Identification of fatty acid synthase from the Pacific white shrimp, Litopenaeus vannamei and its specific expression profiles during white spot syndrome virus infection

Effects of dietary chenodeoxycholic acid supplementation in a low fishmeal diet on growth performance, lipid metabolism, autophagy and intestinal health of Pacific white shrimp, Litopenaeus vannamei

An 8-week feeding trial was conducted to evaluate the effects of chenodeoxycholic acid (CDCA) on growth performance, body composition, lipid metabolism, and intestinal health of juvenile white shrimp, Litopenaeus vannamei fed a low fishmeal diet. Four practical diets were formulated: HFM (25% fishmeal), LFM (15% fishmeal), LB1 (LFM + 0.04% CDCA), LB2 (LFM + 0.08% CDCA). Each diet was assigned to four tanks with forty shrimp (initial weight 0.33 ± 0.03 g) per tank. The results indicated that the growth performance of shrimp were similar between the four groups; the crude lipid content of shrimp fed the LB2 diet was significantly lower than those fed the HFM diet (P < 0.05). The lipase activity content in hepatopancreatic were significantly higher in the two CDCA supplemented groups than that in LFM group; the contents of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol in hemolymph were significantly lower in LFM group, LB1 group and LB2 group than that in HFM group (P < 0.05). The shrimp fed LB1 diet was significantly decreased the intestinal expression levels of tube than those fed in HFM diet; the intestinal gene expression of imd and toll were significantly lower in LB2 group than those in HFM group (P < 0.05). The results of hepatopancreas gene expression suggest that shrimp fed the LFM diet showed significantly upregulated expression levels of sterol regulatory element-binding protein (srebp), acetyl-CoA carboxylase (acc), and carnitine palmitoyltransferase 1 (cpt-1) than those fed the HFM diet; shrimp fed the LB1 diet showed significantly upregulated expression levels of srebp, acc, and AMP-activated protein kinase (ampk) than those fed the HFM diet; shrimp fed the LB2 diet had higher expression levels of srebp, acc, and cpt-1 than those fed the HFM diet (P < 0.05). In the hepatopancreas, the shrimp fed the LFM diet shown significantly up-regulated the expression levels of beclin1 compared to those fed HFM diet; the expression levels of autophagy-related protein13 (atg3), autophagy-related protein 12 (atg12) of in shrimp fed the LB1 diet were significantly higher than those fed the HFM diet; and the expression levels of autophagy-related protein13 (atg13), beclin1, atg3, atg12, autophagy-related protein 9 (atg9) of shrimp fed LB2 diet were significantly higher than those fed the HFM diet (P < 0.05). The atg3 in intestine of shrimp fed the LB2 diet were significantly higher than those fed the HFM diet (P < 0.05). Intestinal mucous fold were damaged, hepatic tubules were disorganized and B cells appeared to be swollen in LFM group. The fold height and width of shrimp fed the diets supplemented with CDCA increased significantly than those fed the LFM diet (P < 0.05), the hepatic tubules were neatly arranged, and R cells increased. In conclusion, supplementary CDCA in a low fishmeal diet promoted lipid metabolism, enhanced autophagy of shrimp, also improved the health of the intestine and hepatopancreas.

Comprehensive transcriptome analysis reveals the effect of feeding rhythm on the immunity and metabolism of Acipenser dabryanus

