Cricket paralysis virus and drosophila C virus: serological analysis and comparison of capsid polypeptides and host range

Investigating the Evolution of Drosophila STING-Dependent Antiviral Innate Immunity by Multispecies Comparison of 2'3'-cGAMP Responses

Viruses represent a major threat to all animals, which defend themselves through induction of a large set of virus-stimulated genes that collectively control the infection. In vertebrates, these genes include interferons that play a critical role in the amplification of the response to infection. Virus- and interferon-stimulated genes include restriction factors targeting the different steps of the viral replication cycle, in addition to molecules associated with inflammation and adaptive immunity. Predictably, antiviral genes evolve dynamically in response to viral pressure. As a result, each animal has a unique arsenal of antiviral genes. Here, we exploit the capacity to experimentally activate the evolutionarily conserved stimulator of IFN genes (STING) signaling pathway by injection of the cyclic dinucleotide 2'3'-cyclic guanosine monophosphate-adenosine monophosphate into flies to define the repertoire of STING-regulated genes in 10 Drosophila species, spanning 40 million years of evolution. Our data reveal a set of conserved STING-regulated factors, including STING itself, a cGAS-like-receptor, the restriction factor pastel, and the antiviral protein Vago, but also 2 key components of the antiviral RNA interference pathway, Dicer-2, and Argonaute2. In addition, we identify unknown species- or lineage-specific genes that have not been previously associated with resistance to viruses. Our data provide insight into the core antiviral response in Drosophila flies and pave the way for the characterization of previously unknown antiviral effectors.

Israeli Acute Paralysis Virus Infection Leads to an Enhanced RNA Interference Response and Not Its Suppression in the Bumblebee Bombus terrestris

RNA interference (RNAi) is the primary antiviral defense system in insects and its importance for pollinator health is indisputable. In this work, we examined the effect of Israeli acute paralysis virus (IAPV) infection on the RNAi process in the bumblebee, Bombus terrestris, and whether the presence of possible functional viral suppressors could alter the potency of the host's immune response. For this, a two-fold approach was used. Through a functional RNAi assay, we observed an enhancement of the RNAi system after IAPV infection instead of its suppression, despite only minimal upregulation of the genes involved in RNAi. Besides, the presence of the proposed suppressor 1A and the predicted OrfX protein in IAPV could not be confirmed using high definition mass spectrometry. In parallel, when bumblebees were infected with cricket paralysis virus (CrPV), known to encode a suppressor of RNAi, no increase in RNAi efficiency was seen. For both viruses, pre-infection with the one virus lead to a decreased replication of the other virus, indicating a major effect of competition. These results are compelling in the context of Dicistroviridae in multi-virus/multi-host networks as the effect of a viral infection on the RNAi machinery may influence subsequent virus infections.

Viruses and antiviral immunity in Drosophila

Viral pathogens present many challenges to organisms, driving the evolution of a myriad of antiviral strategies to combat infections. A wide variety of viruses infect invertebrates, including both natural pathogens that are insect-restricted, and viruses that are transmitted to vertebrates. Studies using the powerful tools in the model organism Drosophila have expanded our understanding of antiviral defenses against diverse viruses. In this review, we will cover three major areas. First, we will describe the tools used to study viruses in Drosophila. Second, we will survey the major viruses that have been studied in Drosophila. And lastly, we will discuss the well-characterized mechanisms that are active against these diverse pathogens, focusing on non-RNAi mediated antiviral mechanisms. Antiviral RNAi is discussed in another paper in this issue.

Convergent evolution of argonaute-2 slicer antagonism in two distinct insect RNA viruses

RNA interference (RNAi) is a major antiviral pathway that shapes evolution of RNA viruses. We show here that Nora virus, a natural Drosophila pathogen, is both a target and suppressor of RNAi. We detected viral small RNAs with a signature of Dicer-2 dependent small interfering RNAs in Nora virus infected Drosophila. Furthermore, we demonstrate that the Nora virus VP1 protein contains RNAi suppressive activity in vitro and in vivo that enhances pathogenicity of recombinant Sindbis virus in an RNAi dependent manner. Nora virus VP1 and the viral suppressor of RNAi of Cricket paralysis virus (1A) antagonized Argonaute-2 (AGO2) Slicer activity of RNA induced silencing complexes pre-loaded with a methylated single-stranded guide strand. The convergent evolution of AGO2 suppression in two unrelated insect RNA viruses highlights the importance of AGO2 in antiviral defense.

