ORF018R, a highly abundant virion protein from Singapore grouper iridovirus, is involved in serine/threonine phosphorylation and virion assembly

Singapore grouper iridovirus VP018 abrogates the interferon response by targeting STING-TBK1-IRF3 axis

Singapore grouper iridovirus (SGIV), causes high mortality rate in grouper aquaculture. Previous study showed that SGIV VP018 was a highly abundant virulence factor, but the potential mechanism underlying the actions of VP018 still remained largely uncertain. Here, we firstly demonstrated that VP018 was interacted with major capsid protein (MCP) and VP075, and recruited into viral assembly sites in SGIV infected cells. Of note, VP018 was identified as a novel iridoviral protein that interacted with TANK-binding kinase 1 (EcTBK1) and IFN regulatory factor 3 (EcIRF3) by yeast two-hybrid screening and co-immunoprecipitation assay. In addition, the adaptor protein stimulator of interferon genes (EcSTING) was also found to interact with VP018. Furthermore, VP018 degraded EcSTING, EcTBK1 and EcIRF3 proteins in vitro, and suppressed their induction of interferon response. VP018 also disrupted the formation of EcSTING-EcTBK1 and EcTBK1-EcIRF3 complexes, leading to the reduction of EcIRF3 nuclear translocation. In addition, VP018 negatively regulated the antiviral actions of EcSTING, EcTBK1 and EcIRF3 against red-spotted grouper nervous necrosis virus (RGNNV) infection. Together, our findings provided the evidence that VP018 was involved in SGIV assembly, but also firstly demonstrated that VP018 functioned as a novel immune evasion protein which antagonized the host antiviral response via STING-TBK1-IRF3 axis.

The morphogenesis of different giant viruses as additional evidence for a common origin of Nucleocytoviricota

Large and giant DNA viruses are a monophyletic group constituting the recently established phylum Nucleocytoviricota. The virus particle morphogenesis of these viruses exhibit striking similarities. Viral factories are established in the host cells where new virions are assembled by recruiting host membranes, forming an inner lipid layer. An outer protein layer starts as a lamellar structure, commonly referred to as viral crescents, coded by the major capsid protein gene. Also, these viruses have a conserved ATPase-coding gene related to genome encapsidation. Similar properties are described for tectiviruses, putative small ancestors of giant viruses. Here we review the morphogenesis of giant viruses and discuss how the process similarities constitute additional evidence to the common origin of Nucleocytoviricota.

The interactome of Singapore grouper iridovirus protein ICP18 as revealed by proximity-dependent BioID approach

Singapore grouper iridovirus (SGIV) is a large double-stranded DNA virus that is a major threat to grouper aquaculture. The pathogenesis of SGIV is not well understood so far. Previous studies have revealed that ICP18, an immediate early protein encoded by SGIV ORF086R gene, promotes viral replication by regulating cell proliferation and virus assembly. In the present study, the potential functions of ICP18 were further explored by probing into its interactors using a proximity-dependent BioID method. Since our in-house grouper embryonic cells (a natural host cell of SGIV) could not be efficiently transfected with the plasmid DNA, and the grouper genome data for mass spectrometry-based protein identification is not currently available, we chosen a non-permissive cell (HEK293 T) as a substitute for this study. A total of 112 cellular proteins that potentially bind to ICP18 were identified by mass spectrometry analysis. Homology analysis showed that among these identified proteins, 110 candidate ICP18-interactors had homologous proteins in zebrafish (a host of SGIV), and shared high sequence identity. Further analysis revealed that the identified ICP18-interacting proteins modulate various cellular processes such as cell cycle and cell adhesion. In addition, the interaction between ICP18 and its candidate interactor, i.e., cyclin-dependent kinase1 (CDK1), was confirmed using Co-immunoprecipitation (Co-IP) and Pull-down assays. Collectively, our present data provides additional insight into the biological functions of ICP18 during viral infection, which could help in further unraveling the pathogenesis of SGIV.

Proteomic analysis of the Heliothis virescens ascovirus 3i (HvAV-3i) virion

Ascoviruses are enveloped, circular, double-stranded DNA viruses that can effectively control the appetite of lepidopteran larvae, thereby reducing the consequent damage and economic losses to crops. In this study, the virion of a sequenced Heliothis virescens ascovirus 3i (HvAV-3i) strain was used to perform proteomic analysis using both in-gel and in-solution digestion. A total of 81 viral proteins, of which 67 were associated with the virions, were identified in the proteome of HvAV-3i virions. Among these proteins, 23 with annotated functions were associated with DNA/RNA metabolism/transcription, virion assembly, sugar and lipid metabolism, signalling, cellular homoeostasis and cell lysis. Twenty-one viral membrane proteins were also identified. Some of the minor 'virion' proteins identified may be non-virion contaminants of viral proteins synthesized during replication, identified by more recent and highly sensitive methods. The extensive identification of the ascoviral proteome will establish a foundation for further investigation of ascoviral replication and infection.

