Widespread Genome Reorganization of an Obligate Virus Mutualist

The family Polydnaviridae is of interest because it provides the best example of viruses that have evolved a mutualistic association with their animal hosts. Polydnaviruses in the genus Bracovirus are strictly associated with parasitoid wasps in the family Braconidae, and evolved ∼100 million years ago from a nudivirus. Each wasp species relies on its associated bracovirus to parasitize hosts, while each bracovirus relies on its wasp for vertical transmission. Prior studies establish that bracovirus genomes consist of proviral segments and nudivirus-like replication genes, but how these components are organized in the genomes of wasps is unknown. Here, we sequenced the genome of the wasp Microplitis demolitor to characterize the proviral genome of M. demolitor bracovirus (MdBV). Unlike nudiviruses, bracoviruses produce virions that package multiple circular, double-stranded DNAs. DNA segments packaged into MdBV virions resided in eight dispersed loci in the M. demolitor genome. Each proviral segment was bounded by homologous motifs that guide processing to form mature viral DNAs. Rapid evolution of proviral segments obscured homology between other bracovirus-carrying wasps and MdBV. However, some domains flanking MdBV proviral loci were shared with other species. All MdBV genes previously identified to encode proteins required for replication were identified. Some of these genes resided in a multigene cluster but others, including subunits of the RNA polymerase that transcribes structural genes and integrases that process proviral segments, were widely dispersed in the M. demolitor genome. Overall, our results indicate that genome dispersal is a key feature in the evolution of bracoviruses into mutualists.     

Systematic analysis of a wasp parasitism arsenal

Parasitoid wasps are among the most diverse insects on earth with many species causing major mortality in host populations. Parasitoids introduce a variety of factors into hosts to promote parasitism, including symbiotic viruses, venom, teratocytes and wasp larvae. Polydnavirus‐carrying wasps use viruses to globally suppress host immunity and prevent rejection of developing parasites. Although prior results provide detailed insights into the genes viruses deliver to hosts, little is known about other products. RNAseq and proteomics were used to characterize the proteins secreted by venom glands, teratocytes and larvae from Microplitis demolitor, which carries M. demolitor bracovirus (MdBV). These data revealed that venom glands and teratocytes secrete large amounts of a small number of products relative to ovaries and larvae. Venom and teratocyte products exhibited almost no overlap with one another or MdBV genes, which suggested that M. demolitor effector molecules are functionally partitioned according to their source. This finding was well illustrated in the case of MdBV and teratocytes. Many viral proteins have immunosuppressive functions that include disruption of antimicrobial peptide production, yet this study showed that teratocytes express high levels of the antimicrobial peptide hymenoptaecin, which likely compensates for MdBV‐mediated immunosuppression. A second key finding was the prevalence of duplications among genes encoding venom and teratocyte molecules. Several of these gene families share similarities with proteins from other species, while also showing specificity of expression in venom glands or teratocytes. Overall, these results provide the first comprehensive analysis of the proteins a polydnavirus‐carrying wasp introduces into its host.     

Origin and evolution of polydnaviruses by symbiogenesis of insect DNA viruses in endoparasitic wasps

During oviposition, many endoparasitic wasps inject virus-like particles into their insect hosts that enable these parasitoids to evade or directly suppress their hosts' immune system, especially encapsulation by hemocytes. These particles are defined as virions that belong to viruses of the two genera that comprise the family Polydnaviridae, bracoviruses (genus Bracovirus) transmitted by braconid wasps, and ichnoviruses (genus Ichnovirus) transmitted by ichneumonid wasps. Structurally, bracovirus virions resemble nudivirus and baculovirus virions (family Baculoviridae), and ichnovirus virions resemble those of ascoviruses (family Ascoviridae). Whereas nudiviruses, baculoviruses and ascoviruses replicate their DNA and produce progeny virions, polydnavirus DNA is integrated into and replicated from the wasp genome, which also directs virion synthesis. The structural similarity of polydnavirus virions to those of viruses that attack the wasps' lepidopteran hosts, along with polydnavirus transmission and replication biology, suggest that these viruses evolved from insect DNA viruses by symbiogenesis, the same process by which mitochondia and chloroplasts evolved from bacteria. Molecular evidence supporting this hypothesis comes from similarities among structural proteins of ascoviruses and the Campoletis sonorensis ichnovirus. Implications of this hypothesis are that polydnaviruses evolved from viruses, but are no longer viruses, and that DNA packaged into polydnavirus virions is not viral genomic DNA per se, but rather wasp genomic DNA consisting primarily of wasp genes and non-coding DNA. Thus, we suggest that a better understanding of polydnaviruses would result by viewing these not as viruses, but rather as a wasp organelle system that evolved to shuttle wasp genes and proteins into hosts to evade and suppress their immune response.     

