iTRAQ-based proteomic study of the effects of Spiroplasma eriocheiris on Chinese mitten crab Eriocheir sinensis hemocytes

Integrated Information for Pathogenicity and Treatment of Spiroplasma

Spiroplasma, belonging to the class Mollicutes, is a small, helical, motile bacterium lacking a cell wall. Its host range includes insects, plants, and aquatic crustaceans. Recently, a few human cases of Spiroplasma infection have been reported. The diseases caused by Spiroplasma have brought about serious economic losses and hindered the healthy development of agriculture. The pathogenesis of Spiroplasma involves the ability to adhere, such as through the terminal structure of Spiroplasma, colonization, and invasive enzymes. However, the exact pathogenic mechanism of Spiroplasma remains a mystery. Therefore, we systematically summarize all the information about Spiroplasma in this review article. This provides a reference for future studies on virulence factors and treatment strategies of Spiroplasma.

The crosstalk between Toll and AMPK signaling pathways mediates growth inhibition of Eriocheir sinensis under deltamethrin stress

Hepatopancreatic necrosis disease (HPND) broke out in 2015 in the Eriocheir sinensis aquaculture region of Xinghua, Jiangsu Province; however, the specific cause of HPND remains unclear. A correlation was found between HPND outbreak and the use of deltamethrin by farmers. In this study, E. sinensis specimens developed the clinical symptoms of HPND after 93 days of deltamethrin stress. The growth of E. sinensis with HPND was inhibited. Adenosine monophosphate-activated protein kinase (AMPK) is a central regulator of energy homeostasis, and its expression was up-regulated in the intestine of E. sinensis with HPND. Growth inhibitory genes (EsCabut, Es4E-BP, and EsCG6770) were also up-regulated in the intestine of E. sinensis with HPND. The expression levels of EsCabut, Es4E-BP, and EsCG6770 decreased after EsAMPK knockdown. Therefore, AMPK mediated the growth inhibition of E. sinensis with HPND. Further analysis indicated the presence of a crosstalk between the Toll and AMPK signaling pathways in E. sinensis with HPND. Multiple genes in the Toll signaling pathway were upregulated in E. sinensis under 93 days of deltamethrin stress. EsAMPK and its regulated growth inhibition genes were down-regulated after the knockdown of genes in the Toll pathway. In summary, the crosstalk between the Toll and AMPK signaling pathways mediates the growth inhibition of E. sinensis under deltamethrin stress.

Hemolymph exosomes inhibit Spiroplasma eriocheiris infection by promoting Tetraspanin-mediated hemocyte phagocytosis in crab

Exosomes released from infected cells are thought to play an important role in the dissemination of pathogens, as well as in host-derived immune molecules during infection. As an intracellular pathogen, Spiroplasma eriocheiris is harmful to multiple crustaceans. However, the immune mechanism of exosomes during Spiroplasma infection has not been investigated. Here, we found exosomes derived from S. eriocheiris-infected crabs could facilitate phagocytosis and apoptosis of hemocytes, resulting in increased crab survival and suppression of Spiroplasma intracellular replication. Proteomic analysis revealed the altered abundance of EsTetraspanin may confer resistance to S. eriocheiris, possibly by mediating hemocyte phagocytosis in Eriocheir sinensis. Specifically, knockdown of EsTetraspanin in E. sinensis increased susceptibility to S. eriocheiris infection and displayed compromised phagocytic ability, whereas overexpression of EsTetraspanin in Drosophila S2 cells inhibited S. eriocheiris infection. Further, it was confirmed that intramuscular injection of recombinant LEL domain of EsTetraspanin reduced the mortality of S. eriocheiris-infected crabs. Blockade with anti-EsTetraspanin serum could exacerbate S. eriocheiris invasion of hemocytes and impair hemocyte phagocytic activity. Taken together, our findings prove for the first time that exosomes modulate phagocytosis to resist pathogenic infection in invertebrates, which is proposed to be mediated by exosomal Tetraspanin, supporting the development of preventative strategies against Spiroplasma infection.

Proteomics of the haemolymph of the terrestrial crustacean Porcellio scaber reveals components of its innate immunity under baseline conditions

The terrestrial crustacean Porcellio scaber is an established test organism in environmental research. We analysed the haemolymph proteome of P. scaber using a classical proteomic approach based on one-dimensional gel electrophoresis and tandem mass spectrometry. Using a publicly available protein database and our P. scaber transcriptome data, we have identified 76 proteins involved in cytoskeleton formation, protein degradation, vesicular transport, genetic information processing, detoxification, carbohydrate and lipid metabolism reflecting haemocyte metabolic activity, active intracellular transport, and intercellular communication. Compared with the data reported for other crustaceans, 28 of these P. scaber proteins have been linked to its immunity, among them hemocyanin, α-2-macroglobulin, phenoloxidase 3, superoxide dismutase, glutathione S-transferase, haemolymph clottable protein, and histones H4 and H2B. Our results thus provide a firm base for studying the innate immune response of P. scaber at the level of the haemolymph proteome. This knowledge is of particular importance in ecotoxicity studies with various environmental stressors where understanding physiological changes is important to reveal possible modes of action.

Current Disease Threats for Cultivated Crab Eriocheir sinensis in China

The Chinese mitten crab, Eriocheir sinensis, is a commercially important crustacean in China due to its great commercial value and compatibility in a variety of aquaculture systems. However, increases in its production have been accompanied by the emergence of various diseases affecting yield, profit, and trading potential. In this study, we review the pathogenic agents associated with E. sinensis since the start of its commercial culture. The history of crab cultivation implies that increased pathogen transfer can occur as E. sinensis aquaculture grows because polyculture of E. sinensis with other aquaculture species is a prevalent practice. With this in mind, a special focus of this review is placed on pathogens that were initially discovered in other crustacean species but have since been demonstrated to infect and cause disease in E. sinensis. We expect that this review will not only offer recommendations for disease management in the E. sinensis aquaculture sector but will also advance other crustacean cultivation.

iTRAQ-based proteomic analysis reveals the underlying mechanism of postmortem tenderization of refrigerated porcine Longissimus thoracis et lumborum muscle

The isobaric tags for relative and absolute quantitation (iTRAQ) technology was used for differential proteomic analysis of refrigerated porcine Longissimus thoracis et lumborum (LTL) muscle at different time points postmortem (45 min, 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h) to mechanistically elucidate the postmortem tenderization. Compared with the proteins identified in porcine LTL muscle at 45 min postmortem (control), 862 proteins were significantly expressed at 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h postmortem. Moreover, clustering and path analysis showed that the quality traits of porcine LTL muscle, including pH, shear force, myofibril fragmentation index, correlated significantly with 2, 6 and 6 differentially expressed proteins, respectively, with the lowest or highest expression at 8 h or 12 h postmortem. Overall, the tenderness of refrigerated porcine LTL muscle might be significantly affected by changes in quality traits at 8 h and 12 h postmortem.

Comparative transcriptome, digital gene expression and proteome profiling analyses provide insights into the brachyurization from the megalopa to the first juvenile in Eriocheir sinensis

Eriocheir sinensis larva normally experiences 11 stages. The reduced abdomen folded beneath the thorax is the most prominent characteristic of morphological alteration from megalopa to juvenile crab. Up to date, the molecular mechanisms of brachyurization remain a mystery. Here, transcriptome library, digital gene expression (DGE) libraries and proteome libraries at two developmental stages [the megalopa stage of E. sinensis (stage M) and the first stage of juvenile crab (stage J1)] of the Chinese mitten crab larva were constructed for RNA sequencing and iTRAQ approaches followed by bioinformatics analysis, respectively. In total, 1106 genes and 871 proteins were differentially expressed between the stage M and stage J1. Moreover, several important pathways were identified, including biosynthesis of secondary metabolites, metabolic pathways, focal adhesion, and some disease pathways. Besides, muscle contraction, oxidative phosphorylation, calcium signaling, PI3K-Akt, DNA replication pathway, and integrin signaling pathway also had important functions in brachyurization process. Furthermore, the components, actin, actin-related protein, collagens, filamin-A/B, laminin, integrins, paxillin, and fibronectin had up-regulated expression levels in M stage compared to J1 stage.

