Glutathione S-transferase in the white shrimp Litopenaeus vannamei: Characterization and regulation under pH stress

Identifying Relationships between Glutathione S-Transferase-2 Single Nucleotide Polymorphisms and Hypoxia Tolerance and Growth Traits in Macrobrachium nipponense

Investigating hypoxia tolerance and growth trait single nucleotide polymorphisms (SNPs) in Macrobrachium nipponense is conducive to cultivating prawns with hypoxia tolerance and good growth characteristics. The glutathione S-transferase-2 gene (GST-2) has been shown to regulate hypoxia responses in M. nipponense. In this study, we identified a single GST-2 SNP in M. nipponense, and analyzed its regulatory relationship with hypoxia tolerance and growth. The GST-2 sequence was amplified with a polymerase chain reaction from 197 "Taihu Lake No. 3", "Taihu Lake No. 2", and Pearl River population samples to identify SNP loci. The full-length Mn-GST2 sequence was 2317 bp, including three exons and two introns. In total, 38 candidate SNP loci were identified from GST-2 using Mega11.0 comparisons, with most loci moderately polymorphic in terms of genetic diversity. Locus genotypes were also analyzed, and basic genetic parameters for loci were calculated using Popgene32 and PIC_CALC. The expected heterozygosity of the 38 SNP loci ranged from 0.2334 to 0.4997, with an average of 0.4107, while observed heterozygosity ranged from 0.1929 to 0.4721, with an average of 0.3401. The polymorphic information content ranged from 0.21 to 0.37. From SPSS analyses, the G+256A locus was significantly correlated with hypoxia tolerance across all three M. nipponense populations, while the SNP loci A+261C, C+898T, A+1370C, and G+1373T were significantly associated with growth traits. Further analyses revealed that the T+2017C locus was significantly correlated with hypoxia tolerance in "Taihu Lake No. 2" populations, G+256A, A+808T, C+1032T, and A+1530G loci were significantly correlated with hypoxia tolerance in "Taihu Lake No. 3" populations, while no SNP loci were correlated with hypoxia tolerance in Pearl River populations. A+1370C and G+1373T loci, which were associated with growth traits, exhibited a high degree of linkage disequilibrium (r2 = 0.89 and r2 > 0.8), suggesting potential genetic linkage. Our data suggest associations between hypoxia tolerance and growth trait SNP loci in M. nipponense, and provide valuable evidence for the genetic improvement of growth and hypoxia tolerance in this prawn species.

Glutathione S-transferase gene diversity and their regulation by Nrf2 in Chinese mitten crab (Eriocheir sinensis) during nitrite stress

Eriocheir sinensis is one of the most important economic aquatic products in China. However, nitrite pollution has become a serious threat to the healthy culture of E. sinensis. Glutathione S-transferase (GST) is an important phase II detoxification enzyme, which plays a leading role in the cellular detoxification of exogenous substances. In this study, we obtained 15 GST genes (designated as EsGST1-15) from E. sinensis, and their expression and regulation in E. sinensis under nitrite stress were studied. EsGST1-15 belonged to different GST subclasses. EsGST1, EsGST2, EsGST3, EsGST4, and EsGST5 belonged to Delta-class GSTs; EsGST6 and EsGST7 are Theta-class GSTs; EsGST8 is a mGST-3-class GST; EsGST9 belonged to mGST-1-class GSTs; EsGST10 and EsGST11 belonged to Sigma-class GSTs; EsGST12, EsGST13, and EsGST14 are Mu-class GSTs; EsGST15 is a Kappa-class GST. Tissue distribution experiments showed that EsGSTs were widely distributed in all detected tissues. The expression level of EsGST1-15 was significantly increased in the hepatopancreas under nitrite stress, indicating that EsGSTs were involved in the detoxification of E. sinensis under nitrite stress. Nuclear factor-erythroid 2 related factor 2 (Nrf2) is a transcription factor that can activate the expression of detoxification enzyme. We detected the expression of EsGST1-15 after interfering with EsNrf2 in the hepatopancreas of E. sinensis with or without nitrite stress. Results showed that EsGST1-15 were all regulated by EsNrf2 with or without nitrite stress. Our study provides new information about the diversity, expression, and regulation of GSTs in E. sinensis under nitrite stress.

Analysis of hybrid combining ability for growth and multiple stress tolerance traits in the Pacific white shrimp, Litopenaeus vannamei

To identify optimal mating combinations for Litopenaeus vannamei, a linear mixed model was used to estimate the general combining ability (GCA) and specific combining ability (SCA) for growth and multiple stress tolerance [high salt (35‰), low pH (6 ± 0.1), and high ammonia nitrogen (70 mg/L) co-stress] traits in 47 combinations of L. vannamei. The results showed that the SCA in the parents played a dominant role in the offspring traits. The highest GCAs were observed for females of strain O and males of strain B (0.602 and 8.889, respectively), indicating that the dams of strain O and sires of strain B could be used as maternal and paternal lines to increase multiple stress resistance in the next generation. The growth traits of the hybrid combination strain G♂ × strain H♀ exhibited the highest degree of heterosis (9.838%–46.518%) and a generally high SCA (0.643–8.596) among all mating combinations. The SCA was the highest for the strain N♂ × strain O♀ multiple stress tolerance (30.131), while the heterosis for that combination strain was the third-highest. The combinations of strain G♂ × strain H♀ and strain N♂ × strain O♀ can be used as candidate combinations for rapid growth and multiple stress tolerance, respectively.