When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses

The Polydnaviridae (PDV), including the Bracovirus (BV) and Ichnovirus genera, originated from the integration of unrelated viruses in the genomes of two parasitoid wasp lineages, in a remarkable example of convergent evolution. Functionally active PDVs represent the most compelling evolutionary success among endogenous viral elements (EVEs). BV evolved from the domestication by braconid wasps of a nudivirus 100 Ma. The nudivirus genome has become an EVE involved in BV particle production but is not encapsidated. Instead, BV genomes have co-opted virulence genes, used by the wasps to control the immunity and development of their hosts. Gene transfers and duplications have shaped BV genomes, now encoding hundreds of genes. Phylogenomic studies suggest that BVs contribute largely to wasp diversification and adaptation to their hosts. A genome evolution model explains how multidirectional wasp adaptation to different host species could have fostered PDV genome extension. Integrative studies linking ecological data on the wasp to genomic analyses should provide new insights into the adaptive role of particular BV genes. Forthcoming genomic advances should also indicate if the associations between endoparasitoid wasps and symbiotic viruses evolved because of their particularly intimate interactions with their hosts, or if similar domesticated EVEs could be uncovered in other parasites.     

Interspecific discrimination and larval competition amongMicroplitis croceipes,Microplitis demolitor,Cotesia kazak (Hym.: Braconidae), andHyposoter didymator (Hym.: Ichneumonidae), parasitoids ofHeliothis virescens (Lep.: Noctuidae)

Interspecific host discrimination by adults, and larval competition among the endoparasitoidsMicroplitis croceipes (Cresson),Microplitis demolitor Wilkinson,Cotesia kazak (Telenga) andHyposoter didymator (Thunberg) were investigated usingHeliothis virescens (F.) as the host. In ovipositional choice tests, the mean number of encounters and ovipositions for unparasitized hosts was not significantly different from the mean number of encounters and ovipositions for parasitized hosts for each treatment combination (P>0.05). Thus, none of the parasitoid species discriminated between host larvae recently parasitized once by a female of another species und unparasitized hosts. However, in all but two cases, females did discriminate between unparasitized hosts and hosts in which an early first instar of the first-attacking species was developing.Cotesia kazak andH. didymator did not discriminate between unparasitized hosts and hosts parasitized by an early first instar ofM. demolitor. Larval competition among these parasitoid species was studied for three time intervals between the first and second species parasitization: 1) second species attack immediately (5–15 sec) after the first; 2) second species attack 24 h after the first; and 3) second species attack 48 h after the first. Time until egg eclosion was shortest forM. demolitor, thenC. kazak, thenM. croceipes, and longest forH. didymator. When the second parasitoid species attacked a host immediately after the first species, the species in which egg eclosion occurred first was the victor more frequently, except whenM. demolitor competed withC. kazak andH. didymator. With a 24 h delay between the first and second species to attack, the older first instar from the first parasitization usually outcompeted the younger first instar from the second attack. A first instar from the second species to attack generally outcompeted the second instar of the first species when the second parasitization had been delayed 48 h. Competiors were eliminated mainly by physical attack, butC. kazak andM. croceipes apparently also killedH. didymator eggs by physiological processes.     

Host discrimination of a larval parasitoid: the quick movement of Microplitis demolitor

Many parasitoids discriminate previously parasitised hosts from unparasitised ones to avoid mortality of offspring. Parasitoids that parasitise aggressive hosts such as lepidopteran larvae are known to attack hosts very quickly to avoid being attacked. However, little is known about host discrimination of such quick attacking parasitoids. We investigated host discrimination of Microplitis demolitor (Wilkinson) (Hymenoptera: Braconidae) a quick attacking parasitoid of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). Results showed that ratios of female wasps that rejected the hosts after antennal examination did not differ between parasitised and unparasitised hosts, indicating that M. demolitor did not discriminate hosts by antennal examination. However, 95% of females that inserted ovipositor into unparasitised hosts actually laid eggs, whereas it was only 31% for parasitised hosts, indicating that females discriminated hosts by oviposition insertion. Analyzing video recordings revealed that the ovipositor exploration of the host took 0.3 s. Female wasps that had experienced high-host density of unparasitised hosts readily rejected parasitised hosts, while wasps with experience of low host availability of parasitised hosts tended to accept parasitised hosts. This suggests that host discrimination behaviour of M. demolitor is affected by previous experience of different host availability and host quality.

