Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis

Abstract

Background: Female endoparasitic ichneumonid wasps inject virus-like particles into their caterpillar hosts to suppress immunity. These particles are classified as ichnovirus virions and resemble ascovirus virions, which are also transmitted by parasitic wasps and attack caterpillars. Ascoviruses replicate DNA and produce virions. Polydnavirus DNA consists of wasp DNA replicated by the wasp from its genome, which also directs particle synthesis. Structural similarities between ascovirus and ichnovirus particles and the biology of their transmission suggest that ichnoviruses evolved from ascoviruses, although molecular evidence for this hypothesis is lacking.

Results: Here we show that a family of unique pox-D5 NTPase proteins in the Glypta fumiferanae ichnovirus are related to three Diadromus pulchellus ascovirus proteins encoded by ORFs 90, 91 and 93. A new alignment technique also shows that two proteins from a related ichnovirus are orthologs of other ascovirus virion proteins.

Conclusion: Our results provide molecular evidence supporting the origin of ichnoviruses from ascoviruses by lateral transfer of ascoviral genes into ichneumonid wasp genomes, perhaps the first example of symbiogenesis between large DNA viruses and eukaryotic organisms. We also discuss the limits of this evidence through complementary studies, which revealed that passive lateral transfer of viral genes among polydnaviral, bacterial, and wasp genomes may have occurred repeatedly through an intimate coupling of both recombination and replication of viral genomes during evolution. The impact of passive lateral transfers on evolutionary relationships between polydnaviruses and viruses with large double-stranded genomes is considered in the context of the theory of symbiogenesis.

Figure 1

Map of the 13-kbp region of the DpAV4 genome (EMBL Acc. N°CU469068andCU467486) that contains the gene cluster with direct homologs in the genome of the Glypta fumiferanae ichnovirus. DpAV-4 ORF with well-characterized direct homologs among other ascovirus and iridovirus genomes are represented by white arrows. Homologous ORF of the GfIV genes are represented by black arrows. The sequence and the features of the protein encoded by these ORF are detailed in fig. S1. Below, the graph is scaled in kbp.

Figure 2

Amino acid sequence comparison resulting from a BLAST search done with the DpAV4 ORF90 as a query, and the best hit corresponding to the protein encoded by the ORF1 of the ichnovirus segment GfV-C20 (Subject; Genbank Acc. N° YP_001029423).

Figure 3

Sequence (lanes 1 to 3) and secondary structure (lanes 4 to 6) comparisons among (a) MCP and (b) SfAV1a ORF061 orthologs from CsIV (lanes 1 and 4, typed in black), DpAV4 (lanes 2 and 5, typed in blue) and SfAV1a (lanes 3 and 6, typed in purple). Conserved positions among the amino acid sequence of CsIV and those of DpAV4 and SfAV1a are highlighted in grey. Secondary structures in the three SfAV1a ORF061 orthologs were calculated with the Network Protein Sequence Analysis at http://npsa-pbil.ibcp.fr/ and the statistical relevance of the secondary structures were evaluated with Psipred at http://bioinf.cs.ucl.ac.uk/psipred/. C, E and H in lanes 4 to 6 respectively indicated for each amino acid that it is involved in a coiled, b sheet or a helix structure. Using default parameters of Psipred, upper case letters indicate that the predicted secondary structure is statically significant in Psipred results. Significant secondary structures are highlighted in yellow. In (a), the comparisons were limited to three of the seven conserved domains (Additional file 3a, b and 3c), the 2, 5 and 7. Indeed, classical in silico methods appeared to be inappropriate to predict statistically significant secondary structures in conserved structural protein rich in b strand such as iridovirus and ascovirus MCP. In contrast, a complete and coherent domain comparison was obtained by HCA profiles (fig. S3b, c).

Figure 4

Amino acid sequence analysis of the N-acetyl-L-glutamate 5-phosphotransferase-like proteins encoded by one gene in SfAV1a (ORF1bis), two genes in HvAV3e (ORFs 002 and 112) and TnAV2c (ORFs 024 and 148), and one gene in CcBV. Identical residues between sequences are highlighted in black typed in white, those that are similar are highlighted in grey.

Figure 5

Hypothetical mechanism for the integration and evolution of ascovirus genomes in endoparasitic wasps. Schematic representation of the three-step process of symbiogenesis, and DNA rearrangements that putatively occurred in the germ line of the wasp ancestors in the Banchinae and Campopleginae lineages, from the integration of an ascoviral genome to the proviral ichnoviral genome. Sequences that originate from the ascovirus are in blue, those of the wasp host and its chromosomes are in pink. Genes of ascoviral origin are surrounded by a thin black or white line, depending on their final chromosomal location. Two solutions can account for the final chromosomal organisation of the proviral ichnovirus genome, monolocus or multilocus, since this question is not fully understood in either wasp lineage. More complex alternatives to this three-step process might also be proposed and would involve, for example, the complete de novo creation of a mono or multi locus proviral genome from the recruitment by recombination or transposition of ascoviral and host genes located elsewhere in the wasp chromosomes. This model for the chromosomal organization of proviral DNA in polydnaviruses is consistent with data recently published [58].