Differentially proteomic analysis of the Chinese shrimp at WSSV latent and acute infection stages by iTRAQ approach

Variation in Shrimp Allergens: Place of Origin Effects on Food Safety Assessment

Due to the widespread use of shellfish ingredients in food products, accurate food labelling is urgently needed for consumers with shellfish allergies. Most crustacean allergen detection systems target the immunorecognition of the allergenic protein tropomyosin. However, this mode of detection may be affected by an origin-dependent protein composition. This study determined if the geographic location of capture, or aquaculture, influenced the allergenic protein profiles of Black Tiger Shrimp (Penaeus monodon), one of the most farmed and consumed shrimp species worldwide. Protein composition was analysed in shrimp from nine different locations in the Asia-Pacific by SDS-PAGE, immunoblotting, and mass spectrometry. Ten of the twelve known shrimp allergens were detected, but with considerable differences between locations. Sarcoplasmic calcium-binding protein, myosin light chain, and tropomyosin were the most abundant allergens in all locations. Hemocyanin-specific antibodies could identify up to six different isoforms, depending on the location of origin. Similarly, tropomyosin abundance varied by up to 13 times between locations. These findings suggest that allergen abundance may be related to shrimp origin and, thus, shrimp origin might directly impact the readout of commercial crustacean allergen detection kits, most of which target tropomyosin, and this should be considered in food safety assessments.

Single-cell RNA-seq revealed heterogeneous responses and functional differentiation of hemocytes against white spot syndrome virus infection in Litopenaeus vannamei

Shrimp hemocytes are the vital immune cells participating in innate immune response to defend against viruses. However, the lack of specific molecular markers for shrimp hemocyte hindered the insightful understanding of their functional clusters and differential roles in combating microbial infections. In this study, we used single-cell RNA sequencing to map the transcriptomic landscape of hemocytes from the white spot syndrome virus (WSSV)-infected Litopenaeus vannamei and conjointly analyzed with our previous published single-cell RNA sequencing technology data from the healthy hemocytes. A total of 16 transcriptionally distinct cell clusters were identified, which occupied different proportions in healthy and WSSV-infected hemocytes and exerted differential roles in antiviral immune response. Following mapping of the sequencing data to the WSSV genome, we found that all types of hemocytes could be invaded by WSSV virions, especially the cluster 8, which showed the highest transcriptional levels of WSSV genes and exhibited a cell type-specific antiviral response to the viral infection. Further evaluation of the cell clusters revealed the delicate dynamic balance between hemocyte immune response and viral infestation. Unsupervised pseudo-time analysis of hemocytes showed that the hemocytes in immune-resting state could be significantly activated upon WSSV infection and then functionally differentiated to different hemocyte subsets. Collectively, our results revealed the differential responses of shrimp hemocytes and the process of immune-functional differentiation post-WSSV infection, providing essential resource for the systematic insight into the synergistic immune response mechanism against viral infection among hemocyte subtypes.

IMPORTANCE

Current knowledge of shrimp hemocyte classification mainly comes from morphology, which hinder in-depth characterization of cell lineage development, functional differentiation, and different immune response of hemocyte types during pathogenic infections. Here, single-cell RNA sequencing was used for mapping hemocytes during white spot syndrome virus (WSSV) infection in Litopenaeus vannamei, identifying 16 cell clusters and evaluating their potential antiviral functional characteristics. We have described the dynamic balance between viral infestation and hemocyte immunity. And the functional differentiation of hemocytes under WSSV stimulation was further characterized. Our results provided a comprehensive transcriptional landscape and revealed the heterogeneous immune response in shrimp hemocytes during WSSV infection.

Integrated characterizations of intestinal bacteria and transcriptomics revealed the acute stress response to carbonate alkalinity in white shrimp Penaeusvannamei

The impact of carbonate alkalinity in saline-alkaline water on aquatic organisms, particularly Penaeus vannamei, a significant species in aquaculture, remains a critical area of study. To elucidate the acute response mechanisms of P. vannamei to elevated carbonate alkalinity environments, we utilized 16S rRNA gene and transcriptome sequencing technologies to analyze intestinal bacteria and gene expressions within various tissues. Our investigation revealed notable changes in specific intestinal bacterial OTUs, whose abundances varied preceding the overall bacterial community, indicating the sensitivity to carbonate alkalinity exposure. These shifts are accompanied by a simplification in bacterial networks and alterations in pathogenic OTUs, notably Aeromonas OTU. Concurrently, gene expression variations were observed across the hepatopancreas, gills, muscles, and intestines, with decreasing numbers of DEGs in the mentioned order. Annotation of these DEGs revealed enrichments in pathways related to transport, catabolism, immune responses, circulatory functions, and lipid metabolism. Notably, correlations between specific intestinal bacterial OTUs and gene expression shifts were identified across these tissues. Several OTUs, attributed to Rhizobiales, Saccharimonadales, Acidovora, and Aeromona, exhibited a correlation with DEGs in all four tissues, primarily associated with amino acid metabolism, signal transduction, and transport and catabolism pathways. Our study provides comprehensive insights into the dynamic responses of P. vannamei to elevated carbonate alkalinity stress. These findings contribute crucial knowledge for effective P. vannamei cultivation in saline-alkaline water, advancing our understanding in this field.