Comparative proteomic profiling in Chinese shrimp Fenneropenaeus chinensis under low pH stress

Lower pH gives rise to a harmful stress to crustacean. Here, we analyzed the proteomic response of Fenneropenaeus chinensis from control pH (pH value 8.2) and low pH (pH value 6.5) - treated groups by employing absolute quantitation-based quantitative proteomic (iTRAQ) analysis. Among the identified proteins, a total of 76 proteins differed in their abundance levels, including 45 upregulated and 31 downregulated proteins. The up-regulation of proteins like citrate synthase, cytochrome c oxidase, V-type proton ATPase, glyceraldehyde-3-phosphate dehydrogenase and fructose 1,6-bisphosphate-aldolase as well as the enrichment of the DEPs in multiple metabolic processes and pathways illustrated that increased energy and substrates metabolism was essential for F. chinensis to counteract low pH stress. Ion transporting related proteins, such as Na⁺/K⁺/2Cl^- cotransporter and calmodulin, participated in the homeostatic maintenance of pH in F. chinensis. There were significant downregulation expressions of lectin, lipopolysaccharide- and beta-1,3-glucan binding protein, chitinase, cathepsin L and beta-glucuronidase, which indicating the immune dysfunction of F. chinensis when exposure to low pH condition. These findings can extend our understanding on the defensive mechanisms of the low pH stress and accelerate the breeding process of low pH tolerance in F. chinensis.

Raising the water temperature: consequences in behavior and biochemical biomarkers of the freshwater crab Aegla longirostri (Crustacea, Anomura)

Understanding how temperature alone affects biomarkers commonly used in ecotoxicology studies and biomonitoring programs is important to obtain a more real response in field studies, especially in freshwater. Thus, we analyzed the behavioral responses, the lethality, and the biochemical biomarkers in the freshwater crustacean Aegla longirostri at different water temperatures. Animals were exposed under laboratory conditions, to 18 °C, 21 °C, 24 °C, and 26 °C for 48 h. There were significant changes in biochemical parameters in different tissues (hepatopancreas, gills, and muscle) and in the behavioral tests in A. longirostri. Hepatopancreas was especially affected by the elevation of temperature, as showed by the high levels of carbonyl proteins. The activity of acetylcholinesterase increased in a temperature-dependent manner in muscle. Glutathione S-transferase activity decreased with the elevation of temperature in all tissues sampled. The results obtained in this study indicate that when assessing the health of polluted limnic ecosystems through the use of organisms in situ, the intrinsic effect of abiotic factors, such as temperature, on biomarkers must be considered.

Growth, Metabolite, Antioxidative Capacity, Transcriptome, and the Metabolome Response to Dietary Choline Chloride in Pacific White Shrimp Litopenaeus vannamei

Simple Summary

Choline is a vitamin-like nutrient and has many metabolic and physiological functions in aquatic animals. Unfortunately, the information on the optimal requirement of dietary choline in Litopenaeus vannamei is limited, and the molecular and metabolic mechanisms of choline on L. vannamei are unclear. Hence, in this study, the growth performance, whole-body composition, serum characteristics, hepatopancreatic antioxidant indexes, serum metabolome and hepatopancreas transcriptome were performed. In this study, the growth of L. vannamei was not affected by dietary choline. Dietary choline played an important role in arachidonic acid and glycerophospholipid metabolism and decreased the oxidant damage of L. vannamei, while excessive choline can inhibit the digestion of protein and reduce the whole-body crude protein in shrimp. Based on the results of weight gain and lipid peroxidation reduction, 1082 mg/kg dietary choline could meet the growth requirement of L. vannamei, but 2822 mg/kg dietary choline was needed to reduce peroxidation damage. The present study would provide valuable information on the requirement of choline in L. vannamei, and help to understand the molecular and metabolic mechanisms of choline in shrimp.

