iTRAQ-based proteomic analysis of the hepatopancreas from Litopenaeus vannamei after trans-vp28 gene Synechocystis sp. PCC6803 immunization

Combined transcriptome and metabolome analysis reveal key regulatory genes and pathways of feed conversion efficiency of oriental river prawn Macrobrachium nipponense

BACKGROUND

Oriental river prawn Macrobrachium nipponense is an economically important aquaculture species in China, Japan, and Vietnam. In commercial prawn farming, feed cost constitutes about 50 to 65% of the actual variable cost. Improving feed conversion efficiency in prawn culture will not only increase economic benefit, but also save food and protect the environment. The common indicators used for feed conversion efficiency include feed conversion ratio (FCR), feed efficiency ratio (FER), and residual feed intake (RFI). Among these, RFI is much more suitable than FCR and FER during the genetic improvement of feed conversion efficiency for aquaculture species.

RESULTS

In this study, the transcriptome and metabolome of hepatopancreas and muscle of M. nipponense from high RFI low RFI groups, which identified after culture for 75 days, were characterized using combined transcriptomic and metabolomic analysis. A total of 4540 differentially expressed genes (DEGs) in hepatopancreas, and 3894 DEGs in muscle were identified, respectively. The DEGs in hepatopancreas were mainly enriched in KEGG pathways including the metabolism of xenobiotics by cytochrome P450 (down-regulated), fat digestion and absorption (down-regulated) and aminoacyl-tRNA biosynthesis (up-regulated), etc. The DEGs in muscle were mainly enriched in KEGG pathways including the protein digestion and absorption (down-regulated), glycolysis/gluconeogenesis (down-regulated), and glutathione metabolism (up-regulated), etc. At the transcriptome level, the RFI of M. nipponense was mainly controlled in biological pathways such as the high immune expression and the reduction of nutrients absorption capacity. A total of 445 and 247 differently expressed metabolites (DEMs) were identified in the hepatopancreas and muscle, respectively. At the metabolome level, the RFI of M. nipponense was affected considerably by amino acid and lipid metabolism.

CONCLUSIONS

M. nipponense from higher and lower RFI groups have various physiological and metabolic capability processes. The down-regulated genes, such as carboxypeptidase A1, 6-phosphofructokinase, long-chain-acyl-CoA dehydrogenase, et. al., in digestion and absorption of nutrients, and the up-regulated metabolites, such as aspirin, lysine, et. al., in response to immunity could be potential candidate factors contributed to RFI variation for M. nipponense. Overall, these results would provide new insights into the molecular mechanism of feed conversion efficiency and assist in selective breeding to improve feed conversion efficiency in M. nipponense.

Combined dynamic transcriptomics and metabolomics analyses revealed the effects of trans-vp28 gene Synechocystis sp. PCC6803 on the hepatopancreas of Litopenaeus vannamei

Litopenaeus vannamei is the most important shrimp species throughout the world. However, diseases are increasing with the development of the industry, so enhancing the immunity of shrimp is of great significance. In this study, 1800 shrimp were divided into two groups randomly: the control group (N, feed with brine shrimp flake) and the experimental group (M, feed with mutant of Synechocystis sp. cells) (300 shrimp/group/replication) and each trial was conducted in triplicates. After immunization, sixty shrimp (with three replicates of twenty) were collected at 0 h in group N and 24, 72, and 144 h in group M, respectively, and the hepatopancreas were isolated for transcriptomic and metabolomic analysis. Transcriptome data revealed that compared with group N, genes related to antimicrobial peptides, cytoskeleton remodeling, detoxification, apoptosis, blood coagulation, immune defense, and antioxidant systems were differentially expressed in group M. In addition, combined transcriptomic and metabolomic analysis revealed that some immune-related differential genes or differential metabolites were consistently expressed in both omics. All the above results indicated that trans-vp28 gene Synechocystis sp. PCC6803 could improve the immunity of L. vannamei. This is the first report of the integration of dynamic transcriptomics combined with metabolomics to study the effect of trans-vp28 gene Synechocystis sp. PCC6803 in the hepatopancreas of L. vannamei and provided important information about the defense and immune mechanisms used by invertebrates against pathogens.

Comprehensive Transcriptomic and Metabolomic Analysis of the Litopenaeus vannamei Hepatopancreas After WSSV Challenge

Litopenaeus vannamei is the major farmed shrimp species worldwide. White spot disease due to white spot syndrome virus (WSSV) is severely affecting shrimp worldwide, causing extensive economic losses in L. vannamei culture. This is the first study that applied combined transcriptomic and metabolomic analysis to study the effects on the L. vannamei hepatopancreas after WSSV challenge. Our transcriptomic data revealed differentially expressed genes (DEGs) associated with immunity, apoptosis, the cytoskeleton and the antioxidant system in the hepatopancreas of L. vannamei. Metabolomic results showed that WSSV disrupts metabolic processes including amino acid metabolism, lipid metabolism and nucleotide metabolism. After challenged by WSSV, immune-related DEGs and differential metabolites (DMs) were detected in the hepatopancreas of L. vannamei, indicating that WSSV may damage the immune system and cause metabolic disorder in the shrimp. In summary, these results provide new insights into the molecular mechanisms underlying L. vannamei's response to WSSV.

