Inhibition of white spot syndrome virus replication in Penaeus monodon by combined silencing of viral rr2 and shrimp PmRab7

VP28 interacts with PmRab7 irrespective of its nucleotide state

In shrimp aquaculture, white spot syndrome virus (WSSV) infections severely impact production. Previous research highlighted the crucial role of the Penaeus monodon Rab7 (PmRab7) protein in WSSV entry, specifically its interaction with the viral envelope protein VP28. PmRab7 exists in two conformations: GDP-bound (inactive) and GTP-bound (active). This study, using ELISA and isothermal titration calorimetry (ITC), reveals that the PmRab7-VP28 interaction occurs irrespective of the nucleotide binding state of PmRab7. Comparing the binding affinity between VP28 and different PmRab7 conformations, including wild-type (WT, 22.5 nM), a fast nucleotide exchange (L129F, 128 nM), a GDP-bound form (T22N, 334 nM), and a favorably GTP-bound form (Q67L, 1990 nM), PmRab7-WT exhibits the strongest binding affinity, especially at a lower temperature (25 °C). The binding of PmRab7-WT and VP28 in the presence of excess nucleotide (WT with excess GDP, 924 nM, and WT with excess GTP, 826 nM) shows a 2-fold higher binding affinity than in the absence (WT, 1920 nM) indicating that the addition of excess nucleotide for PmRab7-WT enhanced the affinity for VP28. Together, these findings support the potential of PmRab7-WT as a promising therapeutic candidate for WSSV control in shrimp. Furthermore, from an industrial point of view, the ITC platform developed to study the VP28-PmRab7 interactions provides a high-throughput method for screening additives for shrimp feed that can inhibit this interaction.

RNA Interference Applied to Crustacean Aquaculture

RNA interference (RNAi) is a powerful tool that can be used to specifically knock-down gene expression using double-stranded RNA (dsRNA) effector molecules. This approach can be used in aquaculture as an investigation instrument and to improve the immune responses against viral pathogens, among other applications. Although this method was first described in shrimp in the mid-2000s, at present, no practical approach has been developed for the use of dsRNA in shrimp farms, as the limiting factor for farm-scale usage in the aquaculture sector is the lack of cost-effective and simple dsRNA synthesis and administration procedures. Despite these limitations, different RNAi-based approaches have been successfully tested at the laboratory level, with a particular focus on shrimp. The use of RNAi technology is particularly attractive for the shrimp industry because crustaceans do not have an adaptive immune system, making traditional vaccination methods unfeasible. This review summarizes recent studies and the state-of-the-art on the mechanism of action, design, use, and administration methods of dsRNA, as applied to shrimp. In addition, potential constraints that may hinder the deployment of RNAi-based methods in the crustacean aquaculture sector are considered.

RNA interference targeting WSSV ribonucleotide reductase 2 provides long-term protection against infection in Litopenaeus vannamei

Many studies have demonstrated that long double-stranded RNAs (dsRNAs) targeting essential genes of white spot syndrome virus (WSSV) can induce a sequence-specific antiviral RNA interference (RNAi) response in shrimp, thereby offering protection against WSSV infection. However, further experimental data on the required dose of dsRNAs and the duration of protection from a single administration are necessary to establish RNAi-mediated methods as effective and practical antiviral measures. In this study, we evaluated the protective efficacy and the duration of protection provided by a single administration of various doses of long dsRNA targeting WSSV ribonucleotide reductase 2 (rr2) in white-leg shrimp Litopenaeus vannamei. The protective efficacy of long dsRNA targeting WSSV rr2 was not diminished by the reduction of the dose to 100 ng g-1 of body weight, suggesting that a relatively low dose can effectively induce an RNAi response in shrimp. Furthermore, shrimp were well-protected against WSSV challenges for up to 4 wk post-administration of the rr2-targeting long dsRNA, although the protective effect almost disappeared at 6 wk post-administration. These results suggest that long dsRNAs can provide protection against WSSV for at least 1 mo, and monthly administration of long dsRNAs could serve as a long-term protective strategy for shrimp against WSSV.