Correlative analysis of transcriptome and proteome in Penaeus vannamei reveals key signaling pathways are involved in IFN-like antiviral regulation mediated by interferon regulatory factor (PvIRF)

Interferon regulatory factors (IRFs) are crucial transcription factors that regulate interferon (IFN) induction in response to pathogen invasion. The regulatory mechanism of IRF has been well studied in vertebrates, but little has been known in arthropods. Therefore, in order to obtain new insights into the potential molecular mechanism of Peneaus vannamei IRF (PvIRF) in response to viral infection, comprehensive comparative analysis of the transcriptome and proteome profiles in shrimp infected with WSSV after knocking down PvIRF was conducted by using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ). The sequence characterization, molecular functional evolution and 3D spatial structure of PvIRF were analyzed by using bioinformatics methods. PvIRF share the higher homology with different species in N-terminal end (containing DNA binding domain (DBD) including DNA sequence recognition sites and metal binding site) than that in C-terminal end. Within 4 IRF subfamilies of vertebrates, PvIRF had closer relationship with IRF1 subfamily. The DBD of PvIRF and C. gigas IRF1a were composed of α-helices and β-folds which was similar with the DBD structure of M. musculus IRF2. Interestingly, different from the five Tryptophan repeats highly homologous in the DBD of vertebrate IRF, the first and fifth tryptophans of PvIRF mutate to Phenylalanine and Leucine respectively, while the mutations were conserved among shrimp IRFs. RNAi knockdown of PvIRF gene by double-strand RNA could obviously promote the in vivo propagation of WSSV in shrimp and increase the mortality of WSSV-infected shrimp. It suggested that PvIRF was involved in inhibiting the replication of WSSV in shrimp. A total of 8787 transcripts and 2846 proteins were identified with significantly differential abundances in WSSV-infected shrimp after PvIRF knockdown, among which several immune-related members were identified and categorized into 10 groups according to their possible functions. Furthermore, the variation of expression profile from members of key signaling pathways involving JAK/STAT and Toll signaling pathway implied that they might participate IRF-mediated IFN-like regulation in shrimp. Correlative analyses indicated that 722 differentially expressed proteins (DEPs) shared the same expression profiles with their corresponding transcripts, including recognition-related proteins (CTLs and ITGs), chitin-binding proteins (peritrophin), and effectors (ALFs and SWD), while 401 DEPs with the opposite expression profiles across the two levels emphasized the critical role of post-transcriptional and post-translational modification. The results provide candidate signaling pathway including pivotal genes and proteins involved in the regulatory mechanism of interferon mediated by IRF on shrimp antiviral response. This is the first report in crustacean to explore the IFN-like antiviral regulation pathway mediated by IRF on the basis of transcriptome and proteomics correlative analysis, and will provide new ideas for further research on innate immune and defense mechanisms of crustacean.

The MEF2 homolog of Penaeus vannamei is essential for maintaining the WSSV latent infection

White spot syndrome virus (WSSV) is a lethal shrimp pathogen that has a latent infection cycle. The latent virus can easily turn into an acute infection when the culture environment changes, leading to widespread shrimp mortality. However, the mechanism of WSSV latent infection is poorly understood. Bioinformatic analysis revealed that the promoters of WSSV latency-related genes (i.e., wsv151, wsv366, wsv403, and wsv427) contained putative myocyte enhancer factor 2 (MEF2) binding sites. This suggested that the transcription factor MEF2 may be involved in WSSV latent infection. To further investigate this, a MEF2 homolog (PvMEF2) was cloned from Penaeus vannamei and its role in WSSV latent infection was explored. The results showed that knockdown of PvMEF2 led to an increase in the copy number of WSSV, indicating reactivation of WSSV from a latent infection. It was further demonstrated that suppression of PvMEF2 significantly decreased expression of the viral latency-related genes in WSSV-latent shrimp, while overexpression of PvMEF2 in Drosophila S2 cells activated the promoter activity of the viral latency-related gene. Additionally, we demonstrated that silencing of PvMEF2 was able to upregulate the expression of pro-apoptosis genes, thereby promoting cell apoptosis during latent infection. Collectively, the present data suggest that PvMEF2 could promote the expression of virus latency-related genes and enhance cell survival to maintain WSSV latent infection. This finding would contribute to a better understanding of the maintenance mechanism of WSSV latent infection.

