Functional characterization of the RNase III gene of rock bream iridovirus

Megalocytivirus and Other Members of the Family Iridoviridae in Finfish: A Review of the Etiology, Epidemiology, Diagnosis, Prevention and Control

Aquaculture has expanded to become the fastest growing food-producing sector in the world. However, its expansion has come under threat due to an increase in diseases caused by pathogens such as iridoviruses commonly found in aquatic environments used for fish farming. Of the seven members belonging to the family Iridoviridae, the three genera causing diseases in fish comprise ranaviruses, lymphocystiviruses and megalocytiviruses. These three genera are serious impediments to the expansion of global aquaculture because of their tropism for a wide range of farmed-fish species in which they cause high mortality. As economic losses caused by these iridoviruses in aquaculture continue to rise, the urgent need for effective control strategies increases. As a consequence, these viruses have attracted a lot of research interest in recent years. The functional role of some of the genes that form the structure of iridoviruses has not been elucidated. There is a lack of information on the predisposing factors leading to iridovirus infections in fish, an absence of information on the risk factors leading to disease outbreaks, and a lack of data on the chemical and physical properties of iridoviruses needed for the implementation of biosecurity control measures. Thus, the synopsis put forth herein provides an update of knowledge gathered from studies carried out so far aimed at addressing the aforesaid informational gaps. In summary, this review provides an update on the etiology of different iridoviruses infecting finfish and epidemiological factors leading to the occurrence of disease outbreaks. In addition, the review provides an update on the cell lines developed for virus isolation and culture, the diagnostic tools used for virus detection and characterization, the current advances in vaccine development and the use of biosecurity in the control of iridoviruses in aquaculture. Overall, we envision that the information put forth in this review will contribute to developing effective control strategies against iridovirus infections in aquaculture.

Using long, sequence-specific dsRNA to knockdown inducible protein expression and virus production via an RNAi-like mechanism

RNA interference (RNAi) is a powerful innate immune mechanism to knock down translation of specific proteins whose machinery is conserved from plants to mammals. The template used to determine which mRNA's translation is inhibited is dsRNA, whose origin can range from viruses (long dsRNA, ∼100-1000s bp) to host (micro(mi)RNA, ∼20mers). While miRNA-mediated RNAi is well described in vertebrates, the ability of long dsRNA to guide RNAi-mediated translation inhibition in vertebrates is controversial. Indeed, as long dsRNA is so effective at inducing type I interferons (IFNs), and IFNs down-regulate RNAi machinery, it is believed that IFN-competent cells are not capable of using long dsRNA for RNAi. In the present study the ability of long, sequence specific dsRNA to knock down both host protein expression and viral replication is investigated in IFN-competent rainbow trout cells. Before exploring RNAi effects, the optimal dsRNA concentration that would funnel into RNAi without triggering the IFN response was determined. After which, the ability of sequence specific long dsRNA to target knockdown via RNAi was evaluated in: (1) uninfected host cells using inducible luciferase gene expression and (2) host cells infected with chum salmon reovirus (CSV), frog virus 3 (FV3) or viral hemorrhagic septicemia virus genotype IVa (VHSV-IVa). Induced expression studies utilized RTG-P1, a luciferase reporter cell line, and dsRNA containing luciferase sequence (dsRNA-Luc) or a mis-matched sequence (dsRNA-GFP), and subsequent luminescence intensity was measured. Anti-CSV studies used dsRNA-CSVseg7 and dsRNA-CSVseg10 to target CSV segment 7 and CSV segment 10 respectively. Inhibition of virus replication was measured by viral titration and RT-qPCR. Taking advantage of the fact that long dsRNA can accommodate more sequences than miRNAs, the antiviral capability of dsRNA molecules containing both CSV segment 7 and segment 10 simultaneously was also measured. Target sequence appears important, as dsRNA-FV3MCP did not knock down FV3 titres, and while dsRNA-VHSV-N knocked down VHSV-IVa, dsRNA-VHSV-G and dsRNA-VHSV-M did not. This is the first study in fish to provide evidence that sequence specific long dsRNA induces potent gene expression silencing and antiviral responses in vitro via an RNAi-like mechanism instead of an IFN-dependent response.