Effects of length and sequence of long double-stranded RNAs targeting ribonucleotide reductase 2 of white spot syndrome virus (WSSV) on protective efficacy against WSSV

Long double-stranded RNA (dsRNA)-mediated RNA interference (RNAi) has been a well-known mechanism against white spot syndrome virus (WSSV) in cultured shrimp. In the present study, we investigated the protective efficacy of dsRNAs targeting the ribonucleotide reductase 2 (rr2) gene of WSSV according to length and target sequence location. To produce different lengths of dsRNAs, the 640 bp rr2 fragment (fragment I) was split into two equal 320 bp fragments (fragment II and III), then each 320 bp fragment was redivided into two 160 bp fragments (fragment IV, V, VI, and VII). After the synthesis of seven kinds of dsRNA fragments, dsRNAs with the same length were mixed with each other, then used for the evaluation of dsRNA's length effect in Penaeus vannamei. The result showed that 160 bp long dsRNAs were as effective as 320 and 640 bp long dsRNAs in the protection of shrimp against WSSV infection, suggesting that the dsRNA length of 160 bp would be enough to be used as RNAi-mediated WSSV suppression in P. vannamei. However, as the 160 bp long dsRNAs used in the length effect experiment were not a single dsRNA population but a mixture of 160 bp dsRNA fragments covering the parent 640 bp long dsRNA, the sequence effect was not included in this RNAi efficacy. In the experiments to know the effect of not only length but also sequence of rr2-targeting long dsRNAs on the protective efficacy against WSSV, dsRNAs with a length of 640 bp (fragment I) and 320 bp (fragment II, III) showed a constant high defense ability, but the protection degree of long dsRNAs with a length of 160 bp was different depending on the kinds of the fragment, suggesting that the RNAi efficacy of some rr2-targeting long dsRNAs with a length of 160 bp might have sequences that are variable according to experimental conditions. In conclusion, this study showed that the protective ability of long dsRNAs in shrimp against WSSV infection can be affected by the length and sequence of the long dsRNAs.

Natural component geniposide enhances survival rate of crayfish Procambarus clarkii infected with white spot syndrome virus

White Spot Disease (WSD), caused by white spot syndrome virus (WSSV), is an acute and highly lethal viral disease of shrimp. Currently, there are no commercially available drugs to control WSD. It is urgent and necessary to find anti-WSSV drugs. Natural compounds are an important source of antiviral drug discovery. In this study, the anti-WSSV activity of natural compound geniposide (GP) was investigated in crayfish Procambarus clarkii. Results showed that GP had a concentration-dependent inhibitory effect on WSSV replication in crayfish at 24 h, and highest inhibition was more than 98%. In addition, GP significantly inhibited the expression of WSSV immediate-early gene ie1, early gene DNApol, late gene VP28. The mortality of WSSV-infected crayfish in control groups was 100%, while it reduced by 70.0% when treated with 50 mg/kg GP. Co-incubation, pre-treatment and post-treatment experiments showed that GP could prevent and treat WSSV infection in crayfish by significantly inhibiting WSSV multiplication. Mechanistically, the syntheses of WSSV structural proteins VP19, VP24, VP26 and VP28 were significantly inhibited by GP in S2 cells. Furthermore, GP could also suppress WSSV replication by blocking the expression of antiviral immunity-related factor STAT to reduce ie1 transcription. Moreover, GP possessed anti-inflammatory and anti-oxidative activity in crayfish. Overall, GP has the potential to be developed as a preventive or therapeutic agent against WSSV infection.

Role of Cellular Receptors in the Innate Immune System of Crustaceans in Response to White Spot Syndrome Virus

Innate immunity is the only defense system for resistance against infections in crustaceans. In crustaceans, white spot diseases caused by white spot syndrome virus (WSSV) are a serious viral disease with high accumulative mortality after infection. Attachment and entry into cells have been known to be two initial and important steps in viral infection. However, systematic information about the mechanisms related to WSSV infection in crustaceans is still limited. Previous studies have reported that cellular receptors are important in the innate immune system and are responsible for the recognition of foreign microorganisms and in the stimulation of the immune responses during infections. In this review, we summarize the current understanding of the functions of cellular receptors, including Toll, C-type lectin, scavenger receptor, β-integrin, polymeric immunoglobulin receptor, laminin receptor, globular C1q receptor, lipopolysaccharide-and β-1,3-glucan-binding protein, chitin-binding protein, Ras-associated binding, and Down syndrome cell adhesion molecule in the innate immune defense of crustaceans, especially shrimp and crabs, in response to WSSV infection. The results of this study provide information on the interaction between viruses and hosts during infections, which is important in the development of preventative strategies and antiviral targets in cultured aquatic animals.