Proteomic analysis of exosomes in pacific oyster Crassostrea gigas during bacterial stimulation

Exosomes are 30-150 nm-sized extracellular vesicles of endocytic origin that are released into the extracellular environment and play roles in cell-cell communication. Accumulating research achievements demonstrated that exosomes could act as innate immune effectors that contribute to the host defense mechanism. To better understand the immune functions of exosomes in Crassostrea gigas against bacterial stimulation, the iTRAQ LC-MS/MS approach was applied to identifying differentially expressed proteins (DEPs) of exosomes in oyster post Staphylococcus aureus and Vibrio splendidus stimulation. A total of 9467 unique peptides corresponding to 1634 proteins were identified. Among them, 99 proteins were upregulated and 152 were downregulated after S. aureus infection. After V. splendidus infection, 431 proteins were identified as differentially abundant, including 76 that were upregulated and 355 were downregulated. Several proteins related to apoptosis, including E3 ubiquitin-protein ligase, eukaryotic translation initiation factor 3, and protein kinase C delta type were found up-regulated in the S. aureus stimulation group, indicating that the apoptosis process was involved in the response to S. aureus stimulation. Thirty up-regulated and 123 down-regulated proteins were identified as differentially abundant after both bacterial stimuli. Among them, some proteins related to the actin-myosin cytoskeleton process were down-regulated, indicating that phagocytosis may be inhibited in both bacterial stimuli. This study would enrich the C. gigas proteome database and provide information for further understanding the immune functions of oyster exosomes against bacterial infection.

Proteomic changes involved in water holding capacity of frozen bovine longissimus dorsi muscles based on DIA strategy

As freeze/thaw procedure leads to inevitable drip loss, elucidation of mechanism on dynamic changes in water holding capacity (WHC) of muscle is urgently needed. In this study, the proteomic profile by DIA-based strategy, muscle microstructure, water mobility, and WHC indices of bovine longissimus dorsi muscles were investigated under different freezing conditions as well as the correlations among them. Results indicated that slow freezing (SF) sample exhibited significantly higher water mobility, thaw loss, total loss, and shear force value than the samples subjected to fast freezing (FF) and non-frozen control (CON). According to the protein profile, we have identified 272 differential abundance proteins (DAPs), in which more significant proteome changes were found in SF/CON samples as compared with FF/CON. Among the 132 DAPs in FF/SF comparison, correlation analysis revealed that MYL3, DES, SYNE2, EXR, RPL35A, RPS6, and Hsp40 were closely correlated with T₂₃ , thaw loss, and total loss. Accordingly, we considered those seven proteins as potential biomarkers related to WHC of frozen muscle. Our study should give a further understanding on mechanisms behind the various WHC of muscle when subjected to different freezing conditions. PRACTICAL APPLICATIONS: Freezing plays a key role in the preservation method for meat and meat products. However, the drip loss during freezing and subsequent thawing procedure causes considerable economic and nutritional losses. To minimize the losses, elucidation of mechanism on the mechanism of thaw loss formation is urgently needed. DIA-based proteomics is a novel, robust method that provides further understanding on the mechanisms behind the dynamic changes in water holding capacity of muscle. The screened protein biomarkers in frozen muscle would play key roles in the development of WHC, especially for the thaw loss formation. Through this perspective, we can explain the origin of thaw loss and the variation under different freezing conditions, which should provide the meat industries with theoretical basis for reducing losses.

Strategy for understanding the biological defense mechanism involved in immune priming in kuruma shrimp

Since the 1970s, individuals that survive a specific infectious disease among crustaceans reportedly develop resistance to the given virulence factors. Quasi-immune response is a similar phenomenon of acquired resistance against white spot syndrome virus, also found in kuruma shrimp. This phenomenon, resembling immunological memory, is collectively called immune priming and recently attracts increasing attention. In this study, I review, along with recent findings, past attempts to immunize shrimp by administration of the pathogen itself or recombinant proteins of viral constituent factors. Moreover, I aimed at investigating the diversity of pattern recognition receptors in kuruma shrimp from the currently available information that allows for a better understanding of immune priming. This review would potentially help to elucidate the underlying mechanisms of immune priming in the future.

iTRAQ-based quantitative proteomic analysis of differentially expressed proteins in the hepatopancreas of Litopenaeus vannamei after WSSV infection