Effects of hydrogen peroxide on Scenedesmus obliquus: Cell growth, antioxidant enzyme activity and intracellular protein fingerprinting

Hydrogen peroxide (H₂O₂) is an environmental-friendly algicide and it is widely used to control algal blooms in aquatic ecosystems. However, the response of algal cell metabolic characteristics and intracellular protein profile under H₂O₂ stress is still not well understood. In the present study, the green alga Scenedesmus obliquus was exposed to different concentrations of H₂O₂ (0, 2, 6, 8 and 10 mg L^-1) to evaluate the changes in algal morphological, physiological, and proteomic features to H₂O₂ exposure. The results showed that 8 mg L^-1 of H₂O₂ could effectively inhibit the cell growth and photosynthetic activity of S. obliquus including chlorophyll-a content and chlorophyll fluorescence parameters. The increased activities of superoxide dismutase (SOD) and catalase (CAT) observed in this study indicate that cells exposure to H₂O₂ caused oxidative stress. The metabolic activity of S. obliquus was significantly decreased by H₂O₂ treatment. In terms of proteomic analysis, 251 differentially expressed proteins (DEPs) were successfully identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed significant protein enrichment in the metabolic pathways, photosynthesis, ascorbic acid, and alginate metabolism and phenylpropane biosynthesis of S. obliquus. The analysis of protein-protein interaction system shows that the pathways of photosynthesis and metabolic pathways of S. obliquus were essential to resist oxidative stress. Taking together, these results shed new lights on exploring the cell physiological metabolism and intracellular protein mechanisms of H₂O₂ inhibition on algal blooms.

A proteomics investigation of 'immune priming' in Penaeus vannamei as shown by isobaric tags for relative and absolute quantification

Invertebrates are considered completely dependent on their innate immunity to defend themselves against pathogens as they lack an adaptive immunity. However, a growing body of evidence has indicated a specific acquired immunity called 'immune priming' may exist. The Pacific white shrimp, Penaeus vannamei is one of the most economically important shrimp species in the world. In the previous research, we investigated the hepatopancreas immune response of shrimp immunized with trans -vp28 gene Synechocystis sp. PCC6803 at the protein level. In this study, on the basis of the previous research, the shrimp were then challenged with WSSV, and hepatopancreas analyzed using isobaric tags for relative and absolute quantification (i TRAQ) labeling. In total, 308 differentially expressed proteins (DEPs) were identified including 84 upregulated and 224 downregulated. Upregulated proteins such as calmodulin B and calreticulin, and downregulated proteins such as calnexin, and signaling pathways like Ras, mTOR were differentially expressed in both studies. Data from this study are more significant than previous work and indicate increased sensitivity to WSSV after immunization with trans-vp28 gene Synechocystis sp. PCC6803. In addition, selected DEPs (upregulated: A0A3R7QHH6 and downregulated: A0A3R7PEF6, A0A3R7MGX8, A0A423TPJ4, and A0A3R7QCC2) were randomly analyzed using parallel reaction monitoring (PRM). These data preliminarily confirm immune priming in P. vannamei, and show that the initial stimulation with trans -vp28 gene Synechocystis sp. PCC6803 regulate P. vannamei immune responses and they provide shrimp with enhanced immune protection against secondary stimulation.

Quantitative proteomic analysis of trachea in fatting pig exposed to ammonia

Ammonia (NH₃) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH₃ is lacking, which is crucial to understanding how NH₃ induces respiratory damage. In this study, we performed labeled quantitative proteomic (TMT-MS) analysis in the trachea of fatting pigs exposed to NH₃ for 30 days. The proteomic results were then validated by Immunohistochemistry (IHC) and Parallel Reaction Monitoring (PRM). The results showed that a total of 126 differentially abundant proteins (DAPs) were identified (fold change <0.83 or > 1.2 and P < 0.05), including 70 differentially up-regulated proteins (DUPs) and 56 differentially down-regulated proteins (DDPs). These proteins were mainly located in intracellular regions and involved in immune response, metabolism and protein synthesis. The results of DAPs (EHHADH, RPL28, SLC25A6, TUBB6, CD14, CTSS, RPS11, RPL19, SLC25A5, RPS8, FABP3, RPL21, RPL34, RPL32, PDIA3, FBP1, HSPH1, SAR1A and SEC24C) verified by IHC and PRM were consistent with the proteomic results. The results of this study provided a basis and a novel insight for understanding the mechanism of NH₃-induced tracheal injury. SIGNIFICANCE: Ammonia (NH₃) is considered as the main pollutant in livestock houses and air environment, and its adverse effects on animal and human health have attracted widespread attention. However, trachea proteomics respond to NH₃ is lacking, which is crucial to understanding how NH₃ induces respiratory damage. Therefore, in this study, labeled quantitative proteomics (TMT-MS) was used to detect trachea tissue samples from finishing pigs in NH₃ exposure group and control group, and PRM method was used to further verify the highly abundant proteins in NH₃ exposure samples, so as to identify new diagnostic markers for NH₃ poisoning. The results of this study provided a basis and a novel insight for understanding the molecular pathological mechanism of NH₃-induced tracheal injury.

