The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome FN1

Abstract

The gene complement of wild-type human cytomegalovirus (HCMV) is incompletely understood, on account of the size and complexity of the viral genome and because laboratory strains have undergone deletions and rearrangements during adaptation to growth in culture. We have determined the sequence (241 087 bp) of chimpanzee cytomegalovirus (CCMV) and have compared it with published HCMV sequences from the laboratory strains AD169 and Toledo, with the aim of clarifying the gene content of wild-type HCMV. The HCMV and CCMV genomes are moderately diverged and essentially collinear. On the basis of conservation of potential proteincoding regions and other sequence features, we have discounted 51 previously proposed HCMV ORFs, modified the interpretations for 24 (including assignments of multiple exons) and proposed ten novel genes. Several errors were detected in the published HCMV sequences. We presently recognize 165 genes in CCMV and 145 in AD169; this compares with an estimate of 189 unique genes for AD169 made in 1990. Our best estimate for the complement of wild-type HCMV is 164 to 167 genes. INTRODUCTIONHuman cytomegalovirus (HCMV; human herpesvirus 5) is ubiquitous and largely inapparent, but poses a risk of serious disease to those lacking a competent immune system, such as neonates, transplant patients and sufferers from AIDS (reviewed in Pass, 2001). HCMV is the prototype of subfamily Betaherpesvirinae, and is the most complex of the eight human herpesvirus species. HCMV is isolated routinely on human fibroblast cell lines, and several strains in common laboratory use, such as AD169 and Towne, were derived by multiple passages on such cells (reviewed in Mocarski & Tan Courcelle, 2001).The linear, double-stranded DNA genome of AD169 comprises two covalently linked segments (L and S), each consisting of a unique region (U L and U S ) flanked by an inverted repeat (TR L and IR L , TR S and IR S ), yielding the overall genome configuration TR L -U L -IR L -IR S -U S -TR S (reviewed in Mocarski & Tan Courcelle, 2001). In addition, the genome is terminally redundant, possessing a short region (the a sequence) as a direct repeat at the termini and also in inverse orientation at the IR L -IR S junction. Some genomes contain tandemly reiterated copies of the a sequence at these locations. U L and U S can invert relative to each other by recombination between inverted repeats in replicating DNA, resulting in four equimolar genome arrangements in virion DNA. The complete DNA sequence of AD169 was published in a seminal paper by Chee et al. (1990), and at that time was the largest viral genome sequence available. The total genome size was 229 354 bp, with U L being 166 972 bp, U S 35 418 bp, R L (a collective term for TR L and IR L ) 11 247 bp, R S (TR S and IR S ) 2524 bp and the a sequence (part of R L and R S in the sizes given above) 578 bp.As a primary criterion for identifying protein-coding regions, Chee et al. (1990) focused on open reading frames (ORFs) of 100 or more contiguous amino acidencoding codons that ov...

Human Cytomegalovirus Encodes an MHC Class I-Like Molecule (UL142) That Functions to Inhibit NK Cell Lysis

“…We predicted HCMV gpUL142 to be an MHC class I-related molecule using a bioinformatics tool (3D-PSSM). This structural homology was also independently predicted by sequence alignment of UL142 with HCMV UL18, human MHC class I and chimpanzee CMV (18), providing independent confirmation of our suggested class I-like secondary structure for UL142. It is clear from experiments using polyclonal NK cell lines, either by knockdown or over expression, that UL142 is able to inhibit NK function.…”

“…We also analyzed the UL142 ORF using an alternative method Pfam (͗http://pfam.wustl.edu/͘) which, again, predicted that UL142 had MHC class I-related domains. Independently, a comparison of the chimpanzee CMV genome with HCMV had identified UL142 as containing an MHC class I-like domain (18). UL142 is predicted to have an N-terminal signal peptide with a cleavage site between aa 19 -20 and also to encode an ␣1 and disulphide bonded ␣2 domain.…”

“…It has been recognized since 1996 that clinical isolates of the virus have a larger genome: comparison of the AD169 and Toledo genomes shows a 13.5-kb insert (ULbЈ) in Toledo, which is absent from AD169 and codes for a putative 20 ORFs (17). This ULbЈ region has recently been reanalyzed and some of the genes in this region reassigned (18). It thus seemed likely that genes encoded in the ULbЈ region might be responsible for rendering infected fibroblasts resistant to lysis by NK cells, and we consequently sought to characterize these genes.…”

Structural and Functional Dissection of the Human Cytomegalovirus Immune Evasion Protein US6

“…In order to further evaluate the sequence requirements for TAP inhibition and binding by HCMV US6, we characterized the CCMV homologue of US6 (10). CCMV US6 shares 35.2% sequence identity with HCMV US6, and like its HCMV orthologue, it is predicted to be a type I integral membrane protein with an N-terminal signal sequence (Fig.…”

A história da disseminação dos microrganismos

“…that ancestral animal common to both man and the chimpanzee carried a herpes virus that it passed on to the chimp line as well as the human, with modern chimpanzees presenting strains of labial and genital herpes genetically very similar to our own (Lacoste et al, 2005;Luebeke et al, 2006;davison et al, 2003).…”