White spot syndrome virus (WSSV) is the most destructive virus among invertebrates. In this study, we analyzed the immune response after WSSV infection in Pacific white shrimp Litopenaeus vannamei using isobaric tags for relative and absolute quantitation (iTRAQ). We identified 325 differentially expressed proteins (DEPs) in the hepatopancreas of L. vannamei. Among them, 212 were up-regulated proteins, and several of them might be related to immunity (e.g. arginine kinase and peroxiredoxin). Of the 113 down-regulated proteins, some were related to immunity (e.g. cathepsin C and cathepsin L) and others to the antioxidant defense process (e.g. glutathione peroxidase and catalase). One down-regulated DEP (C7M84_014268) and 3 up-regulated DEPs (C7M84_003456, C7M84_020702, and C7M84_007135) were randomly selected and analyzed using parallel reaction monitoring. This study is an important step for a comprehensive understanding of the immune relationship between L. vannamei and WSSV and provides valuable information for the prevention of viral diseases in the crustacean aquaculture industry.

Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp

White Spot Disease (WSD) presents a major barrier to penaeid shrimp production. Mechanisms underlying White Spot Syndrome Virus (WSSV) susceptibility in penaeids are poorly understood due to limited information related to early infection. We investigated mRNA and miRNA transcription in Penaeus vannamei over 36 h following infection. Over this time course, 6192 transcripts and 27 miRNAs were differentially expressed—with limited differential expression from 3–12 h post injection (hpi) and a more significant transcriptional response associated with the onset of disease symptoms (24 hpi). During early infection, regulated processes included cytoskeletal remodelling and alterations in phagocytic activity that may assist WSSV entry and translocation, novel miRNA-induced metabolic shifts, and the downregulation of ATP-dependent proton transporter subunits that may impair cellular recycling. During later infection, uncoupling of the electron transport chain may drive cellular dysfunction and lead to high mortalities in infected penaeids. We propose that post-transcriptional silencing of the immune priming gene Dscam (downregulated following infections) by a novel shrimp miRNA (Pva-pmiR-78; upregulated) as a potential mechanism preventing future recognition of WSSV that may be suppressed in surviving shrimp. Our findings improve our understanding of WSD pathogenesis in P. vannamei and provide potential avenues for future development of prophylactics and treatments.

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.

The iTRAQ-based quantitative proteomics reveals metabolic changes in Scylla paramamosain under different light intensities during indoor overwintering

Light intensity is one of the ecological factors that appreciably affects the metabolism of Scylla paramamosain during overwintering. This study adopted the isobaric tag for relative and absolute quantitation (iTRAQ) method to investigate metabolic changes of S. paramamosain under three illumination levels (0, 1.43 and 40.31 μmol m^-2·s^-1) for four months during indoor overwintering. The iTRAQ identified 3282 proteins, among which 267 exhibited significant differential expression (122 upregulated and 145 downregulated) in the low light group, and 299 with significant differential expression (252 upregulated and 47 downregulated) in the high light group. Analysis of these results showed that there were different metabolic regulatory patterns under different light intensities. Low light is more conducive to the survival of S. paramamosain, which needs to produce and consume relatively less energy to sustain physiological activities. Thus, the essential proteins associated with physiological activities were significantly upregulated, while those related to energy production were significantly downregulated. In contrast, high light exerts a certain stress on the survival of S. paramamosain and required more energy to cope with this stress, which forced a significant upregulation of proteins related to stress response and energy production. The findings of this study highlighted the metabolic regulatory mechanisms of S. paramamosain under different light intensities.

iTRAQ and PRM-based comparative proteomic profiling in gills of white shrimp Litopenaeus vannamei under copper stress

Crustaceans are particularly sensitive to heavy metal pollution. Copper (Cu) is one of typical heavy metal pollutants in aquatic ecosystems. However, limited attention has been paid on the proteomic responses of shrimp under Cu stress. White shrimp Litopenaeus vannamei held in 5‰ seawater were exposed to 5 mg L^-1 Cu for 3 h, and the regulatory mechanism in the gills was elucidated using iTRAQ-based quantitative proteomics. The results showed that a total of 5034 proteins were identified, 385 differentially expressed proteins (DEPs), including 147 differentially up-regulated proteins (DUPs) and 238 differentially down-regulated proteins (DDPs) were found. Bioinformatics analysis indicated the DEPs responding to Cu stress mainly involved in cytoskeleton, immune response, stress response, protein synthesis, detoxification, ion homeostasis and apoptosis. Furthermore, we still performed PRM analysis on sarcoplasmic calcium binding protein (SCP), serine proteinase inhibitor B3 (SPIB3), C-type lectin 4 (CTL4), cathepsin L (CATHL), JHE-like carboxylesterase 1 (CXE1) and paramyosin (PMY), and biochemical analysis on Cu/Zn-superoxide dismutase (Cu/Zn-SOD) to validate the iTRAQ results, respectively. The present proteome analysis revealed that Cu stress disrupted the ion homeostasis and protein synthesis, and L.vannamei mainly regulates a series of molecular pathways which contained many key proteins involved in the immune process to protect the organism from Cu stress. Our data provides more insight about the underlying mechanisms that related to the stress response of Cu exposure in crustacean.