Aquatic animal viruses mediated immune evasion in their host

Viruses are important and lethal pathogens that hamper aquatic animals. The result of the battle between host and virus would determine the occurrence of diseases. The host will fight against virus infection with various responses such as innate immunity, adaptive immunity, apoptosis, and so on. On the other hand, the virus also develops numerous strategies such as immune evasion to antagonize host antiviral responses. Here, We review the research advances on virus mediated immune evasions to host responses containing interferon response, NF-κB signaling, apoptosis, and adaptive response, which are executed by viral genes, proteins, and miRNAs from different aquatic animal viruses including Alloherpesviridae, Iridoviridae, Nimaviridae, Birnaviridae, Reoviridae, and Rhabdoviridae. Thus, it will facilitate the understanding of aquatic animal virus mediated immune evasion and potentially benefit the development of novel antiviral applications.

RNase III Nucleases and the Evolution of Antiviral Systems

Every living entity requires the capacity to defend against viruses in some form. From bacteria to plants to arthropods, cells retain the capacity to capture genetic material, process it in a variety of ways, and subsequently use it to generate pathogen-specific small RNAs. These small RNAs can then be used to provide specificity to an otherwise non-specific nuclease, generating a potent antiviral system. While small RNA-based defenses in chordates are less utilized, the protein-based antiviral invention in this phylum appears to have derived from components of the same ancestral small RNA machinery. Based on recent evidence, it would seem that RNase III nucleases have been reiteratively repurposed over billions of years to provide cells with the capacity to recognize and destroy unwanted genetic material. Here we describe an overview of what is known on this subject and provide a model for how these defenses may have evolved.

The Ambystoma tigrinum virus (ATV) RNase III gene can modulate host PKR activation and interferon production

The iridovirus RNase III gene is one of 26 conserved core genes among the family Iridoviridae. Initial studies suggest this viral protein functions to suppress RNA interference pathways that may attack viral RNA during infection. Therefore, to determine if the Ambystoma tigrinum virus (ATV) RNase III-like gene (ORF 25R) can modulate the host innate immune response fish and human cells ectopically expressing 25R were treated with polyI:C and monitored for interferon synthesis and phosphorylation of eIF2α and PKR. We found a decrease in cellular IFN production and modulation of the PKR pathway. In addition, ATV deleted of the RNase III gene (ATVΔ25R) shows reduced pathogenicity in tiger salamanders. Collectively our data suggest that the ATV 25R protein is a pathogenesis factor that may function to help evade the host's immune response by masking activators of the IFN pathway.

Plant RNA Regulatory Network and RNA Granules in Virus Infection

Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual components contribute to these processes. In this review we discuss the roles of cellular RNA regulatory mechanisms and RNA granules in plant virus infection in the light of current knowledge and compare the findings to those made in animal virus studies.

Functional characterisation and expression analysis of recombinant serum amyloid P isoform 1 (RbSAP1) from rock bream (Oplegnathus fasciatus)

