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STRUCTURE OF HUMAN CYTOMEGALOVIRUS 71
TABLE I
Location of the Four Major Components of the HSV Capsid Shell and Comparison to the HCMV Homologues
(Gibson, 1996)
HSV-1 HCMV
Copy
Location in capsid number Gene Gene product Gene Gene product
Hexons and pentons 960 UL19 VP5 (149 kDa) UL86 Major capsid protein (154 kDa)
Triplexes 640 UL18 VP23 (34 kDa) UL85 Minor capsid protein (35 kDa)
Triplexes 320 UL38 VP19c (50 kDa) UL46 Minor capsid protein-binding protein (33 kDa)
Hexon tips 900 UL35 VP26 (12 kDa) UL48/49 Smallest capsid protein (8.5 kDa)
difference imaging (Trus et al., 1995; Zhou et al., only limited amino acid homology, but both are small
1988b, 1995) and antibody labeling (Trus et al., 1992) proteins with a basic pI (Baldick and Shenk, 1996;
and are shown in Table I. Herpesvirus capsid assem- Gibson et al., 1996b).
bly and viral DNA packaging takes place in the We report differences between the HCMV and
nucleus of infected cells and is dependent on the HSV-1 capsid shell structures that are relevant to
virus scaffolding proteins [e.g., the product of HSV-1 the observation that the HCMV capsid structure
genes UL26 and UL26.5: and HCMV genes UL80 accommodates a DNA molecule up to 60% larger (at
and UL80.5 (Desai et al., 1994; Preston et al., 1992; 245 kb) (Cha et al., 1996; Chee et al., 1990; Dargan et
Tatman et al., 1994; Welch et al., 1991a,b)]. Three al., 1997) than that of the HSV-1 genome (152 kb)
types of capsid structure are generated: A, which are (McGeoch et al., 1988).
devoid of any core structure; B, which contain a
scaffold structure but lack viral DNA; and C, which MATERIALS AND METHODS
are mature DNA-containing structures (Gibson and
Cells
Roizman, 1972). The B-capsid structures are the
most abundant in the infected cell nucleus and most Human fetal foreskin fibroblast cells (HFFF-2; European Collec-
easily isolated. tion of Animal Cell Cultures, No. 86031405) were propagated in
Dulbecco’s modified Eagle’s medium containing 10% fetal bovine
This paper extends the investigation of capsid serum (DMEM 10% FB).
shell architecture to the b-herpesvirus subfamily.
Using electron cryomicroscopy and image reconstruc- Virus Propagation
tion, we have examined and compared the B-capsid The AD169 (Glasgow) stock of HCMV (Dargan et al., 1997) was
shell structures of two important human pathogens: used throughout. Virus-infected cell preparations were produced
human cytomegalovirus (HCMV), the prototype vi- by infecting HFFF-2 cell monolayers (4 3 106 cells) with HCMV at
rus of the b-herpesvirus subfamily, and HSV-1, the a multiplicity of infection of 0.01 PFU/cell and, when extensive
prototype virus of the a-herpesvirus subfamily. The cytopathic effect was evident, seeding virus-infected cells (,105
cells) onto subconfluent monolayers of HFFF-2 cells in roller
HCMV capsid shell proteins are compared with bottles (,2 3 107 cells/bottle) and incubating at 37°C. At 24 h
those of HSV-1 in Table I. The HSV-1 and HCMV postinfection (PI) the culture medium was replaced with fresh
major capsid proteins (MCPs) are of similar molecu- DMEM 10% FB and the infected cultures were incubated again at
lar size and their respective genes share 25% nucleo- 37°C. Cytopathic effect was usually apparent by the fifth day PI
tide and 26% amino acid homology (Chee et al., and was extensive by the ninth day. The infected cells were
detached from the surface of the roller bottle by gentle shaking
1989). The HSV-1 triplex structures are composed of and then pelleted by centrifugation at 1000g.