Metabolomic and metagenomic analyses of the Chinese mitten crab Eriocheir sinensis after challenge with Metschnikowia bicuspidata

Milky disease caused by Metschnikowia bicuspidata fungus has significantly harmed the Chinese mitten crab Eriocheir sinensis aquaculture industry. However, the effect of M. bicuspidata infection on the metabolism and intestinal flora of the crab remains unclear. In this study, we aimed to explore the changes in the metabolism and intestinal flora E. sinensis after 48 h of infection with M. bicuspidata, using metabolomic and metagenomic analyses. Metabolomic analysis results revealed 420 significantly different metabolites between the infected and control groups, and these metabolites were enriched in 58 metabolic pathways. M. bicuspidata infection decreased the levels of metabolites related to amino acid biosynthesis, the tricarboxylic acid cycle, as well as lysine, histidine, linolenic, arachidonic, and linoleic acid metabolism. These results indicated that M. bicuspidata infection significantly affected the energy metabolism, growth, and immunity of E. sinensis. The results of metagenomic analysis showed that the anaerobes and ascomycetes populations significantly increased and decreased, respectively, after M. bicuspidata infection. These changes in intestinal flora significantly upregulated metabolic and synthetic pathways while downregulating immunity-related pathways. The results of integrated metabolomic and metagenomic analyses showed that 55 differentially expressed genes and 28 operational taxonomic units were correlated with 420 differential metabolites. Thus, the intestinal flora changes caused by M. bicuspidata infection also affected the metabolites. This study provides novel insights into the metabolic-and intestinal microflora-based effects of M. bicuspidata infection in E. sinensis, as well as a theoretical basis for the interaction between fungi and crustaceans.

A proteomics approach reveals digestive and nutritional responses to food intake in anadromous Coilia nasus

The estuarine tapertail anchovy, Coilia nasus, is an anadromous fish that undertakes over a 600-km spawning migration along the Yangtze River of China. They generally cease feeding during this process, but we recently documented that a small proportion of them appear to feed. Research on proteomic responses is essential for understanding the phenomenon of C. nasus feeding. In this study, we used an iTRAQ-based proteomics approach to study the changes in protein expression in response to food intake in C. nasus following voluntary fasting. Coilia nasus in the feeding group (CSI) were fed shrimp or small fish, whereas those in the control group (CSN) were starved. We identified 3279 proteins in the gastric tissue/stomach, of which 279 were significantly differentially expressed. In all, 133 differentially expressed proteins (DEPs) were upregulated and 146 proteins were downregulated in CSI compared with those in CSN C. nasus. In addition to gastric acid secretion caused by gastric distention, a functional analysis suggested that a series of DEPs were involved mainly in the regulation of protein digestion (e.g., carboxypeptidase A1 and chymotrypsin A-like), immune response (e.g., lysozyme and alpha 2-macroglobulin), and nutrition metabolism (e.g., glyceraldehyde 3-phosphate dehydrogenase, glycogenin, long-chain acyl-CoA synthetase, and creatine kinase). Real-time PCR confirmed that the mRNA levels of the DEPs were similar those obtained using iTRAQ. These results indicate that the nutrients obtained through food were effectively utilized by C. nasus, thereby providing energy for swimming, gonadal maturation, primary metabolism, and an enhanced immune function to better resist pathogen interference. This research contributes to the elucidation of nutritional regulation mechanisms of C. nasus to better protect the wild population.

Ubiquitin-modified proteome analysis of Eriocheir sinensis hemocytes during Spiroplasma eriocheiris infection

Spiroplasma eriocheiris, the pathogen of Eriocheir sinensis tremor disease (TD), has bring a huge economic loss to China aquaculture. The hemocytes of crab as the first target cells of S. eriocheiris, but the interactive relationship between the E. sinensis and this pathogen not particularly clear. The present study is the first time to analysis the role of protein ubiquitination in the process of E. sinensis hemocytes response S. eriocheiris infection. By applying label-free quantitative liquid chromatography with tandem mass spectrometry proteomics, 950 lysine ubiquitination sites and 803 ubiquitination peptides on 458 proteins were identified, of which 48 ubiquitination sites on 40 proteins were quantified as significantly changed after the S. eriocheiris infection. Bioinformatics analysis of ubiquitination different proteins suggested many biological process and pathways were participated in the interaction between S. eriocheiris and host cell, such as ubiquitin system, endocytosis, prophenoloxidase system (proPO system), cell apoptosis, glycolysis. Our study can enhance our understanding of interaction between the crab and S. eriocheiris, and also provides basis to study the role of protein ubiquitination in other crustacean innate immune system.

The Elevated Expressions of Anti-lipopolysaccharide Factors After Priming Stimulation Confer Lastingly Humoral Protection in Crab Eriocheir sinensis

Evidence of immune memory in invertebrates (immune priming) has accumulated in various organisms, and both cellular and humoral immune reactions are speculated to be involved in immune priming. However, there is a lack of understanding of the molecular mechanisms involved. In the present study, the protective effect of primed haemolymph was further validated by the increased survival rate of naïve crabs receiving a transfusion of primed haemolymph. By proteomic analysis, there were 474 proteins identified from the primed haemolymph, and most of them were functionally annotated in transport and metabolism classes. A total of 70 proteins were found to be differentially expressed in haemolymph at 12 hours and 7 days after priming stimulation with Aeromonas hydrophila, among which anti-lipopolysaccharide factor 1 (EsALF-1) and 3 (EsALF-3) were identified as the most significant (p < 0.05). After being challenged with A. hydrophila, EsALF-1 and EsALF-3 were highly expressed at both mRNA (in haemocytes) and protein (in haemolymph) levels compared with blank crabs, and the mRNA expressions of components in the EsTLR1-EsMyd88-EsPelle-EsALF pathway also increased significantly (p < 0.05). The EsALF-3 and EsMyd88 were even significantly higher expressed in response to the second A. hydrophila challenge, but their expressions all decreased (p < 0.05) when EsTLR1 was knocked down by RNAi. After the naïve crabs received an injection with the recombinant protein of EsALF-1 (rEsALF-1) or EsALF-3 (rEsALF-3), their survival rate increased significantly (p < 0.05) upon A. hydrophila stimulation. In contrast, the survival rate of the primed crabs reduced significantly (p < 0.05) after they received an injection with the antibody of EsALF-1 or EsALF-3. The enhanced expressions of EsALF-1 and EsALF-3 after A. hydrophilap riming stimulation could sustain for four weeks. All the results suggested that the EsTLR1-mediated productions of EsALF-1 and EsALF-3 in haemolymph played an indispensable role in the month-long humoral immune protection induced by A. hydrophila, which provides solid evidence of immune priming in crabs and a valuable reference for further understanding immune memory in invertebrates.

Proteomic Analysis of the Hemolymph After Metschnikowia bicuspidata Infection in the Chinese Mitten Crab Eriocheir sinensis

The “milky disease” of the Chinese mitten crab, Eriocheir sinensis, is a highly lethal fungal disease caused by Metschnikowia bicuspidata infection. To elucidate the immune responses of the hemolymph of E. sinensis to M. bicuspidata infection, a comparative analysis of the hemolymph of E. sinensis infected with M. bicuspidata and that treated with phosphate buffered saline was performed using label-free quantitative proteomics. A total of 429 proteins were identified. Using a 1.5-fold change in expression as a physiologically significant benchmark, 62 differentially expressed proteins were identified, of which 38 were significantly upregulated and 24 were significantly downregulated. The upregulated proteins mainly included cytoskeleton-related proteins (myosin regulatory light chain 2, myosin light chain alkali, tubulin α-2 chain, and tubulin β-1 chain), serine protease and serine protease inhibitor (clip domain-containing serine protease, leukocyte elastase inhibitor, serine protein inhibitor 42Dd), catalase, transferrin, and heat shock protein 70. Upregulation of these proteins indicated that phenoloxidase system, phagocytosis and the ROS systems were induced by M. bicuspidata. The downregulated proteins were mainly organ and tissue regeneration proteins (PDGF/VEGF-related factor protein, integrin-linked protein kinase homing pat-4 gene) and hemagglutination-associated proteins (hemolymph clottable protein, hemocyte protein-glutamine gamma-glutamyltransferase). Downregulation of these proteins indicated that M. bicuspidata inhibited hemocyte regeneration and hemolymph agglutination. Fifteen differentially expressed proteins related to immunity were verified using a parallel reaction monitoring method. The expression trend of these proteins was similar to that of the proteome. To the best of our knowledge, this is the first report on the proteome of E. sinensis in response to M. bicuspidata infection. These results not only provide new and important information on the immune response of crustaceans to yeast infection but also provide a basis for further understanding the molecular mechanism of complex host pathogen interactions between crustaceans and fungi.

