Genome-Wide Survey for Genes Horizontally Transferred from Cellular Organisms to Baculoviruses

Austin L. Hughes and Robert Friedman1

Department of Biological Sciences, University of South Carolina, Columbia


    Abstract
 TOP
 Abstract
 Introduction
 Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
The phylogeny of 13 viral species in the genera Granulovirus and Nucleopolyhedrovirus (family Baculoviridae) was reconstructed on the basis of 22 conserved protein families shared by all species, and a comprehensive homology search and phylogenetic analysis of the complete genomes of these viruses was used to test for horizontal gene transfer from cellular organisms. Statistically significant evidence of horizontal transfer was found in the case of six protein families (DNA ligase, ribonucleotide reductase 1, SNF2 global transactivator, inhibitor of apoptosis, chitinase, and UDP-glucosyltransferase). Three of these families are known to play key roles in the infection of insect hosts by these viruses. There was evidence that two of these (inhibitor of apoptosis and UDP-glucosyltransferase) were derived from the insect host. By contrast, the gene encoding chitinase in these viruses was evidently derived from a group of bacteria (the gamma subdivision of proteobacteria), which use chitinase to break down fungal chitins.

Key Words: Baculoviridae • chitinase • gene capture • horizontal gene transfer • UDP-glucosyl transferase • viral evolution


    Introduction
 TOP
 Abstract
 Introduction
 Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
Certain DNA viruses parasitic on vertebrates are known to possess genes encoding molecules that show evidence of homology to cytokines or other immune system molecules of their hosts (Barry and McFadden 1997; Lalani and McFadden 1999). In some cases, there is experimental evidence that these viral molecules can disrupt host immune signaling and thus are advantageous to the virus (Liu et al. 1997). Phylogenetic analyses support the hypothesis that immune system genes have been acquired ("captured") from the host genome; for example, interleukin-10 genes have been captured independently by different DNA viruses on at least three different occasions since the radiation of the eutherian mammals (Hughes 2002a).

There is evidence that a similar phenomenon has occurred in the evolutionary history of the Baculoviridae, a family of double-stranded DNA, no RNA-stage viruses parasitic on members of the phylum Arthropoda (Miller 1997; Blissard et al. 2000). Certain Baculoviridae are known to express genes belonging to the inhibitor of apoptosis (IAP) family found also in both vertebrates and insects (Crook, Clem, and Miller 1993; Clem and Miller 1994). These proteins suppress the apoptotic responses that are part of the insect's defense response against viruses (Clem, Fechhemer, and Miller 1991). Phylogenetic analysis supported the hypothesis that baculovirus IAP genes originated by capture of host genes, which occurred on at least two separate occasions in the evolution of this viral family (Hughes 2002b).

In the present paper, we used genome-wide homology searches in a set of 13 complete genomes from the viral family Baculoviridae to discover all genes that may have been horizontally transferred from cellular organisms. We were particularly interested in transfers of genes potentially important in the infection process and in genes captured from the insect host. For all gene families containing potential horizontal transfers, we used phylogenetic analysis to reconstruct the evolutionary relationships among the genes. By comparing these phylogenies with phylogenies of the viruses reconstructed on the basis of a set of conserved gene families shared by all of the baculovirus genomes analyzed and with known phylogenies of cellular organisms, we inferred the source and time of acquisition of horizontally transferred baculovirus genes relative to major cladogenetic events in the phylogeny of these viruses and in that of their hosts.


    Methods
 TOP
 Abstract
 Introduction
 Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
Families Shared by Baculovirus Genomes
The complete sets of predicted protein translations were extracted from the baculovirus genomes listed in table 1. Using the BlastP program (Altschul et al. 1997) and an expect (E) value of 10-50, we conducted all-against-all homology searches for the 14 genomes. We then assembled protein families using a single-link method (Friedman and Hughes 2001). A strict homology search criterion was used in order to identify protein families present in all baculovirus genomes analyzed and homologous through most of the sequence length, rather than homologous only in isolated domains. We then used these conserved protein families as a basis for reconstructing the phylogenetic relationships of these species.


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Table 1 Species in Phylogenetic Analyses.