Lectins are carbohydrate-binding proteins that play important roles in the recognition and elimination of pathogens via the innate immune system. Pentraxins (PTX) are humoral lectins, which are multifunctional proteins in vertebrates. Pentraxins can be divided into two groups based on their primary structure: short (C-reactive protein and serum amyloid P [SAP]) and long pentraxins (PTX3 and neuronal pentraxins). Previously, SAP was shown to have Ca(2+)-dependent binding specificity for various ligands and to be a major acute phase protein. In this study, we identified and characterised the gene encoding SAP isoform 1 in rock bream (Oplegnathus fasciatus) (RbSAP1) and analysed its expression in various tissues after a pathogen challenge. An alignment analysis conducted based on the deduced amino acid sequence of RbSAP1 (1918 bp full-length cDNA with a 699 bp open reading frame encoding 232 amino acids) and SAPs and PTXs isolated from other organisms, revealed that the pentraxin domain and cysteine residues of the deduced protein are conserved. RbSAP1, which was ubiquitously expressed in all tissues examined, was predominantly detected in head kidney, trunk kidney, peripheral blood leukocytes, and gills. RbSAP1 expression was dramatically up-regulated in the kidney and liver after infection with Edwardsiella tarda, Streptococcus iniae, or red seabream iridovirus. Purified rRbSAP1 was able to bind Gram-negative bacteria, Gram-positive bacteria, and pathogen-associated molecular patterns. Interestingly, rRbSAP1 aggregated Gram-negative bacteria in the presence of Ca(2+). The anti-pathogen activity of rRbSAP1 suggests that SAP functions in innate immunity in the rock bream.

Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants

Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV) infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi) pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant) and Caenorhabditis elegans (nematode) and found that it cleaves double-stranded small interfering RNA (ds-siRNA) molecules that are pivotal in the host RNA interference (RNAi) pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA)--mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3) produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are homologous in unrelated RNA and DNA viruses and can be detected in viral genomes using gene modeling and protein structure prediction programs.

Two NF-κB inhibitor-alpha (IκBα) genes from rock bream (Oplegnathus fasciatus): molecular characterization, genomic organization and mRNA expression analysis after immune stimulation

IkBa is a member of IkB family, which sequesters NF-kB in an inactivate form in the cytoplasm and blocks the translocation of NF-kB to nucleus. The IkBa paralogs of rock bream (OfIkBa-A and OfIkBa-B) encoded IkBa proteins with typical features including, highly conserved IkB degradation motif, six ankyrin repeats and a PEST sequence. However, their amino acid identity and similarity were only 55.6 and 69.7%, respectively suggesting that these two genes could be the two different isoforms of IkBa. The number and size of the exons of OfIkBa-A and OfIkBa-B were conserved well with all the compared vertebrate species, although they have significantly different genomic sizes. Phylogenetic analysis revealed that OfIkBa-A and OfIkBa-B proteins cluster with IkBa family members; however, they were grouped with different subclades in IkBa family. Tissue specific expression of OfIkBa mRNA was constitutively detected in all the tested tissues, and they showed the higher transcription level in heart, liver, gill and peripheral blood cells, respectively. The injection of flagellin stimulated the mRNA expression of OfIkBa paralogs in head kidney and intestine. Moreover, the OfIkBa mRNA expression in gill and liver was significantly upregulated by LPS, poly I:C and Edwardsiella tarda challenges. The transcription of OfIkBa was up-regulated in early-phase of injection and then rapidly restored. These results suggest that the OfIkBa paralogs might be involved in rapid immune responsive reactions in rock bream against bacterial and viral pathogens.

Cloning, characterisation, and expression analysis of the cathepsin D gene from rock bream (Oplegnathus fasciatus)

Cathepsins are lysosomal cysteine proteases belonging to the papain family, members of which play important roles in normal metabolism for the maintenance of cellular homeostasis. Rock bream (Oplegnathus fasciatus) cathepsin D (RbCTSD) cDNAs were identified by expressed sequence tag analysis of a lipopolysaccharide-stimulated rock bream liver cDNA library. The full-length RbCTSD cDNA (1644 bp) contained an open reading frame of 1191 bp encoding 396 amino acids. Alignment analysis revealed that the active sites and N-glycosylation sites of the deduced protein were well conserved. Phylogenetic analysis revealed that RbCTSD is most closely related to the Mi-iuy croaker (Miichthys miiuy) cathepsin D. RbCTSD was ubiquitously expressed in all the examined tissues, predominantly in muscle and kidneys. RbCTSD mRNA expression was also examined in several tissues under conditions of bacterial and viral challenge. All examined tissues of fish infected with Edwardsiella tarda (E. tarda), Streptococcus iniae (S. iniae), and red sea bream iridovirus (RSIV) showed significant increases in RbCTSD expression compared with the control. In the kidney and spleen, RbCTSD mRNA expression was markedly upregulated following infection with all tested pathogens. These findings indicate that RbCTSD plays an important role in the innate immune response of rock bream. Furthermore, these results provide important information for the identification of other cathepsin D genes in various fish species.

