Contributions of functional genomics and proteomics to the study of immune responses in the Pacific white leg shrimp Litopenaeus vannamei

Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir

As a new generation of high-throughput sequencing technology, PacBio Iso-Seq technology (Iso-Seq) provides a better alternative sequencing method for the acquisition of full-length unigenes. In this study, a total of 22.27 gigabyte (Gb) subread bases and 128,614 non-redundant unigenes (mean length: 2,324 bp) were obtained from six main tissues of Eriocheir sinensis including the heart, nerve, intestine, muscle, gills and hepatopancreas. In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). In addition, 6696 transcription factors (TFs), 28,458 long non-coding RNAs (lncRNAs) and 94,230 mRNA-miRNA pairs were identified. Hepatospora eriocheir is the primary pathogen of E. sinensis and can cause hepatopancreatic necrosis disease (HPND); the intestine is the main target tissue. Here, we attempted to identify the key genes related to H. eriocheir infection in the intestines of E. sinensis. By combining Iso-Seq and Illumina RNA-seq analysis, we identified a total of 12,708 differentially expressed unigenes (DEUs; 6,696 upregulated and 6,012 downregulated) in the crab intestine following infection with H. eriocheir. Based on the biological analysis of these DEUs, several key processes were identified, including energy metabolism-related pathways, cell apoptosis and innate immune-related pathways. Twelve selected genes from these DEUs were subsequently verified by quantitative real-time PCR (qRT-PCR) analysis. Our findings enhance our understanding of the E. sinensis transcriptome and the specific association between E. sinensis and H. eriocheir infection.

Application of proteomics in shrimp and shrimp aquaculture

Since proteins play an important role in the life of an organism, many researchers are now looking at how genes and proteins interact to form different proteins. It is anticipated that the creation of adequate tools for rapid analysis of proteins will accelerate the determination of functional aspects of these biomolecules and develop new biomarkers and therapeutic targets for the diagnosis and treatment of various diseases. Though shrimp contains high-quality marine proteins, there are reports about the heavy losses to the shrimp industry due to the poor quality of shrimp production and many times due to mass mortality also. Frequent outbreaks of diseases, water pollution, and quality of feed are some of the most recognized reasons for such losses. In the seafood export market, shrimp occupies the top position in currency earnings and strengthens the economy of many developing nations. Therefore, it is vital for shrimp-producing companies they produce healthy shrimp with high-quality protein. Though aquaculture is a very competitive market, global awareness regarding the use of scientific knowledge and emerging technologies to obtain better-farmed organisms through sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful tool, has therefore been increasingly used to address several issues in shrimp aquaculture. In the present paper, efforts have been made to address some of them, particularly the role of proteomics in reproduction, breeding and spawning, immunological responses and disease resistance capacity, nutrition and health, microbiome and probiotics, quality and safety of shrimp production, bioinformatics applications in proteomics, the discovery of protein biomarkers, and mitigating biotic and abiotic stresses. Future challenges and research directions on proteomics in shrimp aquaculture have also been discussed.

Moderate acidification mitigates the toxic effects of phenanthrene on the mitten crab Eriocheir sinensis

Freshwater acidification and phenanthrene may result in complex adverse effects on aquatic animals. Juvenile Chinese mitten crabs (Eriocheir sinensis) were exposed to different pH levels (7.8, 6.5, and 5.5) under phenanthrene (PHE) (0 (control) and 50 μg/L) conditions for 14 days. Antioxidant and transcriptomic responses were determined under stress conditions to evaluate the physiological adaptation of crabs. Under the control pH 7.8, PHE led to significantly reduced activities of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR) and glutathione S-transferase (GST), but increased glutathione peroxidase (GSH-Px), 7-ethoxyresorufin-o-deethylase (EROD) activities, and malondialdehyde (MDA) levels. However, moderate acidification (pH 6.5) changed PHE effects by increasing antioxidant enzymes. Acidification generally reduced SOD, GPx, GST and EROD activities, but increased CAT, GR, MDA. Compared with pH7.8 group, pH7.8 × PHE and pH6.5 × PHE groups had 1148 and 1498 differentially expressed genes, respectively, with "Biological process" being the main category in the two experimental groups. pH7.8 × PHE treatment caused significant enrichment of disease and immune-related pathways, while under pH6.5 × PHE, more pathways related to metabolism, detoxification, environmental information processing, and energy supply were significantly enriched. Thus, PHE had a significant inhibitory effect on antioxidant performance in crabs, while moderate acidification (pH6.5) mitigated the toxic effects of PHE. Overall, moderate acidification has a positive effect on the defense against the negative effects of PHE in Chinese mitten crabs, and this study provides insights into the defense mechanism of crustaceans in response to combined stress of acidification and PHE.