 
Phylogenetic trees were constructed for each protein family ( families) present in all 14 species of Baculoviridae analyzed. Likewise phylogenetic trees were constructed for each protein family ( families) found each of the 13 species analyzed from the genera Granulovirus and Nucleopolyhedrovirus. The phylogenies for all 14 species were used to infer the root for the families found in Granulovirus and Nucleopolyhedrovirus. Of the 23 protein families found in all members of these two genera, one family (occlusion-derived envelope protein ODV-E66) was found to have a phylogeny very different from the others (data not shown), suggesting that the members were not orthologs. Indeed, a similar result was reported by Herniou et al. (2001), who suggested that the evolutionary history of this gene involved independent duplication and deletion events in different lineages of the Baculoviridae. Phylogenies of the remaining 22 families were used to reconstruct evolutionary relationships among the 13 species of Granulovirus and Nucleopolyhedrovirus. We computed the consensus of the phylogenies of the 22 individual protein families and also the phylogeny based on the concatenated sequence of all 22 proteins. Russo, Takezaki, and Nei (1996) found that concatenated protein sequences provided better resolution of a known phylogeny than the consensus of individual proteins.

The following is a list of the 22 conserved families shared by the 13 species of Granulovirus and Nucleopolyhedrovirus, with accession numbers for the protein translation from AcMNPV: polyhedrin (NP_054037); unknown protein (NP_054122); late expression factor 4 (NP_054120); unknown protein (NP_054111); very late expression factor 1 (NP_054107); p49 (NP_054173); DNA polymerase (NP_054095); late expression factor 8 (NP_054079); late expression factor 9 (NP_054092); occlusion-derived virus envelope protein ODV-E56 (NP_054179); alkaline exonuclease (NP_054163); virion protein vp1054 (NP_054084); serine-threonine kinase (NP_054039); transcriptional regulator (NP_054069); p48 (NP_054133); late expression factor 5 (NP-054129); 38k protein (NP_054128); helicase (NP_054125); capsid-associated protein vp91 (NP_054113); unknown protein (NP_054051); occlusion-derived virus envelope protein p74 (NP_054168); unknown protein (NP_054149).

Families Shared with Cellular Organisms
We used BlastP with an E-value of 10-20 to search all predicted proteins from the set of baculovirus genomes against the following sequences of cellular organisms: the set of complete protein translations (proteome) for Saccharomyces cerevisiae from http://genome-www.stanford.edu/Saccharomyces; for Arabidopsis thaliana from http://www.tigr.org; for Caenorhabditis elegans from http://www.sanger.ac.uk/C_elegans; and for Drosophila melanogaster from ftp://ftp.ebi.ac.uk/pub/databases/edgp/sequence_sets. Proteome data sets from 38 complete genomes of bacteria and all available sequences from a set of other representative organisms (the slime mold Dictyostelium discoideum, the zebrafish Danio rerio, the pufferfish Takifugu rubripes, the frog Xenopus laevis, the human Homo sapiens, and the mouse Mus musculus) were obtained from the National Center for Biotechnology Information (NCBI). A relatively strict homology search criterion was used because preliminary analyses showed that phylogenetic analyses using families assembled by less strict criteria were unlikely to show good resolution of deep branching patterns.

In each case where homology search showed evidence of homology between a baculovirus protein and one or more proteins from cellular organisms, we conducted additional homology searches against the complete NCBI nonredundant database to identify additional potential homologues. For these families, phylogenetic analyses were conducted initially including all homologs identified by these searches. For ease of presentation in figures, only selected sequences were used in the phylogenetic analyses presented here. However, the overall phylogenetic patterns presented were similar when larger data sets were used (data not shown). Organisms used in phylogenetic analyses presented here are listed in table 1.

Phylogenetic Methods
Amino acid sequences were aligned using the ClustalW program (Thompson, Higgins, and Gibson 1994). All alignments are available from the authors by request. In phylogenetic analyses, any site at which the alignment postulated a gap in any sequence was excluded from all pairwise comparisons so that a comparable set of sites was used for each comparison.