Evaluation of the antiviral activity of naringenin, a major constituent of Typha angustifolia, against white spot syndrome virus in crayfish Procambarus clarkii

White spot syndrome virus (WSSV) is a serious pathogen threatening global crustacean aquaculture with no commercially available drugs. Herbal medicines widely used in antiviral research offer a rich reserve for drug discovery. Here, we investigated the inhibitory activity of 13 herbal medicines against WSSV in crayfish Procambarus clarkii and discovered that naringenin (NAR) has potent anti-WSSV activity. In the preliminary screening, the extracts of Typha angustifolia displayed the highest inhibitory activity on WSSV replication (84.62%, 100 mg/kg). Further, NAR, the main active compound of T. angustifolia, showed a much higher inhibition rate (92.85%, 50 mg/kg). NAR repressed WSSV proliferation followed a dose-dependent manner and significantly improved the survival of WSSV-challenged crayfish. Moreover, pre- or post-treatment of NAR displayed a comparable inhibition on the viral loads. NAR decreased the transcriptional levels of vital genes in viral life cycle, particularly for the immediately early-stage gene ie1. Further results showed that NAR could decrease the STAT gene expression to block ie1 transcription. Besides, NAR modulated immune-related gene Hsp70, antioxidant (cMnSOD, mMnSOD, CAT, GST), anti-inflammatory (COX-1, COX-2) and pro-apoptosis-related factors (Bax and BI-1) to inhibit WSSV replication. Overall, these results suggest that NAR may have the potential to be developed as preventive or therapeutic agent against WSSV.

Evaluation of the relationship between the 14-3-3ε protein and LvRab11 in the shrimp Litopenaeus vannamei during WSSV infection

The 14-3-3 proteins interact with a wide variety of cellular proteins for many diverse functions in biological processes. In this study, a yeast two-hybrid assay revealed that two 14-3-3ε isoforms (14-3-3ES and 14-3-3EL) interacted with Rab11 in the white shrimp Litopenaeus vannamei (LvRab11). The interaction of 14-3-3ε and LvRab11 was confirmed by a GST pull-down assay. The LvRab11 open reading frame was 645 bp long, encoding a protein of 214 amino acids. Possible complexes of 14-3-3ε isoforms and LvRab11 were elucidated by in silico analysis, in which LvRab11 showed a better binding energy score with 14-3-3EL than with 14-3-3ES. In shrimp challenged with the white spot syndrome virus (WSSV), the mRNA expression levels of LvRab11 and 14-3-3ε were significantly upregulated at 48 h after challenge. To determine whether LvRab11 and binding between 14-3-3ε and LvRab11 are active against WSSV infection, an in vivo neutralization assay and RNA interference were performed. The results of in vivo neutralization showed that LvRab11 and complexes of 14-3-3ε/LvRab11 delayed mortality in shrimp challenged with WSSV. Interestingly, in the RNAi experiments, the silencing effect of LvRab11 in WSSV-infected shrimp resulted in decreased ie-1 mRNA expression and WSSV copy number. Whereas suppression of complex 14-3-3ε/LvRab11 increased WSSV replication. This study has suggested two functions of LvRab11 in shrimp innate immunity; (1) at the early stage of WSSV infection, LvRab11 might play an important role in WSSV infection processes and (2) at the late stage of infection, the 14-3-3ε/LvRab11 interaction acquires functions that are involved in immune response against WSSV invasion.

A multi-target dsRNA for simultaneous inhibition of yellow head virus and white spot syndrome virus in shrimp

Outbreaks of diseases caused by yellow head virus (YHV) and white spot syndrome virus (WSSV) infection in shrimp have resulted in economic losses worldwide. DsRNA-mediated RNAi has been used to control these viruses, and the best target genes for efficient inhibition of YHV and WSSV are the protease and ribonuleotide reductase small subunit (rr2), respectively. However, one dsRNA can suppress only one virus, and therefore the production of multi-target dsRNA to effectively inhibit both YHV and WSSV is needed. In this study, plasmids pETpro-rr2_one stem and pETpro-rr2_two stems were constructed to produce two different forms of multi-target dsRNA in E. coli, which were designed specifically to both YHV protease and WSSV rr2 genes. The potency of each dsRNA in inhibiting YHV and WSSV and reducing shrimp death were investigated in L. vannamei. Shrimp were injected with the dsRNAs into the hemolymph before challenge with YHV or WSSV. The results showed that both dsRNAs could inhibit the viruses, however the one stem construct was more effective than the two stems construct when shrimp were infected with WSSV. This study establishes a potential strategy for dual inhibition of YHV and WSSV for further application in shrimp aquaculture.