Genomic characterization of interferon regulatory factor 5 from rock bream (Oplegnathus fasciatus) and its role in antiviral defense

The interferon regulatory factor 5 (IRF5) is a key mediator of the Toll-like receptor (TLR)7 and TLR8 signaling pathways. In this study, we describe the identification of IRF5 (Rb-IRF5) from rock bream fish (Oplegnathus fasciatus) and its characteristics features at the genomic and expression levels. The full-length Rb-IRF5 sequence was identified from a cDNA library and its genomic sequence was obtained by screening and sequencing of a bacterial artificial chromosome (BAC) genomic DNA library of rock bream. The genomic sequence is comprised of 8 exons interrupted by 7 introns. The complete coding sequence of Rb-IRF5 is 1497 bp in length and encodes for 498 amino acids. The putative Rb-IRF5 protein consists of 3 important conserved domains: a DNA-binding domain (DBD) at the N-terminus, an IRF-associated domain (IAD), and a virus-activated domain (VAD) at the C-terminus. Based on pairwise sequence analysis, the highest sequence similarity/identity for Rb-IRF5 was observed with the IRF5 gene from turbot fish (>87%) and Japanese flounder (83%). Several important putative transcription factor-binding sites shared by the IRF gene family, including the NF-κB, Ap-1, IRF-1, and ICSBP/ISRE sites, were found in the 5' flanking region of Rb-IRF5. The predicted tertiary structure of the dimerized IAD and VAD of the Rb-IRF5 protein resembled that of its orthologs from humans. In healthy rock bream, the highest constitutive expression of Rb-IRF5 was detected in the liver. After iridovirus and polyinosinic-polycytidylic acid (poly(I:C)) challenge, Rb-IRF5 expression was significantly induced in the head kidney. Furthermore, rock bream recombinant type I interferon (Rb-IFN1) was also found to be an efficient inducer of Rb-IRF5 in a head kidney primary cell culture model. Upon IRF5 transfection, rock bream Mx (Rb-Mx), interferon I (Rb-IFN1) and tumor-necrosis factor α (Rb-TNFα) genes get significantly upregulated in rock bream heart cells. The findings of the present study explain the involvement of Rb-IRF5 in the induction of interferons and pro-inflammatory cytokines and thereby provide a model for how IRF5 modulates immune responses against viral infections in rock bream.

Binding and processing of small dsRNA molecules by the class 1 RNase III protein encoded by sweet potato chlorotic stunt virus

Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae) causes heavy yield losses in sweet potato plants co-infected with other viruses. The dsRNA-specific class 1 RNase III-like endoribonuclease (RNase3) encoded by SPCSV suppresses post-transcriptional gene silencing and eliminates antiviral defence in sweet potato plants in an endoribonuclease activity-dependent manner. RNase3 can cleave long dsRNA molecules, synthetic small interfering RNAs (siRNAs), and plant- and virus-derived siRNAs extracted from sweet potato plants. In this study, conditions for efficient expression and purification of enzymically active recombinant RNase3 were established. Similar to bacterial class 1 RNase III enzymes, RNase3-Ala (a dsRNA cleavage-deficient mutant) bound to and processed double-stranded siRNA (ds-siRNA) as a dimer. The results support the classification of SPCSV RNase3 as a class 1 RNase III enzyme. There is little information about the specificity of RNase III enzymes on small dsRNAs. In vitro assays indicated that ds-siRNAs and microRNAs (miRNAs) with a regular A-form conformation were cleaved by RNase3, but asymmetrical bulges, extensive mismatches and 2'-O-methylation of ds-siRNA and miRNA interfered with processing. Whereas Mg(2+) was the cation that best supported the catalytic activity of RNase3, binding of 21 nt small dsRNA molecules was most efficient in the presence of Mn(2+). Processing of long dsRNA by RNase3 was efficient at pH 7.5 and 8.5, whereas ds-siRNA was processed more efficiently at pH 8.5. The results revealed factors that influence binding and processing of small dsRNA substrates by class 1 RNase III in vitro or make them unsuitable for processing by the enzyme.

