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Polydnavirus-wasp associations: evolution, genome organization, and function
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Polydnavirus-wasp associations: evolution, genome organization, and function Michael R Strand and Gaelen R Burke Viruses replicate to produce virions that transfer the viral genome among hosts, while endogenous viral elements (EVEs) are DNA sequences derived from viruses that integrate into the germline of multicellular organisms and are thereafter inherited like host alleles. Viruses in the family Polydnaviridae are specifically associated with insects called parasitoid wasps and exhibit many traits associated with other viruses. Polydnavirus genomes also persist as EVEs. In this short review we discuss polydnavirus evolution, compare polydnaviruses to other known EVEs of ancient origin, and examine some of the functional similarities polydnaviruses share with phage-like gene transfer agents (GTAs) from prokaryotes Addresses Department of Entomology, University of Georgia, Athens, GA 30602, USA Corresponding author: Strand, Michael R ([email protected])
Current Opinion in Virology 2013, 3:587–594 This review comes from a themed issue on Virus evolution Edited by Valerian V Dolja and Mart Krupovic For a complete overview see the Issue and the Editorial Available online 29th June 2013 1879-6257/$ – see front matter, # 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.coviro.2013.06.004
Introduction Viruses infecting multicellular organisms exhibit a continuum of co-evolutionary interactions with their hosts. At one end of this continuum are the majority of viruses, which replicate in one host to produce virions that horizontally transfer the viral genome to another [1]. Such life cycles are also usually parasitic, which leads to selection favoring adaptations in viruses that promote transmission and counter-adaptations in hosts that resist infection. At the other end of this continuum are endogenous virus elements (EVEs), which are DNA sequences derived from viruses that chromosomally integrate and become fixed in the germline of a host [2,3]. This results in EVEs being inherited like host alleles. Mutation accumulation renders most EVEs nonfunctional, but some EVEs have been coopted by hosts to perform new functions [4,5]. Viruses in the family Polydnaviridae are of interest because their interactions with insects called parasitoid wasps exhibit features intermediate between other known animal viruses and EVEs [6]. Here, we highlight key aspects of polydnavirus (PDV) evolution and function. www.sciencedirect.com
Polydnaviruses exhibit several traits associated with other viruses The Polydnaviridae was formally recognized as a virus family in 1995 because all isolates share a common life cycle and possess several traits found in other viruses [7]. PDVs are associated with an extremely species-rich group of insects called parasitoid wasps (Hymenoptera) that reproduce by laying eggs on or in the bodies of other insects their progeny consume. Approximately 40,000 wasp species in two families named the Braconidae and Ichneumonidae carry PDVs, which are correspondingly divided into two genera named the Bracovirus (BVs) and Ichnovirus (IVs) [7]. Each BV or IV from a given wasp species persists in the germline and all somatic cells of the wasp’s body as a provirus (Figure 1). Replication, however, only occurs in pupal and adult stage female wasps in the nuclei of a specific population of cells located in the ovaries called calyx cells [8,9] (Figure 1). Enveloped nucleocapsids package multiple circular, double-stranded DNAs with large aggregate sizes (190–600 kb), which are released from calyx cells by either lysis (BVs) or budding (IVs) [10– 15]. Virions are then stored in the lumen of the reproductive tract with wasp eggs. Each PDV-carrying wasp parasitizes only one or a few species of host insects that are primarily larval stage Lepidoptera (moths). Wasps parasitize hosts by injecting eggs, which contain the proviral genome, plus virions into the body cavity (hemocoel) (Figure 1). Virions thereafter rapidly infect and express virulence genes that: firstly, disable the host’s immune system, which allows wasp offspring to survive, and secondly, alter growth, which causes the host to ultimately die while promoting wasp offspring development [16,17]. Many viruses besides PDVs exhibit both a proviral and replication phase, or infect different species. The key feature of the life cycle that differs from viruses in any other family is that PDVs cannot replicate in the hosts of wasps because none of the genes required to produce virus particles are packaged into virions. As a result, PDVs are only transmitted vertically through the germline of wasps as proviruses, yet the survival of wasps fully depends on the genes PDV virions deliver to parasitized hosts.
Polydnaviruses also exhibit traits associated with many EVEs Since EVEs are any DNA sequence of viral origin in a host germline, proviruses capable of producing infectious virus represent a type of EVE. Such EVEs, however, are rare outside of retroviruses that integrate into the genomes of animal hosts as part of their replication cycle [4]. Instead, most EVEs identified from animals are fragments Current Opinion in Virology 2013, 3:587–594
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Figure 1
PDV persists in wasp somatic and germ cells as a provirus
Wasp ovaries PDV replication in calyx cells PDV virions accumulate in the lumen of the reproductive tract Female wasp parasitizes host insect
Provirus in wasp egg
PDV virions infect host cells
Adult wasp
Pupa
PDV replication begins in calyx cells
Wasp larva develops and then emerges from host to pupate Current Opinion in Virology
The life cycle of parasitoid wasps and PDVs. See main text for discussion.
of a parental genome that in most cases have also been rendered non-functional through mutation [2,3–5]. In the case of PDVs, the evolutionary origin of IVs is unclear [18]. In contrast, all BV-carrying braconids form a monophyletic group called microgastroids that evolved ca. 100 million years ago (Mya) [19,20]. This finding suggested BVs evolved from a virus that infected the common ancestor of microgastroids. The first insights into the identity of this ancestor derived from transcriptome studies of wasp ovaries, which identified several genes expressed in calyx cells during BV replication that share weak but recognizable homology with genes in another group of insect-infecting viruses called nudiviruses [21,22,23]. Nudiviruses are relatively poorly studied but they are the sister taxon of baculoviruses, which have been extensively characterized [24,25,26]. Most baculoviruses and nudiviruses are virulent pathogens that establish systemic, fatal infections by replicating in the nuclei of all cells of an infected insect. Some nudiviruses, however, infect the reproductive system of insects, and establish persistent infections associated with integration into the host genome [27,28]. BVs thus likely evolved from an ancient nudivirus that integrated into the germline of the microgastroid ancestor. Current Opinion in Virology 2013, 3:587–594
Nudiviruses package a single large, circular dsDNA genome (ca. 200 kb) into virions [25]. Integration into the germline of the ancestral wasp therefore presumably occurred as a linear DNA with the resulting provirus retaining the ability to produce infectious virus (Figure 2). In contrast, BV proviral genomes consist of two functional components that are dispersed in the wasp genome [6]. The first of these components is the aforementioned nudivirus-like genes, while the second is the virulence gene-encoding proviral segments that are packaged into virions during replication. Several of the nudivirus-like genes are integrated in close proximity to one another in the wasp genome, forming a cluster, while the rest are located elsewhere in the wasp genome [21]. A majority of the proviral segments are also clustered in a tandem array that forms a macrolocus, while other proviral segments are integrated elsewhere in the wasp genome as either individual segments or as smaller loci that contain 1–3 segments [29]. Conserved synteny of some proviral segments between wasp species provides support for orthology, while differences in the number of proviral segments between species are due to lineage-specific duplication events [9,29]. However, the precise location of the nudivirus-like genes and proviral domains relative www.sciencedirect.com
Polydnavirus evolution Strand and Burke 589
Figure 2
Virus
Functional replication and production of infectious virus particles
Germline integration and fixation
Provirus
Episomal dsDNA viral genome Fragmentation, gene duplication, gene loss, rearrangements - BVs
mRNA
AAAA
Non-functional for production of infectious virus particles
Interaction with host cell factors dsDNA Germline integration and fixation
Scenarios for further gene loss, rearrangements, and accumulation of inactivating mutations Cooption by host and neofunctionalization Most EVEs Current Opinion in Virology
Genome organization of BVs relative to known ancestors and other types of EVEs. Nudiviruses and baculoviruses package large, circular dsDNA genomes that replicate in host cell nuclei. Baculovirus and nudivirus genomes normally persist in host cell nuclei as episomes, and viral replication usually begins shortly after infection with the regulated expression of numerous viral genes that amplify the genome, transcribe virion structural components, and produce infectious virus (upper left). EVEs from a nudivirus could arise by either anomalous integration of a dsDNA derived from a viral transcript (middle left) or integration of the episomal genome into the germline of a host (upper right). In the case of BVs, the ancestor likely integrated into the germline of the ancestor wasp as a provirus that was initially capable of reestablishing a productive infection given evidence from known nudiviruses (see text). The ancestral genome thereafter underwent numerous alterations that led to the evolution of BVs. However, these alterations still maintained a conserved gene set that produces infectious virus particles (upper right). In contrast, most other EVEs of ancient origin [2,3–5] are fragments of a parental genome that have been rendered nonfunctional by rearrangements, deletions and inactivating mutations (boxes with crosses) (lower left and right). Some examples are known of viral regulatory sequences or genes that have been coopted by hosts for novel functions (red boxes) (lower left and right) [2,3–5]. These functions though do not include producing infectious virus particles.