Phylogenetic analyses were conducted by three methods: (1) minimum evolution (ME) (Rzhetsky and Nei 1992); (2) maximum parsimony (MP) (Swofford 2000); and (3) quartet maximum likelihood (QML) (Strimmer and von Haeseler 1996), using the TreePuzzle-5.0 program. ME trees were based on the gamma-corrected amino acid distance (Ota and Nei 1994), using the parameter for the gamma distribution estimated by TreePuzzle-5.0. QML trees were based on the JTT model of amino acid sequence evolution (Jones, Taylor, and Thornton 1992) with rates assumed to vary among sites according to a gamma distribution. Nei, Xu, and Glazko (2001) provide theoretical justification for use of gamma distances for concatenated amino acid sequences.

The significance of internal branches in ME trees was tested by the standard error test, and the standard errors of branch length were computed by the bootstrap method implemented in the MEGA2 program (Kumar et al. 2001). The reliability of each internal branch in MP trees was assessed by bootstrapping; 1,000 bootstrap samples were used. The reliability of each internal branch in QML trees was assessed by the proportion of 10,000 puzzling steps supporting the branch (Strimmer and von Haeseler 1996).


    Results
 TOP
 Abstract
 Introduction
 Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
Baculovirus Phylogeny
Figure 1A shows the consensus of the trees based on 22 conserved protein families shared by the 13 species of Granulovirus and Nucleopolyhedrovirus. The tree was rooted on the basis of four families, which also included CnBV from the genus Baculovirus (data not shown). Figure 1B shows the ME tree based on the concatenated sequences of the 22 proteins, rooted as in Figure 1A. Although there were differences among the genes analyzed and among the different methods of phylogenetic tree reconstruction, all genes and methods agreed in certain broad patterns. First, Granulovirus species were separated from Nucleopolyhedrovirus by an internal branch seen in the trees for all 22 protein families constructed by each method (fig. 1A). The same branch received strong statistical support in the trees based on the concatenated proteins reconstructed by all three methods (fig. 1B). Thus, our results supported monophyly of the genera Granulovirus and Nucleopolyhedrovirus. In trees constructed by ME and QML methods for all 22 families, AcMNPV, BmMNPV, OpMNPV, and EpMNPV clustered together (fig. 1A). These four species clustered together in 21 of 22 MP trees (fig. 1A), and the same cluster received strong support in the trees based on the concatenated proteins reconstructed by all three methods (fig. 1B).



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FIG. 1. (A) Consensus of phylogenies of 22 orthologous conserved proteins present in 13 genomes of the viral genera Granulovirus and Nucleopolyhedrovirus. Numbers on the branches represent the number of families in which the branch was supported in the following analyses (from left to right): ME based on gamma-corrected amino acid distance, MP, and QML. (B) ME tree of 22 concatenated proteins (9,306 aligned amino acid sites) based on gamma corrected distance (the parameter used to model rate variation among sites was ). Numbers on branches represent the confidence level of the interior branch test in the ME tree (only ); numbers in parentheses (from left to right) represent the bootstrap support for the branch in MP analysis (only ) and the percent of 1,000 puzzling steps supporting the branch in QML analysis (only ). Trees were rooted based on four families for which CnBV homologs were available

 
Potential Horizontal Transfers
A total of 20 protein families were found that contained members in the Baculoviridae and in cellular organisms. In the phylogenies of 10 families, sequences from Baculoviridae formed a monophyletic group apart from those of cellular organisms (table 2); thus in these 10 families, there was no evidence of horizontal gene transfer. In the phylogenies of four families, although the sequences from Baculoviridae did not form a monophyletic group, this pattern was not supported by a significant internal branch in the ME tree (table 2). Therefore, in these four cases, the question of horizonal transfer was not resolved by the phylogenetic analysis. In this section, only the results of ME analyses are shown; other methods yielded similar results (data not shown).


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Table 2 Gene Families of Baculoviruses with Homologs in Cellular Organisms.

 
In six other families, the phylogeny provided evidence, supported by statistically significant internal branches, of horizontal gene transfer from cellular organisms to Baculoviridae. This evidence took two different forms. First, there were three families in which the sequences from Baculoviridae did not form a monophyletic group, but clustered with different groups of molecules from cellular organisms: DNA ligase, IAP, and ribonucleotide reductase 1 (table 2). Second, there were three families in which the sequences from Baculoviridae formed a monophyletic group, but that group clustered with one subset of the sequences from cellular organisms: chitinase, SNF2, and UDP glucosyl transferase (table 2). In the following sections, we discuss each of the six protein families showing evidence of horizontal transfer.