A teleostean counterpart of ferritin M subunit from rock bream (Oplegnathus fasciatus): an active constituent in iron chelation and DNA protection against oxidative damage, with a modulated expression upon pathogen stress

Ferritins are biological iron chelators that can sequestrate excess iron to maintain iron homeostasis in the body. Ferritins basically consist of 2 types of subunits, designated as H and L. However, another new subunit, ferritin "M" which possesses characteristic features of both the H and L subunits, was recently identified in lower vertebrates, mostly in fish. In this study, a ferritin M-like subunit from rock bream (Oplegnathus fasciatus) (RbFerM) was characterized at the molecular level, and its transcriptional profile was analyzed in healthy fish, as well as in pathogen- and mitogen-stimulated fish. Furthermore, its functional properties were evaluated using the recombinant protein. The complete coding sequence of RbFerM was 528 bp in length, encoding a 176-amino acid peptide with a calculated molecular mass of 20 kDa. In silico analysis of RbFerM revealed that it has features similar to both the mammalian ferritin subunits, H and L. Phylogenetic analysis depicted the higher evolutionary proximity of RbFerM with its fish counterparts. Quantitative real time polymerase chain reaction (PCR) analysis detected a ubiquitous transcriptional profile of RbFerM in selected tissues of rock bream, in which more pronounced expression was observed in blood and liver tissues. Significant transcriptional inductions of RbFerM were detected in liver tissues upon lipopolysaccharides (LPS), Edwardsiella tarda, Streptococcus iniae, and rock bream irido virus (RBIV) exposures in time-course immune-challenge experiments. The purified recombinant protein of RbFerM demonstrated detectable iron chelating activity that varied with the temperature. Moreover, the recombinant RbFerM rendered a detectable protection effect against iron (II) and H2O2-mediated DNA damage.

Genomic characterization and transcriptional evidence for the involvement of complement component 7 in immune response of rock bream (Oplegnathus fasciatus)

The complement component 7 (C7) is the central mediator of pathogenic attack at the membrane surface and its binding to the C5b-7 complex triggers cytolytic signaling. In this study, C7 of rock bream (Oplegnathus fasciatus) was identified (Rb-C7) and characterized at the genomic level. The Rb-C7 gene contains 18 exons and 17 introns and is composed of a 2490 bp complete open reading frame (ORF). The encoded polypeptide (830 amino acids) contains a number of well-conserved C7 signature domains. Important putative transcription factor binding sites, including those for NF-κB, SP-1, C/EBP, AP-1 and OCT-1, are present in the 5'-flanking region of Rb-C7. Phylogenetic analysis revealed a close proximity of Rb-C7 with the orthologues in tilapia and Japanese flounder. Quantitative real-time PCR (qPCR) analysis confirmed constitutive Rb-C7 expression throughout all the examined tissue of healthy rock bream, with highest expression in liver. In immune challenge experiment, Rb-C7 expression was up-regulated in head kidney and liver in response to Edwardsiella tarda, Streptococcus iniae, lipopolysaccharide and rock bream iridovirus (RBIV). Furthermore, significant increases of both intracellular expression level and the number of Rb-C7-expressing cells were detected by in situ hybridization assay in head kidney and liver tissues upon E. tarda infection. These results suggested that Rb-C7 is lytic pathway gene in complement system and its transcriptional regulation may be an important immune response in pathogenic defense mechanism of rock bream.