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Figure 3
Proviral genome Proviral segments
Excision, amplification and circularization of proviral segments
Nudivirus-like conserved gene set
Integrases (vlf-1, int-1)
Early gene transcription
RNA polymerase (lef-4, lef-8, lef-9, p47)
Circularized proviral segments packaged into virions
Late gene transcription Virion assembly
Structural components: nucleocapsid proteins (vp39, vlf-1) envelope proteins (p74, pif-1)
Replication-defective BV virions Current Opinion in Virology
BV nudivirus-like genes exhibit ancestral functions to produce infectious but replication defective virions. BV proviral genomes consist of two functional components: a conserved nudivirus-like gene set (upper right) and proviral DNAs (red) that encode virulence genes (yellow) and share conserved flanking excision motifs (black) (upper left). The location of the nudivirus-like genes and proviral DNAs in genomes of wasps are incompletely characterized and are thus indicated by double slash marks. BV replication in the nuclei of calyx cells begins in the early pupal stage of female wasps with expression of several nudivirus-like RNA polymerase subunit and integrase genes (Early gene transcription). This is followed by expression of nucleocapsid and envelope genes required for virion formation (Late gene transcription) and excision, amplification, and circularization of proviral DNAs that are packaged into virions. This results in formation of large numbers of virions. Each individual virion contains only one circularized proviral segment [10,11] but none of the nudivirus-like genes required for virion formation or excision/amplification of the proviral segments. See text for additional information.
to one another in the genomes of wasps remains unclear [21,29,30]. BVs thus derive from a virus ancestor and similar to many other EVEs of ancient origin the components of the parental genome that are still recognizable have become fragmented (Figure 2). Unlike most EVEs, however, the fragmented genomes of BVs still consist of many genes that are transcribed in a highly coordinated manner to produce virions that are infectious but package only a portion of the proviral genome (Figure 2).
Several BV nudivirus-like genes have predicted roles in replication while proviral segments share flanking domains associated with packaging into virions Current understanding of how BV proviral genomes function derives from a combination of comparative genomic, expression, and functional data. Consider first the nudivirus-like genes in relation to the relatives of BVs. Current Opinion in Virology 2013, 3:587–594
Baculoviruses exhibit high diversity in gene content but all sequenced isolates share 31 core genes of which approximately half are essential for replication [24]. These include a DNA polymerase that replicates the viral genome, four subunits of a novel DNA dependent RNA polymerase, and several structural genes coding for capsid and envelope proteins with promoter sequences that are specifically recognized by the viral RNA polymerase [24]. The six nudivirus genomes sequenced to date encode homologs of 20 baculovirus core genes that include the DNA polymerase, baculovirus-like RNA polymerase subunits, and select structural genes [24,25]. The function of these genes, however, is unknown beyond inferences from baculoviruses. The three BV proviral genomes for which data are available lack a recognizable baculovirus/nudivirus DNA polymerase, but each encodes four baculovirus/nudivirus-like RNA polymerase subunits, select transcription factors, www.sciencedirect.com
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and several structural genes with baculovirus-like promoter sequences [21,22,23]. Other predicted members of a BV conserved gene set are eleven nudivirus-like genes that include integrases unknown from baculoviruses [21,22,23]. Consider next the proviral segments that are packaged into virions. Unlike the conservation seen for the nudivirus-like genes, the number of proviral segments and the genes they encode differs with BVs from closely related wasp species sharing more genes than distantly related species [6–9]. The origin of these genes is also diverse with some being recent acquisitions from wasps, others showing evidence of acquisition from other organisms by horizontal gene transfer (HGT), and others still being of uncertain ancestry [31,32]. In contrast, all proviral segments in all BV isolates examined to date are flanked by a conserved direct repeat motif that identifies their site of excision from the wasp genome during replication in calyx cells [29,33,34]. These motifs are absent, however, from DNA flanking any of the nudivirus-like genes [21].
Nudivirus-like RNA polymerase subunits and integrases are essential for virion formation Expression studies show that BV replication begins in calyx cells when female wasps pupate [21,22,23,35]. First, the nudivirus-like RNA polymerase subunits and integrases are transcribed, which is then followed by transcription of the nudivirus-like structural genes plus excision, amplification, and circularization of proviral segments for packaging into virions [21,23,35,36] (Figure 3). Proteomic studies indicate that BV virions contain predicted nudivirus-like structural gene products [21,22,37]. As previously alluded to, the identity between BV and more closely related nudivirus proteins is low (19–41%), while algorithms like BLAST have difficulty detecting homology between BV and more distantly related baculovirus-like core genes. This finding is consistent with the ancient divergence times between BVs, nudiviruses and baculoviruses. Yet, recent functional studies indicate: firstly, the predicted viral RNA polymerase subunits of BVs produce a functional enzyme that transcribes the nudivirus-like structural genes but does not transcribe wasp genes, secondly, the nudivirus-like integrase genes are required for excision of the proviral segments from the wasp genome, and finally select nudivirus-like genes are essential for capsid and envelope formation [37] (Figure 3). In all other cells of the wasp including the germline, all of the nudivirus-like genes and nearly all of the genes on proviral segments are silent [21,23,38]. Taken together, proviral segments are packaged into virions comprised of nudivirus-like gene products but no nudivirus-like genes are packaged because none are excised and amplified (Figure 3). This in turn prevents any viral replication in the hosts wasps parasitize while assuring that transmission of the proviral genome is www.sciencedirect.com
entirely vertical through the germline of the wasp. Finally, BVs cause no disease in wasps because replication is restricted to calyx cells and almost none of the virulence genes on proviral segments are transcribed [21,23,35,36,37]. However, BVs cause severe disease in the hosts wasps parasitize because virions establish a systemic infection in which all virulence genes are expressed [34,38]. It remains unclear what restricts BV replication to calyx cells when most baculoviruses and nudiviruses replicate in many cell types of infected insects. One obvious component is calyx cell-specific expression of the nudivirus-like RNA polymerase subunits and integrases but the signal(s) controlling activation of these genes following pupation of female wasps is unknown [37]. Another factor of potential importance in restricting replication to calyx cells is the absence of a recognizable nudivirus-like DNA polymerase, which suggests that proviral segment amplification has shifted from the virus to control by the wasp [23]. Also unclear are the evolutionary events that led to the dispersed organization of BV genomes. Assuming both components of BV genomes derive from the nudivirus ancestor, dispersal of the genome could have occurred by either duplication of the ancestral genome or integration of several copies of the ancestral genome followed by elimination of conserved replication genes from some copies and elimination of the direct repeat motifs required for excision from the wasp genome from others [6,9,32]. The requirement of nudivirus-like integrases for excision of proviral segments from the wasp genome circumstantially supports the conserved repeat domains flanking each proviral segment derived from the ancestral nudivirus genome. However, it is also possible the proviral segments are not of nudivirus origin given that: firstly, genes on proviral segments are unrelated to any genes from known nudiviruses, and secondly, no sequences homologous to the repeat domains that flank proviral segments have been identified from nudiviruses and shown to play a role in integration. Resolving these issues will undoubtedly benefit from whole genome sequencing, which should clarify where the nudiviruslike genes and proviral segments of BV genomes reside within different wasp species and whether components of the genome are integrated in similar positions in the different lineages of microgastroids.