Identification of β tubulin IVb as a pattern recognition receptor with opsonic activity

Previous studies have shown that tubulins play important role in immune responses of both plants and animals, but no experiments have been performed to study the mode of action of tubulins in immune defense. In addition, there is little convincing experimental evidence of functional commitment for specific tubulin isotypes in animals. In the present, we showed that expression of β-tubulin IVb gene was affected by both LPS and LTA, hinting its involvement in anti-infectious response. We also showed that recombinant zebrafish β-tubulin IVb not only interacted with LPS and LTA as well as Gram-negative and -positive bacteria but also agglutinated both Gram-negative and -positive bacteria in a Ca²⁺-dependent fashion. Interestingly, recombinant β-tubulin IVb could enhance the phagocytosis of bacteria by macrophages. Moreover, we demonstrated that β-tubulin IVb was present extracellularly in the serum of zebrafish and mouse. Collectively, these suggest that β-tubulin IVb may be physiologically involved in the systematic immunity of host via acting as a pattern recognition receptor and an opsonin. This also provides a new angle to understand the roles of β-tubulin IVb.

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.

Integrated transcriptomic and proteomic analyses of grass carp intestines after vaccination with a double-targeted DNA vaccine of Vibrio mimicus

Intestinal mucosal immunity plays a vital role against Vibrio mimicus infection because it is an enteric pathogen causing serious vibriosis in fish. In the previous studies, we developed an oral double-targeted DNA vaccine of V. mimicus and demonstrated that the vaccine could elicit significantly higher intestinal mucosal immune response than did naked DNA vaccine. But, little is known underlying regulatory molecular mechanisms of the enhanced intestinal mucosal immunity. Here the transcriptome and proteome in the intestines of the grass carps immunized or not with the double-targeted DNA vaccine were investigated by using RNA-seq and iTRAQ-coupled LC-MS/MS. Compared with the control group, a total of 5339 differentially expressed genes (DEGs) and 1173 differentially expressed proteins (DEPs) were identified in the immunized fish intestines. Subsequently, the integrated analysis between transcriptome and proteome data revealed that 250 DEPs were matched with the corresponding DEGs (named associated DEPs/DEGs) at both transcriptome and proteome levels. Fifty of all the associated DEPs/DEGs were immune-related and mainly enriched in phagosome, antigen-processing and presentation, complement and coagulation cascades, NLRs and MAPK signaling pathways via Gene Ontology and KEGG pathway analyses, which suggested the coordination of the five activated pathways was essential to the enhanced intestinal mucosal immune response in the immunized fish. The protein-protein interaction analysis showed that 60 of the 63 immune-related DEPs to form an integrated network. Additionally, randomly selected DEGs and DEPs were respectively validated by quantitative real-time RT-PCR and multiple reaction monitoring (MRM) assay, indicating that the both RNA-Seq and iTRAQ results in the study were reliable. Overall, our comprehensive transcriptome and proteome data provide some key genes and their protein products for further research on the regulatory molecular mechanisms underlying the enhanced intestinal mucosal immunity.

Transcriptome analysis of hepatopancreas of Eriocheir sinensis with hepatopancreatic necrosis disease (HPND)

Hepatopancreatic necrosis disease (HPND) is a newly emerging disease in the Chinese mitten crab, Eriocheir sinensis, which has resulted in large economic losses. However, the underlying cause of this disease remains unclear. To better understand the pathogenesis and pathogenic mechanism of HPND, we compared the transcriptome differences of the hepatopancreas of E. sinensis with and without HPND. The analysis yielded > 30 million reads for each sample of three test (with HPND) and three control groups (without HPND). We observed 978 downregulated genes and 644 upregulated genes. Among the gene ontology categories "biological process," "cellular component," and "molecular function", the subcategories cellular process, single-organism process, biological regulation, metabolic process, cell part, organelle, organelle part, binding, and catalytic were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that "metabolism of xenobiotics by cytochrome P450," "drug metabolism-cytochrome P450," "chemical carcinogenesis," and "material metabolism" were the "five" most significantly enriched pathways in the hepatopancreas of E. sinensis with HPND. The results revealed that material metabolic abnormalities and drug effects from the external environment might be associated with HPND in the Chinese mitten crab. Considering the wide use of pyrethroids for pond cleaning in Xinghua city, we speculated that pyrethroids might cause HPND in the Chinese mitten crab. Our study provided useful information about the cause and pathogenetic mechanisms of HPND and could help to prevent this disease in production practice.

Comparative Proteomics on Deep-Sea Amphipods after in Situ Copper Exposure

The interest in deep-sea mining increased along with the environmental concerns of these activities to the deep-sea fauna. The discovery of optimal biomarkers of deep-sea mining activities in deep-sea species is a crucial step toward the supply of important ecological information for environmental impact assessment. In this study, an in situ copper exposure experiment was performed on deep-sea scavenging amphipods. Abyssorchomene distinctus individuals were selected among all the exposed amphipods for molecular characterization. Copper concentration within the gut was assessed, followed by a tandem mass tag-based coupled with two-dimensional liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) applied to identify and quantify the protein expression changes after 48 h of exposure. 2937 proteins were identified and annotated, and 1918 proteins among all identified proteins were assigned by at least two nonambiguous peptides. The screening process was performed based on the differences in protein abundance and the specific correlation between the proteins and copper in previous studies. These differentially produced proteins include Na⁺/K⁺ ATPase, cuticle, chitinase, and proteins with unknown function. Their abundances showed correlation with copper and had high sensitivity to indicate the copper level, being here proposed as biomarker candidates for deep-sea mining activities in the future. This is a key step in the development of environmental impact assessment of deep-sea mining activities integrating ecotoxicological data.

Transcriptomic analysis of Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in response to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus

Acute hepatopancreatic necrosis disease (AHPND), caused by marine bacteria Vibrio Parahaemolyticus, is a huge problem in shrimp farms. The V. parahaemolyticus infecting material is contained in a plasmid which encodes for the lethal toxins PirABVp, whose primary target tissue is the hepatopancreas, causing sloughing of epithelial cells, necrosis, and massive hemocyte infiltration. To get a better understanding of the hepatopancreas response during AHPND, juvenile shrimp Litopenaeus vannamei were infected by immersion with V. parahaemolyticus. We performed transcriptomic mRNA sequencing of infected shrimp hepatopancreas, at 24 hours post-infection, to identify novel differentially expressed genes a total of 174,098 transcripts were examined of which 915 transcripts were found differentially expressed after comparative transcriptomic analysis: 442 up-regulated and 473 down-regulated transcripts. Gene Ontology term enrichment analysis for up-regulated transcripts includes metabolic process, regulation of programmed cell death, carbohydrate metabolic process, and biological adhesion, whereas for down-regulated transcripts include, microtubule-based process, cell activation, and chitin metabolic process. The analysis of protein- protein network between up and down-regulated genes indicates that the first gene interactions are connected to oxidation-processes and sarcomere organization. Additionally, protein-protein networks analysis identified 20-top highly connected hub nodes. Based on their immunological or metabolic function, ten candidate transcripts were selected to measure their mRNA relative expression levels in AHPND infected shrimp hepatopancreas by RT-qPCR. Our results indicate a close connection between the immune and metabolism systems during AHPND infection. Our RNA-Seq and RT-qPCR data provide the possible immunological and physiological scenario as well as the molecular pathways that take place in the shrimp hepatopancreas in response to an infectious disease.