Genomic characterization and expression analysis of complement component 8α and 8β in rock bream (Oplegnathus fasciatus)

The complement component 8α and 8β are glycoproteins that mediate formation of the membrane attack complex (MAC) on the surface of target cells. Full-length complement C8α (Rb-C8α) and C8β (Rb-C8β) sequences were identified from a cDNA library of rock bream (Oplegnathus fasciatus), and their genomic sequences were obtained by screening and sequencing of a bacterial artificial chromosome (BAC) genomic DNA library of rock bream. The Rb-C8α gene contains 64bp of 5'-UTR, open reading frame (ORF) of 1794bp, which encodes a polypeptide of 598 amino acids, 212bp of 3'-UTR. The Rb-C8β gene contains 5'-UTR of 27bp, open reading frame (ORF) of 1761bp, which encodes a polypeptide of 587 amino acids, 3'-UTR of 164bp. Rb-C8α consists of 11 exons interrupted by 10 introns and Rb-C8β consists of 12 exons interrupted by 11 introns. Sequence analysis revealed that both Rb-C8α and Rb-C8β contain thrombospondin type-1, a low-density lipoprotein receptor domain class A, membrane attack complex/perforin (MACPF) domain and epidermal growth factor like domain. The promoter regions of both genes contain important putative transcription factor binding sites including those for NF-κB, SP-1, C/EBP, AP-1, and OCT-1. Rb-C8α and Rb-C8β showed the highest amino acid identity of 62% and 83% to rainbow trout C8α and Japanese flounder C8β respectively. Quantitative real-time PCR analysis confirmed that Rb-C8α and Rb-C8β were constitutively expressed in all examined tissues, isolated from healthy rock bream, with highest expression occurring in liver. Pathogen challenge, including Edwardsiella tarda, Streptococcus iniae, and rock bream iridovirus led to up regulation of Rb-C8α and Rb-C8β in liver. Positive regulations upon bacterial and viral challenges, and high degree of evolutionary relationship to respective orthologues, confirmed that Rb-C8α and Rb-C8β important immune genes, likely involved in the complement system lytic pathway of rock bream.

Genomic characterization and expression analysis of complement component 9 in rock bream (Oplegnathus fasciatus)

The complement component 9 (C9) is a single-chain glycoprotein that mediates formation of the membrane attack complex (MAC) on the surface of target cells. Full-length C9 sequence was identified from a cDNA library of rock bream (Oplegnathus fasciatus), and its genomic sequence was obtained by screening and sequencing of a bacterial artificial chromosome (BAC) genomic DNA library of rock bream. The rock bream complement component 9 (Rb-C9) gene contains 11 exons and 10 introns and is composed of a 1782 bp complete open reading frame (ORF) that encodes a polypeptide of 593 amino acids. Sequence analysis revealed that the Rb-C9 protein contains two thrombospondin type-1domains, a low-density lipoprotein receptor domain class A, a membrane attack complex & perforin (MACPF) domain, and an epidermal growth factor (EGF)-like domain. Important putative transcription factor binding sites, including those for NF-κB, SP-1, C/EBP, AP-1 and OCT-1, were found in the 5' flanking region. Phylogenetic analysis revealed a close proximity of Rb-C9 with the orthologues in puffer fish, and Japanese flounder. Quantitative real-time RT-PCR analysis confirmed that Rb-C9 was constitutively expressed in all the examined tissues isolated from healthy rock bream, with highest expression occurring in liver. Pathogen challenge, including Edwardsiella tarda, Streptococcus iniae, lipopolysaccharide endotoxin and rock bream iridovirus led to up-regulation of Rb-C9 in liver but no change in peripheral blood cells. The observed response to bacterial and viral challenges and high degree of evolutionary relationship to respective orthologues, confirmed that Rb-C9 is an important immune gene, likely involved in the complement system lytic pathway of rock bream.