The two components of BV genomes are subject to different selection pressures Members of large dsDNA virus families, like baculoviruses, typically share a core gene set with roles in conserved processes like replication. Overall genome size and content, however, is also variable because of specialization onto different hosts and the capture of genes from diverse sources that become fixed due to the Current Opinion in Virology 2013, 3:587–594
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advantageous phenotypes they confer [24]. As hosts become genetically isolated and speciate, so do the viruses resulting in host-associated lineages and patterns of diversity. Despite an overall slower rate of evolution due to fewer replication events per unit time, BV genomes exhibit these features while also showing that selection pressures differ for the nudivirus-like genes required for virion formation in wasps versus the proviral segments and virulence genes required for parasitism of hosts. Strikingly, selection has maintained the ancestral functions of the BV RNA polymerase subunits, capsid, and envelope genes over 100 Mya since divergence from nudiviruses and more than 300 Mya since the last common ancestor shared by nudiviruses and baculoviruses [26,37]. In contrast, the variation among BVs in the number of proviral segments, the types of virulence genes packaged into virions, and the diversification of several genes into multimember families with diverged functions provides strong evidence that arms race dynamics are at play as BVs and wasps in different wasp lineages adapt to parasitize hosts, and hosts evolve counter adaptations to evade the effects of gene products delivered by BVs [6,9,31,32,39–47].
[2,3,4]. The small number of EVEs that have been coopted by hosts for novel functions are also appropriately viewed as selfish elements that derive from viruses but which are no longer viruses themselves [3–5]. BVs in contrast present a much more complicated interaction in that their proviral genomes are fragmented and have been coopted to perform functions of novel benefit to wasps, yet do so by producing infectious virus particles and functioning in many respects like the viruses they evolved from. Unlike most viruses, BVs do not package a complete genome into virions that can be transferred to other cells and replicate. However, their ability to produce virions that package a portion of the genome, which is essential for the survival of wasps and in the process their own transmission as proviruses, is consistent with the view that BVs and wasps are mutualists [6].
Acknowledgements This work was supported in part by grants from the National Science Foundation (IOS 1145953), US Department of Agriculture (2009-3530205250) and National Institutes of Health (F32 AI096552).
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:
Functional parallels between BVs and prokaryotic gene transfer agents While no other EVEs from animals or plants function like BVs, phage-like entities from prokaryotes called gene transfer agents (GTAs) show interesting parallels. Four genetically distinct lineages of GTAs have thus far been identified with each using host chromosomally-encoded genes to produce phage-like particles that package host DNA but few or none of the genes required for GTA particle formation [48]. GTAs functionally differ from transducing phages that occasionally package host DNA rather than the viral genome during the process of replication but resemble BVs in the sense that both package DNAs largely unrelated to the genes required for particle formation. Other parallels with BVs include: firstly, several of the genes required for GTA formation derive from phage ancestors, secondly, these genes are organized in host genomes as clusters and single ORFs, and finally, GTA particles horizontally transfer the DNAs they package from one host to another [49,50]. Unlike the specific proviral segments packaged by BVs, however, GTAs package relatively small (4 kb) and random pieces of DNA from donor cells [51]. In addition, while BVs cause no disease in wasps, GTA production is lethal to donor cells because particles are released by lysis [48,51]. Thus unlike BV-mediated gene transfer to host insects, which directly benefits the wasp and its provirus, the potential fitness benefits of GTAs for the prokaryotes that produce them are likely indirect and complex [52].
of special interest of outstanding interest 1.
Roossinck MJ: The good viruses: viral mutualistic symbioses. Nat Rev Microbiol 2011, 9:99-108.
2. Katzourkakis A, Gifford RJ: Endogenous viral elements in animal genomes. PLoS Genet 2010, 6:e1001191. This paper presents survey data on the diversity of non-retroviral EVEs in animal genomes. 3.
Holmes EC: The evolution of endogenous viral elements. Cell Host Microbe 2011, 10:368-377.
4.
Feschotte C, Gilbert C: Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012, 13:283-296.
5.
Aswad A, Katzourakis A: Paleovirology and virally derived immunity. Trends Ecol Evol 2012, 27:627-636.
6.
Strand MR, Burke GR: Polydnaviruses as symbionts and gene delivery systems. PLoS Pathogens 2012, 8:e1002757.
7.
Strand MR, Drezen J-M: Family Polydnaviridae. In Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Edited by King AMQ, Adams MJ, Castens EB, Lefkowitz EJ. Elsevier; 2012:237-248.
8.
Strand MR: Polydnaviruses. In Insect Virology. Edited by Asgari S, Johnson KN. Caister Academic Press; 2010:171-197.
9.
Gundersen-Rindal D, Dupuy C, Huguet E, Drezen J-M: Parasitoid polydnaviruses: evolution, pathology and applications. Biocontrol Sci Technol 2013, 23:1-61.
10. Albrecht U, Wyler T, Pfister-Wilhelm R, Gruber A, Stettler P, Heiniger P, Schumperli D, Lanzrein B: PDV of the parasitic wasp Chelonus inanitus (Braconidae): characterization, genome organization and time point of replication. J Gen Virol 1994, 75:3353-3363.
Conclusions
11. Beck MH, Inman RB, Strand MR: Microplitis demolitor bracovirus genome segments vary in abundance and are individually packaged in virions. Virology 2007, 359:179-189.
Most ancient EVEs in animal genomes consist of nonfunctional viral fragments that are evolutionary dead ends
12. Espagne E, Dupuy C, Huguet E, Cattolico L, Provost B, Martins N, Poirie M, Periquet G, Drezen J-M: Genome sequence of a
Current Opinion in Virology 2013, 3:587–594
www.sciencedirect.com
Polydnavirus evolution Strand and Burke 593
polydnavirus: insights into symbiotic virus evolution. Science 2004, 306:286-289. 13. Webb BA, Strand MR, Dickey SE, Beck MH, Hilgarth RS, Kadash K, Kroemer JA, Lindstrom KG, Rattanadechakul W, Shelby KS et al.: Polydnavirus genomes reflect their dual roles as mutualists and pathogens. Virology 2006, 347:160-174. 14. Lapointe R, Tanaka K, Barney WE, Whitfield JB, Banks JC, Beliveau C, Stoltz D, Webb BA, Cusson M: Genomic and morphological features of a banchine polydnavirus: comparison with bracoviruses and ichnoviruses. J Virol 2007, 81:6491-6501. 15. Chen YF, Gao F, Ye XQ, Wei SJ, Shi M, Zheng HJ, Chen XX: Deep sequencing of Cotesia vestalis bracovirus reveals the complexity of a polydnavirus genome. Virology 2011, 414:42-50. 16. Strand MR: Polydnavirus gene products that interact with the host immune system. In Parasitoid Viruses Symbionts and Pathogens. Edited by Beckage NE, Drezen J-M. Academic Press; 2012:149-161. 17. Beckage NE: Polydnaviruses as endocrine regulators. In Parasitoid Viruses Symbionts and Pathogens. Edited by Beckage NE, Drezen J-M. Academic Press; 2012:163-168. 18. Volkoff AN, Jouan V, Urbach S, Samain S, Bergoin M, Wincker P, Demettre E, Cousserans F, Provost B, Coulibaly F et al.: Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. PLoS Pathog 2010, 6:e1000923. This paper presents evidence that IVs likely evolved from a virus ancestor but whether this ancestor is now extinct or is related to an as yet undiscovered virus taxon is unclear. 19. Whitfield JB: Estimating the age of the polydnavirus/braconid wasp symbiosis. Proc Natl Acad Sci U S A 2002, 99:7508-7513. 20. Murphy N, Banks JC, Whitfield JB, Austin AD: Phylogeny of the parasitic microgastroid subfamilies (Hymenoptera: Braconidae) based on sequence data from seven genes, with an improved time estimate of the origin of the lineage. Mol Phylogenet Evol 2008, 47:378-395. 21. Bezier A, Annaheim M, Herbiniere J, Wetterwald C, Gyapay G, Bernard-Samain S, Wincker P, Rodidi I, Heller M, Belghaazi M et al.: Polydnaviruses of braconid wasps derive from an ancestral nudivirus. Science 2009, 323:926-930. This paper presents the first evidence that BVs evolved from a nudivirus ancestor. 22. Wetterwald C, Roth T, Kaeslin M, Annaheim M, Wespi G, Heller M, Ma¨ser P, Roditi I, Pfister-Wilhelm R, Be`zier A et al.: Identification of bracovirus particle proteins and analysis of their transcript levels at the stage of virion formation. J Gen Virol 2010, 91:2610-2619.