iTRAQ-Based Quantitative Proteomics Analysis Reveals the Invasion Mechanism of Spiroplasma eriocheiris in 3T6 Cells

Background:

Spiroplasma eriocheiris is a novel pathogen of freshwater crustaceans and is closely related to S. mirum. They have no cell wall and a helical morphology. They have the ability to infect mammals with an unclear mechanism.

Objective:

In this study, our aim was to investigate the profile of protein expression in 3T6 cells infected with S. eriocheiris.

Methods:

The proteome of 3T6 cells infected by S. eriocheiris was systematically investigated by iTRAQ.

Results:

We identified and quantified 4915 proteins, 67 differentially proteins were found, including 30 up-regulated proteins and 37 down-regulated proteins. GO term analysis shows that dysregulation of adhesion protein , interferon and cytoskeletal regulation are associated with apoptosis. Adhesion protein Vcam1 and Interferon-induced protein GBP2, Ifit1, TAPBP, CD63 ,Arhgef2 were up-regulated. A key cytoskeletal regulatory protein, ARHGEF17 was down-regulated. KEGG pathway analysis showed the NF-kappa B signaling pathway, the MAPK signaling pathway , the Jak-STAT signaling pathway and NOD-like receptor signaling are closely related to apoptosis in vivo.

Conclusion:

Analysis of the signaling pathways involved in invasion may provide new insights for understanding the infection mechanisms of S. eriocheiris.

The State of "Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization

Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.

Functional elucidation of LvToll 3 receptor from P. vannamei through RNA interference and its potential role in the shrimp antiviral response

There is a continuing debate on whether an antiviral immunity similar to vertebrate interferon response exists in invertebrates. Recent advances in penaeid immunology identified several new members of the Toll receptor family and one of these is LvToll3 (Litopenaeus vannamei Toll3). It is hypothesized in this study that LvToll3 responds to pathogen associated molecular patterns (PAMPs) such as dsRNA, which then activates certain antiviral pathways in penaeids. RNA interference (RNAi) was used to determine differences in the expression levels of specific genes putatively involved in the antiviral response through qPCR. Results showed that LvToll3 upregulation could be elicited through the introduction of double stranded RNA (dsRNA) regardless of sequence relative to initial levels in the 3rd hour. Furthermore, statistically intriguing trend in the overall expression of Vago 4/5 and Interferon regulatory factor (IRF) suggests that both these genes are affected by the expression of LvToll3. Dicer showed no statistical difference between the experimentally treated (LvToll3-dsRNA), positive control (GFP-dsRNA), and control (PBS) samples corroborating the assertion that dicer is part of another antiviral mechanism that acts in concert with Toll system. These findings suggests that LvToll3 plays a critical role in penaeid antiviral immunity when molecular patterns associated with viruses are detected.

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.

Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response

Hematophagous insects transmit infectious diseases. Sand flies are vectors of leishmaniasis, but can also transmit viruses. We have been studying immune responses of Lutzomyia longipalpis, the main vector of visceral leishmaniasis in the Americas. We identified a non-specific antiviral response in L. longipalpis LL5 embryonic cells when treated with non-specific double-stranded RNAs (dsRNAs). This response is reminiscent of interferon response in mammals. We are investigating putative effectors for this antiviral response. Secreted molecules have been implicated in immune responses, including interferon-related responses. We conducted a mass spectrometry analysis of conditioned medium from LL5 cells 24 and 48 h after dsRNA or mock treatment. We identified 304 proteins. At 24 h, 19 proteins had an abundance equal or greater than 2-fold change, while the levels of 17 proteins were reduced when compared to control cells. At the 48 h time point, these numbers were 33 and 71, respectively. The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. The transcription profile of most candidates did not follow the pattern of secreted protein abundance.