Multi-cellular organisms require a potent immune response to ensure survival under the ongoing assault by microbial pathogens. Co-evolution of virus and host shapes the genome of both pathogen and host. Using Drosophila melanogaster as a model, we study virus-host interactions in infections by Nora virus, a non-lethal natural pathogen of fruit flies. Insects depend on the RNA interference (RNAi) pathway for antiviral defense. A hallmark of the antiviral RNAi response is the production of viral small RNAs during infection. We detected Nora virus small RNAs during infection of Drosophila, demonstrating that Nora virus is a target of the antiviral RNAi pathway. Furthermore, we show that Nora virus viral protein 1 (VP1) inhibits the catalytic activity of Argonaute-2, a key protein of the RNAi pathway. The 1A protein of Cricket paralysis virus suppresses RNAi via a similar mechanism. Importantly, whereas Nora virus persistently infects Drosophila, Cricket paralysis virus induces a lethal infection. Our findings thus indicate that two distantly related viruses independently evolved an RNAi suppressor protein that targets the Argonaute-2 protein. Altogether, our results emphasize the critical role of Argonaute-2 in insect antiviral defense, both in lethal and persistent infections.

A DNA virus of Drosophila

Little is known about the viruses infecting most species. Even in groups as well-studied as Drosophila, only a handful of viruses have been well-characterized. A viral metagenomic approach was used to explore viral diversity in 83 wild-caught Drosophila innubila, a mushroom feeding member of the quinaria group. A single fly that was injected with, and died from, Drosophila C Virus (DCV) was added to the sample as a control. Two-thirds of reads in the infected sample had DCV as the best BLAST hit, suggesting that the protocol developed is highly sensitive. In addition to the DCV hits, several sequences had Oryctes rhinoceros Nudivirus, a double-stranded DNA virus, as a best BLAST hit. The virus associated with these sequences was termed Drosophila innubila Nudivirus (DiNV). PCR screens of natural populations showed that DiNV was both common and widespread taxonomically and geographically. Electron microscopy confirms the presence of virions in fly fecal material similar in structure to other described Nudiviruses. In 2 species, D. innubila and D. falleni, the virus is associated with a severe (∼80-90%) loss of fecundity and significantly decreased lifespan.

Host range and specificity of the Drosophila C virus

BACKGROUND

The Drosophila C virus (DCV) is a common and well-studied Drosophila pathogen. Although natural infections are known from Drosophila melanogaster and D. simulans, and artificial infections have been reported from several Drosophila species and other insects, it remains unclear to date whether DCV infections also occur naturally in other Drosophila species.

METHODS/PRINCIPAL FINDINGS

Using reverse transcription PCR, we detected natural infections in six Drosophila species, which have not been previously known as natural hosts. By subsequent Sanger sequencing we compared DCV haplotypes among eight Drosophila host species. Our data suggest that cross-infections might be frequent both within and among species within the laboratory environment. Moreover, we find that some lines exhibit multiple infections with distinct DCV haplotypes.

CONCLUSIONS

Our results suggest that the natural host range of DCV is much broader than previously assumed and that cross-infections might be a common phenomenon in the laboratory, even among different Drosophila hosts.

Host and viral translational mechanisms during cricket paralysis virus infection

The dicistrovirus is a positive-strand single-stranded RNA virus that possesses two internal ribosome entry sites (IRES) that direct translation of distinct open reading frames encoding the viral structural and nonstructural proteins. Through an unusual mechanism, the intergenic region (IGR) IRES responsible for viral structural protein expression mimics a tRNA to directly recruit the ribosome and set the ribosome into translational elongation. In this study, we explored the mechanism of host translational shutoff in Drosophila S2 cells infected by the dicistrovirus, cricket paralysis virus (CrPV). CrPV infection of S2 cells results in host translational shutoff concomitant with an increase in viral protein synthesis. CrPV infection resulted in the dissociation of eukaryotic translation initiation factor 4G (eIF4G) and eIF4E early in infection and the induction of deIF2alpha phosphorylation at 3 h postinfection, which lags after the initial inhibition of host translation. Forced dephosphorylation of deIF2alpha by overexpression of dGADD34, which activates protein phosphatase I, did not prevent translational shutoff nor alter virus production, demonstrating that deIF2alpha phosphorylation is dispensable for host translational shutoff. However, premature induction of deIF2alpha phosphorylation by thapsigargin treatment early in infection reduced viral protein synthesis and replication. Finally, translation mediated by the 5' untranslated region (5'UTR) and the IGR IRES were resistant to impairment of eIF4F or eIF2 in translation extracts. These results support a model by which the alteration of the deIF4F complex contribute to the shutoff of host translation during CrPV infection, thereby promoting viral protein synthesis via the CrPV 5'UTR and IGR IRES.

