases after hypoxia stress except the transcript of liver in H2 group 6 h after hypoxia. The assessment of asHSP70 and asHSP90 mRNA levels under crowding and hypoxia stresses indicated that asHSP70 and asHSP90 gene might be good indicators of stressful situations for Amur sturgeon. Taking serum globulin and electrolytes account, we suggest that crowding and hypoxia stress can result in considerable stress for Amur sturgeon.

Molecular characterization of heat shock protein 70 (HSP 70) promoter in Japanese flounder (Paralichthys olivaceus), and the association of Pohsp70 SNPs with heat-resistant trait

Ambient temperature is one of the major abiotic environmental factors determining the main parameters of fish vital activity. HSP70 plays an essential role in heat response. In this investigation, the promoter and structure of Paralichthys olivaceus hsp70 (Pohsp70) gene was cloned and predicted. 2558 bp upstream regulatory region of Pohsp70 was annotated with four potential promoter elements and four putative binding sites of transcription factors heat shock elements (HSE, nGAAn) in the upstream of the transcription start site. In addition, one intron with 454 bp in the 5'-noncoding region was found. Quantitative Real Time PCR analysis indicated that the transcript level of Pohsp70 was raised markedly after 1 h by heat shocked. Furthermore, 25 SNPs were identified in Pohsp70 by resequencing, seven of which was associated with heat resistance. In addition, two of the seven SNPs, namely SNP14 and SNP16, were observed in strong linkage disequilibrium. The haplotype with association analysis showed TAGGAG haplotype was more represented in heat susceptible group while (DEL/T) GAATA haplotype was more frequent in heat resistant group. The heat resistant SNPs and haplotype could be candidate markers potentially serving for selective breeding programs of Japanese flounder aimed at improving anti-stress and production.