Human Cytomegalovirus Genome - Human Cytomegalovirus - page 1

Human Cytomegalovirus Genome

E. Murphy , T. Shenk ( ü )

Contents
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Genome Organization and cis -Acting Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Clinical Isolates and Laboratory Strains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Protein-Coding ORFs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Genomic Organization: Evolution and Function. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Perspectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Referencce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Abstract Human cytomegalovirus (HCMV) contains a large and complex E-type
genome. There are both clinical isolates of the virus that have been passaged
minimally in fibroblasts and so-called laboratory strains that have been extensively
passaged and adapted to growth in fibroblasts. The genomes of laboratory strains
have undergone rearrangements. To date, the genomes of five clinical isolates have
been sequenced. We have re-evaluated the coding content of clinical isolates by
identifying the set of open reading frames (ORFs) that are conserved in all five
sequenced clinical isolates. We have further determined which of these ORFs are
present in the chimpanzee cytomegalovirus (CCMV) genome. A total of 173 ORFs
are present in all HCMV genomes and the CCMV genome, and we conclude that
these ORFs are very likely to be functional. An additional 59 ORFs are present in
the genomes of all five HCMV isolates, but not in CCMV. We have discounted 26
of this latter set of ORFs, because they reside in regions of the genome unlikely to
encode functional ORFs. The remaining 33 ORFs are potentially functional ORFs
that are specific to HCMV.

T. Shenk
Department of Molecular Biology , Princeton University , Princeton , NJ 08544-1014 , USA
[e-mail]