two proteins, VP23 (gene UL18) and VP19c (gene
UL38), in the ratio of 2:1. Similarly, the HCMV Capsid Preparation
triplex structures are composed of the minor capsid
Nuclei were isolated from the infected cell pellets by washing
protein-binding protein (mC-BP, gene UL46) and the the cells with NTE buffer (0.5 M NaCl, 20 mM Tris, pH 7.4, 1 mM
minor capsid protein (mCP, gene UL85), also in the EDTA) containing 1% Nonidet P-40. (NP40). The resulting nuclei
ratio of 2:1. However, while the HCMV mCP shares were pooled and stored at 270°C until required. The nuclei were
22.5% amino acid homology with HSV-1 UL18, the resuspended in NTE containing 1% NP40 and subjected to three
cycles of freeze–thawing. This suspension was then probe soni-
HCMV mC-BP protein is only two-thirds of the size cated to break residual nuclei open and the cellular debris
of its HSV-1 functional homologue and shares no pelleted at 1000g. The virus particles present in the supernatant
appreciable amino acid homology (Gibson et al., were pelleted through a 40% (w/v in NTE) sucrose cushion
1996a). The small HSV-1 protein, VP26, located at (Sorvall TST41, 25 000 rpm, 1 h, 4°C), resuspended in 1% NP40 in
the tip of the hexons is not required for capsid shell NTE, and banded on a 10–40% sucrose gradient in NTE (Sorvall
TST41, 40 000 rpm, 20 min, 4°C). The B-capsid band was har-
assembly (Tatman et al., 1994). HSV-1 VP26 and its vested, pelleted (Sorvall TST41, 25 000 rpm, 1 h, 4°C), and
HCMV counterpart, the ‘‘smallest capsid protein’’ resuspended in 0.15 M NaCl, 20 mM Tris, pH 7.4, 1 mM EDTA.
(SCP, reported as gene UL48.5, or UL48/49), have HSV capsids were purified from baby hamster kidney cells
72 BUTCHER ET AL.
infected for 16 h at 37°C with 5 PFU HSV-1 (strain 17) per cell, as
described previously (Zhou et al., 1994).
Electron Cryomicroscopy
Electron cryomicroscopy allows us to examine samples under
native, hydrated conditions free from some of the artifacts that
are commonly associated with negatively stained specimens, as
well as reveal internal details. Freshly prepared capsids were
vitrified on holey carbon coated grids by plunge freezing into
liquid ethane (Adrian et al., 1984; Fukami and Adachi, 1965).
Samples were held at less than 2170°C in an Oxford CT3500
cryostage and observed using low-dose techniques in a Jeol
JEM-1200 EX II electron microscope (120 kV, tungsten filament)
fitted with an Oxford TAC100 twin-blade anticontaminator. Focal
pairs were recorded on Kodak SO163 film using a dose of 10–15
e/Å2 at a nominal magnification of 25 000 or 30 000 at defocus
values between 3 and 4 µm. FIG. 1. Electron cryomicrograph of B capsids from HCMV.
Image Processing than those for HSV1 (see Results). The data from the Jeol
Selected micrographs were scanned on a Zeiss-SCAI scanner micrographs were then scaled accordingly. In addition the scaling
using a step size of 14 µm per pixel, corresponding to 0.58 nm per of the HSV-1 reconstruction was checked against that of a 1.9-nm
pixel (14/24 100) and 0.48 nm per pixel (14/29 000) on the speci- HSV-1 reconstruction kindly provided by Dr. Hong Zhou (Zhou et
men. Image quality was assessed and the defocus estimated by al., 1995).
evaluating the position of the first zero in the sum of power
spectra from the particles of each micrograph. In total six RESULTS
micrographs were scanned from which 144 particles were se-
lected, boxed, floated, and normalized using SPIDER (Frank et al., Electron Cryomicroscopy and Image Reconstruction
1981). Orientations and centers were determined and refined
We have studied the structure of the HCMV capsid
using the common lines procedure (Crowther, 1971; Fuller et al.,
1996). The polar Fourier transform method was used to check the by electron cryomicroscopy and image processing.
accuracy of the model, further refinement, and orientation searches Figure 1 shows part of an electron micrograph of
for new data (Baker and Cheng, 1996). Three-dimensional recon- vitrified HCMV B capsids. The capsids have a diam-
structions were calculated using cylindrical expansion methods eter of approximately 130 nm. This can also be seen
(Crowther, 1971). Only particles with icosahedral phase residuals
below 75° at 3.5-nm resolution were included in the reconstructions.
from the radial density profile (Fig. 2). The capso-
The map of HCMV was calculated to 3.5-nm resolution from a meres covering the surface of each capsid are clearly
subset of 59 particles from four micrographs (taken at 3 µm under evident as projections at the edge of the particle and
focus). All the eigenvalues were greater than 10 and 97% were as regularly spaced dots across the surface (,15 nm
greater than 100, showing that reciprocal space was adequately in diameter). In addition the scaffold can be seen as a
sampled. Independent reconstructions calculated from subsets of
the data were consistent with all the features described below. For
dense area, roughly in the center of each particle.
comparison, a micrograph of HSV-1 B capsids (taken at 3 µm The HCMV capsids were difficult to fully dissoci-
under focus) was also processed in a similar fashion. Here, 38 of 43 ate from the nuclear matrix without breakage, and
particles were included in the reconstruction that was also could not be stored at 270, 220, or 4°C without
calculated to 3.5-nm resolution. For this reconstruction, all of the further breakage occurring. Consequently, only rela-
eigenvalues were greater than 1 and 87% were greater than 100,
reflecting the lower number of particles included in the reconstruc- tively few particles from each field could be used
tion. Visualization and rendering of the reconstructions were done (typically 30 particles were processed per micro-
in SPIDER. All of the programs were run on a Digital Alpha 255/233
AXP running Digital Unix OSF1 v3.2, an SGI Indigo Elan 4000
running IRIX 5.2, and a Digital Alpha 2100 running Open VMS 7.0.