VP19 is important for the envelope coating of white spot syndrome virus

VP19 is a major envelope protein of white spot syndrome virus (WSSV), an important pathogen of farmed shrimp. However, the exact function of VP19 in WSSV assembly and infection is unknown. To understand the function of VP19, the gene was knocked down by RNA interference. We found that the dsRNA specific for vp19 gene dramatically reduced the replication of WSSV genomic DNA in infected animals. Further investigation by transmission electron microscopy showed that inhibition of VP19 prevented envelope coating of progeny virions, resulting in a high amount of immature virus particles without outer layer (envelope) in the host cells. This finding was further confirmed by SDS-PAGE analysis, which showed the loss of VP19 and other envelope proteins from the improperly assembled virions. These results suggest that VP19 is essential for WSSV envelope coating.

Molecular cloning of the Rab7 effector RILP (Rab-interacting lysosomal protein) in Litopenaeus vannamei and preliminary analysis of its role in white spot syndrome virus infection

To investigate the role of the Rab7 effector RILP (Rab-interacting lysosomal protein) in white spot syndrome virus (WSSV) infection, the full-length cDNA of RILP (LvRILP) was cloned in Litopenaeus vannamei, which consists of 1595 bp and encodes a polypeptide of 411 amino acids. Sequence analysis and multiple sequence alignment displayed that LvRILP contained a conserved RILP region from 277 amino acid to 325 amino acid. Both the LvRILP and Rab7 mRNA were most highly expressed in stomach and most lowly expressed in hemocyte, which were significantly up-regulated and exhibited similar kinetics post WSSV infection. The interaction of Rab7 with LvRILP was verified by both GST Pull-down and ELISA. Meanwhile, the results of Pull-down assays showed that the GST-tagged VP28 (GST-VP28), His-tagged Rab7 (His-Rab7) and His-RILP formed a tripartite complex. After silencing by specific LvRILP dsRNA, the LvRILP mRNA level exhibited a significant reduction, and the expression levels of three WSSV genes ie1, wsv477 and vp28 all exhibited decreases at 24, 36 and 48 h post WSSV infection. These results suggested that the Rab7 effector RILP was involved in WSSV infection.

Suppression of argonautes compromises viral infection in Penaeus monodon

Argonaute (Ago) proteins, the catalytic component of an RNA-induced silencing complex (RISC) in RNA interference pathway, function in diverse processes, especially in antiviral defense and transposon regulation. So far, cDNAs encoding four members of Argonaute were found in Penaeus monodon (PmAgo1-4). Two PmAgo proteins, PmAgo1 and PmAgo3 shared high percentage of amino acid identity to Ago1 and Ago2, respectively in other Penaeid shrimps. Therefore, the possible roles of PmAgo1 and PmAgo3 upon viral infection in shrimp were characterized in this study. The level of PmAgo1 mRNA expression in shrimp hemolymph was stimulated upon YHV challenge, but not with dsRNA administration. Interestingly, silencing of either PmAgo1 or PmAgo3 using sequence-specific dsRNAs impaired the efficiency of PmRab7-dsRNA to knockdown shrimp endogenous PmRab7 expression. Inhibition of yellow head virus (YHV) replication and delayed mortality rate were also observed in both PmAgo1-and PmAgo3-knockdown shrimp. In addition, silencing of PmAgo3 transcript, but not PmAgo1, revealed partial inhibition of white spot syndrome virus (WSSV) infection and delayed mortality rate. Therefore, our study provides insights into PmAgo1and PmAgo3 functions that are involved in a dsRNA-mediated gene silencing pathway and play roles in YHV and WSSV replication in the shrimp.

Meta-analysis of antiviral protection of white spot syndrome virus vaccine to the shrimp

Currently, white spot syndrome virus (WSSV) is one of the most serious pathogens that impacts shrimp farming around the world. A WSSV vaccine provides a significant protective benefit to the host shrimp. Although various types of vaccines against WSSV have emerged, the immune effects among them were not compared, and it remains unclear which type of vaccine has the strongest protective effect. Meanwhile, due to the lack of effective routes of administration and immunization programs, WSSV vaccines have been greatly limited in the actual shrimp farming. To answer these questions, this study conducted a comprehensive meta-analysis over dozens of studies and compared all types WSSV vaccines, which include sub-unit protein vaccines, whole virus inactivated vaccines, DNA vaccines and RNA-based vaccines. The results showed that the RNA-based vaccine had the highest protection rate over the other three types of vaccines. Among the various sub-unit protein vaccines, VP26 vaccine had the best protective effects than other sub-unit protein vaccines. Moreover, this study demonstrated that vaccines expressed in eukaryotic hosts had higher protection rates than that of prokaryotic systems. Among the three immunization modes (oral administration, immersion and injection) used in monovalent protein vaccines, oral administration had the highest protection rate. In natural conditions, shrimp are mostly infected by the virus orally. These results provide a guide for exploration of a novel WSSV vaccine and help facilitate the application of WSSV vaccines in shrimp farming.