Integrated Analysis of Transcriptomic, miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis

Heterosis is a complex biological phenomenon in which hybridization produces offspring that exhibit superior phenotypic characteristics compared with the parents. Heterosis is widely utilized in agriculture, for example in fish farming; however, its underlying molecular basis remains elusive. To gain a comprehensive and unbiased molecular understanding of fish heterosis, we analyzed the mRNA, miRNA, and proteomes of the livers of three catfish species, Pelteobagrus fulvidraco, P. vachelli, and their hybrid, the hybrid yellow catfish "Huangyou-1" (P. fulvidraco ♀ × P. vachelli ♂). Using next-generation sequencing and mass spectrometry, we show that the nonadditive, homoeolog expression bias and expression level dominance pattern were readily identified at the transcriptional, post-transcriptional, or protein levels, providing the evidence for the widespread presence of dominant models during hybridization. A number of predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM assays. Furthermore, several diverse key pathways were identified, including immune defense, metabolism, digestion and absorption, and cell proliferation and development, suggesting the vital mechanisms involved in the generation of the heterosis phenotype in progenies. We propose that the high parental expression of genes/proteins (growth, nutrition, feeding, and disease resistance) coupled with low parental miRNAs of the offspring, are inherited from the mother or father, thus indicating that the offspring were enriched with the advantages of the father or mother. We provide new and important information about the molecular mechanisms of heterosis, which represents a significant step toward a more complete elucidation of this phenomenon.

Proteomic and metabolomic responses in hepatopancreas of whiteleg shrimp Litopenaeus vannamei infected by microsporidian Enterocytozoon hepatopenaei

Enterocytozoon hepatopenaei (EHP) causes hepatopancreatic microsporidiosis (HPM) in shrimp. HPM is not normally associated with shrimp mortality, but is associated with significant growth retardation. In this study, the responses induced by EHP were investigated in hepatopancreas of shrimp Litopenaeus vannamei using proteomics and metabolomics. Among differential proteins identified, several (e.g., peritrophin-44-like protein, alpha2 macroglobulin isoform 2, prophenoloxidase-activating enzymes, ferritin, Rab11A and cathepsin C) were related to pathogen infection and host immunity. Other proteomic biomarkers (i.e., farnesoic acid o-methyltransferase, juvenile hormone esterase-like carboxylesterase 1 and ecdysteroid-regulated protein) resulted in a growth hormone disorder that prevented the shrimp from molting. Both proteomic KEGG pathway (e.g., "Glycolysis/gluconeogenesis" and "Glyoxylate and dicarboxylate metabolism") and metabolomic KEGG pathway (e.g., "Galactose metabolism" and "Biosynthesis of unsaturated fatty acids") data indicated that energy metabolism pathway was down-regulated in the hepatopancreas when infected by EHP. More importantly, the changes of hormone regulation and energy metabolism could provide much-needed insight into the underlying mechanisms of stunted growth in shrimp after EHP infection. Altogether, this study demonstrated that proteomics and metabolomics could provide an insightful view into the effects of microsporidial infection in the shrimp L. vannamei.

iTRAQ analysis of liver immune-related proteins from darkbarbel catfish (Pelteobagrus vachelli) infected with Edwardsiella ictaluri

Edwardsiella ictaluri causes enteric septicemia of catfish (ESC), a major disease occurring in these siluriform fish. As the liver is an important organ for defending against bacterial pathogens in fish, this study aimed to determine the liver immune response at the protein level. The differential proteomes of the darkbarbel catfish liver in response to E. ictaluri infection were identified with isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using a 1.2-fold change in expression as a physiologically significant benchmark, a total of 819 differentially expressed proteins were reliably quantified using iTRAQ analysis, including 6 up-regulated proteins and 813 down-regulated proteins. GO enrichment analysis indicated that the "complement activation, alternative pathway" and "complement activation, classical pathway" were significantly enriched. KEGG enrichment analysis indicated the "antigen processing and presentation" and "bacterial secretion system" were significantly enriched. We selected the 6 up-regulated proteins and 10 immune-related down-regulated proteins for validation using real-time PCR. The 10 immune-related proteins included complement component C1r, C3, C5, C7, and C9 and plasma protease C1 inhibitor (C1-INH), signal recognition particle 54 kDa protein (SRP54), SRP receptor, proteasome activator complex subunit 1 (PSME1) and major histocompatibility complex class I (MHC class I) were selected from the GO clusters and KEGG pathways. The variations in mRNA expression for these genes were similar to the results of iTRAQ. This is the first report detailing the proteome response in the darkbarbel catfish liver during E. ictaluri infection and markedly contributes to our understanding of the defense mechanisms in the livers of darkbarbel catfish.

ITRAQ-Based Quantitative Proteomics Reveals the Proteome Profiles of Primary Duck Embryo Fibroblast Cells Infected with Duck Tembusu Virus

Outbreaks of duck Tembusu virus (DTMUV) have caused substantial economic losses in the major duck-producing regions of China since 2010. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of DTMUV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with multidimensional liquid chromatography-tandem mass spectrometry to detect the protein changes in duck embryo fibroblast cells (DEFs) infected and mock-infected with DTMUV. In total, 434 cellular proteins were differentially expressed, among which 116, 76, and 339 proteins were differentially expressed in the DTMUV-infected DEFs at 12, 24, and 42 hours postinfection, respectively. The Gene Ontology analysis indicated that the biological processes of the differentially expressed proteins were primarily related to cellular processes, metabolic processes, biological regulation, response to stimulus, and cellular organismal processes and that the molecular functions in which the differentially expressed proteins were mainly involved were binding and catalytic activity. Some selected proteins that were found to be differentially expressed in DTMUV-infected DEFs were further confirmed by real-time PCR. The results of this study provide valuable insight into DTMUV-host interactions. This could lead to a better understanding of DTMUV infection mechanisms.

Proteomic profile in the mussel Perna viridis after short-term exposure to the brown tide alga Aureococcus anophagefferens

Blooms of Aureococcus anophagefferens, referred to as brown tides are responsible for massive mortalities and recruitment failure of some bivalves. However, the molecular mechanisms underlying the toxicity remain elusive despite its biological significance, and the information currently available on the molecular effects is still insufficient. In this study, to evaluate the toxicity and associated mechanism of A. anophagefferens on bivalves, we analyzed the protein expression profiles in digestive glands of the A. anophagefferens-exposed Perna viridis by using iTRAQ. A total of 3138 proteins were identified in the digestive glands of A. anophagefferens-exposed P. viridis based on iTRAQ. Amongst, a repertoire of 236 proteins involved in cell, cell part, catalytic activity, metabolic process, biological regulation, immune system process, and response to stimulus were found to be differentially expressed. Functional analysis of the differentially expressed proteins demonstrated that innate immune system of P. viridis was activated, and some proteins associated with stress response and lipid metabolism were induced after exposure to A. anophagefferens. Additionally, MDA content, SOD activity and GSH-Px activity was increased significantly in the digestive gland of A. anophagefferens-exposed P. viridis. Taken together, our results indicated that the A. anophagefferens could induce oxidative stress, activate complement system and alter fat acid metabolism of P. viridis.

Characterization of cathepsin D from Eriocheir sinensis involved in Spiroplasma eriocheiris infection

Cathepsin D (catD) belongs to a lysosomal aspartic protease superfamily. The full-length catD cDNA from the Chinese mitten crab Eriocheir sinensis (EscatD) was 2748 bp and contained a 1158-bp ORF encoding a protein of 385 amino acids, including a signal peptide and two N-glycosylation sites. Phylogenetic analysis showed that EscatD was clustered into a single group, together with other catD for crustaceans. Quantitative real-time PCR revealed that EscatD was expressed mainly in the eyes, hemocytes, intestine and nerve and was expressed weakly in heart, muscle and gills. After challenge with Spiroplasma eriocheiris, the expression of EscatD was significantly up-regulated from 1 d to 9 d. The copy number of S. eriocheiris in a silencing EscatD group was significantly higher than those in the control groups during S. eriocheiris infection. Meanwhile, the survival rate of crabs decreased in an EscatD-dsRNA group. We further found that knockdown of EscatD by RNA interference resulted in a downward trend of expression levels of JNK, ERK, relish and p38 during the early stage, as well as a reduction in the expression of five antimicrobial peptides genes, namely, crusrin1, crustin2, ALF1, ALF2 and ALF3. The subcellular localization experiment suggested that recombinant EscatD was mainly located in the cytoplasm. The over-expression in Drosophila S2 cells indicated that EscatD could decrease the copy number of S. eriocheiris and increase cell viability. The above results demonstrated that EscatD plays an important immune role in E. sinensis to S. eriocheiris challenge.