Acipenser dabryanus is a species endemic to Yangtze River drainage in China and is listed as a critical endangered species on the IUCN Red List. In the present study, the liver and spleen transcriptomes were analyzed by comparing the data of A. dabryanus that experienced nine different feeding rhythms (once a day diurnal, T1; two times a day diurnal, T2; three times a day diurnal, T3; four times a day, T4; five times a day, T5; six times a day, T6; once a day nocturnal, Tn1; two times a day nocturnal, Tn2; and three times a day nocturnal, Tn3). Transcriptome sequencing generated 1,901,236,482 clean reads, encompassing 570.4 Gb of sequence data. The reads were assembled into 287,372 unigenes with an average length of 803 bp and an N50 of 1004 bp. KEGG analysis showed that 1,080, 1,030, and 1216 unigenes were annotated to lipid metabolism, amino acid metabolism and carbohydrate metabolism, respectively, and 2549 unigenes were annotated to the immune system category. Differentially expressed genes (DEGs) between different feeding frequency groups or between nighttime and daytime feeding were obtained and functionally enriched. Importantly, DEGs participating in nutrition metabolism and various immunoregulation pathways and their expression profiles in A. dabryanus were discussed. Interestingly, the majority of key genes related to lipid metabolism or in immunodependent gene families, such as antimicrobial peptides, Toll-like receptors, chemokines, NOD-like receptors, B cell receptors and the major histocompatibility complex, were all significantly upregulated in animals in the T6 group compared to the characteristics of animals in the T2 group that had a normal feeding frequency. In addition, light/dark rhythm also affected the immunity of A. dabryanus, and fish fed at night possessed an improved immune response than fish fed at daytime. Our study suggested that feeding six times a day is optimal for A. dabryanus juvenile growth as it enhances the organism's nutrition metabolism and immune function.

Characterization and role of PGK from Litopenaeus vannamei in WSSV infection

Phosphoglycerate kinase (EC 2.7.2.3, PGK) catalyses the reversible transfer of a phosphate group from 1,3-diphosphoglyceric acid and ADP to produce 3-phosphoglyceric acid and ATP, which represents the initial production of ATP during glycolysis; therefore, PGK is a key enzyme in the energy metabolism. To study the role of PGK in the resistance to WSSV infection in shrimp, the full-length cDNA of the PGK gene (LvPGK) from Litopenaeus vannamei was obtained by using homology cloning and RACE amplification. The tissue distribution of LvPGK and its expression changes in the main immune tissues after WSSV stimulation were obtained by quantitative real-time PCR. Furthermore, RNA interference (RNAi) was used to study the role of LvPGK in shrimp defending against WSSV infection. The results showed that the full-length cDNA sequence of LvPGK was 1855 bp, contained a 1248 bp open reading frame (ORF) encoding 415 amino acids, and included a conserved PGK domain. LvPGK presented ubiquitous expression in most examined tissues, with the most predominant expression in the muscle and the weakest expression in the intestine. LvPGK transcripts could be induced in the hemocytes and hepatopancreas by injection with WSSV. Both the replication of WSSV and the shrimp cumulative mortality decreased significantly after LvPGK knockdown (P < 0.01). After challenging LvPGK RNAi shrimp with WSSV, the concentration of glucose in the hepatopancreas and muscle tissue did not show significant change; however, the content of pyruvate and lactate decreased significantly (P < 0.05). Moreover, significant decreases in the expression levels of crustin, ALF1, ALF2 and ALF3 were also detected. The results suggested that LvPGK might be involved in WSSV replication by increasing host aerobic and anaerobic metabolism.

SNP markers for the genetic characterization of Mexican shrimp broodstocks

Selective breeding of shrimp has major potential to enhance production traits, including growth and disease resistance. Genetic characterization of broodstock populations is a key element of breeding programs, as it enables decisions on inbreeding restrictions, family structure, and the potential use of genomic selection. Single Nucleotide Polymorphisms (SNPs) are suitable genetic markers for this purpose. A set of SNPs was developed to characterize commercial breeding stocks in Mexico. Individuals from local and imported lines were selected for sequencing using the nextRAD technique, resulting in the identification of 2619 SNPs. Genetic structure analysis showed three to five genetic groups of Ecuadorian and Mexican origins. A subset of 1231 SNPs has potential for stock identification and management. Further, three SNPs were identified as candidate sex-linked markers. The role of SNPs possibly associated with genes related to traits of importance to shrimp farming, such as growth and immune response, should be further investigated.