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.

High CO2 alters the hypoxia response of the Pacific whiteleg shrimp (Litopenaeus vannamei) transcriptome including known and novel hemocyanin isoforms

Acclimation to low O2 in many organisms involves changes at the level of the transcriptome. Here we used high-throughput RNA sequencing (RNA-Seq) to explore the global transcriptomic response and specific involvement of a suite of hemocyanin (Hc) subunits to low O2 alone and in combination with high CO2, which naturally co-occurs with low O2. Hepatopancreas mRNA of juvenile L. vannamei exposed to air-saturated water, low O2, or low O2/high CO2 for 4 or 24 h was pooled, sequenced (HiSeq 2500) and assembled (Trinity: 52,190 contigs) to create a deep strand-specific reference transcriptome. Annotation of the assembly revealed sequences encoding the previously described small Hc subunit (HcS), and three full-length isoforms of the large subunit (HcL1-3). In addition to this, a previously unidentified full-length Hc subunit was discovered. Phylogenetic analysis demonstrated the subunit to be a β-type Hc subunit (denoted HcB), making this the first report of a β-type hemocyanin subunit in the Penaeoidea. RNAs of individual shrimp were sequenced; regulated genes identified from pairwise comparisons demonstrated a distinct pattern of regulation between prolonged low O2 and low O2/high CO2 treatments by GO term enrichment analysis (Roff-Bentzen, P < 0.0001), showcasing the stabilization of energetically costly translational machinery, mobilization of energy stores, and downregulation of the ubiquitin/proteasomal degradation machinery. Exposure to hypoxia for 24 h resulted in an increase in all of the full-length hemocyanin subunits (HcS, HcL1, HcL2, HcL3, and HcB). The addition of CO2 to hypoxia muted the transcriptomic response of all the Hc subunits to low O2, except for the β-type subunit.

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

Spiroplasma eriocheiris is as a novel pathogen of Chinese mitten crab Eriocheir sinensis tremor disease. The hemocytes have been shown to be major target cells in S. eriocheiris infection. The aim of this study was to examine the hemocytes' immune response at the protein levels. The differential proteomes of the crab hemocytes were analyzed immediately prior to injection with the pathogen, and at 10 d post-injection by isobaric tags for relative and absolute quantization (iTRAQ) labeling, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 1075 proteins were identified by LC-MS/MS and de novo sequencing data. Using a 1.2-fold change in expression as a physiologically significant benchmark, 76 differentially expressed proteins (7.07%) were reliably quantified by iTRAQ analysis. Thirty-five (3.26%) proteins were up-regulated and 41 (3.81%) proteins were down-regulated resulting from a S. eriocheiris infection. Approximately 20 differential proteins in hemocytes were involved in the stress and immune responses. Up-regulated proteins included alpha-2-macroglobulin (α2M), prostaglandin D synthase (GST), ferritin, and heat shock protein 60. Down-regulated proteins included two lectins (mannose-binding protein and hemocytin), three kinds of serine proteinase inhibitors (two serpins and pacifastin), three different kinds of serine proteases, mitogen-activated protein kinase kinase (MAPKK), and two thioredoxins (Trx), crustin, etc. Selected bioactive factors (α2M, GST, ferritin, tubulin, crustin, thioredoxin, clip domain serine protease and serpin) are verified by their immune roles in the S. eriocheiris infection using Real-time PCR. The variation trend of immune gene's mRNA expression is similar with the result of iTRAQ, except the tubulin. The prophenoloxidase-activating system, antimicrobial action and antioxidant system involved in the immune responses of E. sinensis is believed to be a resistance to S. eriocheiris infection. This is the first report of the proteome response of crab hemocytes against S. eriocheiris infection. These findings contribute to our understanding of tremor disease processes in crabs, and provide the first evidence to promote a search for potential biomarkers of the disease.