Caspase 3 from rock bream (Oplegnathus fasciatus): genomic characterization and transcriptional profiling upon bacterial and viral inductions

Caspase 3 is a prominent mediator of apoptosis and participates in the cell death signaling cascade. In this study, caspase 3 was identified (Rbcasp3) and characterized from rock bream (Oplegnathus fasciatus). The full-length cDNA of Rbcasp3 is 2683 bp and contains an open reading frame of 849 bp, which encodes a 283 amino acid protein with a calculated molecular mass of 31.2 kDa and isoelectric point of 6.31. The amino acid sequence resembles the conventional caspase 3 domain architecture, including crucial amino acid residues in the catalytic site and binding pocket. The genomic length of Rbcasp3 is 7529 bp, and encompasses six exons interrupted by five introns. Phylogenetic analysis affirmed that Rbcasp3 represents a complex group in fish that has been shaped by gene duplication and diversification. Many putative transcription factor binding sites were identified in the predicted promoter region of Rbcasp3, including immune factor- and cancer signal-inducible sites. Rbcasp3, excluding the pro-domain, was expressed in Escherichia coli. The recombinant protein showed a detectable activity against the mammalian caspase 3/7-specific substrate DEVD-pNA, indicating a functional role in physiology. Quantitative real time PCR assay detected Rbcasp3 expression in all examined tissues, but with high abundance in blood, liver and brain. Transcriptional profiling of rock bream liver tissue revealed that challenge with lipopolysaccharides (LPS) caused prolonged up-regulation of Rbcasp3 mRNA whereas, Edwardsiella tarda (E. tarda) stimulated a late-phase significant transcriptional response. Rock bream iridovirus (RBIV) up-regulated Rbcasp3 transcription significantly at late-phase, however polyinosinic-polycytidylic acid (poly(I:C)) induced Rbcasp3 significantly at early-phase. Our findings suggest that Rbcasp3 functions as a cysteine-aspartate-specific protease and contributes to immune responses against bacterial and viral infections.

The molecular biology of frog virus 3 and other iridoviruses infecting cold-blooded vertebrates

Frog virus 3 (FV3) is the best characterized member of the family Iridoviridae. FV3 study has provided insights into the replication of other family members, and has served as a model of viral transcription, genome replication, and virus-mediated host-shutoff. Although the broad outlines of FV3 replication have been elucidated, the precise roles of most viral proteins remain unknown. Current studies using knock down (KD) mediated by antisense morpholino oligonucleotides (asMO) and small, interfering RNAs (siRNA), knock out (KO) following replacement of the targeted gene with a selectable marker by homologous recombination, ectopic viral gene expression, and recombinant viral proteins have enabled researchers to systematically ascertain replicative- and virulence-related gene functions. In addition, the application of molecular tools to ecological studies is providing novel ways for field biologists to identify potential pathogens, quantify infections, and trace the evolution of ecologically important viral species. In this review, we summarize current studies using not only FV3, but also other iridoviruses infecting ectotherms. As described below, general principles ascertained using FV3 served as a model for the family, and studies utilizing other ranaviruses and megalocytiviruses have confirmed and extended our understanding of iridovirus replication. Collectively, these and future efforts will elucidate molecular events in viral replication, intrinsic and extrinsic factors that contribute to disease outbreaks, and the role of the host immune system in protection from disease.