Jones KM: Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biol 2008, 9:R183. This paper presents the first detailed insights into how the proviral segments of BVs are organized in the genomes of braconid wasps. 30. Belle E, Beckage NE, Rousselet J, Poirie M, Lemeunier F, Drezen J-M: Visualization of polydnavirus sequences in a parasitoid wasp chromosome. J Virol 2002, 76:5793-5796. 31. Huguet E, Serbielle C, Moreau SJM: Evolution and origin of polydnavirus virulence genes. In Parasitoid Viruses Symbionts and Pathogens. Edited by Beckage NE, Drezen J-M. Academic Press; 2012:63-78. 32. Burke GR, Strand MR: Polydnaviruses of parasitic wasps: domestication of viruses to act as gene delivery vectors. Insects 2012, 3:91-119. 33. Annaheim M, Lanzrein B: Genome organization of the Chelonus inanitus polydnavirus: excision sites, spacers, and abundance of proviral and excised segments. J Gen Virol 2007, 8:450-457. 34. Beck MH, Zhang S, Bitra K, Burke GR, Strand MR: The encapsidated genome of Microplitis demolitor bracovirus integrates into the host Pseudoplusia includens. J Virol 2011, 85:11685-11696. This study presents the first experimental evidence that BV segments in virions integrate into the genomes of host insects parasitized by wasps. The paper also shows that the conserved flanking motifs which identify sites of integration in the wasp genome differ from the repeat motifs that mediate integration into the genome of parasitized host insects. 35. Gruber A, Stettler P, Heiniger P, Schumperli D, Lanzrein B: Polydnavirus DNA of the braconid wasp Chelonus inanitus is integrated in the wasp’s genome and excised only in later pupal and adult stages of the female. J Gen Virol 1996, 77:2873-2879. 36. Savary S, Beckage N, Tan F, Periquet G, Drezen J-M: Excision of the polydnavirus chromosomal integrated EP1 sequence of the parasitoid wasp Cotesia congregata (Braconidae, Microgastrinae) at potential recombinase binding sites. J Gen Virol 1997, 78:3125-3134. 37. Burke GR, Thomas SA, Eum JH, Strand MR: Mutualistic polydnaviruses share essential replication gene functions with pathogenic ancestors. PLoS Pathog 2013, 9:e1003348. This study presents the first experimental evidence for the functions of several nudivirus-like genes in BV replication. 38. Bitra K, Zhang S, Strand MR: Transcriptomic profiling of Microplitis demolitor bracovirus reveals host, tissue, and stage-specific patterns of activity. J Gen Virol 2011, 92:20602071.
23. Burke GR, Strand MR: Deep sequencing identifies viral and wasp genes with potential roles in replication of Microplitis demolitor bracovirus. J Virol 2012, 86:3293-3306.
39. Pruijssers AJ, Strand MR: PTP-H2 and PTP-H3 from Microplitis demolitor bracovirus localize to focal adhesions and are antiphagocytic in insect immune cells. J Virol 2007, 81:1209-1219.
24. Rohrmann GF: Baculovirus Molecular Biology. Bethesda: National Library of Medicine, National Center for Biotechnology Information; 2008, .
40. Beck MH, Strand MR: A novel polydnavirus protein inhibits the insect prophenoloxidase activation pathway. Proc Natl Acad Sci U S A 2007, 104:19267-19272.
25. Wang J, Jehle JA: Nudiviruses and other large, doublestranded circular DNA viruses of invertebrates: new insights on an old topic. J Invert Pathol 2009, 101:187-193.
41. Lu Z, Beck MH, Jiang H, Wang Y, Strand MR: The viral protein Egf1.0 is a dual activity inhibitor of prophenoloxidase activating proteinases 1 and 3 from Manduca sexta. J Biol Chem 2008, 283:21325-21333.
26. Theze J, Bezier A, Periquet G, Drezen JM, Herniou EA: Paleozoic origin of insect large dsDNA viruses. Proc Natl Acad Sci U S A 2011, 108:15931-15935. This paper uses sequence data from BV proviral genomes to generate estimates for the timing of the origin of nudiviruses and baculoviruses. 27. Burand JP: Insect viruses: nonoccluded. In Encyclopedia of Virology. Edited by Mahy BWJ, Van Regenmortel MHV. Oxford; 2008:69-90. 28. Wu YL, Wu CP, Lee ST, Tang H, Chang CH, Chen HH, Chao YC: The early gene hhi1 reactivates Heliothis zea nudivirus 1 in latently infected cells. J Virol 2010, 84:1057-1065. 29. Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fadrosh DW, Fuester RW, Pedroni MJ, Haas BJ, Schatz MC, www.sciencedirect.com
42. Pichon S, Dupas S, Lesobre J, Purisima EO, Drezen J-M, Huguet E: Viral cystatin evolution and three-dimensional structure modelling: a case of directional selection acting on a viral protein involved in a host-parasitoid interaction. BMC Biol 2008, 6:38. 43. Branco A, Le Ru BP, Vavre F, Silvain JF, Dupas S: Intraspecific specialization of the generalist parasitoid Cotesia sesamiae revealed by polydnavirus polymorphism and associated with different Wolbachia infection. Mol Ecol 2011, 20:959-971. 44. Cooper TH, Bailey-Hill K, Leifert WR, McMurchie EJ, Asgari S, Galtz RV: Identification of an in vitro interaction between an insect immune suppressor protein (CrV2) and G alpha proteins. J Biol Chem 2011, 286:10466-10475. Current Opinion in Virology 2013, 3:587–594
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45. Magkrioti C, Katrou K, Labropoulou V: Differential inhibition of BmRelish1-dependent transcription in lepidopteran cells by bracovirus ankyrin-repeat proteins. Insect Bichem Mol Biol 2011, 41:993-1002. 46. Bitra K, Suderman RJ, Strand MR: Polydnavirus ank proteins bind NF-kb homodimers and inhibit processing of relish. PLoS Pathog 2012, 8:e1002722. 47. Serbielle C, Dupas S, Perdereau E, Hericourt F, Dupuy C, Huguet E, Drezen J-M: Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases. BMC Evol Biol 2013, 12:253. 48. Lang AS, Zhaxybayeva O, Beatty JT: Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 2012, 10:472-482.
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49. Lang AS, Beatty JT: Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodabacter capsulatus. Proc Natl Acad Sci U S A 2000, 97:859-864. 50. Chen F, Spano A, Goodman BE, Blasler KR, Sabat A, Jeffery E, Norris A et al.: Proteomic analysis and identification of the structural and regulatory proteins of the Rhodabacter capsulatus gene transfer agent. J Proteome Res 2008, 8:967973. 51. Hynes AP, Mercer RG, Watton DE, Buckley CB, Lang AS: DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA. Mol Microbiol 2012, 85:314-325. 52. Vos M: Why do bacteria engage in homologous recombination? Trends Microbiol 2009, 17:226-232.