Proteomic analysis of hemocyte reveals the immune regulatory mechanisms after the injection of corticosteroid-releasing hormone in mud crab Scylla Paramamosain

Corticosteroid-releasing hormone (CRH) is a crucial neuroendocrine-immune factor regulating the immune response of Scylla paramamosain. To understand the regulatory mechanisms of CRH in S. paramamosain, the hemolymph of S. paramamosain with injection of CRH (1.5 ng/crab) at 24 h were chosen to perform proteomic analysis in this study. Furthermore, quantitative real-time PCR (RT-PCR) method was used to validate the accuracy of proteomic data at 24 h after CRH injection. The proteomic data showed that 255 DEPs were identified, in which 231 and 24 were up- or down-regulated, respectively. Besides, the results of enriched pathways showed that the DEPs were involved in signaling pathways, cellular immunity, humoral immunity and the response of immune related processes. These results revealed that CRH promoted the activation of signal transduction, regulated immune systems and antioxidation, and enhanced the immune related processes (such as protein synthesis, protein transport, carbohydrate mobilization and energy redistribution). These findings will benefit to foster the understanding on the effects of glucocorticoids on neuroendocrine-immune (NEI) networks of crustacean, and supply a substantial material and foundation for further researching of the NEI response. SIGNIFICANCE: Corticotrophin-releasing hormone (CRH) is a 41-amino acid neuropeptide and has been preliminarily studied in aquatic animals. CRH can regulate many important physiological activities comprising protein synthesis, energy metabolism, growth, breeding and behavior in fish, which play an important roles in neuroendocrine-immune (NEI) regulatory network of fish. The neuroendocrine system of crustacean has a primary research, that inspired by fish NEI network. Despite the research on the neuroendocrine system in crustacean has rapidly increased in recent years, our understanding of the regulation between neuroendocrine system and immune system in crustacean is still limited. The research on the strategy of NEI network in crustaceans becomes a significant issue. In the present study, the isobaric tags for relative and absolute quantification (iTRAQ) technology approach were applied to examine the NEI network of Scylla Paramamosain. control group and treatment group (CRH: 1.5 ng/crab) were settled for the iTRAQ experiment, and sampled at 24 h after CRH injection. The study aimed to gain knowledge on the immune response in Scylla Paramamosain after CRH injection and identify related differentially expressed proteins (DEPs) of the crab. The results of this study provide a preliminary resource for analysis the immune mechanism for crustaceans. In general, our work represents the first report of the utilization of the iTRAQ proteomics method for the study of NEI regulatory network in Scylla Paramamosain after CRH injection. We identified a number of DEPs involved in diverse pathways including immune signaling pathways, cellular immunity, humoral immunity, immune related process. These results demonstrated a very complex network involving immune and multiple related metabolic pathways in hemocytes of Scylla Paramamosain and will be of great value in understanding the crab neuroendocrine-immune immune mechanism.

Proteomic analysis of body wall and coelomic fluid in Sipunculus nudus

In order to make clear the protein compositions of Sipunculus nudus and investigate its immune-related proteins, proteomic analysis was performed on body wall and coelomic fluid of Sipunculus nudus. A total of 1659 proteins were identified, and 539 proteins were differentially expressed in the coelomic fluid compared to those in the body wall, of which 415 proteins were up-regulated while 124 proteins were down-regulated. Gene Ontology (GO) analysis showed that the GO terms involved in the two parts of Sipunculus nudus were similar, with metabolic processes, catalytic activity and cell occupying the top categories of biological process, molecular function and cellular component, respectively. KEGG pathway analysis showed that 49 pathways in body wall and 48 in coelomic fluid were mapped respectively, and these pathways were mainly related to cellular processes, environmental information processing, genetic information processing and metabolism. The COG analysis showed that 757 proteins from body wall and 889 from coelomic fluid were classified into 26 COG categories, respectively. Pfam annotation revealed the mainly immune-related proteins contained in Sipunculus nudus, such as insulin-like growth factor binding protein, catalase, basement membrane proteoglycan, titin. Our research provides the first proteomic information of Sipunculus nudus, which contributes to the study of functional proteins in Sipunculus nudus and is of great significance for the application of Sipunculus nudus in functional foods and medicines.