Differentially proteomic analysis of the hemocytes against Aeromonas hydrophila infection in oriental river prawn Macrobrachium nipponense by iTRAQ approach

As the direct executors of biological function, the expression level of proteins in host will reveal the molecular mechanisms regulating bacteria infection more directly. In the present study, the differential proteomes of Macrobrachium nipponense hemocytes response to Aeromonas hydrophila infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography electrospray ionization tandem mass spectrometry. The hemocyte proteins from the unchallenged and A. hydrophila challenged prawn, M. nipponense, at 12, 24 and 36 h post infection were compared. From this, a total of 3372 proteins were identified and 1014 proteins were considered differentially expressed, of which 117 common differentially expressed proteins were indicated between the time points. Hierarchical clustering, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and protein-protein interaction network analyses were performed for the general characterization of overall enriched proteins. Cytoskeletal proteins including myosin heavy chain, myosin regulatory light chain, actin, tubulin alpha/beta chain, troponin I and troponin T as well as antioxidant enzymes such as catalase and cytosolic MnSOD were found significantly up-regulated in hemocytes, indicating that the phagocytosis process and ROS system were induced after challenge with A. hydrophila. And other proteins such as integrin β, innexin inx2-like and heat shock protein 60 also participate in prawn immune response against bacteria. Parallel reaction monitoring analyses were carried out for validation of the expression levels of differentially expressed proteins, which indicated high reliability of the proteomic results. This is the first report on proteome of M. nipponense hemocytes against A. hydrophila infection, which contributes to better understanding on the molecular mechanisms of prawns.

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

Litopenaeus vannamei (Pacific white shrimp) is one of the most commercially important varieties of shrimp cultivated in the world. Shrimp farming is a high-risk, capital-intensive industry that is susceptible to periodic outbreaks of diseases caused by viral and bacterial pathogens. Thus, there is a need to develop economically viable methods of disease control. The hepatopancreas of crustaceans are known to have an important role in their innate immune response. In this study, we have explored the immune response of the hepatopancreas from L. vannamei fed with trans-vp28 gene Synechocystis sp. PCC6803 using iTRAQ-based proteomics. A total of 214 differentially expressed proteins (DEPs) were identified, of which 143 were up-regulated and 71 were down-regulated. These proteins have diverse roles in the cell cytoskeleton and cell phagocytosis, antioxidant defense process and the response of immune related proteins. Among these proteins, the immunity associated with the functional annotation of L. vannamei was further analysed. In addition, 4 DEPs (act1, N/A, H and C7M84_013542) were analysed using parallel reaction monitoring (PRM). This is the first report of proteomics in the hepatopancreas of L. vannamei immunized with trans-vp28 gene Synechocystis sp. PCC6803.

Transcriptomics of Cherax quadricarinatus hepatopancreas during infection with Decapod iridescent virus 1 (DIV1)

Cherax quadricarinatus is a large-sized, highly fecund, and fast-growing species of freshwater crayfish, and has become one of the world's most intensely studied crustaceans. Decapod iridescent virus 1 (DIV1), a newly described species in the family Iridoviridae, is known to infect various crustaceans, including C. quadricarinatus, and may pose a new threat in the shrimp-farming industry. The present study performed de novo transcriptome sequencing of C. quadricarinatus hepatopancreas during DIV1 infection. A total of 114,784 transcripts and 56,418 genes were obtained; 1070 genes were upregulated and 775 genes were downregulated when compared with the uninfected samples (controls). Three pattern recognition receptor genes (fibrinogen-related protein, C-type lectin, and beta-1,3-glucan-binding protein) were upregulated during DIV1 infection. Among the top-30 upregulated unigenes, 9 unigenes were identified as vitellogenin (Vg) genes, and the top-3 upregulated unigenes were identified as involved in Vg lipid transport, lipid localization, and lipid transporter activity, which were all significantly over-representative GO terms in the GO enrichment analysis of total and upregulated differentially expressed genes (DEGs). Many genes associated with Jak-STAT signaling pathway, Endocytosis, Phagosome, MAPK signaling pathway, Apoptosis and Lysosome were positively modified after DIV1 infection. The predicted protein-protein interaction (PPI) analysis showed NF1 and TUBA, CRM1 and TUBB were involved in protein interactions. This research showed that DIV1 infection has a significant impact on the transcriptome profile of C. quadricarinatus hepatopancreas, and the results enhance our understanding of virus-host interactions. Furthermore, the high number of transcripts generated in the present study will provide information for identifying novel genes in the absence of a full C. quadricarinatus genome sequence.