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Polydnavirus-wasp associations: evolution, genome organization, and function Michael R Strand and Gaelen R Burke Viruses replicate to produce virions that transfer the viral genome among hosts, while endogenous viral elements (EVEs) are DNA sequences derived from viruses that integrate into the germline of multicellular organisms and are thereafter inherited like host alleles. Viruses in the family Polydnaviridae are specifically associated with insects called parasitoid wasps and exhibit many traits associated with other viruses. Polydnavirus genomes also persist as EVEs. In this short review we discuss polydnavirus evolution, compare polydnaviruses to other known EVEs of ancient origin, and examine some of the functional similarities polydnaviruses share with phage-like gene transfer agents (GTAs) from prokaryotes Addresses Department of Entomology, University of Georgia, Athens, GA 30602, USA Corresponding author: Strand, Michael R ([email protected])
Current Opinion in Virology 2013, 3:587–594 This review comes from a themed issue on Virus evolution Edited by Valerian V Dolja and Mart Krupovic For a complete overview see the Issue and the Editorial Available online 29th June 2013 1879-6257/$ – see front matter, # 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.coviro.2013.06.004
Introduction Viruses infecting multicellular organisms exhibit a continuum of co-evolutionary interactions with their hosts. At one end of this continuum are the majority of viruses, which replicate in one host to produce virions that horizontally transfer the viral genome to another [1]. Such life cycles are also usually parasitic, which leads to selection favoring adaptations in viruses that promote transmission and counter-adaptations in hosts that resist infection. At the other end of this continuum are endogenous virus elements (EVEs), which are DNA sequences derived from viruses that chromosomally integrate and become fixed in the germline of a host [2,3]. This results in EVEs being inherited like host alleles. Mutation accumulation renders most EVEs nonfunctional, but some EVEs have been coopted by hosts to perform new functions [4,5]. Viruses in the family Polydnaviridae are of interest because their interactions with insects called parasitoid wasps exhibit features intermediate between other known animal viruses and EVEs [6]. Here, we highlight key aspects of polydnavirus (PDV) evolution and function. www.sciencedirect.com
Polydnaviruses exhibit several traits associated with other viruses The Polydnaviridae was formally recognized as a virus family in 1995 because all isolates share a common life cycle and possess several traits found in other viruses [7]. PDVs are associated with an extremely species-rich group of insects called parasitoid wasps (Hymenoptera) that reproduce by laying eggs on or in the bodies of other insects their progeny consume. Approximately 40,000 wasp species in two families named the Braconidae and Ichneumonidae carry PDVs, which are correspondingly divided into two genera named the Bracovirus (BVs) and Ichnovirus (IVs) [7]. Each BV or IV from a given wasp species persists in the germline and all somatic cells of the wasp’s body as a provirus (Figure 1). Replication, however, only occurs in pupal and adult stage female wasps in the nuclei of a specific population of cells located in the ovaries called calyx cells [8,9] (Figure 1). Enveloped nucleocapsids package multiple circular, double-stranded DNAs with large aggregate sizes (190–600 kb), which are released from calyx cells by either lysis (BVs) or budding (IVs) [10– 15]. Virions are then stored in the lumen of the reproductive tract with wasp eggs. Each PDV-carrying wasp parasitizes only one or a few species of host insects that are primarily larval stage Lepidoptera (moths). Wasps parasitize hosts by injecting eggs, which contain the proviral genome, plus virions into the body cavity (hemocoel) (Figure 1). Virions thereafter rapidly infect and express virulence genes that: firstly, disable the host’s immune system, which allows wasp offspring to survive, and secondly, alter growth, which causes the host to ultimately die while promoting wasp offspring development [16,17]. Many viruses besides PDVs exhibit both a proviral and replication phase, or infect different species. The key feature of the life cycle that differs from viruses in any other family is that PDVs cannot replicate in the hosts of wasps because none of the genes required to produce virus particles are packaged into virions. As a result, PDVs are only transmitted vertically through the germline of wasps as proviruses, yet the survival of wasps fully depends on the genes PDV virions deliver to parasitized hosts.
Polydnaviruses also exhibit traits associated with many EVEs Since EVEs are any DNA sequence of viral origin in a host germline, proviruses capable of producing infectious virus represent a type of EVE. Such EVEs, however, are rare outside of retroviruses that integrate into the genomes of animal hosts as part of their replication cycle [4]. Instead, most EVEs identified from animals are fragments Current Opinion in Virology 2013, 3:587–594
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Figure 1
PDV persists in wasp somatic and germ cells as a provirus
Wasp ovaries PDV replication in calyx cells PDV virions accumulate in the lumen of the reproductive tract Female wasp parasitizes host insect
Provirus in wasp egg
PDV virions infect host cells
Adult wasp
Pupa
PDV replication begins in calyx cells
Wasp larva develops and then emerges from host to pupate Current Opinion in Virology
The life cycle of parasitoid wasps and PDVs. See main text for discussion.
of a parental genome that in most cases have also been rendered non-functional through mutation [2,3–5]. In the case of PDVs, the evolutionary origin of IVs is unclear [18]. In contrast, all BV-carrying braconids form a monophyletic group called microgastroids that evolved ca. 100 million years ago (Mya) [19,20]. This finding suggested BVs evolved from a virus that infected the common ancestor of microgastroids. The first insights into the identity of this ancestor derived from transcriptome studies of wasp ovaries, which identified several genes expressed in calyx cells during BV replication that share weak but recognizable homology with genes in another group of insect-infecting viruses called nudiviruses [21,22,23]. Nudiviruses are relatively poorly studied but they are the sister taxon of baculoviruses, which have been extensively characterized [24,25,26]. Most baculoviruses and nudiviruses are virulent pathogens that establish systemic, fatal infections by replicating in the nuclei of all cells of an infected insect. Some nudiviruses, however, infect the reproductive system of insects, and establish persistent infections associated with integration into the host genome [27,28]. BVs thus likely evolved from an ancient nudivirus that integrated into the germline of the microgastroid ancestor. Current Opinion in Virology 2013, 3:587–594
Nudiviruses package a single large, circular dsDNA genome (ca. 200 kb) into virions [25]. Integration into the germline of the ancestral wasp therefore presumably occurred as a linear DNA with the resulting provirus retaining the ability to produce infectious virus (Figure 2). In contrast, BV proviral genomes consist of two functional components that are dispersed in the wasp genome [6]. The first of these components is the aforementioned nudivirus-like genes, while the second is the virulence gene-encoding proviral segments that are packaged into virions during replication. Several of the nudivirus-like genes are integrated in close proximity to one another in the wasp genome, forming a cluster, while the rest are located elsewhere in the wasp genome [21]. A majority of the proviral segments are also clustered in a tandem array that forms a macrolocus, while other proviral segments are integrated elsewhere in the wasp genome as either individual segments or as smaller loci that contain 1–3 segments [29]. Conserved synteny of some proviral segments between wasp species provides support for orthology, while differences in the number of proviral segments between species are due to lineage-specific duplication events [9,29]. However, the precise location of the nudivirus-like genes and proviral domains relative www.sciencedirect.com
Polydnavirus evolution Strand and Burke 589
Figure 2
Virus
Functional replication and production of infectious virus particles
Germline integration and fixation
Provirus
Episomal dsDNA viral genome Fragmentation, gene duplication, gene loss, rearrangements - BVs
mRNA
AAAA
Non-functional for production of infectious virus particles
Interaction with host cell factors dsDNA Germline integration and fixation
Scenarios for further gene loss, rearrangements, and accumulation of inactivating mutations Cooption by host and neofunctionalization Most EVEs Current Opinion in Virology
Genome organization of BVs relative to known ancestors and other types of EVEs. Nudiviruses and baculoviruses package large, circular dsDNA genomes that replicate in host cell nuclei. Baculovirus and nudivirus genomes normally persist in host cell nuclei as episomes, and viral replication usually begins shortly after infection with the regulated expression of numerous viral genes that amplify the genome, transcribe virion structural components, and produce infectious virus (upper left). EVEs from a nudivirus could arise by either anomalous integration of a dsDNA derived from a viral transcript (middle left) or integration of the episomal genome into the germline of a host (upper right). In the case of BVs, the ancestor likely integrated into the germline of the ancestor wasp as a provirus that was initially capable of reestablishing a productive infection given evidence from known nudiviruses (see text). The ancestral genome thereafter underwent numerous alterations that led to the evolution of BVs. However, these alterations still maintained a conserved gene set that produces infectious virus particles (upper right). In contrast, most other EVEs of ancient origin [2,3–5] are fragments of a parental genome that have been rendered nonfunctional by rearrangements, deletions and inactivating mutations (boxes with crosses) (lower left and right). Some examples are known of viral regulatory sequences or genes that have been coopted by hosts for novel functions (red boxes) (lower left and right) [2,3–5]. These functions though do not include producing infectious virus particles.