Regulation of lactate dehydrogenase in response to WSSV infection in the shrimp Litopenaeus vannamei

Lactate dehydrogenase (LDH) is key for anaerobic glycolysis. LDH is induced by the hypoxia inducible factor -1 (HIF-1). HIF-1 induces genes involved in glucose metabolism and regulates cellular oxygen homeostasis. HIF-1 is formed by a regulatory α-subunit (HIF-1α) and a constitutive β-subunit (HIF-1β). The white spot syndrome virus (WSSV) induces anaerobic glycolysis in shrimp hemocytes, associated with lactate accumulation. Although infection and lactate production are associated, the LDH role in WSSV-infected shrimp has not been examined. In this work, the effects of HIF-1 silencing on the expression of two LDH subunits (LDHvan-1 and LDHvan-2) in shrimp infected with the WSSV were studied. HIF-1α transcripts increased in gills, hepatopancreas, and muscle after WSSV infection, while HIF-1β remained constitutively expressed. The expression for both LDH subunits increased in each tissue evaluated during the WSSV infection, translating into increased enzyme activity. Glucose concentration increased in each tissue evaluated, while lactate increased in gills and hepatopancreas, but not in muscle. Silencing of HIF-1α blocked the increase of LDH expression and enzyme activity, along with glucose (all tissues) and lactate (gills and hepatopancreas) concentrations produced by WSSV infection. These results demonstrate that HIF-1 up regulates the expression of LDH subunits during WSSV infection, and that this induction contributes to substrate metabolism in energetically active tissues of infected shrimp.

Advances in the application of high-throughput sequencing in invertebrate virology

Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.

Recombinant baculovirus mediates dsRNA specific to rr2 delivery and its protective efficacy against WSSV infection

White spot syndrome virus (WSSV) is a major causative agent in shrimp farming. Consequently, RNAi technology is an effective strategy to prevent WSSV infection in shrimp especially dsRNA targeting to rr2 of WSSV. In an effort to develop dsRNA expression in shrimp for control of WSSV infection, we developed a recombinant baculovirus expressing recombinant VP28 as the gene delivery system to carry a gene encoding dsRNA specific to rr2 for triggering the RNAi process in shrimp. The results showed that the recombinant baculovirus harboring VP28 was able to express VP28 indicated by Western blot with polyclonal antibody specific to VP28. VP28 transcript was detected in shrimp hemocytes after co-culture hemocytes with the recombinant baculovirus displaying VP28. In addition, we found that shrimp injected with the recombinant baculovirus displaying VP28 and encoding dsRNA synthetic gene specific to rr2 (Bac-VP28-dsrr2) showed the lowest cumulative mortality (33%) at 14days post infection (dpi) when compared to shrimp injected with baculovirus displaying VP28 (Bac-VP28) (64% cumulative mortality) (p<0.05). According to the results, shrimp injected with Bac-VP28-dsrr2 also showed significantly lower WSSV copies than shrimp injected with Bac-VP28 (p<0.05) along with the down-regulation of rr2 expression at 1, 3 and 7dpi. In conclusion, the Bac-VP28-dsrr2 was effective in prevention of WSSV infection. Therefore, the results obtained here can be applied to the prevention of WSSV infection by mixing the recombinant baculovirus with shrimp feed in the future.

Molecular Mechanisms of White Spot Syndrome Virus Infection and Perspectives on Treatments

Since its emergence in the 1990s, White Spot Disease (WSD) has had major economic and societal impact in the crustacean aquaculture sector. Over the years shrimp farming alone has experienced billion dollar losses through WSD. The disease is caused by the White Spot Syndrome Virus (WSSV), a large dsDNA virus and the only member of the Nimaviridae family. Susceptibility to WSSV in a wide range of crustacean hosts makes it a major risk factor in the translocation of live animals and in commodity products. Currently there are no effective treatments for this disease. Understanding the molecular basis of disease processes has contributed significantly to the treatment of many human and animal pathogens, and with a similar aim considerable efforts have been directed towards understanding host-pathogen molecular interactions for WSD. Work on the molecular mechanisms of pathogenesis in aquatic crustaceans has been restricted by a lack of sequenced and annotated genomes for host species. Nevertheless, some of the key host-pathogen interactions have been established: between viral envelope proteins and host cell receptors at initiation of infection, involvement of various immune system pathways in response to WSSV, and the roles of various host and virus miRNAs in mitigation or progression of disease. Despite these advances, many fundamental knowledge gaps remain; for example, the roles of the majority of WSSV proteins are still unknown. In this review we assess current knowledge of how WSSV infects and replicates in its host, and critique strategies for WSD treatment.

