Patterns of divergence in the vCXCL and vGPCR gene clusters in primate cytomegalovirus genomes

Abstract

Primate cytomegalovirus (CMV) genomes contain tandemly repeated gene clusters putatively encoding divergent CXC chemokine ligand-like proteins (vCXCLs) and G protein-coupled receptor-like proteins (vGPCRs). In human, chimpanzee and rhesus CMVs, respectively, the vCXCL cluster contains two, three and six genes, and the vGPCR cluster contains two, two and five genes. We report that (i) green monkey CMV strains fall into two groups, containing either eight and five genes or seven and six genes in the respective clusters, and (ii) owl monkey CMV has two and zero genes. Phylogenetic analysis suggested that the vCXCL cluster evolved from a CXCL chemokine gene (probably GRO-alpha) that was captured in an incompletely spliced form by an ancestor of Old and New World primate CMVs, and that the vGPCR cluster evolved from a GPCR gene captured by an Old World primate CMV. Both clusters appear to have evolved via complex duplication and deletion events.

Figure 1. Organization of tandem-repeat vCXCL and vGPCR gene clusters in primate CMV genomes

The genes are represented as transcribed from left to right. Panels (a) and (b) show schematic representations of the vCXCL and vGPCR clusters, respectively. Genes in grey font are absent from certain GMCMV genomes; vCXCL1B is absent from group II and vGPCR3A is absent from group I. Proposed orthologous relationships are shown for the GMCMV/RhCMV and CCMV/HCMV pairs, but otherwise the numbers used do not imply orthology. The grey shading indicates that the GMCMV and RhCMV vCXCL4 genes are spliced, and the blank box indicates the absence of one of the paralogous genes even within unrearranged, wild type genomes. OMCMV lacks the entire vGPCR cluster. The available data indicate that the gene arrangements in BaCMV are the same as in RhCMV. Panel (c) shows a scale diagram of the vCXCL and vGPCR clusters in GMCMV(2715) (group I) and GMCMV(4915) (group II), respectively, which have the full complement of genes in these regions. vCXCL and vGPCR coding regions are shaded grey and flanking coding regions are shaded white. In the vCXCL cluster, the white bar denotes an intron and the black bar a vestigial vCXCL coding region.

Figure 2. Sequence alignment comparisons among primate CMV vCXCL proteins

The alignment shows predicted primary translation products encoded by the primate CMV vCXCL cluster, plus human GRO-α (CXCL1). Dots indicate gapping characters. The four conserved C residues are shaded, as are residues conserved between human GRO-α and vCXCL3A/vCXCL3B/vCXCL3/vCXCL4 in GMCMV, BaCMV and RhCMV. Bold characters in human GRO-α and GMCMV, BaCMV and RhCMV vCXCL4 correspond to the codons in which exon boundaries are located.

Figure 2. Sequence alignment comparisons among primate CMV vCXCL proteins

The alignment shows predicted primary translation products encoded by the primate CMV vCXCL cluster, plus human GRO-α (CXCL1). Dots indicate gapping characters. The four conserved C residues are shaded, as are residues conserved between human GRO-α and vCXCL3A/vCXCL3B/vCXCL3/vCXCL4 in GMCMV, BaCMV and RhCMV. Bold characters in human GRO-α and GMCMV, BaCMV and RhCMV vCXCL4 correspond to the codons in which exon boundaries are located.

Figure 3. Phylogenetic grouping of primate CMV vCXCL proteins

Bayesian phylogenetic tree of proteins encoded by the primate CMV vCXCL cluster, rooted at the midpoint. Nodes supported by at least 95% of trees are indicated. The tree includes all recognized versions of HCMV vCXCL1 (G1–G14) and vCXCL3 (as accession numbers), plus primate versions of GRO-α (CXCL1).

Figure 4. Sequence alignment comparisons among primate CMV vGPCR proteins

The alignment shows predicted primary translation products encoded by the primate CMV vGPCR cluster, plus those from the primate CMV UL33 and UL78 GPCRs. For GMCMV and RhCMV, only sequences from GMCMV(4915) and RhCMV(22659) are included. The functionally important [DE]RY motif is in bold type. Dots indicate gapping characters, and highly conserved residues are shaded. Arrowheads indicate N- or C-terminal extensions (not shown) in certain proteins. The seven predicted TMDs in GMCMV vGPCR1 (as an example) are indicated by dashes above the alignment.

Figure 5. Phylogenetic grouping of primate CMV vGPCR proteins

Bayesian phylogenetic tree of proteins encoded by the primate CMV vGPCR cluster, rooted at the midpoint. Nodes supported by at least 95% of trees are indicated. The tree includes primate CMV versions of vGPCRs encoded by genes UL33 and UL78.

Figure 6. Vestigial genes provide evidence for recent deletion events in the GMCMV vCXCL and vGPCR gene clusters

Both parts show an alignment of the relevant DNA sequences of GMCMV(2715) and GMCMV(4915), which belong to groups I and II, respectively. The alignment for the vCXCL cluster proceeds from the end of the UL145 coding region, through a vestigial vCXCL, the inititation and then the termination codon of vCXCL1A, and the initiation and termination codon of vCXCL1B. Repeated sequences that are largely conserved at the 5’-end of vCXCL1A and in the vestigial vCXCL are underlined, and those conserved at the initiation and termination codons of vCXCL1A and vCXCL1B are underlined in bold. The alignment for the vGPCR cluster proceeds from the end of vGPCR2, through the initiation and then the termination codon for vGPCR3A, to the initiation codon for vGPCR3B. The vestigial vGPCR sequence is underlined. In both alignments, tildes indicate coding sequences (lengths in bp) that are not shown, and dots indicate gapping characters.

Figure 7. Phylogenetic grouping of complete primate CMV DNA polymerase proteins

The ClustalW-based tree is rooted with TSCMV as the outgroup. Bootstrap values were 100% at each node.