DNA Ligase
In the DNA ligase family, homologs were found in all three species of Granulovirus but in only one species of Nucleopolyhedrovirus, LdMNPV (fig. 2). However, the sequence from LdMNPV did not cluster with the Granulovirus sequences (fig. 2). Although the rooting of the tree was not certain, there were two major clusters separated by a significant internal branch (fig. 2). One cluster included DNA ligase of Granulovirus and DNA ligase I of eukaryotes; the other cluster included DNA ligase of LdMNPV, DNA ligase of poxviruses, and DNA ligase III of eukaryotes (fig. 2).



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FIG. 2. ME tree of DNA ligase of baculoviruses and homologs, based on the gamma-corrected amino acid distance () at 445 aligned sites. Numbers on branches represent the confidence level of the interior branch test (only )

 
This topology is consistent with the hypothesis that the DNA ligase of the ancestral Granulovirus species was derived by capture of a eukaryotic DNA ligase I gene, while LdMNPV independently captured a eukaryotic DNA ligase III gene. Alternatively, the results are also consistent with the hypothesis that an ancestor of both Granulovirus and Nucleopolyhedrovirus captured both eukaryotic DNA ligase I and DNA ligase III, after which DNA ligase III was lost in Granulovirus, DNA ligase I was lost in LdMNPV, and both were lost in other Nucleopolyhedrovirus. In either case, horizontal gene transfer from eukaryotes is implicated because of the fact that baculovirus members of this family cluster with different eukaryotic molecules. It is also of interest that DNA ligase of LdMNPV did not cluster with those of poxviruses, even though both clustered with eukaryotic DNA ligase III (fig. 2). This topology supports the hypothesis that the baculoviruses and the poxviruses acquired eukaryotic DNA ligase III by independent events of horizontal transfer.

IAP
Because the phylogeny of baculovirus inhibitor of apoptosis (IAP) was the subject of a recent paper (Hughes 2002b), the phylogenetic tree is not shown here. In the phylogentic tree of IAP, baculovirus IAP clustered with those of insects, and at least two separate events of transfer of genes in this family from insect hosts to baculoviruses were supported (Hughes 2002b).

Ribonucleotide Reductase 1
In the phylogeny of ribonucleotide reductase 1, there were two major clusters, separated by a highly significant internal branch (fig. 3). One cluster included sequences from one species of Granulovirus (CpGV) and two species of Nucleopolyhedrovirus (LdMNPV and OpMNPV), together with bacterial sequences from the Firmicutes (fig. 3). The other cluster included sequences from Archaea, from other groups of bacteria, from eukaryotes, and from poxviruses, along with sequences from two species of Nucleopolyhedrovirus, SeMNPV and SlMNPV (fig. 3). Within the latter cluster, SeMNPV fell outside a cluster that included SlMNPV and sequences from insects and other animals, which was supported by a highly significant internal branch (fig. 3). Ribonucleotide reductase 1 from SlMNPV clustered with those of insects, although the branch supporting this pattern was not significantly supported (fig. 3).



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FIG. 3. ME tree of ribonucleotide reductase 1 of baculoviruses and homologs, based on the gamma-corrected amino acid distance () at 522 aligned sites. Numbers on branches represent the confidence level of the interior branch test (only )

 
The phylogenetic analysis thus supported three distinct events of origin of baculovirus ribonucleotide reductase 1 genes from cellular organisms. The fact that sequences from both Granulovirus and Nucleopolyhedrovirus clustered with those from Firmicutes (fig. 3) suggests that the common ancestor of these two viral genera possessed a ribonucleotide reductase 1 gene related to these bacterial molecules. The fact that the sequences from SlMNPV and SeMNPV fell within a cluster of sequences from eukaryotes (fig. 3) supports the hypothesis that gene transfer occurred from eukaryotes to baculoviruses rather than in the opposite direction. The sequence from SlMNPV clustered with animal molecules and in particular those of insects (fig. 3); this suggests a recent transfer of the gene encoding ribonucleotide reductase 1 to this viral species from its host. On the other hand, the sequence in SeMNPV appears to have originated from a separate transfer of a eukaryotic gene. Two events of transfer of ribonucleotide reductase 1 genes to baculoviruses were previously proposed on the basis of a phylogenetic analysis with a smaller number of sequences by van Strien et al. (1997).