First detection of white spot syndrome virus (WSSV) in the mud shrimp Austinogebia edulis in Taiwan

The white spot syndrome virus (WSSV) causes mass mortalities in the aquaculture of shrimps worldwide. The mud shrimp Austinogebia edulis (Ngoc-Ho & Chan, 1992) is an economically important sea food item occurring along the west coast of Taiwan. While the population of A. edulis began to decrease with some fluctuations in the last decade, the current study aims to discover the causes for such sporadic population decline. This study explores the effects of microbial pathogens and innate immunity on the populations of A. edulis. Here, we report firstly about WSSV infection of A. edulis from the coastal zone of western Taiwan which is one of the possible causes of population decrease of A. edulis in Shengang. However, WSSV infection is not the only reason for its population decrease because a similar infection rate of WSSV was found in Wangong. Population changes may be related to both environmental pollution stress and WSSV. Both factors likely caused a massive reduction of hemocytes and an abnormal increase of phenoloxidase and superoxide dismutase activity, which were spectrophotometrically measured. Since there is no effective way to treat WSSV infection, improving the coastal environment appears the most effective way to increase the population size of feral shrimps.

Comparative proteomic investigation of Marsupenaeus japonicus hepatopancreas challenged with Vibrio parahaemolyticus and white spot syndrome virus

This study aimed to use isobaric tags (IBTs) to investigate the immune response of the hepatopancreas of Marsupenaeus japonicas infected with Vibrio parahaemolyticus or white spot syndrome virus (WSSV). Liquid chromatography-tandem mass spectrometry and protein sequencing identified 1005 proteins. Among them, 109 proteins were upregulated and 94 were downregulated after V. parahaemolyticus infection. After WSSV infection, 130 proteins were identified as differentially abundant, including 88 that were upregulated and 42 were downregulated. Fifty-four proteins were identified as differentially abundant after both V. parahaemolyticus and WSSV infection. A number of proteins related to cytoskeletal processes, including actin and myosin, and apoptosis-related proteins were upregulated in shrimp after V. parahaemolyticus and WSSV infection, indicating that phagocytosis and apoptosis may be involved in the response to in V. parahaemolyticus or WSSV infection. Quantitative real-time PCR was carried out to verify the reliability of the proteomic data. These data provide a basis to characterize the immunity-related processes of shrimp in response to infection with WSSV or V. parahaemolyticus.

The risk of neonicotinoid exposure to shrimp aquaculture

Widespread agricultural use of systemic neonicotinoid insecticides has resulted in the unintended contamination of aquatic environments. Water quality surveys regularly detect neonicotinoids in rivers and waterways at concentrations that could impact aquaculture stock. The toxicity of neonicotinoids to non-target aquatic insect and crustacean species has been recognised, however, there is a paucity of information on their effect on commercial shrimp aquaculture. Here, we show that commercially produced shrimp are likely to be exposed to dietary, sediment and waterborne sources of neonicotinoids; increasing the risks of disease and accidental human consumption. This review examines indicators of sublethal neonicotinoid exposure in non-target species and analyses their potential usefulness for ecotoxicology assessment in shrimp. The identification of rapid, reliable responses to neonicotinoid exposure in shrimp will result in better decision making in aquaculture management.

Proteomic profiling of the white shrimp Litopenaeus vannamei (Boone, 1931) hemocytes infected with white spot syndrome virus reveals the induction of allergy-related proteins

To elucidate the proteomic responses of shrimp hemocytes to white spot syndrome virus (WSSV) infection at the proteome level, a quantitative shotgun proteomic analysis was performed to detect differentially synthesized proteins in infected hemocytes of white shrimp (Litopenaeus vannamei). We identified 1528 proteins associated to 203 gene ontology (GO) categories. The most representative GO categories were regulation of cellular processes, organic substance metabolic processes and nitrogen compound metabolic processes. Most of the 83 detected up-regulated proteins are involved in DNA regulation and organization and cell signaling. In contrast, most of the 40 down-regulated proteins were related to immune defense processes, protein folding, and development. Differentially induced proteins were further analyzed at the transcript level by RT-qPCR to validate the results. This work provides new insights into the alterations of L. vannamei hemocytes at the protein level at 12 h post-infection with WSSV. Interestingly, several of the up-regulated proteins are allergy-related proteins in humans. Based on our results, we suggest a deeper analysis of the effects of this interaction on the regulation of allergy related-proteins as their up-regulation during WSSV could represent a threat to human health.