Protein profiling in the gut of Penaeus monodon gavaged with oral WSSV-vaccines and live white spot syndrome virus

White spot syndrome virus (WSSV) is a pathogen that causes considerable mortality of the farmed shrimp, Penaeus monodon. Candidate 'vaccines', WSSV envelope protein VP28 and formalin-inactivated WSSV, can provide short-lived protection against the virus. In this study, P. monodon was orally intubated with the aforementioned vaccine candidates, and protein expression in the gut of immunised shrimps was profiled. The alterations in protein profiles in shrimps infected orally with live-WSSV were also examined. Seventeen of the identified proteins in the vaccine and WSSV-intubated shrimps varied significantly compared to those in the control shrimps. These proteins, classified under exoskeletal, cytoskeletal, immune-related, intracellular organelle part, intracellular calcium-binding or energy metabolism, are thought to directly or indirectly affect shrimp's immunity. The changes in the expression levels of crustacyanin, serine proteases, myosin light chain, and ER protein 57 observed in orally vaccinated shrimp may probably be linked to immunoprotective responses. On the other hand, altered expression of proteins linked to exoskeleton, calcium regulation and energy metabolism in WSSV-intubated shrimps is likely to symbolise disturbances in calcium homeostasis and energy metabolism.

Transcriptome analysis of the initial stage of acute WSSV infection caused by temperature change

White spot syndrome virus (WSSV) is the most devastating virosis threatening the shrimp culture industry worldwide. Variations of environmental factors in shrimp culture ponds usually lead to the outbreak of white spot syndrome (WSS). In order to know the molecular mechanisms of WSS outbreak induced by temperature variation and the biological changes of the host at the initial stage of WSSV acute infection, RNA-Seq technology was used to analyze the differentially expressed genes (DEGs) in shrimp with a certain amount of WSSV cultured at 18°C and shrimp whose culture temperature were raised to 25°C. To analyze whether the expression changes of the DEGs were due to temperature rising or WSSV proliferation, the expression of selected DEGs was analyzed by real-time PCR with another shrimp group, namely Group T, as control. Group T didn't suffer WSSV infection but was subjected to temperature rising in parallel. At the initial stage of WSSV acute infection, DEGs related to energy production were up-regulated, whereas most DEGs related to cell cycle and positive regulation of cell death and were down-regulated. Triose phosphate isomerase, enolase and alcohol dehydrogenase involved in glycosis were up-regulated, while pyruvate dehydrogenase, citrate synthase and isocitrate dehydrogenase with NAD as the coenzyme involved in TCA pathway were down-regulated. Also genes involved in host DNA replication, including DNA primase, DNA topoisomerase and DNA polymerase showed down-regulated expression. Several interesting genes including crustin genes, acting binding or inhibiting protein genes, a disintegrin and metalloproteinase domain-containing protein 9 (ADAM9) gene and a GRP 78 gene were also analyzed. Understanding the interactions between hosts and WSSV at the initial stage of acute infection will not only help to get a deep insight into the pathogenesis of WSSV but also provide clues for therapies.

Proteomic analysis of differentially expressed proteins in Fenneropenaeus chinensis hemocytes upon white spot syndrome virus infection

To elucidate molecular responses of shrimp hemocytes to white spot syndrome virus (WSSV) infection, two-dimensional gel electrophoresis was applied to investigate differentially expressed proteins in hemocytes of Chinese shrimp (Fenneropenaeus chinensis) at 24 h post infection (hpi). Approximately 580 protein spots were detected in hemocytes of healthy and WSSV-infected shrimps. Quantitative intensity analysis revealed 26 protein spots were significantly up-regulated, and 19 spots were significantly down-regulated. By mass spectrometry, small ubiquitin-like modifier (SUMO) 1, cytosolic MnSOD, triosephosphate isomerase, tubulin alpha-1 chain, microtubule-actin cross-linking factor 1, nuclear receptor E75 protein, vacuolar ATP synthase subunit B L form, inositol 1,4,5-trisphosphate receptor, arginine kinase, etc., amounting to 33 differentially modulated proteins were identified successfully. According to Gene Ontology annotation, the identified proteins were classified into nine categories, consisting of immune related proteins, stimulus response proteins, proteins involved in glucose metabolic process, cytoskeleton proteins, DNA or protein binding proteins, proteins involved in steroid hormone mediated signal pathway, ATP synthases, proteins involved in transmembrane transport and ungrouped proteins. Meanwhile, the expression profiles of three up-regulated proteins (SUMO, heat shock protein 70, and arginine kinase) and one down-regulated protein (prophenoloxidase) were further analyzed by real-time RT-PCR at the transcription level after WSSV infection. The results showed that SUMO and heat shock protein 70 were significantly up-regulated at each sampling time point, while arginine kinase was significantly up-regulated at 12 and 24 hpi. In contrast, prophenoloxidase was significantly down-regulated at each sampling time point. The results of this work provided preliminary data on proteins in shrimp hemocytes involved in WSSV infection.

