Evolution Of Large DNA Viruses Research Articles

Divergent Traits and Ligand-Binding Properties of the Cytomegalovirus CD48 Gene Family

The genesis of gene families by the capture of host genes and their subsequent duplication is a crucial process in the evolution of large DNA viruses. CD48 is a cell surface molecule that interacts via its N-terminal immunoglobulin (Ig) domain with the cell surface receptor 2B4 (CD244), regulating leukocyte cytotoxicity. We previously reported the presence of five CD48 homologs (vCD48s) in two related cytomegaloviruses, and demonstrated that one of them, A43, binds 2B4 and acts as a soluble CD48 decoy receptor impairing NK cell function. Here, we have characterized the rest of these vCD48s. We show that they are highly glycosylated proteins that display remarkably distinct features: divergent biochemical properties, cellular locations, and temporal expression kinetics. In contrast to A43, none of them interacts with 2B4. Consistent with this, molecular modeling of the N-terminal Ig domains of these vCD48s evidences notable changes as compared to CD48, suggesting that they interact with alternative targets. Accordingly, we demonstrate that one of them, S30, tightly binds CD2, a crucial T- and NK-cell adhesion and costimulatory molecule. Thus, our findings show how a key host immune receptor gene captured by a virus can be subsequently remodeled to evolve new immunoevasins with altered binding properties.

The divergent evolution of cytomegalovirus-encoded CD48 homologs contributes to the expansion of the immunevasin repertoire

Abstract The genesis of gene families by capture of host genes and their subsequent duplication is a crucial process in the evolution of large DNA viruses. CD48 is a GPI-linked cell surface protein containing two extracellular immunoglobulin (Ig) domains. Via its N-terminal Ig domain, CD48 interacts with the cell surface receptor 2B4, modulating leukocyte cytotoxicity. We previously reported the presence of five CD48 homologs (vCD48s) in two related cytomegaloviruses, derived from a common host CD48 ancestor gene acquired by retrotranscription. Recently, we examined one member of this family, A43, showing that it acts as a functional viral decoy receptor, impairing 2B4-mediated NK cell cytotoxicity. Here, we have characterized the rest of the vCD48s. We show that they are highly glycosylated type I transmembrane proteins which display remarkably distinct structures, biochemical properties, locations, and temporal kinetic classes. Molecular modeling of the N-terminal Ig domains of these vCD48s evidence significant changes in the number and length of their β-strands and inter-sheet loops that participate in the interaction of CD48 with 2B4, and accordingly we found that none of these molecules binds to 2B4. Interestingly, we determined that two of them, S30 and S31, have new targets in T or B lymphocytes. In particular, S30 tightly interacts with CD2, a T- and NK-cell adhesion and costimulatory molecule whose primary ligand is CD58. Thus, altogether our results show how a key host immune receptor captured by a virus can be subsequently remodeled during viral evolution to yield new molecules with shifted binding specificities to additional immune targets, expanding the repertoire of viral immunevasins.

Comparative Genomics of Amphibian-like Ranaviruses, Nucleocytoplasmic Large DNA Viruses of Poikilotherms.

Recent research on genome evolution of large DNA viruses has highlighted a number of incredibly dynamic processes that can facilitate rapid adaptation. The genomes of amphibian-like ranaviruses – double-stranded DNA viruses infecting amphibians, reptiles, and fish (family Iridoviridae) – were examined to assess variation in genome content and evolutionary processes. The viruses studied were closely related, but their genome content varied considerably, with 29 genes identified that were not present in all of the major clades. Twenty-one genes had evidence of recombination, while a virus isolated from a captive reptile appeared to be a mosaic of two divergent parents. Positive selection was also found to be acting on more than a quarter of Ranavirus genes and was found most frequently in the Spanish common midwife toad virus, which has had a severe impact on amphibian host communities. Efforts to resolve the root of this group by inclusion of an outgroup were inconclusive, but a set of core genes were identified, which recovered a well-supported species tree.