Comparative transcriptomic analysis of crab hemocytes in response to white spot syndrome virus or Vibrio alginolyticus infection

To assess the immune response of hemocytes to white spot syndrome virus (WSSV) or Vibrio alginolyticus infection in the mud crab Scylla paramamosain, a transcriptome analysis was performed. We report the analysis of 45131 transcripts from S. paramamosain hemocytes by de novo assembly. A comparison with GenBank protein and nucleotide sequences identified 33699 genes as previously known. The length distribution of the genes was 8147 genes ≥200 bp, 4714 genes ≥300 bp, and 3517 genes ≥2000 bp. A total of 21579 simple sequence repeats (SSRs) were found in the transcriptomic dataset, including 9% monomers, 53.34% dimers and 32.55% trimers. A total of 13172 and 5087 differentially expressed transcripts were found in the V. alginolyticus-infected group and WSSV-infected group, respectively. Of these, 5920 transcripts were up-regulated and 7252 were down-regulated in the V. alginolyticus-infected crabs and 2302 transcripts were up-regulated and 2785 were down-regulated in the WSSV-infected crabs. Additionally, 3096 transcripts were differentially expressed simultaneously in the V. alginolyticus-infected crabs and the WSSV-infected crabs. Several known immune-related genes such as heat shock protein, Janus kinase, STAT, relish, caspase, Ca²⁺-transporting ATPase and lysosomal alpha-mannosidase were found among the differentially expressed transcripts. Transcription and its regulation were significant biological processes, and ATP binding and zinc ion binding were significant molecular functions. This is the first report of comparative transcriptomic analysis of crab hemocytes in response to WSSV or V. alginolyticus infection. These findings will contribute to our understanding of the immune response to WSSV and V. alginolyticus infection in crustaceans.

The function of Eriocheir sinensis transferrin and iron in Spiroplasma eriocheiris infection

Transferrin, a member of the iron binding superfamily protein, plays an extremely important role in the transport of iron in the biological process of cells. The result of preliminary proteomic study on E. sinensis hemocytes infected Spiroplasma eriocheiris showed the expression of transferrin (EsTF) and ferrin (EsFe) significantly changed. In addition, other reports have confirmed that transferrin, ferritin and iron are involved in the immune response of hosts. In order to validate the immune function of EsTF, the whole length of EsTF was successfully amplified by the gene cloning and RACE technique. The results showed that the full-length cDNA of the EsTF gene was 2748 bp, including a 2193 bp open reading frame which encodes 730 amino acids. The result of bioinformatics analysis showed EsTF contains two highly conserved TR_FER domains. Evolutionary analysis showed that EsTF has a close genetic relationship with other TFs of invertebrates. In addition, EsTF mRNA was highly transcripted in nerve and intestine tissues, followed by hemocytes. The expression of EsTF, EsFe1 and EsFe2 increased after exogenous supplemental of iron under the concentration of 100 nmol/L in water. After exogenous supplement of iron and injection with S. eriocheiris, these three gene transcription of mRNA levels were higher than that of PBS group, while lower than the S. eriocheiris group and the iron group. Besides, the copy number of S. eriocheiris in the experimental group was significantly reduced, and the death rate decreased. As can be seen, iron made transferrin and ferritin return to normal levels during the infection of S. eriocheiris and help the host maintain normal immunity levels to resist S. eriocheiris. These results further demonstrated that EsTF, EsFe1, EsFe2 and iron play a role in the immune defense mechanism of the crabs to resist S. eriocheiris infection.

iTRAQ-based quantitative proteomic analysis of Procambarus clakii hemocytes during Spiroplasma eriocheiris infection

As a new-found aquaculture pathogen, Spiroplasma eriocheiris, has resulted in inconceivable economic losses in aquaculture. In the infection of S. eriocheiris, the Procambarus clakii hemocytes have indicated to be major target cells. What was designed to examine in our study is the hemocytes' immune response at the protein levels. Before the pathogen was injected and after 192 h of post-injection, the differential proteomes of the crayfish hemocytes were analyzed immediately by isobaric tags for relative and absolute quantization (iTRAQ) labeling, followed by liquid chromatogramphytandem mass spectrometry (LC-MS/MS). This research had identified a total of 285 differentially expressed proteins. Eighty-three and 202 proteins were up-regulated and down-regulated, respectively, caused by the S. eriocheiris infection. Up-regulated proteins included alpha-2-macroglobulin (α2M), vitellogenin, ferritin, etc. Down-regulated proteins, involved with serine protease, peroxiredoxin 6, 14-3-3-like protein, C-type lectin, cdc42 homolog precursor, etc. The prophenoloxidase-activating system, antimicrobial action involved in the immune responses of P. clarkii is considered to be damaged due to S. eriocheiris infection. The present work could lay the foundation for future research on the proteins related to the susceptibility/resistance of P. clarkii to S. eriocheiris. In addition, it is helpful for our understanding molecular mechanism of disease processes in crayfishes.

Understanding the regulatory mechanisms of milk production using integrative transcriptomic and proteomic analyses: improving inefficient utilization of crop by-products as forage in dairy industry

BACKGROUND

Bovine milk is an important nutrient source for humans. Forage plays a vital role in dairy husbandry via affecting milk quality and quantity. However, the differences in mammary metabolism of dairy cows fed different forages remain elucidated. In this study, we utilized transcriptomic RNA-seq and iTRAQ proteomic techniques to investigate and integrate the differences of molecular pathways and biological processes in the mammary tissues collected from 12 lactating cows fed corn stover (CS, low-quality, n = 6) and alfalfa hay (AH, high-quality, n = 6).

RESULTS

A total of 1631 differentially expressed genes (DEGs; 1046 up-regulated and 585 down-regulated) and 346 differentially expressed proteins (DEPs; 138 increased and 208 decreased) were detected in the mammary glands between the CS- and AH-fed animals. Expression patterns of 33 DEPs (18 increased and 15 decreased) were consistent with the expression of their mRNAs. Compared with the mammary gland of AH-fed cows, the marked expression changes found in the mammary gland of CS group were for genes involved in reduced mammary growth/development (COL4A2, MAPK3, IKBKB, LGALS3), less oxidative phosphorylation (ATPsynGL, ATP6VOA1, ATP5H, ATP6VOD1, NDUFC1), enhanced lipid uptake/metabolism (SLC27A6, FABP4, SOD2, ACADM, ACAT1, IDH1, SCP2, ECHDC1), more active fatty acid beta-oxidation (HMGCS1), less amino acid/protein transport (SLC38A2, SLC7A8, RAB5a, VPS18), reduced protein translation (RPS6, RPS12, RPS16, RPS19, RPS20, RPS27), more proteasome- (PSMC2, PSMC6, PSMD14, PSMA2, PSMA3) and ubiquitin-mediated protein degradation (UBE2B, UBE2H, KLHL9, HSPH1, DNAJA1 and CACYBP), and more protein disassembly-related enzymes (SEC63, DNAJC3, DNAJB1, DNAJB11 and DNAJC12).

CONCLUSION

Our results indicate that the lower milk production in the CS-fed dairy cows compared with the AH-fed cows was associated with a network of mammary gene expression changes, importantly, the prime factors include decreased energy metabolism, attenuated protein synthesis, enhanced protein degradation, and the lower mammary cell growth. The present study provides insights into the effects of the varying quality of forages on mammary metabolisms, which can help the improvement of strategies in feeding dairy cows with CS-based diet.

iTRAQ-based proteomic analysis identifies proteins involved in limb regeneration of swimming crab Portunus trituberculatus

The swimming crab (Portunus trituberculatus) has a striking capacity for limb regeneration, which has drawn the interest of many researchers. In this study, isobaric tag for relative and absolute quantitation (iTRAQ) approach was utilised to investigate protein abundance changes during limb regeneration in this species. A total of 1830 proteins were identified, of which 181 were significantly differentially expressed, with 94 upregulated and 87 downregulated. Our results highlight the complexity of limb regeneration and its regulation through cooperation of various biological processes including cytoskeletal changes, extracellular matrix (ECM) remodelling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism. Additionally, real-time PCR confirmed that mRNA levels of differentially expressed genes were correlated with protein levels. Our results provide a basis for studying the regulatory mechanisms associated with crab limb regeneration.

Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.)

The fleshy taproot of radish is an important storage organ determining its yield and quality. Taproot thickening is a complex developmental process in radish. However, the molecular mechanisms governing this process remain unclear at the proteome level. In this study, a comparative proteomic analysis was performed to analyze the proteome changes at three developmental stages of taproot thickening using iTRAQ approach. In total, 1862 differentially expressed proteins (DEPs) were identified from 6342 high-confidence proteins, among which 256 up-regulated proteins displayed overlapped accumulation in S1 (pre-cortex splitting stage) vs. S2 (cortex splitting stage) and S1 vs. S3 (expanding stage) pairs, whereas 122 up-regulated proteins displayed overlapped accumulation in S1 vs. S3 and S2 vs. S3 pairs. Gene Ontology (GO) and pathway enrichment analysis showed that these DEPs were mainly involved in several processes such as "starch and sucrose metabolism", "plant hormone signal transduction", and "biosynthesis of secondary metabolites". A high concordance existed between iTRAQ and RT-qPCR at the mRNA expression levels. Furthermore, association analysis showed that 187, 181, and 96 DEPs were matched with their corresponding differentially expressed genes (DEGs) in S1 vs. S2, S1 vs. S3, and S2 vs. S3 comparison, respectively. Notably, several functional proteins including cell division cycle 5-like protein (CDC5), expansin B1 (EXPB1), and xyloglucan endotransglucosylase/hydrolase protein 24 (XTH24) were responsible for cell division and expansion during radish taproot thickening process. These results could facilitate a better understanding of the molecular mechanism underlying taproot thickening, and provide valuable information for the identification of critical genes/proteins responsible for taproot thickening in root vegetable crops.

Changes in the gut microbiome of the Chinese mitten crab (Eriocheir sinensis) in response to White spot syndrome virus (WSSV) infection

Intestinal microorganisms play important roles in maintaining host health, but their functions in aquatic animal hosts have yet to be fully elucidated. The Chinese mitten crab, Eriocheir sinensis, is one such example. We attempted to identify the shift of gut microbiota that occurred in response to infection of white spot syndrome virus (WSSV), an emerging viral pathogen in the crab aquaculture industry. The microbiota may exert some control over aspects of the viral pathogenesis. We investigated the changes in composition and structure of the crab gut microbiome during various WSSV infection stages of 6 h post-infection (hpi) and 48 hpi, using a 16S rRNA approach on the MiSeq Illumina sequencing platform. Four phyla (Firmicutes, Proteobacteria, Tenericutes and Bacteroidetes) were most dominant in the gut of E. sinensis regardless of the WSSV infection stages. However, further analysis revealed that over 12 bacterial phyla, 44 orders and 68 families were significantly different in abundance at various states of WSSV infection. Several intriguing aspects of E. sinensis gut bacteria that had not been previously reported were also uncovered, such as class Mollicutes was dominant here, but absent in crabs from Yangtze River estuary and Chongming Islands. Overall, this study provided the first evidence that changes in gut microbiome were closely associated with the severity of WSSV infection and that indicator taxa could be used to evaluate the crab health status.

Immune regulation effect of lienal polypeptides extract in Lewis lung carcinoma-bearing mice treated with cyclophosphamide

Polypeptides extracted from animal immune organs have been proved to exert immunomodulatory activities in previous reports. However, relative experimental data regarding the influence of a polypeptide mixture extracted from healthy calf spleen (lienal polypeptide [LP]) on the immune function in tumor therapy are limited, and the components in LP remain unclear. In the present study, the immune regulatory effect of LP was investigated in normal mice and Lewis lung carcinoma (LLC)-bearing mice treated with cyclophosphamide (CTX). The components of LP were identified by liquid chromatography-electrospray ionization-coupled with tandem mass spectrometry (LC-MS/MS) analysis and bioinformatic analysis. In LLC-bearing mice, LP showed a synergic antitumor effect with CTX, whereas LP alone did not present direct antitumor activity. Further, LP was found to enhance immune organ indexes, splenocyte number, and T lymphocyte subsets in normal mice and LLC-bearing mice treated with CTX. The decline of white blood cell and platelet counts, splenocyte proliferation activity, and peritoneal macrophage phagocytic function caused by CTX were also significantly suppressed by LP treatment in LLC-bearing mice. Notably, LP treatment significantly decreased the expression of phagocytosis-related proteins including CD47/signal regulatory protein α/Src homology phosphatase-1 in the tumor tissue of LLC-bearing mice treated with CTX. LC-MS/MS-based peptidomics unraveled the main polypeptides in LP with a length from 8 to 25 amino acids. Bioinformatics analysis further confirmed the possibility of LP to regulate immunity, especially in phagocytosis-related pathway. Our above findings indicated that LP can relieve the immunosuppression induced by chemotherapy and is a beneficial supplement in cancer therapy. Impact statement The immunomodulatory activities of polypeptides extracted from animal immune organs have incurred people's interests since a long time ago. In this study, we investigated the immune regulation effects of a polypeptide mixture extracted from health calf spleen (lienal polypeptide [LP]) in Lewis lung carcinoma-bearing mice treated with cyclophosphamide (CTX). Liquid chromatography-electrospray ionization-coupled with tandem mass spectrometry-based peptidomics and bioinformatics analysis unraveled the main polypeptides in LP and further confirmed that LP is mainly associated with immune regulating pathway, especially in tumor cell phagocytosis-related pathway. Our study for the first time revealed that polypeptides from spleen can relieve the immunosuppression induced by CTX and is a beneficial supplement in cancer therapy.

Transcriptional responses in the hepatopancreas of Eriocheir sinensis exposed to deltamethrin

Deltamethrin is an important pesticide widely used against ectoparasites. Deltamethrin contamination has resulted in a threat to the healthy breeding of the Chinese mitten crab, Eriocheir sinensis. In this study, we investigated transcriptional responses in the hepatopancreas of E. sinensis exposed to deltamethrin. We obtained 99,087,448, 89,086,478, and 100,117,958 raw sequence reads from control 1, control 2, and control 3 groups, and 92,094,972, 92,883,894, and 92,500,828 raw sequence reads from test 1, test 2, and test 3 groups, respectively. After filtering and quality checking of the raw sequence reads, our analysis yielded 79,228,354, 72,336,470, 81,859,826, 77,649,400, 77,194,276, and 75,697,016 clean reads with a mean length of 150 bp from the control and test groups. After deltamethrin treatment, a total of 160 and 167 genes were significantly upregulated and downregulated, respectively. Gene ontology terms "biological process," "cellular component," and "molecular function" were enriched with respect to cell killing, cellular process, other organism part, cell part, binding, and catalytic. Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes showed that the metabolic pathways were significantly enriched. We found that the CYP450 enzyme system, carboxylesterase, glutathione-S-transferase, and material (including carbohydrate, lipid, protein, and other substances) metabolism played important roles in the metabolism of deltamethrin in the hepatopancreas of E. sinensis. This study revealed differentially expressed genes related to insecticide metabolism and detoxification in E. sinensis for the first time and will help in understanding the toxicity and molecular metabolic mechanisms of deltamethrin in E. sinensis.

Comparative Proteomic Analysis of Paulownia fortunei Response to Phytoplasma Infection with Dimethyl Sulfate Treatment

Paulownia fortunei is a widely cultivated economic forest tree species that is susceptible to infection with phytoplasma, resulting in Paulownia witches' broom (PaWB) disease. Diseased P. fortunei is characterized by stunted growth, witches' broom, shortened internodes, and etiolated and smaller leaves. To understand the molecular mechanism of its pathogenesis, we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography coupled with tandem mass spectrometry approaches to study changes in the proteomes of healthy P. fortunei, PaWB-infected P. fortunei, and PaWB-infected P. fortunei treated with 15 mg·L⁻¹ or 75 mg·L⁻¹ dimethyl sulfate. We identified 2969 proteins and 104 and 32 differentially abundant proteins that were phytoplasma infection responsive and dimethyl sulfate responsive, respectively. Based on our analysis of the different proteomes, 27 PaWB-related proteins were identified. The protein-protein interactions of these 27 proteins were analyzed and classified into four groups (photosynthesis-related, energy-related, ribosome-related, and individual proteins). These PaWB-related proteins may help in developing a deeper understanding of how PaWB affects the morphological characteristics of P. fortunei and further establish the mechanisms involved in the response of P. fortunei to phytoplasma.