Chitinase
Chitinase sequences from Granulovirus and Nucleopolyhedrovirus formed a monophyletic group that clustered with sequences from the gamma subdivision of Proteobacteria, and this pattern was supported by a highly significant branch (fig. 4). A chitinase from a member of the viral family Phycodnaviridae (PbCV1) fell outside the cluster of sequences from baculoviruses and the gamma division of Proteobacteria, as did other bacterial sequences and eukaryotic sequences (fig. 4). Thus, the phylogeny supported the hypothesis that the gene encoding chitinase was transferred from the gamma division of Proteobacteria to the common ancestor of Granulovirus and Nucleoplyhedrovirus. In the phylogenetic tree, chitinases of baculoviruses clustered with one clade of bacterial chitinases but within a larger clade that included other bacterial sequences (fig. 4). This topology supports the hypothesis that horizontal gene transfer occurred from bacteria to baculoviruses rather than in the opposite direction.



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FIG. 4. ME tree of chitinase of baculoviruses and homologs, based on the gamma-corrected amino acid distance () at 256 aligned sites. Numbers on branches represent the confidence level of the interior branch test (only )

 
SNF2
Members of the SNF2 family of global transactivators were found in AcMNPV, BmMNPV, OpMNPV, and EpMNPV (fig. 5); that is, the species corresponding to the so-called "Group I" of Nucleopolyhedrovirus (Herniou et al. 2001). These sequences clustered with a group of sequences from fungi, plants, and animals homologous to Drosophila lodestar, and this clustering pattern was supported by a significant internal branch (fig. 5). Although the branch supporting this pattern was not significantly supported, the baculovirus sequences clustered closer to the animal lodestar homologs than to plant or fungal sequences (fig. 5). Because other sequences from eukaryotes fell with bacterial sequences outside the cluster of lodestar homologs and baculovirus SNF2, the phylogeny supported the hypothesis that baculovirus SNF2 is more closely related to the lodestar group of eukaryotic SNF2 than to other SNF2. This, in turn, suggests that baculovirus SNF2 originated through horizonal transfer of a gene encoding a lodestar-like protein, probably from an animal host, to the common ancestor of the clade that includes AcMNPV, BmMNPV, OpMNPV, and EpMNPV.



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FIG. 5. ME tree of SNF2 global transactivator of baculoviruses and homologs, based on the gamma-corrected amino acid distance () at 329 aligned sites. Numbers on branches represent the confidence level of the interior branch test (only )

 
UDP-Glucosyltransferase
UDP-glucosyltransferases constitute a large multigene family in the completely sequenced genome of Drosophila melanogaster and in the partially sequences genome of Anopheles gambiae; representative members were included in our analysis of this family (fig. 6). UDP-glucosyltransferases from Granulovirus and Nucleopolyhedrovirus clustered with insect sequences, apart from homologs from C. elegans and vertebrates (fig. 6). Moreover, the baculovirus UDP-glucosyltransferase molecules clustered with a single sequence from A. gambiae, and this pattern was supported by a significant internal branch (fig. 6). Because the baculoviruses sequences clustered with a particular insect sequence (fig. 6), the phylogenetic analysis supports the hypothesis of O'Reilly (1995) that the baculovirus gene encoding UDP-glucosyltransferase was transferred from an insect host. Because the baculovirus cluster included sequences from Granulovirus and Nucleopolyhedrovirus, the phylogeny supports the hypothesis that the horizontal transfer occurred in the common ancestor of the two genera.