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Figure 3
Proviral genome Proviral segments
Excision, amplification and circularization of proviral segments
Nudivirus-like conserved gene set
Integrases (vlf-1, int-1)
Early gene transcription
RNA polymerase (lef-4, lef-8, lef-9, p47)
Circularized proviral segments packaged into virions
Late gene transcription Virion assembly
Structural components: nucleocapsid proteins (vp39, vlf-1) envelope proteins (p74, pif-1)
Replication-defective BV virions Current Opinion in Virology
BV nudivirus-like genes exhibit ancestral functions to produce infectious but replication defective virions. BV proviral genomes consist of two functional components: a conserved nudivirus-like gene set (upper right) and proviral DNAs (red) that encode virulence genes (yellow) and share conserved flanking excision motifs (black) (upper left). The location of the nudivirus-like genes and proviral DNAs in genomes of wasps are incompletely characterized and are thus indicated by double slash marks. BV replication in the nuclei of calyx cells begins in the early pupal stage of female wasps with expression of several nudivirus-like RNA polymerase subunit and integrase genes (Early gene transcription). This is followed by expression of nucleocapsid and envelope genes required for virion formation (Late gene transcription) and excision, amplification, and circularization of proviral DNAs that are packaged into virions. This results in formation of large numbers of virions. Each individual virion contains only one circularized proviral segment [10,11] but none of the nudivirus-like genes required for virion formation or excision/amplification of the proviral segments. See text for additional information.
to one another in the genomes of wasps remains unclear [21,29,30]. BVs thus derive from a virus ancestor and similar to many other EVEs of ancient origin the components of the parental genome that are still recognizable have become fragmented (Figure 2). Unlike most EVEs, however, the fragmented genomes of BVs still consist of many genes that are transcribed in a highly coordinated manner to produce virions that are infectious but package only a portion of the proviral genome (Figure 2).
Several BV nudivirus-like genes have predicted roles in replication while proviral segments share flanking domains associated with packaging into virions Current understanding of how BV proviral genomes function derives from a combination of comparative genomic, expression, and functional data. Consider first the nudivirus-like genes in relation to the relatives of BVs. Current Opinion in Virology 2013, 3:587–594
Baculoviruses exhibit high diversity in gene content but all sequenced isolates share 31 core genes of which approximately half are essential for replication [24]. These include a DNA polymerase that replicates the viral genome, four subunits of a novel DNA dependent RNA polymerase, and several structural genes coding for capsid and envelope proteins with promoter sequences that are specifically recognized by the viral RNA polymerase [24]. The six nudivirus genomes sequenced to date encode homologs of 20 baculovirus core genes that include the DNA polymerase, baculovirus-like RNA polymerase subunits, and select structural genes [24,25]. The function of these genes, however, is unknown beyond inferences from baculoviruses. The three BV proviral genomes for which data are available lack a recognizable baculovirus/nudivirus DNA polymerase, but each encodes four baculovirus/nudivirus-like RNA polymerase subunits, select transcription factors, www.sciencedirect.com
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and several structural genes with baculovirus-like promoter sequences [21,22,23]. Other predicted members of a BV conserved gene set are eleven nudivirus-like genes that include integrases unknown from baculoviruses [21,22,23]. Consider next the proviral segments that are packaged into virions. Unlike the conservation seen for the nudivirus-like genes, the number of proviral segments and the genes they encode differs with BVs from closely related wasp species sharing more genes than distantly related species [6–9]. The origin of these genes is also diverse with some being recent acquisitions from wasps, others showing evidence of acquisition from other organisms by horizontal gene transfer (HGT), and others still being of uncertain ancestry [31,32]. In contrast, all proviral segments in all BV isolates examined to date are flanked by a conserved direct repeat motif that identifies their site of excision from the wasp genome during replication in calyx cells [29,33,34]. These motifs are absent, however, from DNA flanking any of the nudivirus-like genes [21].
Nudivirus-like RNA polymerase subunits and integrases are essential for virion formation Expression studies show that BV replication begins in calyx cells when female wasps pupate [21,22,23,35]. First, the nudivirus-like RNA polymerase subunits and integrases are transcribed, which is then followed by transcription of the nudivirus-like structural genes plus excision, amplification, and circularization of proviral segments for packaging into virions [21,23,35,36] (Figure 3). Proteomic studies indicate that BV virions contain predicted nudivirus-like structural gene products [21,22,37]. As previously alluded to, the identity between BV and more closely related nudivirus proteins is low (19–41%), while algorithms like BLAST have difficulty detecting homology between BV and more distantly related baculovirus-like core genes. This finding is consistent with the ancient divergence times between BVs, nudiviruses and baculoviruses. Yet, recent functional studies indicate: firstly, the predicted viral RNA polymerase subunits of BVs produce a functional enzyme that transcribes the nudivirus-like structural genes but does not transcribe wasp genes, secondly, the nudivirus-like integrase genes are required for excision of the proviral segments from the wasp genome, and finally select nudivirus-like genes are essential for capsid and envelope formation [37] (Figure 3). In all other cells of the wasp including the germline, all of the nudivirus-like genes and nearly all of the genes on proviral segments are silent [21,23,38]. Taken together, proviral segments are packaged into virions comprised of nudivirus-like gene products but no nudivirus-like genes are packaged because none are excised and amplified (Figure 3). This in turn prevents any viral replication in the hosts wasps parasitize while assuring that transmission of the proviral genome is www.sciencedirect.com
entirely vertical through the germline of the wasp. Finally, BVs cause no disease in wasps because replication is restricted to calyx cells and almost none of the virulence genes on proviral segments are transcribed [21,23,35,36,37]. However, BVs cause severe disease in the hosts wasps parasitize because virions establish a systemic infection in which all virulence genes are expressed [34,38]. It remains unclear what restricts BV replication to calyx cells when most baculoviruses and nudiviruses replicate in many cell types of infected insects. One obvious component is calyx cell-specific expression of the nudivirus-like RNA polymerase subunits and integrases but the signal(s) controlling activation of these genes following pupation of female wasps is unknown [37]. Another factor of potential importance in restricting replication to calyx cells is the absence of a recognizable nudivirus-like DNA polymerase, which suggests that proviral segment amplification has shifted from the virus to control by the wasp [23]. Also unclear are the evolutionary events that led to the dispersed organization of BV genomes. Assuming both components of BV genomes derive from the nudivirus ancestor, dispersal of the genome could have occurred by either duplication of the ancestral genome or integration of several copies of the ancestral genome followed by elimination of conserved replication genes from some copies and elimination of the direct repeat motifs required for excision from the wasp genome from others [6,9,32]. The requirement of nudivirus-like integrases for excision of proviral segments from the wasp genome circumstantially supports the conserved repeat domains flanking each proviral segment derived from the ancestral nudivirus genome. However, it is also possible the proviral segments are not of nudivirus origin given that: firstly, genes on proviral segments are unrelated to any genes from known nudiviruses, and secondly, no sequences homologous to the repeat domains that flank proviral segments have been identified from nudiviruses and shown to play a role in integration. Resolving these issues will undoubtedly benefit from whole genome sequencing, which should clarify where the nudiviruslike genes and proviral segments of BV genomes reside within different wasp species and whether components of the genome are integrated in similar positions in the different lineages of microgastroids.