Molecular signatures at imminent death: hemocyte gene expression profiling of shrimp succumbing to viral and fungal infections

Infectious diseases represent the most serious threat to shrimp farming worldwide. Understanding the molecular mechanisms driving shrimp-pathogen interactions is necessary for developing strategies to control disease outbreaks in shrimp production systems. In the current study, we experimentally reproduced mortality events using standardized infections to characterize the hemocyte transcriptome response of the shrimp Litopenaeus vannamei succumbing to infectious diseases. By using a high-throughput microfluidic RT-qPCR approach, we identified molecular signatures in shrimp during lethal infections caused by the White Spot Syndrome Virus (WSSV) or the filamentous fungus Fusarium solani. We successfully identified gene expression signatures shared by both infections but also pathogen-specific gene responses. Interestingly, whereas lethal WSSV infection induced the expression of antiviral-related genes, the transcript abundance of many antimicrobial effectors was reduced by lethal F. solani infection. To our knowledge, this is the first report of the immune-gene repertoire of infected shrimp at the brink of death.

Comparison of protein expression profiles of the hepatopancreas in Fenneropenaeus chinensis challenged with heat-inactivated Vibrio anguillarum and white spot syndrome virus

Fenneropenaeus chinensis (Chinese shrimp) culture industry, like other Penaeidae culture, has been seriously affected by the shrimp diseases caused by bacteria and virus. To better understand the mechanism of immune response of shrimp to different pathogens, proteome research approach was utilized in this study. Firstly, the soluble hepatopancreas protein samples in adult Chinese shrimp among control, heat-inactivated Vibrio-challenged and white spot syndrome virus-infected groups were separated by 2-DE (pH range, 4-7; sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and pH range, 3-10; tricine-SDS-PAGE). Then the differentially expressed protein spots (≥1.5-fold or ≤0.67-fold averagely of controls) were analyzed by LC-ESI-MS/MS. Using Mascot online database searching algorithm and SEQUEST searching program, 48 and 49 differentially expressed protein spots were successfully identified in response to Vibrio and white spot syndrome virus infection, respectively. Based on these results, we discussed the mechanism of immune response of the shrimp and shed light on the differences between immune response of shrimp toward Vibrio and white spot syndrome virus. This study also set a basis for further analyses of some key genes in immune response of Chinese shrimp.

Signaling pathways regulating innate immune responses in shrimp

The first line of defense against microbial infections in animals is innate immune response which triggers diverse humoral and cellular activities via signal transduction pathways. Toll, IMD and JAK/STAT pathways are regarded as the main pathways regulating the immune response of invertebrates. This paper reviews the main progress of the investigation on the immune response to pathogen's infection in shrimp and supposes that these three signal pathways exist in shrimp. Most of the components (proteins or genes) involved in Toll pathway of Drosophila have been cloned also in shrimp which suggested the existence of Toll pathway in shrimp. The data update shows that the Toll pathway of shrimp is responsive not only to Gram-positive bacteria, Gram-negative bacteria, but also to WSSV. Challenge of WSSV can lead to the variation of transcription level of all identified components in shrimp Toll pathway, which supported that Toll pathway in shrimp played important roles during WSSV infection. Two major homologs to the components of IMD pathway of Drosophila, IMD and Relish, have been identified in shrimp, which indicated that IMD pathway should be existed in shrimp and might play important roles in regulating the immune response of shrimp to bacteria and virus infection. Relish in IMD pathway and dorsal in Toll pathway of shrimp were both involved in the immune response of shrimp to bacteria and virus infection, which implied that these two pathways are not completely separated during the immune response of shrimp. The transcription of STAT in shrimp was modulated after WSSV infection, which suggested that a putative JAK/STAT pathway might exist in shrimp and be very important to virus infection. Study on the signaling pathway regulating the immune response in shrimp could help us to understand the innate immune system, and would provide instructions to shrimp disease control. Obviously, to get more clear ideas about the innate immunological pathways in shrimp, more solid functional studies should be done in the future.