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FIG. 6. ME tree of UDP glucosyltransferases of baculoviruses and homologs, based on the gamma-corrected amino acid distance () at 339 aligned sites. Numbers on branches represent the confidence level of the interior branch test (only )

 

    Discussion
 TOP
 Abstract
 Introduction
 Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
A phylogenetic analysis of 13 species in the viral genera Granulovirus and Nucleopolyhedrovirus (family Baculoviridae) was conducted on the basis of 22 conserved protein families with putative orthologs in all species. Both the consensus of the phylogenies for each family and phylogenies based on the concatenated species strongly supported the monophyly of each of the two genera. Previous analyses of smaller numbers of species of Granulovirus and Nucleopolyhedrovirus, by Zanotto, Kessing, and Maruniak (1993) and by Herniou et al. (2001) found support for two groups within the genus Nucleopolyhedrovirus: Group I, which included AcMNPV, BmMNPV, and OpMNPV; and Group II, which included HaMNPV, SeMNPV, and LdMNPV. Our analyses supported monophyly of the former group but not the latter group (fig. 1).

In a survey of the complete genomes of the 13 species of Granulovirus and Nucleopolyhedrovirus, six protein families showed phylogenetic tree topologies indicative of horizontal gene transfer. In the case of DNA ligase, the phylogenetic tree showed two clusters, each of which contained sequences from both baculoviruses and cellular organisms (fig. 2). Theoretically, this topology is consistent with the hypothesis that horizontal transfer occurred from baculoviruses to cellular organisms. However, given the widespread occurrence of DNA ligases in all groups of eukaryotes, the hypothesis that horizontal transfer occurred from eukaryotes to DNA viruses seems much more plausible. By contrast, in the other five families, the baculovirus sequences fell within clusters of sequences from cellular organisms (figs. 3–6GoGoGo and Hughes 2002b). Thus, in these families, the phylogenies supported horizontal transfer from cellular organisms to viruses, rather than in the opposite direction.

Two of the six families showing evidence of horizontal gene transfer, DNA ligase and ribonucleotide reductase 1, play roles in the metabolism of DNA. The animal lodestar protein, of which a homolog is found in certain baculovirus species, is involved in transcription termination (Liu, Xie, and Price 1998). The other three families for which there is evidence of horizontal transfer are all known to be directly involved in the infection process. The role of baculovirus IAP in suppressing the insect host's apoptotic defense response (Clem, Fechhemer, and Miller 1991) has been mentioned previously. Chitinase breaks down chitin, the polysaccharide that is a major constituent of arthropod cuticle. During infection of insect cells by AcMNPV, chitinase is localized mainly in the endoplasmic reticulum and is released into the extracellular medium on cell lysis. There it is important for the liquefaction of tissues that characterizes infection of insect larvae by these viruses (Savile et al. 2002). Baculovirus UDP-glucosyltransferase is involved in viral suppression of host metamorphosis through inactivation of host ecdysosteroid hormones (Evans and O'Reilly 1999).

Phylogenetic analyses provided evidence that genes encoding baculovirus IAP (Hughes 2002b) and UDP-glucosyltransferase (fig. 6) were horizontally transferred from insects. These transfers thus presumably occurred after the ancestor of baculoviruses began to infect insects, and the acquisition of these genes improved the adaptation of this family of viruses to their insect hosts. The baculovirus gene encoding chitinase, by contrast, was shown to be of bacterial origin, being derived from an ancestor from the gamma division of Proteobacteria. Hatwin et al. (1995) previously proposed that the baculovirus chitinase gene was transferred from a species of Proteobacteria. However, they included only one baculovirus chitinase in their phylogenetic analysis, and that sequence clustered with a bacterial chitinase from the genus Serratia (Hatwin et al. 1995). Thus, their tree suggested a transfer directly from one bacterial species. By contrast, our analysis included a much larger number of species, and baculoviruses chitinases clustered with a group of species from the gamma division of Protobacteria. This result places the horizontal transfer event before speciation of this group of bacteria. Hatwin et al. (1995) speculated that since Proteobacteria include enteric pathogens of insects, horizontal transfer from bacteria to virus may have occurred in the insect host.

