Biology Reference
In-Depth Information
The utility of the isomerization of the HCMV and CCMV genomes is not yet
understood. Herpes simplex virus type 1 (HSV-1) mutants that are frozen in indi-
vidual isomeric orientations replicate perfectly well (Poffenberger et al. 1983;
Jenkins and Roizman 1986). Consequently, there is no evidence for a functional
consequence of the isomerization, although it remains possible that the multiple
isomers are useful in cell types that have not yet been investigated or within
infected hosts. It is conceivable that the inverted repeats provide a convenient
mechanism for the genome to be segmented by recombination and then maintained
in two segments under certain conditions.
Cytomegalovirus genomes contain
cis
-acting elements that direct DNA replica-
tion, packaging and transcription. In HCMV the replication origin, ori
Lyt
, has been
mapped to an approximately 1500-bp domain (Anders et al. 1992; Masse et al.
1992; Borst and Messerle 2005) located near the middle of the U
L
domain. The core
of ori
Lyt
includes various repeated elements, transcription factor binding sites and
sites at which RNA-DNA structures form (see the chapter by G.S. Pari, this vol-
ume). It is possible that a second specific origin functions to initiate replication of
the viral genome within latently infected cells, where the HCMV genome is thought
to persist as an episome (Bolovan-Fritts et al. 1999). As yet, however, a latency ori-
gin has not been identified. It is possible that the cellular DNA replication machin-
ery initiates randomly on latent genomes or that the viral genome is not replicated
during latency (see the chapter by M. Reeves and J. Sinclair, this volume). The
a
regions of HCMV are comprised of multiple head-to-tail repeats of
a
sequences
(Tamashiro and Spector 1986), which include two
cis
-acting packaging elements,
pac1
and
pac2
(Kemble and Mocarski 1989). The number of
a
repeats can vary
among strains and among different passages of the same strain due to amplifica-
tions and deletions. These relatively short sequences with AT-rich cores flanked by
GC-rich sequences are recognized by the viral DNA cleavage and encapsidation
machinery (Bogner et al. 1998; W. Gibson, this volume). Cleavage of the sequences
adjacent to the
pac
1 and
pac
2 sequences leaves a single 3′ base overhang which, as
noted above, is utilized for circularization of the linear viral genome upon entry. A
variety of transcriptional control regions have been characterized on the HCMV
genome, most notably the large and complex major immediate-early promoter/
enhancer. It is located within the U
L
domain, and it plays a pivotal role in the regula-
tion of viral gene expression at the start of infection (see the chapter by M.F. Stinski
and D.T. Petrik, this volume).
Clinical Isolates and Laboratory Strains
Five different HCMVs that are generally referred to as clinical isolates have been
sequenced. Four of these viruses were passaged to a limited, but not precisely
defined, extent in fibroblasts before they were cloned as bacterial artificial chro-
mosomes (BACs) and then sequenced (FIX, TR, PH and Toledo; Murphy et al.
2003b). Toledo has suffered an inversion event that likely enhanced its growth in