Insights into the antiviral functions of the RNAi machinery in penaeid shrimp

Over the last decade, RNA interference pathways have emerged in eukaryotes as critical regulators of many diverse biological functions including, among others, transcriptional gene regulation, post-transcriptional gene silencing, heterochromatin remodelling, suppression of transposon activity, and antiviral defences. Although this gene silencing process has been reported to be relatively well conserved in species of different phyla, there are important discrepancies between plants, invertebrates and mammals. In penaeid shrimp, the existence of an intact and functional RNAi machinery is supported by a rapidly growing body of evidence. However, the extent to which this process participates to the host immune responses remains poorly defined in this non-model organism. This review summarizes our current knowledge of RNAi mechanisms in shrimp and focuses on their implication in antiviral activities and shrimp immune defences.

Comparative proteomic identification of the hemocyte response to cold stress in white shrimp, Litopenaeus vannamei

To understand molecular responses of crustacean hemocytes to cold stress, flow cytometer analysis and two-dimensional electrophoresis proteomic approach were used to investigate altered proteins in hemocytes of Litopenaeus vannamei during cold stress treatment. Through flow cytometer analysis, 13°C for 24h post-cold stress was selected as the suitable temperature and condition for cold stress treatment. MALDI-TOF/TOF MS analysis revealed that 6 forms of 6 proteins were significantly up-regulated, including three enzymes (cystathionase, glyceraldehyde 3-phosphate dehydrogenase and glyoxalase 1) and one immune-related protein (oncoprotein nm23), whereas 24 forms of 3 proteins were significantly down-regulated in the treated shrimp (hemocyanin, hemocyte transglutaminase and transketolase). There were 20 spots identified as hemocyanin meaning that it may play important roles in environmental regulation in shrimp. Real-time fluorescence quantitative PCR confirmed that the levels of transcription of the hemocyanin, partial mRNA for hemocyanin, cystathionase, glyoxalase 1 and oncoprotein nm23 genes were found to relate well with that of their translation products after cold stress treated, while only the levels of hemocyte transglutaminase transcripts were not corresponded with that of their translation products. Further investigation of these data may lead to better understanding of the molecular responses of crustacean hemocytes to cold stress.

Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery

BACKGROUND

Giant freshwater prawn (Macrobrachium rosenbergii or GFP), is the most economically important freshwater crustacean species. However, as little is known about its genome, 454 pyrosequencing of cDNA was undertaken to characterise its transcriptome and identify genes important for growth.

METHODOLOGY AND PRINCIPAL FINDINGS

A collection of 787,731 sequence reads (244.37 Mb) obtained from 454 pyrosequencing analysis of cDNA prepared from muscle, ovary and testis tissues taken from 18 adult prawns was assembled into 123,534 expressed sequence tags (ESTs). Of these, 46% of the 8,411 contigs and 19% of 115,123 singletons possessed high similarity to sequences in the GenBank non-redundant database, with most significant (E value < 1e(-5)) contig (80%) and singleton (84%) matches occurring with crustacean and insect sequences. KEGG analysis of the contig open reading frames identified putative members of several biological pathways potentially important for growth. The top InterProScan domains detected included RNA recognition motifs, serine/threonine-protein kinase-like domains, actin-like families, and zinc finger domains. Transcripts derived from genes such as actin, myosin heavy and light chain, tropomyosin and troponin with fundamental roles in muscle development and construction were abundant. Amongst the contigs, 834 single nucleotide polymorphisms, 1198 indels and 658 simple sequence repeats motifs were also identified.