Abstract

To determine the response of Pacific white shrimp Litopenaeus vannamei to different levels of dietary choline, juvenile white shrimp (1.75 ± 0.09 g) were fed six semi-purified diets supplemented with 0 (control), 2000, 4000, 6000, 8000, and 12,000 mg/kg choline chloride for eight weeks. Growth performance, whole-body composition, serum characteristics and hepatopancreatic antioxidant indexes were evaluated. Meanwhile, serum metabolome and hepatopancreas transcriptome were performed to examine the overall difference in metabolite and gene expression. The weight gain, survival, specific growth rate, condition factor and hepatosomatic index were not affected by dietary choline levels. The shrimp fed 6000 mg/kg dietary choline chloride gained the maximal whole-body crude protein, which was significantly higher than that of shrimp fed with 12,000 mg/kg dietary choline. Serum total cholesterol of shrimp fed 6000 mg/kg dietary choline was higher than that in shrimp fed 4000 mg/kg choline. Dietary choline significantly decreased malondialdehyde content, superoxide dismutase, and glutathione peroxidase activities in shrimp hepatopancreas. Compared with the shrimp fed 6000 mg/kg dietary choline chloride, the glycerophospholipid metabolism pathway was significantly enriched in the shrimp fed 0 mg/kg dietary choline chloride, and the choline content and bile salt-activated lipase-like expression were upregulated. The expression of trypsin-1-like in protein digestion and absorption pathway was significantly downregulated in the shrimp fed 12,000 mg/kg dietary choline chloride. Apolipoprotein D might be a potential biomarker in shrimp, and dietary choline played an important role in lipid metabolism, especially in the reduction of oxidative damage in L. vannamei. Based on the results of weight gain and degree of oxidative damage, 1082 mg/kg dietary choline could meet the growth requirement of L. vannamei, but 2822 mg/kg dietary choline was needed to reduce peroxidation damage.

Seasonal factors driving biochemical biomarkers in two fish species from a subtropical reservoir in southern Brazil: An integrated approach

Reservoirs are lentic man-made waterbodies resulting from river damming processes. Pollutants coming from adjacent areas can accumulate in the water and sediment of these modified freshwater environments. Fish are often found in reservoirs occupying several trophic niches. Biochemical biomarkers are early warning signals of environmental disturbance to an organism. It is essential to understand how pollutants, abiotic variables and biochemical biomarker responses behave throughout the seasons to implement biomonitoring programs. Loricariichthys anus and Geophagus brasiliensis were collected, and abiotic variables were seasonally measured for one year, at six sampling sites in Passo Real reservoir, in a subtropical region of Southern Brazil. Biochemical biomarkers were analyzed in four tissues of both fish species, as well as metal and pesticide concentrations in the reservoir's water and sediment. Redundancy analysis (RDA) was carried out to find the temporal relationship between biomarkers and environmental variables. RDA has clearly shown the separation of seasons for both species. Azoxystrobin, simazine and propoxur were the pesticides mostly contributing to the variation, whereas metals had lesser contribution to it. Seasonality appears to be the main factor explaining biomarkers' variability. PERMANOVA has confirmed the effect of temperature and dissolved oxygen on biomarkers of both fish species. Thus, it is hard to differentiate if the fluctuation in biomarkers' responses only reflects the normal state of organisms or it is a biological consequence from negative effects of fish exposure to several types of pollution (sewage, pesticides, and fertilizers) entering this aquatic system. In this study, to circumvent the seasonality issue on biomonitoring, the analysis of biomarkers on these fish should not be carried out in organs directly affected by temperature (such as liver and gills), or during reproduction periods (mainly in Spring).

How do abiotic environmental conditions influence shrimp susceptibility to disease? A critical analysis focussed on White Spot Disease

White Spot Syndrome Virus (WSSV) causes White Spot Disease (WSD) and is historically the most devastating disease in the shrimp industry. Global losses from this disease have previously exceeded $3 bn annually, having a major impact on a global industry worth US$19 bn per annum. Shrimp are cultured predominantly in enclosed ponds that are subject to considerable fluctuations in abiotic conditions and WSD outbreaks are increasingly linked to periods of extreme weather, which may cause major fluctuations in pond culture conditions. Combined with the intensity of production in these systems, the resulting suboptimal physicochemical conditions have a major bearing on the susceptibility of shrimp to infection and disease. Current knowledge indicates that pond temperature and salinity are major factors determining outbreak severity. WSSV appears to be most virulent in water temperatures between 25 and 28 °C and salinities far removed from the isoosmotic point of shrimp. Elevated temperatures (>30 °C) may protect against WSD, depending on the stage of infection, however the mechanisms mediating this effect have not been well established. Other factors relating to water quality that may play key roles in determining outbreak severity include dissolved oxygen concentration, nitrogenous compound concentration, partial pressure of carbon dioxide and pH, but data on their impacts on WSSV susceptibility in cultured shrimps is scarce. This illustrates a major research gap in our understanding of the influence of environmental conditions on disease. For example, it is not clear whether temperature manipulations can be used effectively to prevent or mitigate WSD in cultured shrimp. Therefore, developing our understanding of the impact of environmental conditions on shrimp susceptibility to WSSV may provide insight for WSD mitigation when, even after decades of research, there is no effective practical prophylaxis or treatment.

The role of Mu-type glutathione S-transferase in the mud crab (Scylla paramamosain) during ammonia stress

Glutathione S-transferase (GST) plays important roles in cellular detoxification and antioxidant defense. A Mu-type glutathione S-transferase (designated as SpMu-GST) was obtained from the mud crab Scylla paramamosain. The open reading frame of SpMu-GST was comprised a 690 bp, which encoded a putative protein of 229 amino acids. Quantitative real-time PCR (qRT-PCR) revealed that the SpMu-GST mRNA was expressed in all examined tissues, with highest expression in hepatopancreas. During ammonia exposure, the SpMu-GST transcriptions in hepatopancreas and gill were significantly up-regulated at early exposure time. Moreover, RNA interference (RNAi) experiment was designed to understand the roles of SpMu-GST under ammonia exposure. Ammonia exposure reduced the levels of glutathione S-transferase (GST), superoxide dismutase (SOD), catalase (CAT) and total antioxidative capacity (T-AOC), and increased the formation of malondialdehyde (MDA). After knockdown of the SpMu-GST level, GST activity and T-AOC were significantly decreased at some exposure time after ammonia exposure. However, the mortality of mud crabs and malondialdehyde (MDA) contents significantly increased under ammonia exposure. These results further suggested that SpMu-GST played a critical role in mud crab antioxidant defenses in response to environmental stress.