Changes in the Intestine Microbial, Digestive, and Immune-Related Genes of Litopenaeus vannamei in Response to Dietary Probiotic Clostridium butyricum Supplementation

The intestine barrier serves as the front-line defense in shrimp. Clostridium butyricum (CB) can produce butyric acid that provides energy for the intestine epithelial cells of the host. However, the effects of dietary CB on the intestine microbiome and the digestion and immunity of the host is not clear. In this study, we therefore investigated the composition and metabolic activity of the intestine microbiome, and digestive and immune-related gene expression in Litopenaeus vannamei fed with diets containing different levels of CB: basal diet (control), 2.5 × 10⁹ CFU kg^-1 diet (CB1), 5.0 × 10⁹ CFU kg^-1 diet (CB2), and 1.0 × 10¹⁰ CFU kg^-1 diet (CB3) for 56 days. Dietary CB altered the composition of the intestine microbiome. Specifically, the dominant bacterial phylum Proteobacteria was enriched in the CB3 group and weakened in the CB1 and CB2 groups. The Bacteroidetes was enriched in the CB1 and CB2 groups and weakened in the CB3 group. The Firmicutes was enriched in all three CB groups. At the genus level, the potential pathogen (Desulfovibrio and Desulfobulbus) were weakened, and beneficial bacteria (Bacillus, Clostridium, Lachmoclostridium, Lachnospiraceae, and Lactobacillus) were enriched in response to dietary CB; these might contribute to the expression of the host digestive genes (α-amylase, lipase, trypsin, fatty acid-binding protein, and fatty acid synthase) and immune-related genes (prophenoloxidase, lipopolysaccharide and β-1,3-glucan binding protein, lysozyme, crustin, and superoxide dismutase). Additionally, CB enhanced the bacterial metabolism, especially that of carbohydrates, polymers, amino acids, carboxylic acids, and amines. These results revealed that dietary CB had a beneficial effect on the intestine health of L. vannamei by modulating the composition of the intestine microbiome, enhancing the microbial metabolism activity, and promoting the digestion and immunity of the host. The optimal dietary supplementation dosage was found to be 5.0 × 10⁹ CFU kg^-1 in the diet.

Identification of MicroRNAs and Their Target Genes Associated with Ovarian Development in Black Tiger Shrimp (Penaeus monodon) Using High-Throughput Sequencing

Plenty of evidence showing that microRNAs (miRNAs) post-transcriptionally regulate gene expression and are involved in a wide range of biological processes. However, the roles of miRNAs in ovarian development process remain largely unknown in shrimp. In the present study, high-throughput sequencing of small RNAs was performed to find specific miRNAs that are involved in ovarian development process in Penaeus monodon. Two small RNA libraries were constructed from undeveloped (UNDEV group) and developed (DEV group) ovarian tissues in P. monodon. In total, 43 differentially expressed miRNAs were identified between the two groups (P ≤ 0.05, |log2 ratio| ≥1), and their expression profiles were validated by qRT-PCR. In order to further clarify the functional roles of these differentially expressed miRNAs during ovarian development process, target gene prediction was performed. In total, 4,102 target genes of 43 miRNAs were predicted, then clustered by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database; only four specific pathways related to ovarian development were obtained (P < 0.05). Dual-luciferase reporter assays and integrated expression analysis were also conducted to further clarify the interaction between the miRNAs and their target mRNAs. This study provides important information about the function of miRNAs involved in ovarian developmental stages in P. monodon.