The polypeptides induced in Drosophila cells by Drosophila C virus (strain Ouarzazate)

The Ouarzazate strain of Drosophila virus (DCV0) was grown in Drosophila melanogaster tissue culture cells, and [35S]methionine-labeled virions were found to contain a group of major structural proteins with a molecular weight of approximately 30,000 as well as several minor proteins of higher molecular weight and a protein of approximately 10,000 daltons. Using a range of pulses, chases and gel systems, examination of the intracellular proteins induced by DCV0 showed the presence of 17 polypeptides not found in uninfected cells. The synthesis of virus-induced polypeptides was extremely asymmetric with a rapid appearance of the major virus structural proteins and a much slower appearance of the lowest molecular weight structural protein (VP4). Processing of virus-induced proteins including the appearance of VP4 was demonstrated using pulse-chase after pulsing with [35S]methionine. While the highest molecular weight induced protein found in infected cells was 146,000, pretreatment of cells with iodoacetamide resulted in the appearance of a protein with a molecular weight of approximately 200,000. The evidence presented in this paper supports the inclusion of DCV0 in the Picornaviridae group.

A glassy-winged sharpshooter cell line supports replication of Rhopalosiphum padi virus (Dicistroviridae)

Rhopalosiphum padi virus (RhPV) (family Dicistroviridae; genus Cripavirus) is an icosahedral aphid virus with a 10kb positive-sense RNA genome. To study the molecular biology of RhPV, identification of a cell line that supports replication of the virus is essential. We screened nine cell lines derived from species within the Lepidoptera, Diptera and Hemiptera for susceptibility to RhPV following RNA transfection. We observed cytopathic effects (CPE) only in cell lines derived from hemipterans, specifically GWSS-Z10 cells derived from the glassy winged sharp shooter, Homalodisca coagulata and DMII-AM cells derived from the corn leaf hopper, Dalbulus maidis. Translation and appropriate processing of viral gene products, RNA replication and packaging of virus particles in the cytoplasm of GWSS-Z10 cells were examined by Western blot analysis, Northern blot hybridization and electron microscopy. Infectivity of the GWSS-Z10 cell derived-virus particles to the bird cherry-oat aphid, R. padi, was confirmed by RT-PCR and Western blot. The GWSS-Z10 cell line provides a valuable tool to investigate replication, structure and assembly of RhPV.

Divergent IRES elements in invertebrates

Viruses have evolved unique strategies and mechanisms to recruit ribosomes to ensure continued translation of their viral RNA during infection. The Dicistroviridae family of invertebrate viruses contains an unusual internal ribosome entry site (IRES), which can directly recruit ribosomes in the absence of initiation factors. Moreover, this IRES initiates translation at a non-AUG codon independent of an initiator Met-tRNA. Recent studies have shown that the IRES mimicks a tRNA to interact with and manipulate the ribosome. The presence of this divergent IRES likely allows translation of the dicistroviral RNA during infection when host translation is compromised. This review will explore the unique properties of this unprecedented mechanism of gene expression. Specific topics will examine structural components of the IRES, the mechanism of initiating translation at non-AUG codons and the regulation of this IRES in vivo. The existence of this mechanism suggests that the repertoire of open reading frames in our genome may be greater than anticipated.

Entry is a rate-limiting step for viral infection in a Drosophila melanogaster model of pathogenesis

The identification of host factors that control susceptibility to infection has been hampered by a lack of amenable genetic systems. We established an in vivo model to determine the host factors that control pathogenesis and identified viral entry as a rate-limiting step for infection. We infected Drosophila melanogaster cells and adults with drosophila C virus and found that the clathrin-mediated endocytotic pathway is essential for both infection and pathogenesis. Heterozygosity for mutations in genes involved in endocytosis is sufficient to protect flies from pathogenicity, indicating the exquisite sensitivity and dependency of the virus on this pathway. Thus, this virus model provides a sensitive and efficient approach for identifying components required for pathogenesis.