The two components of BV genomes are subject to different selection pressures Members of large dsDNA virus families, like baculoviruses, typically share a core gene set with roles in conserved processes like replication. Overall genome size and content, however, is also variable because of specialization onto different hosts and the capture of genes from diverse sources that become fixed due to the Current Opinion in Virology 2013, 3:587–594
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advantageous phenotypes they confer [24]. As hosts become genetically isolated and speciate, so do the viruses resulting in host-associated lineages and patterns of diversity. Despite an overall slower rate of evolution due to fewer replication events per unit time, BV genomes exhibit these features while also showing that selection pressures differ for the nudivirus-like genes required for virion formation in wasps versus the proviral segments and virulence genes required for parasitism of hosts. Strikingly, selection has maintained the ancestral functions of the BV RNA polymerase subunits, capsid, and envelope genes over 100 Mya since divergence from nudiviruses and more than 300 Mya since the last common ancestor shared by nudiviruses and baculoviruses [26,37]. In contrast, the variation among BVs in the number of proviral segments, the types of virulence genes packaged into virions, and the diversification of several genes into multimember families with diverged functions provides strong evidence that arms race dynamics are at play as BVs and wasps in different wasp lineages adapt to parasitize hosts, and hosts evolve counter adaptations to evade the effects of gene products delivered by BVs [6,9,31,32,39–47].
[2,3,4]. The small number of EVEs that have been coopted by hosts for novel functions are also appropriately viewed as selfish elements that derive from viruses but which are no longer viruses themselves [3–5]. BVs in contrast present a much more complicated interaction in that their proviral genomes are fragmented and have been coopted to perform functions of novel benefit to wasps, yet do so by producing infectious virus particles and functioning in many respects like the viruses they evolved from. Unlike most viruses, BVs do not package a complete genome into virions that can be transferred to other cells and replicate. However, their ability to produce virions that package a portion of the genome, which is essential for the survival of wasps and in the process their own transmission as proviruses, is consistent with the view that BVs and wasps are mutualists [6].
Acknowledgements This work was supported in part by grants from the National Science Foundation (IOS 1145953), US Department of Agriculture (2009-3530205250) and National Institutes of Health (F32 AI096552).
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as:
Functional parallels between BVs and prokaryotic gene transfer agents While no other EVEs from animals or plants function like BVs, phage-like entities from prokaryotes called gene transfer agents (GTAs) show interesting parallels. Four genetically distinct lineages of GTAs have thus far been identified with each using host chromosomally-encoded genes to produce phage-like particles that package host DNA but few or none of the genes required for GTA particle formation [48]. GTAs functionally differ from transducing phages that occasionally package host DNA rather than the viral genome during the process of replication but resemble BVs in the sense that both package DNAs largely unrelated to the genes required for particle formation. Other parallels with BVs include: firstly, several of the genes required for GTA formation derive from phage ancestors, secondly, these genes are organized in host genomes as clusters and single ORFs, and finally, GTA particles horizontally transfer the DNAs they package from one host to another [49,50]. Unlike the specific proviral segments packaged by BVs, however, GTAs package relatively small (4 kb) and random pieces of DNA from donor cells [51]. In addition, while BVs cause no disease in wasps, GTA production is lethal to donor cells because particles are released by lysis [48,51]. Thus unlike BV-mediated gene transfer to host insects, which directly benefits the wasp and its provirus, the potential fitness benefits of GTAs for the prokaryotes that produce them are likely indirect and complex [52].
of special interest of outstanding interest 1.
Roossinck MJ: The good viruses: viral mutualistic symbioses. Nat Rev Microbiol 2011, 9:99-108.
2. Katzourkakis A, Gifford RJ: Endogenous viral elements in animal genomes. PLoS Genet 2010, 6:e1001191. This paper presents survey data on the diversity of non-retroviral EVEs in animal genomes. 3.
Holmes EC: The evolution of endogenous viral elements. Cell Host Microbe 2011, 10:368-377.
4.
Feschotte C, Gilbert C: Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012, 13:283-296.
5.
Aswad A, Katzourakis A: Paleovirology and virally derived immunity. Trends Ecol Evol 2012, 27:627-636.
6.
Strand MR, Burke GR: Polydnaviruses as symbionts and gene delivery systems. PLoS Pathogens 2012, 8:e1002757.
7.
Strand MR, Drezen J-M: Family Polydnaviridae. In Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. Edited by King AMQ, Adams MJ, Castens EB, Lefkowitz EJ. Elsevier; 2012:237-248.
8.
Strand MR: Polydnaviruses. In Insect Virology. Edited by Asgari S, Johnson KN. Caister Academic Press; 2010:171-197.
9.
Gundersen-Rindal D, Dupuy C, Huguet E, Drezen J-M: Parasitoid polydnaviruses: evolution, pathology and applications. Biocontrol Sci Technol 2013, 23:1-61.
10. Albrecht U, Wyler T, Pfister-Wilhelm R, Gruber A, Stettler P, Heiniger P, Schumperli D, Lanzrein B: PDV of the parasitic wasp Chelonus inanitus (Braconidae): characterization, genome organization and time point of replication. J Gen Virol 1994, 75:3353-3363.
Conclusions
11. Beck MH, Inman RB, Strand MR: Microplitis demolitor bracovirus genome segments vary in abundance and are individually packaged in virions. Virology 2007, 359:179-189.
Most ancient EVEs in animal genomes consist of nonfunctional viral fragments that are evolutionary dead ends
12. Espagne E, Dupuy C, Huguet E, Cattolico L, Provost B, Martins N, Poirie M, Periquet G, Drezen J-M: Genome sequence of a
Current Opinion in Virology 2013, 3:587–594
www.sciencedirect.com
Polydnavirus evolution Strand and Burke 593
polydnavirus: insights into symbiotic virus evolution. Science 2004, 306:286-289. 13. Webb BA, Strand MR, Dickey SE, Beck MH, Hilgarth RS, Kadash K, Kroemer JA, Lindstrom KG, Rattanadechakul W, Shelby KS et al.: Polydnavirus genomes reflect their dual roles as mutualists and pathogens. Virology 2006, 347:160-174. 14. Lapointe R, Tanaka K, Barney WE, Whitfield JB, Banks JC, Beliveau C, Stoltz D, Webb BA, Cusson M: Genomic and morphological features of a banchine polydnavirus: comparison with bracoviruses and ichnoviruses. J Virol 2007, 81:6491-6501. 15. Chen YF, Gao F, Ye XQ, Wei SJ, Shi M, Zheng HJ, Chen XX: Deep sequencing of Cotesia vestalis bracovirus reveals the complexity of a polydnavirus genome. Virology 2011, 414:42-50. 16. Strand MR: Polydnavirus gene products that interact with the host immune system. In Parasitoid Viruses Symbionts and Pathogens. Edited by Beckage NE, Drezen J-M. Academic Press; 2012:149-161. 17. Beckage NE: Polydnaviruses as endocrine regulators. In Parasitoid Viruses Symbionts and Pathogens. Edited by Beckage NE, Drezen J-M. Academic Press; 2012:163-168. 18. Volkoff AN, Jouan V, Urbach S, Samain S, Bergoin M, Wincker P, Demettre E, Cousserans F, Provost B, Coulibaly F et al.: Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. PLoS Pathog 2010, 6:e1000923. This paper presents evidence that IVs likely evolved from a virus ancestor but whether this ancestor is now extinct or is related to an as yet undiscovered virus taxon is unclear. 19. Whitfield JB: Estimating the age of the polydnavirus/braconid wasp symbiosis. Proc Natl Acad Sci U S A 2002, 99:7508-7513. 20. Murphy N, Banks JC, Whitfield JB, Austin AD: Phylogeny of the parasitic microgastroid subfamilies (Hymenoptera: Braconidae) based on sequence data from seven genes, with an improved time estimate of the origin of the lineage. Mol Phylogenet Evol 2008, 47:378-395. 21. Bezier A, Annaheim M, Herbiniere J, Wetterwald C, Gyapay G, Bernard-Samain S, Wincker P, Rodidi I, Heller M, Belghaazi M et al.: Polydnaviruses of braconid wasps derive from an ancestral nudivirus. Science 2009, 323:926-930. This paper presents the first evidence that BVs evolved from a nudivirus ancestor. 22. Wetterwald C, Roth T, Kaeslin M, Annaheim M, Wespi G, Heller M, Ma¨ser P, Roditi I, Pfister-Wilhelm R, Be`zier A et al.: Identification of bracovirus particle proteins and analysis of their transcript levels at the stage of virion formation. J Gen Virol 2010, 91:2610-2619.