     

Venom gland extract is not required for successful parasitism in the polydnavirus-associated endoparasitoid Hyposoter didymator (Hym. Ichneumonidae) despite the presence of numerous novel and conserved venom proteins

The venom gland is a conserved organ in Hymenoptera that shows adaptations associated with life-style diversification. Few studies have investigated venom components and function in the highly diverse parasitic wasps and all suggest that the venom regulates host physiology. We explored the venom of the endoparasitoid Hyposoter didymator (Campopleginae), a species with an associated polydnavirus produced in the ovarian tissue. We investigated the effects of the H. didymator venom on two physiological traits of the host Spodoptera frugiperda (Noctuidae): encapsulation response and growth rate. We found that H. didymator venom had no significant effect on host cellular immunity or development, suggesting that it does not contribute to parasitism success. The host physiology seemed to be modified essentially by the ovarian fluid containing the symbiotic polydnaviruses. Proteomic analyses indicated that the H. didymator venom gland produces a large variety of proteins, consistent with the classical hymenopteran venom protein signature, including: reprolysin-like, dipeptidyl peptidase IV, hyaluronidase, arginine kinase or allergen proteins. The venom extracts also contained novel proteins, encoded by venom genes conserved in Campopleginae ichneumonids, and proteins with similarities to active molecules identified in other parasitoid species, such as calreticulin, reprolysin, superoxide dismutase and serpin. However, some of these proteins appear to be produced only in small amounts or to not be secreted. Possibly, in Campopleginae carrying polydnaviruses, the host-modifying activities of venom became redundant following the acquisition of polydnaviruses by the lineage.     

Genomic and morphological features of a banchine polydnavirus: comparison with bracoviruses and ichnoviruses

Many ichneumonid and braconid endoparasitoids inject a polydnavirus (PDV) into their caterpillar hosts during oviposition. The viral entities carried by wasps of these families are referred to as "ichnoviruses" (IVs) and "bracoviruses" (BVs), respectively. All IV genomes characterized to date are found in wasps of the subfamily Campopleginae; consequently, little is known about PDVs found in wasps of the subfamily Banchinae, the only other ichneumonid taxon thus far shown to carry these viruses. Here we report on the genome sequence and virion morphology of a PDV carried by the banchine parasitoid Glypta fumiferanae. With an aggregate genome size of approximately 290 kb and 105 genome segments, this virus displays a degree of genome segmentation far greater than that reported for BVs or IVs. The size range of its genome segments is also lower than those in the latter two groups. As reported for other PDVs, the predicted open reading frames of this virus cluster into gene families, including the protein tyrosine phosphatase (PTP) and viral ankyrin (ank) families, but phylogenetic analysis indicates that ank genes of the G. fumiferanae virus are not embedded within the IV lineage, while its PTPs and those of BVs form distinct clusters. The banchine PDV genome also encodes a novel family of NTPase-like proteins displaying a pox-D5 domain. The unique genomic features of the first banchine virus examined, along with the morphological singularities of its virions (IV-like nucleocapsids, but enveloped in groups like some of the BVs), suggest that they could have an origin distinct from those of IVs and BVs.     

The UGA-CiE1 cell line from Chrysodeixis includens exhibits characteristics of granulocytes and is permissive to infection by two viruses

The soybean looper, Chrysodeixis (Pseudoplusia) includens (Lepidoptera: Noctuidae) is an economically important insect pest and a highly permissive host for the parasitoid Microplitis demolitor and its associated polydnavirus M. demolitor bracovirus (MdBV). Here we established a cell line from C. includens embryos designated UGA-CiE1 cells. CiE1 cells morphologically resemble granulocytes, which are a subpopulation of C. includens hemocytes. Antibody and RT-PCR analyses indicated that CiE1 cells express several molecular and functional markers that identify granulocytes. We further determined that CiE1 cells are permissive to infection by MdBV, exhibiting alterations very similar to MdBV-infected granulocytes, and Autographa californica multiple nucleopolyhedrosis virus (AcMNPV). Combined with the ability to transfect CiE1 cells with high efficiency and knock down expression of viral genes by RNA interference, we conclude this cell line has several attributes of value for studying immune interactions with polydnaviruses and potentially other pathogens.     