The evolutionary origin of viruses remains mysterious (Morse 1994). Since all viruses are parasitic on cellular organisms and require molecular machinery produced by their cellular hosts in order to complete their life cycles, it seems reasonable to hypothesize that viruses originated after cellular organisms and indeed that they originated from genetic elements originally present in cellular organisms. However, it is uncertain how many independent evolutionary events have given rise to new viral lineages. Strauss and Strauss (1998) proposed that all or most RNA viruses constitute a monophyletic group and thus have a common origin. On the other hand, the monophyly of the large DNA viruses (double stranded DNA, no RNA-stage viruses) is much more difficult to establish. Iyer, Aravind, and Koonin (2001) have recently proposed that four families of large DNA viruses (Poxviridae, Asfarviridae, Iridoviridae, and Phycnoviridae) share a common origin. However, these authors did not test this hypothesis with phylogenetic methods; and, even if their hypothesis is correct, the relationship of these four families to other large DNA viruses, including Baculoviridae, remains uncertain.

Phylogenies of genes of large DNA viruses in the families Poxviridae and Herpesviridae with homologs in vertebrates were consistent with the hypothesis that these viruses have captured genes from cellular organisms repeatedly over the course of their evolution (Hughes 2002a). Similarly, an extensive phylogenetic analysis of dUTPase genes from viruses and cellular organisms suggested that different viral lineages have captured dUTPase genes independently at least five times (Baldo and McClure 1999). The present analyses suggested that different families of large DNA viruses independently acquired several genes from cellular organisms. There was evidence of independent acquisition of genes for DNA ligase (fig. 2) and ribonucleotide reductase 1 (fig. 3) in Baculoviridae and Poxviridae and of independent acquisition of genes for chitinase in Baculoviridae and Phycnoviridae (fig. 5). Because homologous genes may have been acquired independently by two different viral lineages, many of the genes of large DNA viruses may not provide reliable phylogenies of the viruses themselves. Indeed, these viruses appear to have been assembled over evolutionary time by numerous independent events of horizontal gene transfer.


    Acknowledgements
 TOP
 Abstract
 Introduction
 Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 
This research was supported by NIH grants GM066710 and GM43940 to A.L.H.


    Footnotes
 
1 Present address: Department of Ecology and Evolution, University of Chicago. Back

William Jeffery, Associate Editor Back

E-mail: austin{at}biol.sc.edu. Back


    Literature Cited
 TOP
 Abstract
 Introduction
 Methods
 Results
 Discussion
 Acknowledgements
 Literature Cited
 

    Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.[Abstract/Free Full Text]

    Baldo, A. M., and M. A. McClure. 1999. Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts. J Virol. 73:7710-7721.[Abstract/Free Full Text]

    Barry, M., and G. McFadden. 1997. Virus encoded cytokines and cytokine receptors. Parasitology 115:(suppl.): S89-S110.[CrossRef][ISI][Medline]

    Blissard, G., B. Black, N. Crook, B. A. Keddie, R. Possee, G. Rohrmann, D. Theilmann, and L. Volkmann. 2000. Family Baculoviridae. Pp. 195–202 in M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle, and R. B. Wickner, eds. Virus taxonomy: classification and nomenclature of viruses. Academic Press, San Diego, Calif.

    Clem, R. J., M. Fechhemer, and L. K. Miller. 1991. Prevention of apoptosis by a baculovirus gene during infection of insect cells. Science 254:1388-1390.[ISI][Medline]

    Clem, R. J., and L. K. Miller. 1994. Control of programmed cell death by the baculovirus genes p35 and iap. Mol. Cell. Biol. 14:5212-5222.[Abstract]

    Crook, N. E., R. J. Clem, and L. K. Miller. 1993. An apoptosis-inhibiting gene with a zinc finger-like motif. J. Virol. 67:2168-2174.[Abstract]

    Evans, O. P., and D. R. O'Reilly. 1999. Expression and structural characterization of a baculovirus ecdysosteroid UDP-glucosyltransferase. J. Gen. Virol. 80:485-492.[Abstract]

    Friedman, R., and A. L. Hughes. 2001. Pattern and timing of gene duplication in animal genomes. Genome Res. 11:1842-1847.[Abstract/Free Full Text]