Molecular characterization of Drosophila C virus isolates

Reverse transcription coupled with polymerase chain reaction and restriction enzyme analysis was used to characterize 12 Drosophila C virus isolates from geographically different regions. A 1.2-kb fragment was amplified from cDNA and profiles from digestion with 20 restriction enzymes were generated. Analysis of the restriction fragment data gave estimates of nucleotide divergence of 0-10% between isolates. The isolates were grouped on the basis of genetic distance estimates derived from the restriction data. For the isolates from which a single genotype could be purified, a geographical pattern in the distribution of viral genotypes was identified. The 4 Moroccan isolates were very closely related to each other, differing in only 1 restriction profile. The 2 Australian isolates were each other's closest relatives, as were the 2 isolates first recovered in France. The PCR-RFLP technique used in this study has provided us with a simple procedure which can be used to characterize DCV isolates. A single enzyme, Taq I, generated 5 distinct and diagnostic restriction fragment patterns, which allowed easy assignment of isolates to one of the five viral genotypes identified in this study.

A simple vacuum dot-blot hybridisation assay for the detection of Drosophila A and C viruses in single Drosophila

Specific cDNA clones were constructed from the single stranded RNA genome of Australian isolates of both Drosophila A and C viruses. These clones were used to develop a nucleic acid hybridisation assay capable of detecting reliably 3.9 ng of DAV and 19.3 ng of DCV virus particles, respectively. The sensitivity of the assays were largely unaffected by soluble host material. Single Drosophila naturally infected or artificially inoculated with DAV or DCV were found to contain in excess of 130 ng of virus. The results presented here demonstrate that the vacuum dot-blotting protocol and the hybridisation assays developed are capable of detecting DAV and DCV in single Drosophila and may therefore be applied to the study of DAV and DCV in natural Drosophila communities.

Queensland fruit fly virus, a probable member of the Picornaviridae

A picornavirus was isolated from various life stages of the Queensland fruit fly, Dacus tryoni. This virus, Queensland fruit fly virus (QFFV) has virions with a diameter of 30 nm and a sedimentation coefficient of 178 S. One third of the particles in preparations were empty capsids or natural top component (NTC) with a sedimentation coefficient of 95 S. The buoyant density (rho) of virions and NTC in CsCl was 1.34 and 1.30 g/ml respectively; small amounts of a dense component (rho = 1.45 g/ml) were also detected. The capsid contained three major protein species of molecular weight (mol.wt.) 41,700, 36,500, and 31,300, in approximately equimolar proportions. NTC contained three major species of mol. wt. 44,700, 41,700, and 31,300. The nucleic acid present only in the bottom component virions was RNA and comprised about 30% of the particle weight and had a mol. wt of 2.88 kd, contained a poly(A) tract, and had a base ratio: G = 20; A = 32; C = 15; U = 33. The mol. wt. of the virion was estimated to be approximately equal to 9.5 kd. When virions were heated at 56 degrees C and above, they converted into artificial top component (ATC), which had the same protein composition as the virion when analysed by SDS-PAGE. In immunodiffusion tests the virions and NTC were indistinguishable, but a minor difference in antigenicity was detected between the virions and ATC. Virions were stable between pH 3 and 9 inclusive, and between 5 and 7 in the presence of 0.14 M NaCl. Immunodiffusion tests showed that QFFV was serologically unrelated to a range of picornaviruses as well as an unclassified virus isolated from the Mediterranean fruit fly, Ceratitis capitata. The data show that QFFV is probably a member of the Picornaviridae, genus Enterovirus.

Cell-free translation of Drosophila C virus RNA: identification of a virus protease activity involved in capsid protein synthesis and further studies on in vitro processing of cricket paralysis virus specified proteins

Drosophila C virus RNA acted as mRNA in rabbit reticulocyte lysates and directed the synthesis of at least one capsid protein and a number of higher molecular weight proteins. Kinetic analysis by pulse-chase experiments showed that a number of high molecular weight products acted as precursors to the capsid protein(s). Various dilution experiments were performed which showed that the virus specified a protease activity essential for the correct processing of precursors to give the capsid protein(s). A similar result was obtained with Cricket paralysis virus, and mixing experiments showed that the protease activity specified by one virus could perform some of the cleavages resulting in the production of the capsid proteins of the other virus. Some of the cleavages involving the highest molecular weight precursors could not be performed by the protease activity of the other virus. We could find no evidence for intramolecular cleavage of the capsid precursors of either of the viruses.