Fatty acid synthase plays a positive role in shrimp immune responses against Vibrio parahaemolyticus infection

Fatty acid synthase (FAS) is an important enzyme that catalyzes the synthesis of fatty acids. In this study, the role of the FAS gene from pacific white shrimp Litopenaeus vannamei (LvFAS) in immune responses against Vibrio parahaemolyticus infection was studied. The expression of LvFAS could be up-regulated upon infection of V. parahaemolyticus and stimulation of lipopolysaccharide and poly (I:C). The promoter of LvFAS was predicted to harbor a NF-κB binding site and dual-luciferase reporter assays demonstrated that the NF-κB family proteins Relish, sRelish and Dorsal could activate the transcription of LvFAS. After knockdown of LvFAS expression using RNAi strategy, both the mortality of V. parahaemolyticus infected shrimps and the bacterial load in shrimp tissues were significantly increased. Meanwhile, the expression of many immune-responsive genes, such as antimicrobial peptides, C-type lectins (CTLs), lysozyme and hemolin, was down-regulated. These suggested that LvFAS could play a positive role in anti-V. parahaemolyticus responses in shrimp. To our knowledge, this is the first study that investigates the role of FAS in antibacterial immunity in animals, which may indicate the relationship between the anabolism of fatty acids and immune responses in crustaceans.

To complete its replication cycle, a shrimp virus changes the population of long chain fatty acids during infection via the PI3K-Akt-mTOR-HIF1α pathway

White spot syndrome virus (WSSV), the causative agent of white spot disease (WSD), is a serious and aggressive shrimp viral pathogen with a worldwide distribution. At the genome replication stage (12 hpi), WSSV induces a metabolic rerouting known as the invertebrate Warburg effect, which boosts the availability of energy and biosynthetic building blocks in the host cell. Here we show that unlike the lipogenesis that is seen in cancer cells that are undergoing the Warburg effect, at 12 hpi, all of the long chain fatty acids (LCFAs) were significantly decreased in the stomach cells of WSSV-infected shrimp. By means of this non-selective WSSV-induced lipolysis, the LCFAs were apparently diverted into β-oxidation and used to replenish the TCA cycle. Conversely, at 24 hpi, when the Warburg effect had ceased, most of the LCFAs were significantly up-regulated and the composition was also significantly altered. In crayfish these changes were in a direction that appeared to favor the formation of WSSV virion particles. We also found that, at 24 hpi, but not at 12 hpi, the PI3K-Akt-mTOR-HIF1α pathway induced the expression of fatty acid synthase (FAS), an enzyme which catalyzes the conversion of acetyl-CoA into LCFAs. WSSV virion formation was impaired in the presence of the FAS inhibitor C75, although viral gene and viral DNA levels were unaffected. WSSV therefore appears to use the PI3K-Akt-mTOR pathway to induce lipid biosynthesis at 24 hpi in order to support viral morphogenesis.

Transcriptome analysis of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Taura syndrome Virus (TSV) experimental infection

Background

The Pacific white shrimp, Litopenaeus vannamei, is a worldwide cultured crustacean species with important commercial value. Over the last two decades, Taura syndrome virus (TSV) has seriously threatened the shrimp aquaculture industry in the Western Hemisphere. To better understand the interaction between shrimp immune and TSV, we performed a transcriptome analysis in the hepatopancreas of L. vannamei challenged with TSV, using the 454 pyrosequencing (Roche) technology.

Methodology/Principal Findings

We obtained 126919 and 102181 high-quality reads from TSV-infected and non-infected (control) L. vannamei cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 15004 unigenes, with an average length of 507 bp. Based on BLASTX search (E-value <10−5) against NR, Swissprot, GO, COG and KEGG databases, 10425 unigenes (69.50% of all unigenes) were annotated with gene descriptions, gene ontology terms, or metabolic pathways. In addition, we identified 770 microsatellites and designed 497 sets of primers. Comparative genomic analysis revealed that 1311 genes differentially expressed in the infected shrimp compared to the controls, including 559 up- and 752 down- regulated genes. Among the differentially expressed genes, several are involved in various animal immune functions, such as antiviral, antimicrobial, proteases, protease inhibitors, signal transduction, transcriptional control, cell death and cell adhesion.

Conclusions/Significance

This study provides valuable information on shrimp gene activities against TSV infection. Results can contribute to the in-depth study of candidate genes in shrimp immunity, and improves our current understanding of this host-virus interaction. In addition, the large amount of transcripts reported in this study provide a rich source for identification of novel genes in shrimp.