Genomic and proteomic analysis of invertebrate iridovirus type 9

Iridoviruses (IV) are nuclear cytoplasmic large DNA viruses that are receiving increasing attention as sublethal pathogens of a range of insects. Invertebrate iridovirus type 9 (IIV-9; Wiseana iridovirus) is a member of the major phylogenetic group of iridoviruses for which there is very limited genomic and proteomic information. The genome is 205,791 bp, has a G+C content of 31%, and contains 191 predicted genes, with approximately 20% of its repeat sequences being located predominantly within coding regions. The repeated sequences include 11 proteins with helix-turn-helix motifs and genes encoding related tandem repeat amino acid sequences. Of the 191 proteins encoded by IIV-9, 108 are most closely related to orthologs in IIV-3 (Chloriridovirus genus), and 114 of the 126 IIV-3 genes have orthologs in IIV-9. In contrast, only 97 of 211 IIV-6 genes have orthologs in IIV-9. There is almost no conservation of gene order between IIV-3, IIV-6, and IIV-9. Phylogenetic analysis using a concatenated sequence of 26 core IV genes confirms that IIV-3 is more closely related to IIV-9 than to IIV-6, despite being from a different genus of the Iridoviridae. An interaction between IIV and small RNA regulatory systems is supported by the prediction of seven putative microRNA (miRNA) sequences combined with XRN exonuclease, RNase III, and double-stranded RNA binding activities encoded on the genome. Proteomic analysis of IIV-9 identified 64 proteins in the virus particle and, when combined with infected cell analysis, confirmed the expression of 94 viral proteins. This study provides the first full-genome and consequent proteomic analysis of group II IIV.

Characterization and expression analysis of the myeloid differentiation factor 88 (MyD88) in rock bream Oplegnathus fasciatus

Myeloid differentiation factor 88 (MyD88) is a universal adaptor protein able to activate nuclear factor-kappa B (NF-κB) through interactions with interleukin-1 receptor (IL-1R) and the Toll-like receptors (TLRs), with the exception of TLR3. Here, we describe the identification of MyD88 from the rock bream fish Oplegnathus fasciatus and its characterization based on GS-FLX™ sequencing. The cDNA of rock bream MyD88 was found to be composed of 1626 bp, with an 867 bp open reading frame that encodes 288 amino acids. The deduced amino acid sequence of MyD88 possessed both a conserved death domain at the amino terminus and a typical Toll-IL-1 receptor (TIR) domain at the carboxyl terminus, similar to that found in other fishes, amphibians, avians, mammals and invertebrates. The mRNA expression pattern of MyD88 in healthy and bacterially challenged rock bream were examined using quantitative real-time polymerase chain reaction (qRT-PCR). MyD88 transcripts were found to be strongly expressed in blood, gill, liver, spleen, head kidney and kidney, moderately expressed in skin, brain and intestine, and weakly expressed in muscle. Expression levels of MyD88 in blood, spleen and head kidney were dramatically up-regulated upon exposure to LPS and the Gram-negative bacteria Edwardsiella tarda, suggesting that MyD88 plays an important role in rock bream defenses against bacterial infection.

An Ascovirus-encoded RNase III autoregulates its expression and suppresses RNA interference-mediated gene silencing

RNase III proteins play vital roles in processing of several types of RNA molecules and gene silencing. Recently, it has been discovered that some plant and animal viruses encode RNase III-like proteins as well. Genome sequencing of four virus species belonging to the Ascoviridae family has revealed sequence conservation of an RNase III open reading frame among the viruses. These have not been explored in ascoviruses, and therefore their role in host-virus interaction is unknown. Here, we confirmed expression of Heliothis virescens ascovirus (HvAV-3e) open reading frame 27 (orf27) that encodes an RNase III-like protein after infection and demonstrated dsRNA specific endoribonuclease activity of the encoded protein. Analysis of the expression patterns of orf27 in virus-infected insect cells and a bacterial expression system revealed autoregulation of this protein over time. Moreover, HvAV-3e RNase III was found essential for virus DNA replication and infection using RNA interference (RNAi)-mediated gene silencing. In addition, using green fluorescent protein gene as a marker, we provide evidence that RNase III is involved in the suppression of gene silencing. To our knowledge, this is the first insect virus-encoded RNase III described and shown to suppress host cell RNAi defense mechanism.