    Hatwin, R. E., L. Arnold, M. D. Ayres, P. M. Zanotto, S. C. Howard, G. W. Gooday, L. H. Chappell, P. A. Kitts, L. A. King, and R. D. Possee. 1995. Identification and preliminary characterization of a chitinase gene in the Autographa californica nuclear polyhedrosis virus genome. Virology 212:673-685.[CrossRef][ISI][Medline]

    Herniou, E. A., T. Luque, X. Chen, J. M. Vlak, D. Winstanley, J. S. Cory, and D. R. O'Reilly. 2001. Use of whole genome sequence data to infer baculovirus phylogeny. J. Virol. 75:8117-8126.[Abstract/Free Full Text]

    Hughes, A. L. 2002a. Origin and evolution of viral interleukin-10 and other DNA virus genes with vertebrate homologues. J. Mol. Evol. 54:90-101.[ISI][Medline]

    Hughes, A. L. 2002b. Evolution of inhibitors of apoptosis in baculoviruses and their insect hosts. Infect. Genet. Evol. 2:3-10.[CrossRef][Medline]

    Iyer, L. M., L. Aravind, and E. V. Koonin. 2001. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75:11720-11734.[Abstract/Free Full Text]

    Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.[Abstract]

    Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics software. 17:1244-1245.

    Lalani, A. S., and G. McFadden. 1999. Evasion and exploitation of chemokines by viruses. Cytokine Growth Factor Rev. 10:219-233.[CrossRef][ISI][Medline]

    Liu, M., Z. Xie, and D. H. Price. 1998. A human RNA polymerase II transcription termination factor is a SWI2/SNF2 family member. J. Biol. Chem. 273:25541-25544.[Abstract/Free Full Text]

    Liu, Y., R. de Waal Malefyt, F. Briere, C. Parham, J.-M. Bridon, J. Banchereau, K. W. Moore, and J. Xu. 1997. The EBV IL-10 homologue is a selective agonist with impaired binding to the IL-10 receptor. J. Immunol. 158:604-613.[Abstract]

    Miller, L. K. 1997. Introduction to the baculoviruses. Pp. 1–6 in L. K. Miller, ed. The baculoviruses. Plenum Press, New York.

    Morse, S. B. 1994. Toward an evolutionary biology of viruses. Pp. 1–28 in S. D. Morse, ed. The evolutionary biology of viruses. Raven Press, New York.

    Nei, M., P. Xu, and G. Glazko. 2001. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proc. Natl. Acad. Sci. USA 98:2497-2502.[Abstract/Free Full Text]

    O'Reilly, D. R. 1995. Baculoviris-encoded ecdysteroid UDP-glucosyltransferases. Insect Biochem. Mol. Biol. 25:541-550.[CrossRef][ISI]

    Ota, T., and M. Nei. 1994. Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol. 38:642-643.[ISI]

    Russo, C. A. M., N. Takezaki, and M. Nei. 1996. Efficiences of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525-536.[Abstract]

    Rzhetsky, A., and M. Nei. 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945-967.[Free Full Text]

    Savile, G. P., C. J. Thomas, R. D. Possee, and L. A. King. 2002. Partial redistribution of the Autographa californica nucleopolyhedrovirus in virus-infected cells accompanies mutation of the carboxy-terminal KDEL ER-retention motif. J. Gen. Virol. 83:685-694.[Abstract/Free Full Text]

    Strauss, J. H., and E. G. Strauss. 1988. Evolution of RNA viruses. Annu. Rev. Microbiol. 42:657-683.[CrossRef][ISI][Medline]

    Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol. Evol. 13:964-969.[Free Full Text]

    Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.

    Thompson, J. D., D. G. Higgins, and T. Gibson. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.[Abstract]

    van Strien, E. A., O. Faktor, Z. H. Hu, D. Zuidema, R. W. Goldbach, and J. M. Vlak. 1997. Baculoviruses contain a gene for the large subunit of ribonucleotide reductase. J. Gen. Virol. 78:2365-2377.[Abstract]

    Zanotto, P. M., B. D. Kessing, and J. E. Maruniak. 1993. Phylogenetic interrelationships among baculoviruses: evolutionary rates and host associations. J. Invert. Pathol. 62:147-164.[CrossRef][ISI][Medline]

Accepted for publication February 13, 2003.