Invertebrate Iridoviruses: A Glance over the Last Decade

Members of the family Iridoviridae (iridovirids) are large dsDNA viruses that infect both invertebrate and vertebrate ectotherms and whose symptoms range in severity from minor reductions in host fitness to systemic disease and large-scale mortality. Several characteristics have been useful for classifying iridoviruses; however, novel strains are continuously being discovered and, in many cases, reliable classification has been challenging. Further impeding classification, invertebrate iridoviruses (IIVs) can occasionally infect vertebrates; thus, host range is often not a useful criterion for classification. In this review, we discuss the current classification of iridovirids, focusing on genomic and structural features that distinguish vertebrate and invertebrate iridovirids and viral factors linked to host interactions in IIV6 (Invertebrate iridescent virus 6). In addition, we show for the first time how complete genome sequences of viral isolates can be leveraged to improve classification of new iridovirid isolates and resolve ambiguous relations. Improved classification of the iridoviruses may facilitate the identification of genus-specific virulence factors linked with diverse host phenotypes and host interactions.

Singapore grouper iridovirus protein VP088 is essential for viral infectivity

Viral infection is a great challenge in healthcare and agriculture. The Singapore grouper iridovirus (SGIV) is highly infectious to numerous marine fishes and increasingly threatens mariculture and wildlife conservation. SGIV intervention is not available because little is known about key players and their precise roles in SGVI infection. Here we report the precise role of VP088 as a key player in SGIV infection. VP088 was verified as an envelope protein encoded by late gene orf088. We show that SGIV could be neutralized with an antibody against VP088. Depletion or deletion of VP088 significantly suppresses SGIV infection without altering viral gene expression and host responses. By precisely quantifying the genome copy numbers of host cells and virions, we reveal that VP088 deletion dramatically reduces SGIV infectivity through inhibiting virus entry without altering viral pathogenicity, genome stability and replication and progeny virus release. These results pinpoint that VP088 is a key player in SGIV entry and represents an ideal target for SGIV intervention.

Visualization of Assembly Intermediates and Budding Vacuoles of Singapore Grouper Iridovirus in Grouper Embryonic Cells

Iridovirid infection is associated with the catastrophic loss in aquaculture industry and the population decline of wild amphibians and reptiles, but none of the iridovirid life cycles have been well explored. Here, we report the detailed visualization of the life cycle of Singapore grouper iridovirus (SGIV) in grouper cells by cryo-electron microscopy (cryoEM) and tomography (ET). EM imaging revealed that SGIV viral particles have an outer capsid layer, and the interaction of this layer with cellular plasma membrane initiates viral entry. Subsequent viral replication leads to formation of a viral assembly site (VAS), where membranous structures emerge as precursors to recruit capsid proteins to form an intermediate, double-shell, crescent-shaped structure, which curves to form icosahedral capsids. Knockdown of the major capsid protein eliminates the formation of viral capsids. As capsid formation progresses, electron-dense materials known to be involved in DNA encapsidation accumulate within the capsid until it is fully occupied. Besides the well-known budding mechanism through the cell periphery, we demonstrate a novel budding process in which viral particles bud into a tubular-like structure within vacuoles. This budding process may denote a new strategy used by SGIV to disseminate viral particles into neighbor cells while evading host immune response.

Characterization of the VP39 envelope protein from Singapore grouper iridovirus

Singapore grouper iridovirus (SGIV) is a major pathogen that causes heavy economic losses to the grouper aquaculture industry in China and Southeast Asian countries. In the present study, a viral envelope protein, VP39, encoded by SGIV ORF39L, was identified and characterized. SGIV ORF39L was found in all sequenced iridoviruses and is now considered to be a core gene of the family Iridoviridae. ORF39L was classified as a late gene during in vitro infection using reverse transcription–polymerase chain reaction, western blotting, and a drug inhibition analysis. An indirect immunofluorescence assay revealed that the VP39 protein was confined to the cytoplasm, especially at viral assembly sites. Western blot and matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry analyses suggested that VP39 is an envelope protein. Immunogold electron microscopy further confirmed that VP39 is a viral envelope protein. Furthermore, a mouse anti-VP39 polyclonal antibody exhibited SGIV-neutralizing activity in vitro, suggesting that VP39 is involved in SGIV infection. Taken together, the current data suggest that VP39 represents a conserved envelope protein of iridoviruses that contributes to viral infection.

Singapore Grouper Iridovirus ORF75R is a Scaffold Protein Essential for Viral Assembly

Singapore Grouper Iridovirus (SGIV) is a member of nucleo cytoplasmic large DNA viruses (NCLDV). This paper reports the functional analysis of ORF75R, a major structural protein of SGIV. Immuno fluorescence studies showed that the protein was accumulated in the viral assembly site. Immunogold-labelling indicated that it was localized between the viral capsid shell and DNA core. Knockdown of ORF75R by morpholinos resulted in the reduction of coreshell thickness, the failure of DNA encapsidation, and the low yield of infectious particles. Comparative proteomics further identified the structural proteins affected by ORF75R knockdown. Two-dimensional gel electrophoresis combined with proteomics demonstrated that ORF75R was phosphorylated at multiple sites in SGIV-infected cell lysate and virions, but the vast majority of ORF75R in virions was the dephosphorylated isoform. A kinase assay showed that ORF75R could be phosphorylated in vitro by the SGIV structural protein ORF39L. Addition of ATP and Mg²⁺ into purified virions prompted extensive phosphorylation of structural proteins and release of ORF75R from virions. These data suggest that ORF75R is a novel scaffold protein important for viral assembly and DNA encapsidation, but its phosphorylation facilitates virion disassembly. Compared to proteins from other viruses, we found that ORF75R shares common features with herpes simplex virus VP22.