Effect of ammonia stress on immune variables of Pacific white shrimp Penaeus vannamei under varying levels of pH and susceptibility to white spot syndrome virus

Of late, Pacific white shrimp Penaeus vannamei culture has intensified globally and is a major contributor to the cultured shrimp produced worldwide. Intensification of its culture has led to elevated ammonia concentration during grow-out. Ammonia toxicity is a function of water pH, temperature, salinity and beyond the optimum range, creates stress to cultured aquatic species which can reduce growth, increase susceptibility to diseases and eventually mortality. The present study was aimed at quantifying the toxic effect of total ammonia nitrogen (TAN) (1, 3, 6 & 9 mg/l) and pH levels (6, 8 & 10) individually and in combination on median survival (50% lethal time) of shrimp (8 g) after exposure for 14 days followed by post-stress challenge with white spot syndrome virus (WSSV) for 9 days. Mortality risk factor and the toxicity effect on the immune variables were evaluated. Individual stressors showed a risk factor of 1-13 times, whereas combined treatments considerably increased the risk of dying compared to control. Low survival (15%) was observed in pH6TAN9 and pH10TAN3 treatments and was substantiated by prominent histological obliteration in gills of shrimp. The cumulative mortality in post-stress WSSV challenged trials was 1-5 times and 1-35 times in individual and combination treatments, respectively compared to control. The study revealed that variations in ammonia and pH beyond the optimal range significantly influence the non-specific immune mechanisms in P.vannamei and increases the susceptibility to WSSV especially in combination treatments.

Genome-wide identification of Chinese shrimp (Fenneropenaeus chinensis) microRNA responsive to low pH stress by deep sequencing

pH has a great impact on the distribution, growth, behavior, and physiology in many aquatic animals. Here, we analyzed miRNA expression profiles of Chinese shrimp (Fenneropenaeus chinensis) from control pH (8.2) and low pH (6.5)-treated shrimp. Expression analysis identified 6 known miRNAs and 23 novel miRNAs with significantly different expression between control pH 8.2 and low pH 6.5; the predicted target genes of differentially expressed miRNAs were significantly enriched in organic acid metabolic process, oxidoreductase activity, coenzyme binding, cofactor binding, and collagen trimer. Moreover, target genes were significantly enriched in several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including citrate cycle, pyruvate metabolism, cytokine-cytokine receptor interaction, tight junction, carbon metabolism, etc. Our survey expanded the number of known shrimp miRNAs and provided comprehensive information about miRNA response to low pH stress.

Characterization, functional analysis, and expression levels of three carbonic anhydrases in response to pH and saline-alkaline stresses in the ridgetail white prawn Exopalaemon carinicauda

Carbonate alkalinity, salinity, and pH are three important stress factors for aquatic animals in saline-alkaline water. Carbonic anhydrases (CAs) catalyze the reversible reaction of CO2 reported to play an important role in the acid-base regulation in vertebrates. To explore the molecular mechanism of CAs efficacy in shrimp after their transfer into saline-alkaline water, the cDNAs of three CAs (EcCAc, EcCAg, and EcCAb) were cloned from Exopalaemon carinicauda. Sequence analysis showed that EcCAc and EcCAg both possessed a conserved α-CA domain and a proton acceptor site, and EcCAb contained a Pro-CA domain. Tissue expression analysis demonstrated that EcCAc and EcCAg were most abundantly in gills, and EcCAb was highly expressed in muscle. The cumulative mortalities remained below 25% under exposure to pH (pH 6 and pH 9), low salinity (5 ppt), or high carbonate alkalinity (5 and 10 mmol/L) after 72 h of exposure. However, mortalities increased up to 70% under extreme saline-alkaline stress (salinity 5 ppt, carbonate alkalinity 10 mmol/L, and pH 9) after 14 days of exposure. The EcCAc and EcCAg expressions in gills were significantly upregulated during the early period of pH and saline-alkaline stresses, while the EcCAb expressions showed no regular or large changes. The two-way ANOVA found significant interactions between salinity and carbonate alkalinity observed in EcCAc, EcCAg, and EcCAb expressions (p < 0.05). Furthermore, an RNA interference experiment resulted in increased mortality of EcCAc- and EcCAg-silenced prawns under saline-alkaline stress. EcCAc knockdown reduced expressions of Na+/H+ exchanger (EcNHE) and sodium bicarbonate cotransporter (EcNBC), and EcCAg knockdown reduced EcCAc, EcNHE, EcNBC, and V-type H+-ATPase (EcVTP) expressions. These results suggest EcCAc and EcCAg as important modulators in response to pH and saline-alkaline stresses in E. carinicauda.

Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress

Soil salinization erodes the farmlands and poses a serious threat to human life, reuse of the saline-alkali lands as cultivated resources becomes increasingly prominent. Pacific white shrimp (Litopenaeus vannamei) is an important farmed aquatic species for the development and utilization of the saline-alkali areas. However, little is known about the adaptation mechanism of this species in terms of high-pH stress. In the present study, a transcriptome analysis on the gill tissues of L. vannamei in response to high-pH stress (pH 9.3 ± 0.1) was conducted. After analyzing, the cyclic nucleotide gated channel-Ca2+ (CNGC-Ca2+) and patched 1 (Ptc1) were detected as the majority annotated components in the cAMP signaling pathway (KO04024), indicating that the CNGC-Ca2+ and Ptc1 might be the candidate components for transducing and maintaining the high-pH stress signals, respectively. The immunoglobulin superfamily (IgSF), heat shock protein (HSP), glutathione s-transferase (GST), prophenoloxidase/phenoloxidase (proPO/PO), superoxide dismutase (SOD), anti-lipopolysaccharide factor (ALF) and lipoprotein were discovered as the major transcribed immune factors in response to high-pH stress. To further detect hub regulation-genes, protein-protein interaction (PPI) networks were constructed; the genes/proteins "Polymerase (RNA) II (DNA directed) polypeptide A" (POLR2A), "Histone acetyltransferase p300" (EP300) and "Heat shock 70kDa protein 8" (HSPA8) were suggested as the top three hub regulation-genes in response to acute high-pH stress; the genes/proteins "Heat shock 70kDa protein 4" (HSPA4), "FBJ murine osteosarcoma viral oncogene homolog" (FOS) and "Nucleoporin 54kDa" (NUP54) were proposed as the top three hub regulation-genes involved in adapting endurance high-pH stress; the protein-interactions of "EP300-HSPA8" and "HSPA4-NUP54" were detected as the most important biological interactions in response to the high-pH stress; and the HSP70 family genes might play essential roles in the adaptation of the high-pH stress environment in L. vannamei. These findings provide the first insight into the molecular and immune basis of L. vannamei in terms of high-pH environments, and the construction of a PPI network might improve our understanding in revealing the hub regulation-genes in response to abiotic stress in shrimp species and might be beneficial for further studies.

Molecular Cloning and Expression of MnGST-1 and MnGST-2 from Oriental River Prawn, Macrobrachium nipponense, in Response to Hypoxia and Reoxygenation

The glutathione-S-transferase (GST) superfamily includes seven classes, and different classes have different functions. GST superfamily members function in various processes including detoxification of xenobiotics, protection against oxidative damage, and intracellular transport of hormones, endogenous metabolites, and exogenous chemicals. Herein, to elucidate the tissue-specific expression pattern of GSTs in response to hypoxia stress, which induces cell death, we investigated the expression of GSTs in response to hypoxia and reoxygenation in oriental river prawn, Macrobrachium nipponense. Full-length cDNAs of two δ class GSTs were cloned from the hepatopancreas, and named MnGST-1 and MnGST-2 based on the established GST nomenclature system. Expression profiles of both GSTs in various tissues were different under acute and chronic experimental hypoxia stress conditions, suggesting that both respond strongly to hypoxia-induced oxidative stress. However, the intensity of responses to hypoxia and reoxygenation were different in different tissues. During acute hypoxia stress, MnGST-1 responds earlier than MnGST-2 in the hepatopancreas and gill, but more slowly in muscle. By contrast, during chronic hypoxia stress, MnGST-2 plays a more important role in the hepatopancreas and gill than MnGST-1.

Seasonal implications on toxicity biomarkers of Loricariichthys anus (Valenciennes, 1835) from a subtropical reservoir

Cropping systems based on intensive land use and continuous application of agricultural chemicals inflict a threat to aquatic organisms since these substances will inevitably be carried in to water bodies where they can accumulate, particularly in lentic sites. Pesticides exposure in aquatic animals can cause changes that can be quantified through biomarkers. Thus, this study aimed to investigate the effects of season on oxidative stress and neurotoxicity biomarkers in Loricariichthys anus from a subtropical reservoir surrounded by agricultural areas in southern Brazil. Ten armored catfish were collected from six sites in February and August 2016. Pesticides present in the water, sediment and muscle were identified and quantified. No pesticides were detected either in sediment nor in muscle. During the winter, the water contained atrazine, imidacloprid, simazine, azoxystrobin, and propoxur; however, in summer, only atrazine was present in the water. In the winter, there was an increase in the hepatic GST activity and in GPx that kept lipid peroxidation (TBARS) constant and, in the summer, there was an increase in metallothioneins levels. In the gills, variables related to summer were possibly responsible for the elevation of GST, GPx and TBARS; during the winter, there was greater carbonylation of proteins. In the winter, the increased AChE activity in brain and muscle tissue was related to carbonylation of proteins in brain. Although the amount of pesticides detected in the water was low, chronic exposure in addition to environmental variations can cause direct and indirect effects on L. anus population.