Development of a primary culture system for haematopoietic tissue cells from Cherax quadricarinatus and an exploration of transfection methods

Various known and unknown viral diseases can threaten crustacean aquaculture. To develop prophylactic and therapeutic strategies against viruses, crustacean cell lines are urgently needed for immunology and virology studies. However, there are currently no permanent crustacean cell lines available. In this study, we developed a new method for preparing crayfish plasma (CP) and found that CP enhanced the proliferative capacity of haematopoietic tissue (hpt) cells from Cherax quadricarinatus by an EdU (5-ethynyl-2'-deoxyuridine) assay. The optimal CP concentration for hpt cell culture and the optimal subculture method are discussed. To achieve efficient expression of a foreign gene in hpt cells cultured in vitro, different transfection methods and vectors were analysed. We found that Lipofectamine 2000 could be used to efficiently transfect a foreign vector into hpt cells and exhibited a lower level of cytotoxicity than the other methods tested, and transfection of pEGFP-N1/w249 and pDHsp70-EGFP-FLAG resulted in high EGFP expression. By transmission electron microscopy (TEM) and virus copy number analysis, we found that white spot syndrome virus (WSSV) could infect hpt cells and multiply efficiently. Our results implied that the crayfish hpt cell culture system we improved could be used as a replacement for immortal crustacean cell lines in viral infection studies. Our findings provide a solid foundation for future immortalization and gene function studies in crustacean cells.

Differential proteome of haemocyte subpopulations responded to white spot syndrome virus infection in Chinese shrimp Fenneropenaeus chinensis

In our previous study, the differentially expressed proteins have been identified by proteomic analysis in total haemocytes of shrimp (Fenneropenaeus chinensis) after white spot syndrome virus (WSSV) infection. To further investigate the differential response of haemocyte subpopulations to WSSV infection, granulocytes and hyalinocytes were separated from healthy and WSSV-infected shrimp by immunomagnetic bead (IMB) method, respectively. Then two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) were used to analyze the differentially expressed proteins in haemocyte subpopulations between healthy and WSSV-infected shrimp. The results of flow cytometry (FCM) showed that about 98% of granulocytes and about 96% of hyalinocytes in purity were obtained. Quantitative intensity analysis revealed that 26 protein spots in granulocytes and 24 spots in hyalinocytes were significantly changed post WSSV infection. Among them, 24 proteins in granulocytes and 23 proteins in hyalinocytes were identified by MS analysis, which could be divided into eight categories according to Gene Ontology. The identification of prophenoloxidase (proPO), proPO 2 and peroxiredoxin in WSSV-infected granulocytes was consistent with the facts that the proPO-activating system and peroxiredoxin were mainly existed in granulocytes. The phagocytosis of hyalinocytes seemed to be enhanced during the infection, because several proteins that involved in phagocytosis, including clathrin heavy chain, ADP ribosylation factor 4 and Alpha2 macroglobulin were up-regulated in hyalinocytes upon WSSV infection. Our results also reflected the vital biological significance of calcium ion binding proteins in granulocytes and ATPase/GTPase in hyalinocytes during WSSV infection. The data in this study verified the roles of granulocytes and hyalinocytes involved in WSSV infection, and differentially expressed proteins identified in granulocytes and hyalinocytes had a close correlation with their function characteristics.

iTRAQ-based comparative proteome analysis for molecular mechanism of defense against acute ammonia toxicity in Pacific White shrimp Litopenaeus vannamei

In the practical farming of Litopenaeus vannamei, the intensive culture system and environmental pollution usually results in a high concentration of ammonia, which brings large detrimental effects to shrimp, such as increasing the susceptibility to pathogens and even causing high mortality. We have revealed that the survival time under acute ammonia stress varied substantially among different families and obtained ammonia-tolerant (LV_T) and ammonia-sensitive (LV_S) families. In order to understand the molecular mechanism of defense against ammonia toxicity in shrimp, we performed iTRAQ LC-MS/MS proteomic analysis between LV_T and LV_S groups of L. vannamei under acute ammonia stress to identify the key proteins and pathways that play an effective role for against ammonia toxicity. By comparative proteome analysis, 202 significantly differentially proteins (DEPs) were identified in LV_T compared to LV_S, and most of the DEPs (60%) were up-regulated. Excepting for the proteins without function reporting, the meaningful finding is that 77.8% of the DEPs have been reported mainly involving in immune defense and stress tolerant in crustacean species, such as hemocyanin, Rab7, Rab GTPase, Rac1, alpha 2 macroglobulin, Bip, peroxiredoxin, Cu/Zn SOD, glutathione peroxidase, thioredoxin, calreticulin, and Elongation Factor 1-alpha, etc. These DEPs might potentially play important role in against ammonia toxicity, and it also reflected a relation between ammonia tolerance and pathogen resistance. In addition, a total of 10 significantly changed KEGG pathways were detected, and the network diagram of these KEGG pathways showed that more critical nodes were up-regulated, which involved in protein synthesis and transport, and against stress stimuli. This study provided important information for understanding the molecular mechanism of defense against ammonia toxicity in shrimp at whole protein level.