Medaka haploid embryonic stem cells are susceptible to Singapore grouper iridovirus as well as to other viruses of aquaculture fish species

Viral infection is a challenge in high-density aquaculture, as it leads to various diseases and causes massive or even complete loss. The identification and disruption of host factors that viruses utilize for infection offer a novel approach to generate viral-resistant seed stocks for cost-efficient and sustainable aquaculture. Genetic screening in haploid cell cultures represents an ideal tool for host factor identification. We have recently generated haploid embryonic stem (ES) cells in the laboratory fish medaka. Here, we report that HX1, one of the three established medaka haploid ES cell lines, was susceptible to the viruses tested and is thus suitable for genetic screening to identify host factors. HX1 cells displayed a cytopathic effect and massive death upon inoculation with three highly infectious and notifiable fish viruses, namely Singapore grouper iridovirus (SGIV), spring viremia of carp virus (SVCV) and red-spotted grouper nervous necrosis virus (RGNNV). Reverse transcription-PCR and Western blot analyses revealed the expression of virus genes. SGIV infection in HX1 cells elicited a host immune response and apoptosis. Viral replication kinetics were determined from a virus growth curve, and electron microscopy revealed propagation, assembly and release of infectious SGIV particles in HX1 cells. Our results demonstrate that medaka haploid ES cells are susceptible to SGIV, as well as to SVCV and RGNNV, offering a unique opportunity for the identification of host factors by genetic screening.

A DNA-binding protein encoded by ORF008L of Singapore grouper iridovirus

Singapore grouper iridovirus (SGIV) is a major viral pathogen that can cause substantial economic losses in aquaculture, but its genome replication, organization and package are largely unknown. We isolated SGIV protein-DNA core by freeze-thaw lysis of viral particles and gradient centrifugation. Twelve proteins were identified from the core by mass spectrometry. ORF008L, one of the core proteins, was identified as a collagen-like protein and its DNA binding ability was demonstrated by electrophoretic mobility shift assay (EMSA). Binding of ORF008L to DNA was neither sequence specific nor pH dependent, and it protected DNA from degradation by DNase I in vitro. These results suggest that ORF008L may play a role in protection or stabilization of the viral genome during infection.

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.

Rana grylio virus as a vector for foreign gene expression in fish cells

In the present study, Rana grylio virus (RGV, an iridovirus) thymidine kinase (TK) gene and viral envelope protein 53R gene were chosen as targets for foreign gene insertion. ΔTK-RGV and Δ53R-RGV, two recombinant RGV, expressing enhanced green fluorescence protein (EGFP) were constructed and analyzed in Epithelioma papulosum cyprinid (EPC) cells. The EGFP gene which fused to the virus major capsid protein (MCP) promoter p50 was inserted into TK and 53R gene loci of RGV, respectively. Cells infected with these two recombinant viruses not only displayed plaques, but also emitted strong green fluorescence under fluorescence microscope, providing a simple method for selection and purification of recombinant viruses. ΔTK-RGV was purified by seven successive rounds of plaque isolation and could be stably propagated in EPC cells. All of the plaques produced by the purified recombinant virus emitted green fluorescence. However, Δ53R-RGV was hard to be purified even through twenty rounds of plaque isolation. The purified recombinant virus ΔTK-RGV was verified by PCR analysis and Western blotting. These results showed EGFP was expressed in ΔTK-RGV infected cells. Furthermore, one-step growth curves and electron microscopy revealed that infection with recombinant ΔTK-RGV and wild-type RGV are similar. Therefore, RGV was demonstrated could be as a viral vector for foreign gene expression in fish cells.

Characterization of Singapore grouper iridovirus (SGIV) ORF086R, a putative homolog of ICP18 involved in cell growth control and virus replication

Singapore grouper iridovirus (SGIV), as a causative agent of serious systemic disease, causes significant economic losses in grouper aquaculture. In this study, a novel ICP18 homolog encoded by SGIV ORF086R was identified and characterized. Strikingly, ICP18 homologs can be found in all ranaviruses, but not in other sequenced large DNA viruses. SGIV ICP18 is an immediate-early gene and begins to be transcribed as early as 2 h post-infection (p.i.). Western blotting indicated that SGIV ICP18 is translated as early as 6 h p.i. and is a viral non-envelope protein. Subcellular localization analysis revealed that the SGIV ICP18 displays a finely punctate cytoplasmic pattern. Furthermore, overexpression of SGIV ICP18 can promote the growth of grouper embryonic cells (GP) and contribute to SGIV replication. These results should offer important insights into the pathogenesis of ranaviruses.