CONCLUSIONS

The M. rosenbergii transcriptome data reported here should provide an invaluable resource for improving our understanding of this species' genome structure and biology. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs.

Shrimp molecular responses to viral pathogens

From almost negligible amounts in 1970, the quantity of cultivated shrimp (~3 million metric tons in 2007) has risen to approach that of the capture fishery and it constitutes a vital source of export income for many countries. Despite this success, viral diseases along the way have caused billions of dollars of losses for shrimp farmers. Desire to reduce the losses to white spot syndrome virus in particular, has stimulated much research since 2000 on the shrimp response to viral pathogens at the molecular level. The objective of the work is to develop novel, practical methods for improved disease control. This review covers the background and limitations of the current work, baseline studies and studies on humoral responses, on binding between shrimp and viral structural proteins and on intracellular responses. It also includes discussion of several important phenomena (i.e., the quasi immune response, viral co-infections, viral sequences in the shrimp genome and persistent viral infections) for which little or no molecular information is currently available, but is much needed.

Molecular cloning, characterization and expression analysis of cathepsin A gene in Chinese mitten crab, Eriocheir sinensis

Cathepsins, a superfamily of hydrolytic enzymes produced and enclosed within lysosomes, function in immune response in vertebrates; however, their function within the innate immune system of invertebrates remains largely unknown. Therefore, we investigated the immune functionality of cathepsin A (catA) in Chinese mitten crab (Eriocheir sinensis), a commercially important and disease vulnerable aquaculture species. The full length catA cDNA (2200 bp) was cloned via PCR based upon an initial expressed sequence tag (EST) isolated from a hepatopancreatic cDNA library. The catA cDNA contained a 1398 bp open reading frame (ORF) that encoded a putative 465 amino acid (aa) protein. Comparisons with other reported vertebrate cathepsins sequences revealed percent identity range from 48 to 51%. CatA mRNA expression in E. sinensis was (a) tissue-specific, with the highest expression observed in gill and (b) responsive in hemocytes to a Vibrio anguillarum challenge, with peak exposure observed 12 h post-injection. Collectively, data demonstrate the successful isolation of catA from the Chinese mitten crab, and its involvement in the innate immune system of an invertebrate.

Environmental proteomics: changes in the proteome of marine organisms in response to environmental stress, pollutants, infection, symbiosis, and development

Environmental proteomics, the study of changes in the abundance of proteins and their post-translational modifications, has become a powerful tool for generating hypotheses regarding how the environment affects the biology of marine organisms. Proteomics discovers hitherto unknown cellular effects of environmental stressors such as changes in thermal, osmotic, and anaerobic conditions. Proteomic analyses have advanced the characterization of the biological effects of pollutants and identified comprehensive and pollutant-specific sets of biomarkers, especially those highlighting post-translational modifications. Proteomic analyses of infected organisms have highlighted the broader changes occurring during immune responses and how the same pathways are attenuated during the maintenance of symbiotic relationships. Finally, proteomic changes occurring during the early life stages of marine organisms emphasize the importance of signaling events during development in a rapidly changing environment. Changes in proteins functioning in energy metabolism, cytoskeleton, protein stabilization and turnover, oxidative stress, and signaling are common responses to environmental change.

Involvement of WSSV-shrimp homologs in WSSV infectivity in kuruma shrimp: Marsupenaeus japonicus