Transcriptome profiling of the Macrobrachium rosenbergii lymphoid organ under the white spot syndrome virus challenge

Macrobrachium rosenbergii is a crustacean with economic importance, and adult prawns are generally thought to be tolerant to white spot syndrome virus (WSSV) infection. Although certain genes are known to respond to WSSV infection and lymphoid tissue is an important immune organ, the response of lymphoid organ to WSSV infection is unclear. Next-generation sequencing was employed in this study to determine the transcriptome differences between WSSV infection and mock lymphoid organs. A total of 44,606,694 and 40,384,856 clean reads were generated and assembled into 73,658 and 72,374 unigenes from the control sample and the WSSV infection sample, respectively. Based on homology searches, KEGG, GO, and COG analysis, 21,323 unigenes were annotated. Among them, 4951 differential expression genes were identified and categorized into 244 metabolic pathways. Coagulation cascades, and pattern recognition receptor signaling pathways were used as examples to discuss the response of host to WSSV infection. We also identified 12,308 simple sequence repeats, which can be further used as functional markers. Results contribute to a better understanding of the immune response of prawn lymphoid organ to WSSV and provide information for identifying novel genes in the absence of the prawn genome.

Molecular Characterization of Viral Responsive Protein 15 and Its Possible Role in Nuclear Export of Virus in Black Tiger Shrimp Penaeus monodon

A viral responsive protein 15 from Penaeus monodon (PmVRP15) has been reported to be important for white spot syndrome virus (WSSV) infection in vivo. This work aims to characterize PmVRP15 and investigate its possible role in nuclear import/export of the virus. Circular dichroism spectra showed that PmVRP15 contains high helical contents (82%). Analytical ultracentrifugation suggested that PmVRP15 could possibly form oligomers in solution. A subcellular fractionation study showed that PmVRP15 was found in heavy and light membrane fractions, indicating that PmVRP15 may be associated with endoplasmic reticulum. Double-stranded RNAi-mediated knockdown of PmVRP15 gene expression in vitro showed no effect on WSSV copy number in whole hemocyte cells. However, PmVRP15 silencing resulted in an accumulation of WSSV DNA in the nucleus of PmVRP15-silenced hemocytes. Immunofluorescence confocal microscopy showed that PmVRP15 knockdown hemocytes had a much lower level of VP28 (WSSV envelope protein), in comparison to that in the control. It is likely that PmVRP15 may play a role in viral nuclear egress.

A Proteomic Study of Hemocyte Proteins from Mud Crab (Scylla paramamosain) Infected with White Spot Syndrome Virus or Vibrio alginolyticus

In this study, we investigated the hemocytes' immune response to white spot syndrome virus (WSSV) or Vibrio alginolyticus infection at the protein level. The differential proteomes from crab hemocytes infected with WSSV or V. alginolyticus were analyzed using the isobaric tags for relative and absolute quantitation approach immediately after infection. Using this approach, we identified 1,799 proteins by their by LC-MS/MS spectra and sequencing data. These included 157 upregulated proteins and 164 downregulated proteins after WSSV infection. Similarly, 243 proteins were determined to be differentially expressed during V. alginolyticus infection, of these, 121 were upregulated and 122 were downregulated after infection. Interestingly, among these differentially expressed proteins, 106 were up- or downregulated significantly in both WSSV and V. alginolyticus infection. Six genes, β-actin, myosin-9, anti-lipopolysaccharide factor isoform 4, anti-lipopolysaccharide factor 4, transketolase-like protein 2-like isoform 1, and sarcoplasmic calcium-binding protein 1 were chosen for further study. The expression of these genes all showed a trend of upregulation at 24 h post-WSSV or V. alginolyticus infection except for myosin-9 in response to WSSV. To confirm the protective effects of the six genes, crabs were injected with specific dsRNAs before WSSV or V. alginolyticus challenge. The results showed that the knockdown of these genes led to an increase in the morbidity and mortality (P < 0.01) rate, and a decrease in infection time in WSSV-infected crabs. During the first 84 h, knockdown of these genes also led to an increase in the morbidity rates in V. alginolyticus -infected crabs, and results of four genes showed a higher mortality rate than that of the control after they were knocked down. This is the first report of the proteome response in crab hemocytes during WSSV or V. alginolyticus infection. These findings will contribute to our understanding of the immune response to WSSV and V. alginolyticus infection in crabs.