Analysis of the First Complete DNA Sequence of an Invertebrate Iridovirus: Coding Strategy of the Genome of Chilo Iridescent Virus

Chilo iridescent virus (CIV), the type species of the genus Iridovirus, a member of the Iridoviridae family, is highly pathogenic for a variety of insect larvae. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The coding capacity and strategy of the CIV genome was elucidated by the analysis of the complete DNA nucleotide sequence of the viral genome (212,482 bp) using cycle sequencing by primer walking technology. Both DNA strands were sequenced independently and the average redundancy for each nucleotide was found to be 1.85. The base composition of the viral genomic DNA sequence was found to be 71.37% A+T and 28.63% G+C. The CIV genome contains 468 open reading frames (ORFs). The size of the individual viral gene products ranges between 40 and 2432 amino acids. The analysis of the coding capacity of the CIV genome revealed that 50% (234 ORFs) of all identified ORFs were nonoverlapping. The comparison of the deduced amino acid sequences to entries in protein data banks led to the identification of several genes with significant homologies, such as the two major subunits of the DNA-dependent RNA polymerase, DNA polymerase, protein kinase, thymidine and thymidylate kinase, thymidylate synthase, ribonucleoside-diphosphate reductase, major capsid protein, and others. The highest homologies were detected between putative viral gene products of CIV and lymphocystis disease virus of fish (LCDV). Although many CIV putative gene products showed significant homologies to the corresponding viral proteins of LCDV, no colinearity was detected when the coding strategies of the CIV and LCDV-1 were compared to each other. An intriguing result was the detection of a viral peptide of 53 amino acid residues (ORF 160L) showing high homology (identity/similarity: 60.0%/30.0%) to sillucin, an antibiotic peptide encoded by Rhizomucor pusillus. Iridovirus homologs of cellular genes possess particular implications for the molecular evolution of large DNA viruses.

Iridovirus homologues of cellular genes--implications for the molecular evolution of large DNA viruses.

Iridoviruses belong to the group of large cytoplasmic deoxyriboviruses and infect either insects or vertebrates. In analogy to other large DNA viruses of eucaryotes it was found that iridoviruses encode a number of cellular protein homologues. The majority of these proteins represent orthologues of cellular enzymes involved in transcription, replication, and nucleotide metabolism. Others may have the potential to interfere with cell cycle regulation or immune defence mechanisms of the host. This raises the question about the phylogenetic origin of the corresponding viral genes. During the evolution of large cytoplasmic DNA viruses such as iridoviruses, poxviruses, and African swine fever virus the acquirement of cellular genes appears to be a crucial event. Each member of this group of viruses encodes a DNA polymerase, two subunits of the DNA-dependent RNA polymerase, and two subunits of the ribonucleotide reductase. It is important to note that all of these viral proteins show a high level of multidomain structure conservation as compared to their cellular orthologues. As a consequence the large cytoplasmic DNAviruses have the ability to replicate independently of the cellular nucleus in the cytoplasm of the infected cell. Assuming a common cellular origin of viral DNA polymerase genes the corresponding amino acid sequences were chosen to construct a phylogenetic tree showing the relatedness among large DNA viruses of eucaryotes.

Chilo iridescent virus encodes a putative helicase belonging to a distinct family within the “Dead/H” superfamily: Implications for the evolution of large DNA viruses

The complete nucleotide sequence of the EcoRI DNA fragment M (7099 bp; 0.310-0.345 map units) of the genome of insect iridescent virus type 6--Chilo iridescent virus (CIV)--was determined. A 606 codon open reading frame located in this region encoded a protein (p69) related to a distinct family of putative DNA and/or RNA helicases belonging to the "DEAD/H" superfamily. Unique sequence signatures were derived that allowed selective retrieval of the putative helicases of the new family from amino acid sequence databases. The family includes yeast, Drosophila, mammalian, and bacterial proteins involved in transcription regulation and in repair of damaged DNA. It is hypothesized that p69 of CIV may be a DNA or RNA helicase possibly involved in viral transcription. A distant relationship was observed to exist between this family of helicases and another group of proteins that consists of putative helicases of poxviruses, African swine fever virus, and yeast mitochondrial plasmids. It is shown that p69 of CIV is much more closely related to cellular helicases than any of the other known viral helicases. Phylogenetic analysis suggested an independent origin for the p69 gene and the genes encoding other viral helicases.