Intraspecific host discrimination and larval competition inMicroplitis croceipes,Microplitis demolitor,Cotesia kazak (HYM.: Braconidae) andHyposoter didymator HYM: Ichneumonidae), parasitoids ofHeliothis virescens (LEP.: Noctuidae)

Intraspecific host discrimination and larval competition were studied forMicroplitis croceipes (Cresson),Microplitis demolitor Wilkinson,Cotesia kazak (Telenga), andHyposoter didymator (Thunberg), solitary endoparasitoids of the tobacco budworm,Heliothis virescens (F.). In ovipositional choice tests between unparasitized and parasitized hosts, the mean number of ovipositions for unparasitized hosts was significantly higher than the mean number of ovipositions for hosts parasitized once by a conspecific female forC. kazak andH. didymator, demonstrating that females of these two species discriminate against hosts recently (within a few seconds) parasitized by a conspecific female. No significant difference in oviposition occurred between these two kinds of hosts forM. croceipes andM. demolitor. Mean percent parasitization by a second conspecific female was determined at 24, 48, and 72 h delays in time between the first and second female attack, and with no delay. Except for the 0 h time delay forC. kazak andH. didymator, percent parasitization by a second conspecific female generally decreased as the delay in time between the first and second female attack increased. When the second parasitization immediately followed the first, one parasitoid larva always eliminated the other by physical combat. With a 24 or 48 h delay between the first and second parasitization, the younger larva was the victor over the older larva forM. croceipes, M. demolitor andC. kazak in at least 50% of the cases. Elimination of older larvae by younger larva was by physical attack. However, forH. didymator, the older instar was the victor, and elimination of younger larvae by older larvae was probably through physiological processes. Further, older larvae ofH. didymator apparently killed the eggs of the second female by physiological processes.      

Cross-protection experiments with parasitoids in the genus Microplitis (Hymenoptera: Braconidae) suggest a high level of specificity in their associated bracoviruses

The immunological and developmental effects of bracoviruses (BVs) from three parasitoids in the genus Microplitis (Braconidae: Microgastrinae) were compared in the hosts Pseudoplusia includens and Heliothis virescens (Lepidoptera: Noctuidae). Southern blotting experiments indicated that viral DNAs from Microplitis demolitor bracovirus (MdBV) cross-hybridized with viral DNAs from Microplitis croceipes bracovirus (McBV) and Microplitis mediator bracovirus (MmBV) under conditions of high stringency. Injection of calyx fluid plus venom from each parasitoid species dose-dependently delayed development of P. includens and H. virescens. Each virus also inhibited pupation of P. includens but not H. virescens. In situ hybridization experiments indicated that MdBV and McBV persistently infect hemocytes in both hosts while MmBV persistently infects hemocytes in P. includens but not H. virescens. While MdBV infection induced a loss of adhesion by most plasmatocytes, McBV and MmBV infection induced a loss of adhesion in less than 50% of cells. Cross-protection experiments indicated that calyx fluid plus venom from one species usually protected progeny of another species from encapsulation but did not always promote successful development.     

The encapsidated genome of Microplitis demolitor bracovirus integrates into the host Pseudoplusia includens

Polydnaviruses (PDVs) are symbionts of parasitoid wasps that function as gene delivery vehicles in the insects (hosts) that the wasps parasitize. PDVs persist in wasps as integrated proviruses but are packaged as circularized and segmented double-stranded DNAs into the virions that wasps inject into hosts. In contrast, little is known about how PDV genomic DNAs persist in host cells. Microplitis demolitor carries Microplitis demolitor bracovirus (MdBV) and parasitizes the host Pseudoplusia includens. MdBV infects primarily host hemocytes and also infects a hemocyte-derived cell line from P. includens called CiE1 cells. Here we report that all 15 genomic segments of the MdBV encapsidated genome exhibited long-term persistence in CiE1 cells. Most MdBV genes expressed in hemocytes were persistently expressed in CiE1 cells, including members of the glc gene family whose products transformed CiE1 cells into a suspension culture. PCR-based integration assays combined with cloning and sequencing of host-virus junctions confirmed that genomic segments J and C persisted in CiE1 cells by integration. These genomic DNAs also rapidly integrated into parasitized P. includens. Sequence analysis of wasp-viral junction clones showed that the integration of proviral segments in M. demolitor was associated with a wasp excision/integration motif (WIM) known from other bracoviruses. However, integration into host cells occurred in association with a previously unknown domain that we named the host integration motif (HIM). The presence of HIMs in most MdBV genomic DNAs suggests that the integration of each genomic segment into host cells occurs through a shared mechanism.     