The proteins expressed by different isolates of Drosophila C virus

Isolates of Drosophila C virus (DCV) from Drosophila flies obtained in geographically different regions were adapted to growth in Drosophila tissue culture cells. The viruses, purified from tissue culture cells, were shown to be serologically related to one of the isolates ("O" from Ouarzazate, Morocco). Analysis of the structural proteins by polyacrylamide gel electrophoresis demonstrated differences between the isolates. Labelling intracellular proteins of infected Drosophila melanogaster cells with 35S-methionine at 28 degrees C demonstrated the presence of the virus structural proteins and their immediate precursors. Raising the temperature to 37 degrees C both before and during the pulse period inhibited the processing of the high molecular weight proteins and resulted in a greater "shut-off" of host cell proteins than viral induced proteins. This allowed the precursor proteins to be compared as well as the structural proteins of the different strains. It was possible to clearly distinguish differences between the isolates on the basis of the induced proteins, although limited proteolysis of corresponding proteins showed marked similarities. Hence it is possible to distinguish between different isolates of the "same" small RNA-virus of insects from geographically different regions.

In vitro translation of cricket paralysis virus RNA

Cricket paralysis virus RNA acted as a messenger in a translation system and directed incorporation of 35S-methionine into protein. Polyacrylamide gel analysis of the proteins demonstrated the presence of proteins of comparable molecular weight to the viral structural proteins and also potential high molecular weight precursors.

The intracellular proteins induced by cricket paralysis virus in Drosophila cells: the effect of protease inhibitors and amino acid analogues

Treatment of Cricket paralysis virus infected Drosophila cells with iodoacetamide before radiolabelling with 35S-methionine results in the appearance of two high molecular weight polypeptides of approximately equal to 200,000 molecular weight, not apparent in untreated infected cells (17). To attempt to differentiate between the effects of iodoacetamide being attributable to either alteration of initial polyprotein or inhibition of the protease (either cellular or viral) the effects of a spectrum of protease inhibitors were examined. These included aprotinin, leupeptin, pepstatin, elevated zinc concentration, phenyl methyl sulphonyl-fluoride, N-tosyl-L-lysine chloromethyl ketone (TLCK) and N-tosyl-L-phenylalanine chloromethyl ketone (TPCK). TLCK and TPCK both inhibited the cleavage of proteins which demonstrates an inhibition of the protease activity. The introduction of amino acid analogues into the infected cells before pulsing also results in the appearance of higher molecular weight proteins. This could be attributed to alternation of the polyprotein making it nonsusceptible to digestion with pre-existing cellular protease or newly synthesized viral protease. The possibility that the presence of the amino acid analogues results in alteration of a viral coded protease cannot be eliminated.

Processing of cricket paralysis virus induced polypeptides in Drosophila cells: production of high molecular weight polypeptides by treatment with iodoacetamide

Infection of Drosophila cells with Cricket paralysis virus in the presence of Actinomycin D results in virtual complete inhibition of host cell protein synthesis by four hours post-infection. Using 35S-methionine or 14C-amino acids to pulse infected cells three major classes of viral induced proteins can be detected, (A) high molecular weight precursor proteins, (B) viral structural proteins and (C) low molecular weight cleavage products. The large number of high molecular weight proteins found in the infected cells suggests that a multiple cleavage cascade mechanism is partially utilized to produce virus structural proteins. In infected cells, even with short pulses, the largest viral induced protein obtained has a molecular weight of 144,000. However with pretreatment of the infected cells with iodoacetamide before pulsing, two further proteins are obtained with molecular weights of 205,000 and 190,000. Other changes occur in viral protein precursors in the presence of iodoacetamide.

Characterization of Cricket Paralysis Virus-Induced Polypeptides in Drosophila Cells

Cricket paralysis virus purified from Galleria mellonella larvae was shown to be similar to virus purified from Drosophila melanogaster cells. Cricket paralysis virus contained three major structural polypeptides of similar molecular weight (around 30,000), had a buoyant density of 1.344 g/ml, and had a capsid diameter of 27 nm. Twenty virus-induced polypeptides could be detected in CrPV-infected Drosophila cells. Two major polypeptides found in the infected cells corresponded to two structural viral polypeptides (VP1 and VP3), whereas the third major intracellular polypeptide was the apparent precursor of the third viral structural polypeptide (VP2). Three of the primary virus-induced polypeptides had molecular weights of 144,000, 124,000, and 115,000. These and other polypeptides were chased into lower-molecular-weight proteins when excess cold methionine was added after a short [ 35 S]methionine pulse. Although cricket paralysis virus has a number of characteristics in common with the mammalian enteroviruses, the extremely fast processing of high-molecular-weight polypeptides into viral proteins seems atypical. Also, no VP4 (8,000 to 10,000 molecular weight) has been found in the virus particles.