White spot syndrome virus (WSSV) is pathogenic and specific to shrimp, and is capable of producing a persistent infection in the host. Moreover, shrimp are capable of persistently carrying a single or multiple viruses, allowing them to survive for long periods with latent infections. In order to identify genes that are specially involved in the intricate WSSV-shrimp association, we focused on homologs between the WSSV and shrimp genomes. We here investigated whether homologous WssvORFs (WssvORF285, WssvORF332) and their homologs in the kuruma shrimp genome (MjORF16, MjORF18) are important for WSSV infectivity by utilizing dsRNA-mediated RNA interference, and further proposed potential roles of homologous WssvORFs associated with the persistent viral infection stage. Homologous MjORFs were found to be highly up-regulated in several tested tissues upon WSSV infection. Injection of dsRNAs specific to homologous MjORFs, followed by WSSV challenge, led to reduced and delayed shrimp mortality when compared to that of shrimp without dsRNA injection. Silencing of homologous WssvORFs by specific dsRNAs sharply increased shrimp survival. WssvORF332 may function as a latency gene especially associated with the persistent WSSV infection stage while WssvORF285 may be classified into the same group as WssvVP28 and may play a role in virus penetration during the infection. Our results suggest that WSSV-shrimp homologs are involved in WSSV infectivity and support the hypothesis that homologous WssvORFs are related to WSSV latency and pathogenesis.

Proteomic analysis of differentially expressed proteins in Penaeus monodon hemocytes after Vibrio harveyi infection

Background

Viral and bacterial diseases can cause mass mortalities in commercial shrimp aquaculture. In contrast to studies on the antiviral response, the responses of shrimps to bacterial infections by high throughput techniques have been reported only at the transcriptional level and not at the translational level. In this study, a proteomic analysis of shrimp hemocytes to identify differentially expressed proteins in response to a luminous bacterium Vibrio harveyi was evaluated for its feasibility and is reported for the first time.

Results

The two-dimensional gel electrophoresis (2-DE) patterns of the hemocyte proteins from the unchallenged and V. harveyi challenged shrimp, Penaeus monodon, at 24 and 48 h post infection were compared. From this, 27 differentially expressed protein spots, and a further 12 weakly to non-differentially regulated control spots, were selected for further analyses by the LC-ESI-MS/MS. The 21 differentially expressed proteins that could be identified by homologous annotation were comprised of proteins that are directly involved in the host defense responses, such as hemocyanin, prophenoloxidase, serine proteinase-like protein, heat shock protein 90 and alpha-2-macroglobulin, and those involved in signal transduction, such as the14-3-3 protein epsilon and calmodulin. Western blot analysis confirmed the up-regulation of hemocyanin expression upon bacterial infection. The expression of the selected proteins which were the representatives of the down-regulated proteins (the 14-3-3 protein epsilon and alpha-2-macroglobulin) and of the up-regulated proteins (hemocyanin) was further assessed at the transcription level using real-time RT-PCR.

Conclusions

This work suggests the usefulness of a proteomic approach to the study of shrimp immunity and revealed hemocyte proteins whose expression were up regulated upon V. harveyi infection such as hemocyanin, arginine kinase and down regulated such as alpha-2-macroglobulin, calmodulin and 14-3-3 protein epsilon. The information is useful for understanding the immune system of shrimp against pathogenic bacteria.

Suitability of the clonal marbled crayfish for biogerontological research: a review and perspective, with remarks on some further crustaceans

This article examines the suitability of the parthenogenetic marbled crayfish for research on ageing and longevity. The marbled crayfish is an emerging laboratory model for development, epigenetics and toxicology that produces up to 400 genetically identical siblings per batch. It is easily cultured, has an adult size of 4-9 cm, a generation time of 6-7 months and a life span of 2-3 years. Experimental data and biological peculiarities like isogenicity, direct development, indeterminate growth, high regeneration capacity and negligible senescence suggest that the marbled crayfish is particularly suitable to investigate the dependency of ageing and longevity from non-genetic factors such as stochastic developmental variation, allocation of metabolic resources, damage and repair, caloric restriction and social stress. It is also well applicable to examine alterations of the epigenetic code with increasing age and to identify mechanisms that keep stem cells active until old age. As a representative of the sparsely investigated crustaceans and of animals with indeterminate growth and extended brood care the marbled crayfish may even contribute to evolutionary theories of ageing and longevity. Some relatives are recommended as substitutes for investigation of topics, for which the marbled crayfish is less suitable like genetics of ageing and achievement of life spans of decades under conditions of low food and low temperature. Research on ageing in the marbled crayfish and its relatives is of practical relevance for crustacean fisheries and aquaculture and may offer starting points for the development of novel anti-ageing interventions in humans.