Intraspecific host discrimination and larval competition inMicroplitis croceipes,Microplitis demolitor,Cotesia kazak (Hym.: Braconidae) andHyposoter didymator (Hym.: Ichneumonidae), parasitoids ofHeliothis virescens (Lep.: Noctuidae)

Intraspecific host discrimination and larval competition were studied forMicroplitis croceipes (Cresson),Microplitis demolitor Wilkinson,Cotesia kazak (Telenga), andHyposoter didymator (Thunberg), solitary endoparasitoids of the tobacco budworm,Heliothis virescens (F.). In ovipositional choice tests between unparasitized and parasitized hosts, the mean number of ovipositions for unparasitized hosts was significantly higher than the mean number of ovipositions for hosts parasitized once by a conspecific female forC. kazak andH. didymator, demonstrating that females of these 2 species discriminate against hosts recently (within a few seconds) parasitized by a conspecific female. No significant difference in oviposition occurred between these 2 kinds of hosts forM. croceipes andM. demolitor. Mean percent parasitization by a 2^nd conspecific female was determined at 24, 48, and 72-h delays in time between the 1^rst and 2^nd female attack, and with no delay. Except for the 0 h time delay forC. kazak andH. didymator, percent parasitization by a 2^nd conspecific female generally decreased as the delay in time between the 1^rst and 2^nd female attack increased. When the 2^nd parasitization immediately followed the 1^rst, one parasitoid larva always eliminated the other by physical combat. With a 24 or 48 h delay between the 1^rst and 2^nd parasitization, the younger larva was the victor over the older larva forM. croceipes, M. demolitor andC. kazak in at least 50% of the cases. Elimination of older larvae by younger larvae was by physical attack. However, forH. didymator, the older instar was the victor, and elimination of younger larvae by older larvae was probably through physiological processes. Further, older larvae ofH. didymator apparently killed the eggs of the 2^nd female by physiological processes.      

Antiviral, anti-parasitic, and cytotoxic effects of 5,6-dihydroxyindole (DHI), a reactive compound generated by phenoloxidase during insect immune response

Phenoloxidase (PO) and its activation system are implicated in several defense responses of insects. Upon wounding or infection, inactive prophenoloxidase (proPO) is converted to active PO through a cascade of serine proteases and their homologs. PO generates reactive compounds such as 5,6-dihydroxyindole (DHI), which have a broad-spectrum antibacterial and antifungal activity. Here we report that DHI and its spontaneous oxidation products are also active against viruses and parasitic wasps. Preincubation of a baculovirus stock with 1.25 mM DHI for 3 h near fully disabled recombinant protein production. The LC₅₀ for lambda bacteriophage and eggs of the wasp Microplitis demolitor were 5.6 ± 2.2 and 111.0 ± 1.6 ??M, respectively. The toxicity of DHI and related compounds also extended to cells derived from insects that serve as hosts for several of the aforementioned pathogens. Pretreatment of Sf9 cells with 1.0 mM DHI for 4 h resulted in 97% mortality, and LC₅₀ values of 20.3 ± 1.2 ??M in buffer and 131.8 ± 1.1 ??M in a culture medium. Symptoms of DHI toxicity in Sf9 cells included DNA polymerization, protein crosslinking, and lysis. Taken together, these data showed that proPO activation and DHI production is strongly toxic against various pathogens but can also damage host tissues and cells if not properly controlled.     

Diversifying selection in a parasitoid's symbiotic virus among genes involved in inhibiting host immunity

During parasitization of their hosts some insect parasitoids deliver resident viruses which encode genes that must be expressed in the host for successful parasitization. Among these viruses the Campoletis sonorensis Ichnovirus has been well studied and encodes a cys-motif gene family implicated in disruption of host immunity and other physiological systems. Members of this gene family encode one or more intercystine-knot structural motifs in which the non-cysteine residues of the motif are variable. We analyzed patterns of synonymous and non-synonymous substitution within the cys-motif to investigate the evolution of this gene family and the likelihood of virus-host gene coevolution. Maximum likelihood techniques suggest positive selection acts on 8 of 51 codons in the aligned cysteine-rich region. Although the detected positive selection was not strong, it likely contributes to the diversification of this gene family. Comparison of selection pressure relative to tertiary structure of the VHv1.1 cys-motif protein suggests that the hypervariable sites are exposed. Furthermore, invariant residues in the motif exhibit a region-specific pattern of codon bias, suggesting there are unusual mechanisms of effecting selection pressure at work in this system, though the mechanism has yet to be studied. The positive selection and duplication of both the gene family and the cys-motif implies either selection is driving the molecular radiation of immune suppressive genes toward novel hosts, or molecular coevolution with host targets.Novel nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AY033945, AY197489, AY197490, AY197491, AY197492, AY197493 and AY197494