Cloning and characterization of PHGPx and its synergistic role with p53 in mediating stress in Penaeus monodon

Phospholipid-hydroperoxide glutathione peroxidase (PHGPx), a ubiquitous antioxidant enzyme in the glutathione peroxidase (GPx) family, plays multiple roles in different organisms. Here, a novel PHGPx (PmPHGPx) was identified from Penaeus monodon. The full-length PmPHGPx cDNA was 1885 bp in length with a 489-bp open reading frame (ORF) containing a selenocysteine codon, TGA^177-179, and a selenocysteine insertion sequence in the 3'-UTR. The typical signature motifs of the GPx family were also detected in the PmPHGPx amino acid sequence. The PmPHGPx expression pattern showed tissue-specific variations, with the highest expression level in the heart and the lowest expression level in the muscle. To examine the relationship between Pmp53 and PmPHGPx, Pmp53 was successfully silenced with a dsRNA-p53 injection, and an obvious down-regulation in PmPHGPx expression was apparent. To clarify the functional roles of Pmp53 and PmPHGPx, their expression patterns were also assessed after pH-induced stress, salinity stress and heavy metal (Cu, Zn, and Cd) challenges. Similar trends in the expression profiles for PmPHGPx and Pmp53 were detected in both the gills and hepatopancreas in response to all stressors. Therefore, we conclude from the results that PmPHGPx acts synergistically and subsequently works cooperatively with Pmp53 toward mediating cell stress. This study improves our understanding of PmPHGPx and its synergistic role with Pmp53 in counteracting stressors in P. monodon.

Molecular characterization of Pacific white shrimp (Litopenaeus vannamei) sodium bicarbonate cotransporter (NBC) and its role in response to pH stress

The sodium bicarbonate cotransporter (NBC) is an integral membrane ion transporter that can transport HCO₃^- (or a related species, such as CO₃^2-) across the plasma membrane. Previous researches revealed that NBC might play an important role in the regulation of intracellular pH in vertebrates. In the present study, an NBC cDNA was identified from Pacific white shrimp (Litopenaeus vannamei) and designated as Lv-NBC. The full-length Lv-NBC cDNA is 4479 bp in size, containing a 5'-untranslated region (UTR) of 59 bp, a 3'-UTR of 835 bp and an open reading frame (ORF) of 3585 bp that encodes a protein of 1194 amino acids with a deduced molecular weight of 134.34 kDa. The Lv-NBC protein contains two functional domains (Band_3_cyto and HCO3_cotransp) and twelve transmembrane (TM) domains. Expression of the Lv-NBC mRNA was ubiquitously detected in all selected tissues, with the highest level in the gill. By in situ hybridization (ISH) with Digoxigenin-labeled probe, the Lv-NBC positive cells were shown mainly located in the secondary gill filaments. After low or high pH challenge, the transcript levels of Lv-NBC in the gill were found to be up-regulated. After knockdown of the Lv-NBC level by siRNA, the mortality of shrimp significantly increased under pH stress. Our study, as a whole, may provide evidences for the role of NBC in shrimp responding to pH stress, and give a new insight of the acid/base homeostasis mechanism in crustaceans.

Characterization and function analysis of Hsp60 and Hsp10 under different acute stresses in black tiger shrimp, Penaeus monodon

Heat shock proteins (Hsps) are a class of highly conserved proteins produced in virtually all living organisms from bacteria to humans. Hsp60 and Hsp10, the most important mitochondrial chaperones, participate in environmental stress responses. In this study, the full-length complementary DNAs (cDNAs) of Hsp60 (PmHsp60) and Hsp10 (PmHsp10) were cloned from Penaeus monodon. Sequence analysis showed that PmHsp60 and PmHsp10 encoded polypeptides of 578 and 102 amino acids, respectively. The expression profiles of PmHsp60 and PmHsp10 were detected in the gills and hepatopancreas of the shrimps under pH challenge, osmotic stress, and heavy metal exposure, and results suggested that PmHsp60 and PmHsp10 were involved in the responses to these stimuli. ATPase and chaperone activity assay indicated that PmHsp60 could slow down protein denaturation and that Hsp60/Hsp10 may be combined to produce a chaperone complex with effective chaperone and ATPase activities. Overall, this study provides useful information to help further understand the functional mechanisms of the environmental stress responses of Hsp60 and Hsp10 in shrimp.

Transciptomic and histological analysis of hepatopancreas, muscle and gill tissues of oriental river prawn (Macrobrachium nipponense) in response to chronic hypoxia

Background

Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China. Chronic hypoxia is a major physiological challenge for prawns in culture, and the hepatopancreas, muscle and gill tissues play important roles in adaptive processes. However, the effects of dissolved oxygen availability on gene expression and physiological functions of those tissues of prawns are unknown. Adaptation to hypoxia is a complex process, to help us understand stress-sensing mechanism and ultimately permit selection for hypoxia- tolerant prawns, we performed transcriptomic analysis of juvenile M. nipponense hepatopancreas, gill and muscle tissues by RNA-Seq.