Large-scale production and antiviral efficacy of multi-target double-stranded RNA for the prevention of white spot syndrome virus (WSSV) in shrimp

BACKGROUND

RNA interference (RNAi) is a specific and effective approach for inhibiting viral replication by introducing double-stranded (ds)RNA targeting the viral gene. In this study, we employed a combinatorial approach to interfere multiple gene functions of white spot syndrome virus (WSSV), the most lethal shrimp virus, using a single-batch of dsRNA, so-called "multi-WSSV dsRNA." A co-cultivation of RNase-deficient E. coli was developed to produce dsRNA targeting a major structural protein (VP28) and a hub protein (WSSV051) with high number of interacting protein partners.

RESULTS

For a co-cultivation of transformed E. coli, use of Terrific broth (TB) medium was shown to improve the growth of the E. coli and multi-WSSV dsRNA yields as compared to the use of Luria Bertani (LB) broth. Co-culture expression was conducted under glycerol feeding fed-batch fermentation. Estimated yield of multi-WSSV dsRNA (μg/mL culture) from the fed-batch process was 30 times higher than that obtained under a lab-scale culture with LB broth. Oral delivery of the resulting multi-WSSV dsRNA reduced % cumulative mortality and delayed average time to death compared to the non-treated group after WSSV challenge.

CONCLUSION

The present study suggests a co-cultivation technique for production of antiviral dsRNA with multiple viral targets. The optimal multi-WSSV dsRNA production was achieved by the use of glycerol feeding fed-batch cultivation with controlled pH and dissolved oxygen. The cultivation technique developed herein should be feasible for industrial-scale RNAi applications in shrimp aquaculture. Interference of multiple viral protein functions by a single-batch dsRNA should also be an ideal approach for RNAi-mediated fighting against viruses, especially the large and complicated WSSV.

Roles of small RNAs in the immune defense mechanisms of crustaceans

Small RNAs, 21-24 nucleotides in length, are non-coding RNAs found in most multicellular organisms, as well as in some viruses. There are three main types of small RNAs including microRNA (miRNA), small-interfering RNA (siRNA), and piwi-interacting RNA (piRNA). Small RNAs play key roles in the genetic regulation of eukaryotes; at least 50% of all eukaryote genes are the targets of small RNAs. In recent years, studies have shown that some unique small RNAs are involved in the immune response of crustaceans, leading to lower or higher immune responses to infections and diseases. SiRNAs could be used as therapy for virus infection. In this review, we provide an overview of the diverse roles of small RNAs in the immune defense mechanisms of crustaceans.

Recent insights into host-pathogen interaction in white spot syndrome virus infected penaeid shrimp

Viral disease outbreaks are a major concern impeding the development of the shrimp aquaculture industry. The viral disease due to white spot syndrome virus (WSSV) observed in early 1990s still continues unabated affecting the shrimp farms and cause huge economic loss to the shrimp aquaculture industry. In the absence of effective therapeutics to control WSSV, it is important to understand viral pathogenesis and shrimp response to WSSV at the molecular level. Identification and molecular characterization of WSSV proteins and receptors may facilitate in designing and development of novel therapeutics and antiviral drugs that may inhibit viral replication. Investigations into host-pathogen interactions might give new insights to viral infectivity, tissue tropism and defence mechanism elicited in response to WSSV infection. However, due to the limited information on WSSV gene function and host immune response, the signalling pathways which are associated in shrimp pathogen interaction have also not been elucidated completely. In the present review, the focus is on those shrimp proteins and receptors that are potentially involved in virus infection or in the defence mechanism against WSSV. In addition, the major signalling pathways involved in the innate immune response and the role of apoptosis in host-pathogen interaction is discussed.

