Complete DNA sequence of the rat cytomegalovirus genome

Abstract

We have determined the complete genome sequence of the Maastricht strain of rat cytomegalovirus (RCMV). The RCMV genome has a length of 229,896 bp and is arranged as a single unique sequence flanked by 504-bp terminal direct repeats. RCMV was found to have counterparts of all but one of the open reading frames (ORFs) that are conserved between murine CMV (MCMV) and human CMV (HCMV). Like HCMV, RCMV lacks homologs of the genes belonging to the MCMV m02 glycoprotein gene family. However, RCMV contains 15 ORFs with homology to members of the MCMV m145 glycoprotein gene family. Four ORFs are predicted to encode homologs of host proteins; R33 and R78 both putatively encode G protein-coupled receptors, whereas r144 and r131 encode homologs of major histocompatibility class I heavy chains and CC chemokines, respectively. An intriguing feature of the RCMV genome is the presence of an ORF, r127, with similarity to the rep gene of parvoviruses as well as ORF U94 of human herpesvirus 6A (HHV-6A) and HHV-6B. Counterparts of these ORFs have not been found in the other sequenced herpesviruses.

FIG. 1

Map of the 229,896-kb RCMV (Maastricht) genome. ORFs are shown as boxes. ORFs on the top strand (coding left to right) are shown above those on the bottom strand (coding right to left). The ORFs are numbered as described in the text and are defined as indicated in Table 1. Members of the five RCMV gene families, the m145, US22, UL25, UL82, and GPCR families, are indicated. The exons of RCMV ORFs that are either known or predicted to encode spliced transcripts, R89 (Y. K. Gruijthuijsen, C. A. Bruggeman, and C. Vink, unpublished data), R112, and R122-123 (3), are connected by lines.

FIG. 2

Alignment of the ORF maps of the genomes of RCMV, HCMV, and MCMV. The line above the HCMV map indicates the UL-US organization of the HCMV genome. For each genome map, the ORFs (boxes) on the top strand (coding left to right) are shown above those on the bottom strand (coding right to left). Boxes that represent ORFs that are conserved between HCMV, RCMV, and MCMV are depicted in light grey; boxes that represent ORFs that are conserved between only two of the three viruses are shown in dark grey. The numbers of most ORFs (without their prefixes) are indicated. ORFs that are conserved between RCMV and the other two CMVs are connected by blocks. The MCMV map is based on Rawlinson et al. (37), and the HCMV map is based on Chee et al. (11) and Cha et al. (9).

FIG. 3

Alignment of the amino acid sequences predicted to be encoded by RCMV r131 and MCMV m131/129. The alignment was carried out by using a CLUSTAL W Multiple Sequence Alignment Program (version 1.7; Human Genome Sequencing Center, Houston, Tex. [http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html]) (45). Blocks of identical (white letters in black boxes) and similar (white letters in grey boxes) residues were generated with program BOXSHADE (version 3.21; The EMBnet Foundation, The Netherlands [http://www.ch.embnet.org/software/BOX_form.html]), with the fraction of sequences that must agree for shading set to 1. Numbers to the left of the sequences indicate the positions of amino acid residues within the polypeptides. Cysteine residues that are conserved among CC chemokines are denoted above the sequence by the letter C. The part of the m131/129-derived amino acid sequence that is encoded by either ORF m131 or ORF m129 is also shown. The m131/129-encoded amino acid sequence was taken from MacDonald et al. (29).

FIG. 4

Alignment of the amino acid sequences predicted to be encoded by RCMV r127, GPV NS1, and HHV-6A U94. The alignment was carried out by using a CLUSTAL W Multiple Sequence Alignment Program (45). Numbers to the left of the sequences indicate the positions of amino acid residues within the polypeptides. Blocks of identical (white letters in black boxes) and similar (white letters in grey boxes) residues were generated with program BOXSHADE (version 3.21), with the fraction of sequences that must agree for shading set to 0.5. The sequence motifs depicted with A, B, B', and C represent strongly conserved putative NTP binding helicase regions (21, 26). The sequences encoded by GPV NS1 and HHV-6A U94 were from Zadori et al. (53) and Thomson et al. (46), respectively.