Results

Approximately 46,472,741; 52,773,612 and 58,195,908 raw sequence reads were generated from hepatopancreas, muscle and gill tissues, respectively. A total of 62,722 unigenes were generated, of the assembled unigenes, we identified 8,892 genes that were significantly up-regulated, while 5,760 genes were significantly down-regulated in response to chronic hypoxia. Genes from well known functional categories and signaling pathways associated with stress responses and adaptation to extreme environments were significantly enriched, including genes in the functional categories “response to stimulus”, “transferase activity” and “oxidoreductase activity”, and the signaling pathways “oxidative phosphorylation”, “glycolysis/gluconeogenesis” and “MAPK signaling”. The expression patterns of 18 DEGs involved in hypoxic regulation of M. nipponense were validated by quantitative real-time reverse-transcriptase polymerase chain reactions (qRT-PCR; average correlation coefficient = 0.94). In addition, the hepatopancreas and gills exhibited histological differences between hypoxia and normoxia groups. These structural alterations could affect the vital physiological functions of prawns in response to chronic hypoxia, which could adversely affect growth and survival of M. nipponense.

Conclusions

Gene expression changes in tissues from the oriental river prawn provide a preliminary basis to better understand the molecular responses of M. nipponense to chronic hypoxia. The differentially expressed genes (DEGs) identified in M. nipponense under hypoxia stress may be important for future genetic improvement of cultivated prawns or other crustaceans through transgenic approaches aimed at increasing hypoxia tolerance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1701-3) contains supplementary material, which is available to authorized users.

RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection

Background

The Malaysian giant freshwater prawn, Macrobrachium rosenbergii, is an economically important crustacean worldwide. However, production of this prawn is facing a serious threat from Vibriosis disease caused by Vibrio species such as Vibrio parahaemolyticus. Unfortunately, the mechanisms involved in the immune response of this species to bacterial infection are not fully understood. We therefore used a high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the hepatopancreas from this freshwater prawn infected with V. parahaemolyticus to gain an increased understanding of the molecular mechanisms underlying the species’ immune response to this pathogenic bacteria.

Result

A total of 59,122,940 raw reads were obtained from the control group, and 58,385,094 reads from the Vibrio-infected group. Via de novo assembly by Trinity assembler, 59,050 control unigenes and 73,946 Vibrio-infected group unigenes were obtained. By clustering unigenes from both libraries, a total of 64,411 standard unigenes were produced. The standard unigenes were annotated against the NCBI non-redundant, Swiss-Prot, Kyoto Encyclopaedia of Genes and Genome pathway (KEGG) and Orthologous Groups of Proteins (COG) databases, with 19,799 (30.73%), 16,832 (26.13%), 14,706 (22.83%) and 7,856 (12.19%) hits respectively, giving a final total of 22,455 significant hits (34.86% of all unigenes). A Gene Ontology (GO) analysis search using the Blast2GO program resulted in 6,007 unigenes (9.32%) being categorized into 55 functional groups. A differential gene expression analysis produced a total of 14,569 unigenes aberrantly expressed, with 11,446 unigenes significantly up-regulated and 3,103 unigenes significantly down-regulated. The differentially expressed immune genes fall under various processes of the animal immune system.

Conclusion

This study provided an insight into the antibacterial mechanism in M. rosenbergii and the role of differentially expressed immune genes in response to V. parahaemolyticus infection. Furthermore, this study has generated an abundant list of transcript from M.rosenbergii which will provide a fundamental basis for future genomics research in this field.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-015-0052-6) contains supplementary material, which is available to authorized users.

Transcriptome changes in Eriocheir sinensis megalopae after desalination provide insights into osmoregulation and stress adaption in larvae

Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups “Energy metabolism,” “Oxidoreductase activity,” “Translation,” “Transport,” “Metabolism,” and “Stress response.” In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or β-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by a series of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.

Chloride and other anions inhibit dichloroacetate-induced inactivation of human liver GSTZ1 in a haplotype-dependent manner

The in vivo elimination rate of dichloroacetate (DCA), an investigational drug; is determined by the rate of its biotransformation to glyoxylate, catalyzed by glutathione transferase ζ1 (GSTZ1). DCA is a mechanism-based inactivator of GSTZ1, thus elimination of DCA is slowed with repeated dosing. We observed that chloride, a physiologically important anion, attenuated DCA-induced GSTZ1 inactivation in human liver cytosol in a concentration and GSTZ1 haplotype-dependent way. In the absence of chloride, incubation with 0.5mM DCA resulted in inactivation of GSTZ1 with a half-life of 0.4h (samples with the KRT haplotype) to 0.5h (EGT haplotype). At the hepatic physiological chloride concentration, 38mM, samples with the EGT haplotype retained more activity (80%) following a 2-h incubation with 0.5mM DCA than those possessing the KRT haplotype (55%). The chloride concentration that protected 50% of the GSTZ1 activity following 2-h incubation with 0.5mM DCA (EC50) was 15.0±3.1mM (mean±S.D., n=3) for EGT samples and 36.2±2.2mM for KRT samples. Bromide, iodide and sulfite also protected GSTZ1 from inactivation by DCA, however fluoride, sulfate, carbonate, acetate, cyanide did not. Protection by bromide varied by GSTZ1 haplotype: EC50 was 1.3±0.3mM for the EGT haplotype and 5.0±0.60mM for the KRT haplotype. The EC50 values for iodide and sulfite in liver cytosol samples with EGT haplotype were respectively 0.14±0.06mM and 9.6±1.1mM (mean±S.D., n=3). Because the in vivo half-life of DCA is determined by the fraction of active GSTZ1 in the liver, identifying factors that regulate GSTZ1 activity is important in determining appropriate DCA dosing in humans.

Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake

Background

Amur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, providing us a valuable material to understand the adaptation mechanism against extreme environmental stress in teleost.

Results

In this study, we generated high-throughput RNA-Seq data from three tissues gill, liver and kidney of L. waleckii living in the soda lake Dali Nor and the fresh water lake Ganggeng Nor, then performed parallel comparisons of three tissues. Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions. We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01and fold-change ≥ 2. Further analysis revealed that well-known functional categories of genes and signaling pathway, which are associated with stress response and extreme environment adaptation, have been significantly enriched, including the functional categories of “response to stimulus”, “transferase activity”, “transporter activity” and “oxidoreductase activity”, and signaling pathways of “mTOR signaling”, “EIF2 signaling”, “superpathway of cholesterol biosynthesis”. We also identified significantly DEGs encoding important modulators on stress adaptation and tolerance, including carbonic anhydrases, heat shock proteins, superoxide dismutase, glutathione S-transferases, aminopeptidase N, and aminotransferases.

Conclusions

Overall, this study demonstrated that transcriptome changes in L. waleckii played a role in adaptation to complicated environmental stress in the highly alkalized Dali Nor lake. The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.

Transcriptome sequencing and analysis of wild Amur Ide (Leuciscus waleckii) inhabiting an extreme alkaline-saline lake reveals insights into stress adaptation

Background

Amur ide (Leuciscus waleckii) is an economically and ecologically important species in Northern Asia. The Dali Nor population inhabiting Dali Nor Lake, a typical saline-alkaline lake in Inner Mongolia, is well-known for its adaptation to extremely high alkalinity. Genome information is needed for conservation and aquaculture purposes, as well as to gain further understanding into the genetics of stress tolerance. The objective of the study is to sequence the transcriptome and obtain a well-assembled transcriptome of Amur ide.

Results

The transcriptome of Amur ide was sequenced using the Illumina platform and assembled into 53,632 cDNA contigs, with an average length of 647 bp and a N50 length of 1,094 bp. A total of 19,338 unique proteins were identified, and gene ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses classified all contigs into functional categories. Open Reading Frames (ORFs) were detected from 34,888 (65.1%) of contigs with an average length of 577 bp, while 9,638 full-length cDNAs were identified. Comparative analyses revealed that 31,790 (59.3%) contigs have a significant similarity to zebrafish proteins, and 27,096 (50.5%), 27,524 (51.3%) and 27,996 (52.2%) to teraodon, medaka and three-spined stickleback proteins, respectively. A total of 10,395 microsatellites and 34,299 SNPs were identified and classified. A dN/dS analysis on unigenes was performed, which identified that 61 of the genes were under strong positive selection. Most of the genes are associated with stress adaptation and immunity, suggesting that the extreme alkaline-saline environment resulted in fast evolution of certain genes.

Conclusions

The transcriptome of Amur ide had been deeply sequenced, assembled and characterized, providing a valuable resource for a better understanding of the Amur ide genome. The transcriptome data will facilitate future functional studies on the Amur ide genome, as well as provide insight into potential mechanisms for adaptation to an extreme alkaline-saline environment.

Seasonal variations of the activity of antioxidant defense enzymes in the red mullet (Mullus barbatus l.) from the Adriatic Sea

This study investigated seasonal variations of antioxidant defense enzyme activities: total, manganese, copper zinc containing superoxide dismutase (Tot SOD, Mn SOD, CuZn SOD), catalase (CAT), glutathione peroxidase (GSH-Px), glutathione reductase (GR) and biotransformation phase II enzyme glutathione-S-transferase (GST) activity in the liver and white muscle of red mullet (Mullus barbatus). The investigations were performed in winter and spring at two localities: Near Bar (NB) and Estuary of the River Bojana (EB) in the Southern Adriatic Sea. At both sites, Mn SOD, GSH-Px, GR and GST activities decreased in the liver in spring. In the white muscle, activities of Mn SOD, GSH-Px, GR and GST in NB decreased in spring. GR decreased in spring in EB, while CAT activity was higher in spring at both sites. The results of Principal Component Analysis (PCA) based on correlations indicated a clear separation of various sampling periods for both investigated tissues and a marked difference between two seasons. Our study is the first report on antioxidant defense enzyme activities in the red mullet in the Southern Adriatic Sea. It indicates that seasonal variations of antioxidant defense enzyme activities should be used in further biomonitoring studies in fish species.