RNAi-based inhibition of infectious myonecrosis virus replication in Pacific white shrimp Litopenaeus vannamei

Disease in Pacific white shrimp Litopenaeus vannamei caused by the infectious myonecrosis virus (IMNV) causes significant socioeconomic impacts in infection-prone shrimp aquaculture regions. The use of synthetic dsRNA to activate an RNA interference (RNAi) response is being explored as a means of disease prophylaxis in farmed shrimp. Here, survival was tracked in L. vannamei injected with long synthetic dsRNAs targeted to IMNV open reading frame (ORF) 1a, ORF1b, and ORF2 genome regions prior to injection challenge with IMNV, and real-time RT-PCR was used to track the progress of IMNV infection and mRNA expression levels of the host genes sid1, dicer2, and argonaute2. Injection of dsRNAs targeting the ORF1a and ORF1b genes but not the ORF2 gene strongly inhibited IMNV replication over a 3 wk period following IMNV challenge, and resulted in 90 and 83% shrimp survival, respectively. Host gene mRNA expression data indicated that the Sid1 protein, which forms a transmembrane channel involved in cellular import/export of dsRNA, increased in abundance most significantly in shrimp groups that were most highly protected by virus-specific dsRNA injection. Subclinical IMNV infections present in the experimental L. vannamei used increased markedly in the 2 d between injection of any of the 4 virus-specific or non-specific dsRNAs tested and IMNV challenge. While handling and injection stress are implicated in increasing IMNV replication levels, the underlying molecular factors that may have been involved remain to be elucidated.

Characterization of two novel ADP ribosylation factors from giant freshwater prawn Macrobrachium rosenbergii and their responses to WSSV challenge

ADP-ribosylation factors (Arfs) are small GTP-binding proteins that have an essential function in intracellular trafficking and organelle structure. To date, little information is available on the Arfs in the economically important giant freshwater prawn Macrobrachium rosenbergii and their relationship to viral infection. Here we identified two Arf genes from M. rosenbergii (MrArf1 and MrArf2) for the first time. Phylogenetic analysis showed that MrArf1, together with MjArf1 from shrimp Marsupenaeus japonicus belonged to Class I Arfs. By contrast, MrArf2 didn't not match any of the Arfs classes of I/II/III, although it could be clustered with an Arf protein from M. japonicas called MjArfn, which may represent an analog of the Arf. MrArf1 was ubiquitously expressed in all the examined tissues, with the highest transcription level in the hepatopancreas, whereas MrArf2 was only highly expressed in the hepatopancreas and exhibited very low levels in the heart, stomach, gills and intestine. The expression level of MrArf1 in the gills was down-regulated post 24 h WSSV challenge, and reached the maximal level at 48 h. MrArf1 in the hepatopancreas went up from 24 to 48 h WSSV challenge. MrArf2 transcript in the gill also went down at 24 h and then was upregulated at 48 h WSSV challenge. MrArf2 increased significantly in the hepatopancreas 24 h after infection and then went down at 48 h WSSV challenge. RNAi results showed that knockdown of MrArf1 or MrArf2 could inhibit the expression of the envelope protein gene vp28 of the WSSV. So, it could be speculated that MrArf1 and MrArf2 might play important roles in the innate immune system against WSSV infection.

Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

We present a new transcriptome assembly of the Pacific whiteleg shrimp (Litopenaeus vannamei), the species most farmed for human consumption. Its functional annotation, a substantial improvement over previous ones, is provided freely. RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality of this assembly and the affiliated targeted homology searches greatly enrich the curated transcripts currently available in public databases for this species. Comparison with the model arthropod Daphnia allows some insights into defining characteristics of decapod crustaceans. This large-scale gene discovery gives the broadest depth yet to the annotated transcriptome of this important species and should be of value to ongoing genomics and immunogenetic resistance studies in this shrimp of paramount global economic importance.

RNA interference technology used for the study of aquatic virus infections

Aquaculture is one of the most important economic activities in Asia and is presently the fastest growing sector of food production in the world. Explosive increases in global fish farming have been accompanied by an increase in viral diseases. Viral infections are responsible for huge economic losses in fish farming, and control of these viral diseases in aquaculture remains a serious challenge. Recent advances in biotechnology have had a significant impact on disease reduction in aquaculture. RNAi is one of the most important technological breakthroughs in modern biology, allowing us to directly observe the effects of the loss of specific genes in living systems. RNA interference technology has emerged as a powerful tool for manipulating gene expression in the laboratory. This technology represents a new therapeutic approach for treating aquatic diseases, including viral infections. RNAi technology is based on a naturally occurring post-transcriptional gene silencing process mediated by the formation of dsRNA. RNAi has been proven widely effective for gene knockdown in mammalian cultured cells, but its utility in fish remains unexplored. This review aims to highlight the RNAi technology that has made significant contributions toward the improvement of aquatic animal health and will also summarize the current status and future strategies concerning the therapeutic applications of RNAi to combat viral disease in aquacultured organisms.