Interaction of heat shock protein 60 (HSP60) with microRNA in Chinese mitten crab during Spiroplasma eriocheiris infection

Heat shock protein 60 from the Chinese mitten crab Eriocheir sinensis (EsHSP60) was previously identified in relation to Spiroplasma eriocheiris infection by isobaric tags for relative and absolute quantitation labelling followed by liquid chromatography-tandem mass spectrometry. In the present study, to validate the immune function of this protein, the cDNA of the EsHSP60 gene was cloned. Various crab tissues were assessed using real-time PCR, which showed that EsHSP60 transcription occurred in all tissues examined. The expression profiles of EsHSP60 in haemolymph at transcription and protein levels when infected with S. eriocheiris were investigated by real-time PCR and Western blot analysis, respectively. A significant increase of EsHSP60 transcription and protein expression appeared post-injection in response to S. eriocheiris infection when compared to the control group. The double-luciferase reporter gene assay showed that the microRNA PC-533-3p interacted with the 3'-untranslated region of EsHSP60 and inhibited the translation of EsHSP60. The expression profiles of PC-533-3p during S. eriocheiris infection were also investigated by real-time PCR. However, the change tendency of PC-533-3p was opposite to that of the EsHSP60 after S. eriocheiris challenge. These data indicate that the EsHSP60 proteins may play an important role in mediating the immune responses of E. sinensis to an S. eriocheiris challenge.

Dissecting the proteome dynamics of the salt stress induced changes in the leaf of diploid and autotetraploid Paulownia fortunei

Exposure to high salinity can trigger acclimation in many plants. Such an adaptative response is greatly advantageous for plants and involves extensive reprogramming at the molecular level. Acclimation allows plants to survive in environments that are prone to increasing salinity. In this study, diploid and autotetraploid Paulownia fortunei seedlings were used to detect alterations in leaf proteins in plants under salt stress. Up to 152 differentially abundant proteins were identified by Multiplex run iTRAQ-based quantitative proteomic and LC-MS/MS methods. Bioinformatics analysis suggested that P. fortunei leaves reacted to salt stress through a combination of common responses, such as induced metabolism, signal transduction, and regulation of transcription. This study offers a better understanding of the mechanisms of salt tolerance in P. fortunei and provides a list of potential target genes that could be engineered for salt acclimation in plants, especially trees.

Development of In situ hybridization and real-time PCR assays for the detection of Hepatospora eriocheir, a microsporidian pathogen in the Chinese mitten crab Eriocheir sinensis

A microsporidian parasite, Hepatospora eriocheir, is an emerging pathogen for the Chinese mitten crab Eriocheir sinensis. Currently, there is scant information about the way it transmits infection in the crustacean of commercial importance, including its pathogenesis, propagation and infection route in vivo. In this study, chromogenic in situ hybridization (ISH) and quantitative real-time PCR (qPCR) assays were developed to address this pressing need, and we provided an advance in the detection methods available. Pathogens can be seen in situ with associated lesions using ISH. Positive hybridization signals were noted inside the epithelial cells of the hepatopancreas, and putative free parasite spores were observed within the tubule lumen, which were associated with lesions detected by electron microscopy and haematoxylin and eosin (H&E) analysis. qPCR allows the determination of parasite loads in infected tissues, which is important for understanding disease progression and transmission. The hepatopancreas displayed the biggest statistical copy numbers among different tissues of infected crabs, confirming a tissue-specific pathogen infection characteristic. The qPCR assay also proved to be suitable for the diagnosis of asymptomatic carrier crabs. Combination of the two methods could facilitate the study of H. eriocheir infection mechanism in E. sinensis, enhance the early diagnosis of the pathogen and improve the management of microsporidian diseases in commercial crustaceans.

Proteome profiling reveals immune responses in Japanese flounder (Paralichthys olivaceus) infected with Edwardsiella tarda by iTRAQ analysis

The liver is an important organ for bacterial pathogen attack in fish. The differential proteomic response of the Japanese flounder liver to Edwardsiella tarda infection was examined using isobaric tags for relative and absolute quantitation (iTRAQ) labeling followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 3290 proteins were identified and classified into categories related to biological process (51.4%), molecular function (63.6%), and cellular component (57.7%). KEGG enrichment analysis indicated the complement and coagulation cascade pathways and the mineral absorption pathway were significantly enriched. Among the differentially expressed proteins, those involved in mediating complement cascade (e.g. complement component C7, C8, C9, complement factor H, complement factor Bf/C2) and mineral absorption (e.g. ferritin, STEAP-4) were most significantly upregulated during infection. Subsequently, five significantly upregulated (C4, C8beta, ferritin middle subunit, PRDX4-like and KRT18) and one significantly downregulated (transferrin) candidate immune proteins were validated by multiple reaction monitoring (MRM) assays. Furthermore, changes in expression of 15 proteins in the complement cascade and mineral absorption pathways were validated at the transcriptional level using quantitative real-time PCR (qPCR). The transcriptional levels of four transcription factors (p21Ras, Rab-31-like, NF-κB, STAT3) were also investigated by qPCR following infection with E. tarda. This study contributes to understanding the defense mechanisms of the liver in fish.

Comparative proteomic analysis of eggplant (Solanum melongena L.) heterostylous pistil development

Heterostyly is a common floral polymorphism, but the proteomic basis of this trait is still largely unexplored. In this study, self- and cross-pollination of L-morph and S-morph flowers and comparison of embryo sac development in eggplant (Solanum melongena L.) suggested that lower fruit set from S-morph flowers results from stigma-pollen incompatibility. To explore the molecular mechanism underlying heterostyly development, we conducted isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis of eggplant pistils for L- and S-morph flowers. A total of 5,259 distinct proteins were identified during heterostyly development. Compared S-morph flowers with L-morph, we discovered 57 and 184 differentially expressed proteins (DEPs) during flower development and maturity, respectively. Quantitative real time polymerase chain reactions were used for nine genes to verify DEPs from the iTRAQ approach. During flower development, DEPs were mainly involved in morphogenesis, biosynthetic processes, and metabolic pathways. At flower maturity, DEPs primarily participated in biosynthetic processes, metabolic pathways, and the formation of ribosomes and proteasomes. Additionally, some proteins associated with senescence and programmed cell death were found to be upregulated in S-morph pistils, which may lead to the lower fruit set in S-morph flowers. Although the exact roles of these related proteins are not yet known, this was the first attempt to use an iTRAQ approach to analyze proteomes of heterostylous eggplant flowers, and these results will provide insights into biochemical events taking place during the development of heterostyly.

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.

Proteome Profiling of Paulownia Seedlings Infected with Phytoplasma

Phytoplasma is an insect-transmitted pathogen that causes witches' broom disease in many plants. Paulownia witches' broom is one of the most destructive diseases threatening Paulownia production. The molecular mechanisms associated with this disease have been investigated by transcriptome sequencing, but changes in protein abundance have not been investigated with isobaric tags for relative and absolute quantitation. Previous results have shown that methyl methane sulfonate (MMS) can help Paulownia seedlings recover from the symptoms of witches' broom and reinstate a healthy morphology. In this study, a transcriptomic-assisted proteomic technique was used to analyze the protein changes in phytoplasma-infected Paulownia tomentosa seedlings, phytoplasma-infected seedlings treated with 20 and 60 mg·L^-1 MMS, and healthy seedlings. A total of 2,051 proteins were obtained, 879 of which were found to be differentially abundant in pairwise comparisons between the sample groups. Among the differentially abundant proteins, 43 were related to Paulownia witches' broom disease and many of them were annotated to be involved in photosynthesis, expression of dwarf symptom, energy production, and cell signal pathways.