Jones KM: Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biol 2008, 9:R183. This paper presents the first detailed insights into how the proviral segments of BVs are organized in the genomes of braconid wasps. 30. Belle E, Beckage NE, Rousselet J, Poirie M, Lemeunier F, Drezen J-M: Visualization of polydnavirus sequences in a parasitoid wasp chromosome. J Virol 2002, 76:5793-5796. 31. Huguet E, Serbielle C, Moreau SJM: Evolution and origin of polydnavirus virulence genes. In Parasitoid Viruses Symbionts and Pathogens. Edited by Beckage NE, Drezen J-M. Academic Press; 2012:63-78. 32. Burke GR, Strand MR: Polydnaviruses of parasitic wasps: domestication of viruses to act as gene delivery vectors. Insects 2012, 3:91-119. 33. Annaheim M, Lanzrein B: Genome organization of the Chelonus inanitus polydnavirus: excision sites, spacers, and abundance of proviral and excised segments. J Gen Virol 2007, 8:450-457. 34. Beck MH, Zhang S, Bitra K, Burke GR, Strand MR: The encapsidated genome of Microplitis demolitor bracovirus integrates into the host Pseudoplusia includens. J Virol 2011, 85:11685-11696. This study presents the first experimental evidence that BV segments in virions integrate into the genomes of host insects parasitized by wasps. The paper also shows that the conserved flanking motifs which identify sites of integration in the wasp genome differ from the repeat motifs that mediate integration into the genome of parasitized host insects. 35. Gruber A, Stettler P, Heiniger P, Schumperli D, Lanzrein B: Polydnavirus DNA of the braconid wasp Chelonus inanitus is integrated in the wasp’s genome and excised only in later pupal and adult stages of the female. J Gen Virol 1996, 77:2873-2879. 36. Savary S, Beckage N, Tan F, Periquet G, Drezen J-M: Excision of the polydnavirus chromosomal integrated EP1 sequence of the parasitoid wasp Cotesia congregata (Braconidae, Microgastrinae) at potential recombinase binding sites. J Gen Virol 1997, 78:3125-3134. 37. Burke GR, Thomas SA, Eum JH, Strand MR: Mutualistic polydnaviruses share essential replication gene functions with pathogenic ancestors. PLoS Pathog 2013, 9:e1003348. This study presents the first experimental evidence for the functions of several nudivirus-like genes in BV replication. 38. Bitra K, Zhang S, Strand MR: Transcriptomic profiling of Microplitis demolitor bracovirus reveals host, tissue, and stage-specific patterns of activity. J Gen Virol 2011, 92:20602071.
23. Burke GR, Strand MR: Deep sequencing identifies viral and wasp genes with potential roles in replication of Microplitis demolitor bracovirus. J Virol 2012, 86:3293-3306.
39. Pruijssers AJ, Strand MR: PTP-H2 and PTP-H3 from Microplitis demolitor bracovirus localize to focal adhesions and are antiphagocytic in insect immune cells. J Virol 2007, 81:1209-1219.
24. Rohrmann GF: Baculovirus Molecular Biology. Bethesda: National Library of Medicine, National Center for Biotechnology Information; 2008, .
40. Beck MH, Strand MR: A novel polydnavirus protein inhibits the insect prophenoloxidase activation pathway. Proc Natl Acad Sci U S A 2007, 104:19267-19272.
25. Wang J, Jehle JA: Nudiviruses and other large, doublestranded circular DNA viruses of invertebrates: new insights on an old topic. J Invert Pathol 2009, 101:187-193.
41. Lu Z, Beck MH, Jiang H, Wang Y, Strand MR: The viral protein Egf1.0 is a dual activity inhibitor of prophenoloxidase activating proteinases 1 and 3 from Manduca sexta. J Biol Chem 2008, 283:21325-21333.
26. Theze J, Bezier A, Periquet G, Drezen JM, Herniou EA: Paleozoic origin of insect large dsDNA viruses. Proc Natl Acad Sci U S A 2011, 108:15931-15935. This paper uses sequence data from BV proviral genomes to generate estimates for the timing of the origin of nudiviruses and baculoviruses. 27. Burand JP: Insect viruses: nonoccluded. In Encyclopedia of Virology. Edited by Mahy BWJ, Van Regenmortel MHV. Oxford; 2008:69-90. 28. Wu YL, Wu CP, Lee ST, Tang H, Chang CH, Chen HH, Chao YC: The early gene hhi1 reactivates Heliothis zea nudivirus 1 in latently infected cells. J Virol 2010, 84:1057-1065. 29. Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fadrosh DW, Fuester RW, Pedroni MJ, Haas BJ, Schatz MC, www.sciencedirect.com
42. Pichon S, Dupas S, Lesobre J, Purisima EO, Drezen J-M, Huguet E: Viral cystatin evolution and three-dimensional structure modelling: a case of directional selection acting on a viral protein involved in a host-parasitoid interaction. BMC Biol 2008, 6:38. 43. Branco A, Le Ru BP, Vavre F, Silvain JF, Dupas S: Intraspecific specialization of the generalist parasitoid Cotesia sesamiae revealed by polydnavirus polymorphism and associated with different Wolbachia infection. Mol Ecol 2011, 20:959-971. 44. Cooper TH, Bailey-Hill K, Leifert WR, McMurchie EJ, Asgari S, Galtz RV: Identification of an in vitro interaction between an insect immune suppressor protein (CrV2) and G alpha proteins. J Biol Chem 2011, 286:10466-10475. Current Opinion in Virology 2013, 3:587–594
594 Virus evolution
45. Magkrioti C, Katrou K, Labropoulou V: Differential inhibition of BmRelish1-dependent transcription in lepidopteran cells by bracovirus ankyrin-repeat proteins. Insect Bichem Mol Biol 2011, 41:993-1002. 46. Bitra K, Suderman RJ, Strand MR: Polydnavirus ank proteins bind NF-kb homodimers and inhibit processing of relish. PLoS Pathog 2012, 8:e1002722. 47. Serbielle C, Dupas S, Perdereau E, Hericourt F, Dupuy C, Huguet E, Drezen J-M: Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases. BMC Evol Biol 2013, 12:253. 48. Lang AS, Zhaxybayeva O, Beatty JT: Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 2012, 10:472-482.
Current Opinion in Virology 2013, 3:587–594
49. Lang AS, Beatty JT: Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodabacter capsulatus. Proc Natl Acad Sci U S A 2000, 97:859-864. 50. Chen F, Spano A, Goodman BE, Blasler KR, Sabat A, Jeffery E, Norris A et al.: Proteomic analysis and identification of the structural and regulatory proteins of the Rhodabacter capsulatus gene transfer agent. J Proteome Res 2008, 8:967973. 51. Hynes AP, Mercer RG, Watton DE, Buckley CB, Lang AS: DNA packaging bias and differential expression of gene transfer agent genes within a population during production and release of the Rhodobacter capsulatus gene transfer agent, RcGTA. Mol Microbiol 2012, 85:314-325. 52. Vos M: Why do bacteria engage in homologous recombination? Trends Microbiol 2009, 17:226-232.
www.sciencedirect.com