Construction and application of a protein interaction map for white spot syndrome virus (WSSV)

White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ∼28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein-protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture.

Endocytic pathway is indicated for white spot syndrome virus (WSSV) entry in shrimp

The white spot syndrome virus (WSSV) has had a serious economic impact on the global shrimp aquaculture industry in the past two decades. Although research has clarified a lot about its genome and structure, the mechanism of how WSSV enters a cell is still unclear. In this study to determine this mechanism, primary cultured hemocytes were used as an experimental model to observe the process of WSSV entry because the stable shrimp cell lines for WSSV infection are lacking. After labeling virions and endosomes with fluorescent dyes followed by observation with a confocal microscope, the results show that the WSSV colocalizes with early endosomes. Hemocytes are further treated with different endocytic inhibitors, methyl-β-cyclodextrin (MβCD) and chlorpromazine (CPZ). WSSV still can be detected in the hemocytes treated with CPZ, but not in the hemocytes treated with MβCD. Thus, we conclude that WSSV adopts the caveolae-mediated endocytosis to enter the shrimp cell.

Exploring RNAi as a therapeutic strategy for controlling disease in aquaculture

Aquatic animal diseases are one of the most significant constraints to the development and management of aquaculture worldwide. As a result, measures to combat diseases of fish and shellfish have assumed a high priority in many aquaculture-producing countries. RNA interference (RNAi), a natural mechanism for post-transcriptional silencing of homologous genes by double-stranded RNA (dsRNA), has emerged as a powerful tool not only to investigate the function of specific genes, but also to suppress infection or replication of many pathogens that cause severe economic losses in aquaculture. However, despite the enormous potential as a novel therapeutical approach, many obstacles must still be overcome before RNAi therapy finds practical application in aquaculture, largely due to the potential for off-target effects and the difficulties in providing safe and effective delivery of RNAi molecules in vivo. In the present review, we discuss the current knowledge of RNAi as an experimental tool, as well as the concerns and challenges ahead for the application of such technology to combat infectious disease of farmed aquatic animals.

Ingestion of bacteria expressing dsRNA triggers specific RNA silencing in shrimp

RNAi activation in shrimp through dsRNA injection has been well demonstrated but oral delivery of dsRNA remains controversial. Therefore, this study was conducted to determine whether RNAi was induced in shrimp by ingestion of bacteria expressing dsRNA. We fed shrimp, Penaeus monodon and Litopenaeus vannamei, with inactivated bacteria expressing dsRNA specific to the shrimp genes (Rab7 and STAT). Forty-eight hours after 6 day-continuous feeding, the level of the targeted gene transcript was measured by semi-quantitative RT-PCR. Significant reduction of Rab7 as well as STAT transcript was observed when compared to that of control shrimp fed with bacteria containing the empty vector or bacteria expressing non-related dsRNA (GFP). Moreover, the suppression was detected not only in the hepatopancreas but also in the gills indicating the successful systemic induction of RNAi via oral delivery of dsRNA. Our results suggested that RNAi in shrimp could be triggered by ingestion of dsRNA expressing bacteria. Therefore, oral feeding is a practical approach which can be used to deliver dsRNA for further viral inhibition in farmed shrimp.

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.

Inhibition of Penaeus monodon densovirus replication in shrimp by double-stranded RNA

Stunted shrimp caused by Penaeus monodon densovirus (PmDNV) infection is one of the main problems leading to a significant economic loss in Thailand. To control this pandemic disease, a double-stranded-RNA-mediated virus-specific gene silencing approach was applied to inhibit viral replication. In this study, two dsRNAs corresponding to the non-structural protein (ns1) and the structural protein (vp) genes of PmDNV were synthesized and introduced into shrimp haemolymph prior to viral challenge. After allowing viral replication for two weeks, the suppression effect by each dsRNA was evaluated by semi-quantitative PCR and compared with the control. A reduction of PmDNV in shrimp treated with each dsRNA was observed. In contrast, a high level of viral infection was detected in the control group (NaCl). Based on a limited sample number, we reached the tentative conclusion that virus-specific dsRNA can inhibit PmDNV replication, in which the dsRNA-ns1 was more effective than the dsRNA-vp.