Identifying Virulence-Associated Genes Using Transcriptomic and Proteomic Association Analyses of the Plant Parasitic Nematode Bursaphelenchus mucronatus

Bursaphelenchus mucronatus (B. mucronatus) isolates that originate from different regions may vary in their virulence, but their virulence-associated genes and proteins are poorly understood. Thus, we conducted an integrated study coupling RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic data of highly and weakly virulent B. mucronatus isolates during the pathogenic processes. Approximately 40,000 annotated unigenes and 5000 proteins were gained from the isolates. When we matched all of the proteins with their detected transcripts, a low correlation coefficient of r = 0.138 was found, indicating probable post-transcriptional gene regulation involved in the pathogenic processes. A functional analysis showed that five differentially expressed proteins which were all highly expressed in the highly virulent isolate were involved in the pathogenic processes of nematodes. Peroxiredoxin, fatty acid- and retinol-binding protein, and glutathione peroxidase relate to resistance against plant defence responses, while β-1,4-endoglucanase and expansin are associated with the breakdown of plant cell walls. Thus, the pathogenesis of B. mucronatus depends on its successful survival in host plants. Our work adds to the understanding of B. mucronatus' pathogenesis, and will aid in controlling B. mucronatus and other pinewood nematode species complexes in the future.

First case of hepatopancreatic necrosis disease in pond-reared Chinese mitten crab, Eriocheir sinensis, associated with microsporidian

An epidemic of hepatopancreatic necrosis disease (HPND) with a high mortality rate (40%-50%) recently occurred in the cultured Chinese mitten crab, Eriocheir sinensis, which is a very important economic crustacean species in China. Histology revealed infection by a microsporidian parasite within the cytoplasm of the epithelial cells of the hepatopancreas. Numerous discrete inclusions in the infected cells and presumably free parasite spores were also observed. By negative staining using electron microscopy, a typical morphology of spores was observed with a protuberant front of the anchoring disc. Infection was confined to the epithelial cells of the hepatopancreas, with no other organ implicated. By sequencing the PCR products using specific primers based on conserved regions of microsporidian small subunit (18S) ribosomal DNA, it was revealed that the parasite from HPND ponds had 99% sequence identity to that of Hepatospora eriocheir. Phylogentic analysis also placed the microsporidian in the same lineage as H. eriocheir. This study reported the first case of widespread infections of H. eriocheir associated with HPND found in the pond-reared Chinese mitten crab, E. sinensis. The description of microsporidian in this important commercial host is fundamental for future consideration of factors affecting stock health and sustainability.

Quantitative Proteomic and Transcriptomic Study on Autotetraploid Paulownia and Its Diploid Parent Reveal Key Metabolic Processes Associated with Paulownia Autotetraploidization

Polyploidy plays a very important role in speciation and plant evolution by way of genomic merging and doubling. In the process of polyploidy, rapid genomic, and transcriptomic changes have been observed and researched. However, proteomic divergence caused by the effects of polyploidization is still poorly understood. In the present study, we used iTRAQ coupled with mass spectrometry to quantitatively analyze proteomic changes in the leaves of autotetraploid Paulownia and its diploid parent. A total of 2963 proteins were identified and quantified. Among them, 463 differentially abundant proteins were detected between autotetraploid Paulownia and its diploid parent, and 198 proteins were found to be non-additively abundant in autotetraploid Paulownia, suggesting the presence of non-additive protein regulation during genomic merger and doubling. We also detected 1808 protein-encoding genes in previously published RNA sequencing data. We found that 59 of the genes that showed remarkable changes at mRNA level encoded proteins with consistant changes in their abundance levels, while a further 48 genes that showed noteworthy changes in their expression levels encoded proteins with opposite changes in their abundance levels. Proteins involved in posttranslational modification, protein turnover, and response to stimulus, were significantly enriched among the non-additive proteins, which may provide some of the driving power for variation and adaptation in autopolyploids. Quantitative real-time PCR analysis verified the expression patterns of related protein-coding genes. In addition, we found that the percentage of differentially abundant proteins that matched previously reported differentially expressed genes was relatively low.

Proteomics Study on Nonallergic Hypersensitivity Induced by Compound 4880 and Ovalbumin

Nonallergic hypersensitivity reaction (NHR) accounts for more than 77% of all immune-mediated immediate hypersensitivity reactions and has become a serious threat to public health. Here, proteomics was used to study the NHR mechanism of two typical substances, the compound 4880 and ovalbumin. Twelve different proteins were suggested as potential biomarkers for examining the NHR mechanism, and our results revealed that the mechanism mainly encompassed 2 processes, i.e., generation and effect processes. The generation process could be classified as direct stimulation, complement (classical and alternative), coagulation, kallikrein-kinin, and integrated pathways. Thus glutathione peroxidase 1, terminal complement complex (complement factor 4d and Bb), coagulation 13, kininogen-1, and IgE could be used as candidate biomarkers for the indication of the corresponding pathways respectively, the proteins were further confirmed by ELISA. And the effect process was mainly composed of histamine as well as proteins such as DCD and MYLPF, which could be used as important indices for the symptoms of NHR. Our study differs from previous studies in that C4880 was found to not only be involved in the direct stimulation pathway, but also in the activated complement and kallikrein-kinin pathways through the coagulation pathway. We also report for the first time that ovalbumin-induced NHR could be a combination of the coagulation, classical complement, and integrated pathways.

iTRAQ-based quantitative proteomic analysis of Macrobrachium rosenbergii hemocytes during Spiroplasma eriocheiris infection

Spiroplasma eriocheiris, as a novel aquaculture pathogen, has led into catastrophic economic losses in aquaculture. The Macrobrachium rosenbergii hemocytes were major target cells in S. eriocheiris infection. Our study was designed to examine the hemocytes' immune response at the protein levels. The differential proteomes of the prawn hemocytes were analyzed immediately prior to injection with the pathogen, and at 192h post-injection by isobaric tags for relative and absolute quantization (iTRAQ) labeling, followed by liquid chromatogramphytandem mass spectrometry (LC-MS/MS). A total of 69 differentially expressed proteins were identified. Forty-nine proteins were up-regulated and 20 proteins were down-regulated resulting from a S. eriocheiris infection. Up-regulated proteins included vertebrate gliacolin-like protein, vitellogenin, Gram-negative binding protein 1, alpha2 macroglobulin isoform 2 (a2M), etc. Down-regulated proteins, involved with beta-1,3-glucan-binding protein (BGBP), immunoglobulin like, Rab7, lipopolysaccharide and β-1,3-glucan (LGBP), actin-related protein, etc. Selected bioactive factors (tachylectin, α2M and vitellogenin, BGBP, C-type lectin, LGBP and Rab7) were verified by their immune roles in the S. eriocheiris infection using real-time PCR. The present work could serve as a basis for future studies on the proteins implicated in the susceptibility/resistance of M. rosenbergii to S. eriocheiris, as well as contribute to our understanding of disease processes in prawns.

BIOLOGICAL SIGNIFICANCE

This is the first time using an iTRAQ approach to analyze proteomes of M. rosenbergii mobilized against S. eriocheiris infection and substantiated the hemocytes' proteomic changes in M. rosenbergii using an infection model. The results reported here can provide a significant step forward toward a more complete elucidation of the immune relationship between M. rosenbergii and the pathogen S. eriocheiris.

Antiphospholipid antibodies bind syncytiotrophoblast mitochondria and alter the proteome of extruded syncytial nuclear aggregates

INTRODUCTION

Antiphospholipid antibodies (aPL) are autoantibodies that increase the risk of women developing the hypertensive disorder pre-eclampsia. aPL are internalised by the syncytiotrophoblast and increase extrusion of necrotic multinucleated syncytial nuclear aggregates (SNAs), which may trigger endothelial dysfunction in pre-eclampsia. The mechanisms by which aPL alter death processes in the syncytiotrophoblast leading to extrusion of SNAs are unknown.

METHODS

First trimester human placentae (n = 10) were dissected into explants and cultured either with aPL (50 μg/mL), isotype-matched control antibody (50 μg/mL), or media for 24 h. Harvested SNAs underwent iTRAQ proteomic analysis. Mitochondria in syncytiotrophoblast treated with aPL labelled with FluoroNanogold were visualised using transmission electron microscopy (TEM).

RESULTS

aPL altered the expression of 72 proteins in SNAs. Thirteen proteins were involved in mitochondrial function. TEM demonstrated that aPL bind to mitochondria in the syncytiotrophoblast and may cause mitochondrial swelling.

DISCUSSION

aPL disrupt mitochondria increasing the extrusion of SNAs with an altered proteome from the syncytiotrophoblast. These altered SNAs may trigger endothelial dysfunction and pre-eclampsia in these pregnancies.