To address the scaling of the micrographs, additional data were
collected on a CM200 FEG microscope at 200 kV, using prepara-
tions mixed with tomato bushy stunt virus [TBSV, 38.5 nm in
diameter in the presence of 1 mM EDTA, pH 7.4 (Robinson and
Harrison, 1982)] to act as an internal standard. These data (taken
at defocus values of 5605 and 6120 nm for HSV-1 and 5200, 5605,
and 5610 nm for HCMV, at a magnification of 319 400, and
scanned with a 7-µm step size) could be corrected for the micro-
scope contrast transfer function due to the presence of several
minima in the power spectra, unlike the original data collected on
the Jeol 1200EX with a tungsten filament. For each micrograph,
at least 90 TBSV particles were aligned and a radial profile made
of the average to check the magnification. The HSV1 data (134
particles) and the HCMV data (70 particles) were averaged FIG. 2. Graph showing the radial density distribution of B
separately and gave rise to radial profiles similar to those shown capsids from HCMV (solid line) and HSV-1 (broken line) calcu-
in Fig. 2, where the shell peaks for HCMV are at a larger radius lated from the reconstructions shown in Fig. 3.
STRUCTURE OF HUMAN CYTOMEGALOVIRUS 73
FIG. 3. Comparison of HCMV and HSV-1 reconstructions. Surface representations of HCMV (A) and HSV-1 (B) viewed down an
icosahedral twofold axis of symmetry contoured at one standard deviation above the mean density value. The inset shows the positions of
hexamers (white dots) and pentamers (green dots) within 1 facet of a T 5 16 lattice, in an orientation similar to that of the reconstructions.
Central 0.58-nm-thick sections through the HCMV (C) and the HSV-1 (D) reconstructions. Bar 5 50 nm.
graph), so data from several micrographs were com- organized on a T 5 16 icosahedral lattice (Fig. 3A).
bined to yield the final reconstruction. There was The relative positions of the capsomers (hexamers
also a high rejection rate during the common lines and pentamers) within a facet are shown in the top
refinement as up to 60% of the particles per micro- inset of Fig. 3.
graph gave icosahedral phase residuals greater than
75°, even at 3.5-nm resolution, and were therefore Capsomers
excluded from the reconstruction. The HCMV hexons and pentons form cylindrical
protrusions (Figs. 3A, 3C, 4) penetrated by an axial
Three-Dimensional Structure channel constricted 7.4 nm from the base of the
The major structural components of the HCMV B capsomer. The hexons appear slightly skewed, so
capsid are 150 hexons, 12 pentons, and 320 triplexes that the axial channel is oval rather than round. The
74 BUTCHER ET AL.
The HCMV capsid is made up of hexamers and smaller channel catfish virus were reported to have
pentamers arranged on a T 5 16 lattice. By analogy similar genome packing densities (Booy et al., 1996).
with HSV-1, we expect that the major capsid protein Alternatively HSV-1 may underutilize its packaging
(MCP) forms the major part of these structures and capacity like bacteriophage l, which can package
that the smallest capsid protein (SCP) forms the tips DNA 9% larger than its genome without affecting
of the hexons. The minor capsid protein (mCP) and viability (Weil et al., 1972). A third possibility is that
the mCP-binding protein (mC-BP), which associate an expansion of the HCMV capsid is associated with
together in a ratio of 2:1, are analogous to the triplex DNA packaging. B capsids from simian CMV have
proteins of HSV-1 and probably form the equivalent been estimated to have a diameter 7% smaller than
structures seen in the HCMV reconstruction at the that of A capsids when examined in thin sections of
positions of local threefold symmetry (Fig. 4). infected cell nuclei (Lee et al., 1988). Studies of the
One of the motivating questions for performing DNA-containing capsid are required to address these
this study was: How does the capsid of HCMV issues in more detail. We have endeavored to isolate
package a genome that is 60% larger than that of such capsids from both virions and infected cells, but
HSV-1? There is, as predicted from a comparative invariably ended up with damaged, empty capsids.
study between HSV-1 and channel catfish virus This implies that HCMV is more fragile than HSV-1.
(Booy et al., 1996), no change in the T number of the In conclusion, this preliminary study of HCMV
capsid to accommodate the larger genome; however, emphasizes the similarities between evolutionary
there is an increase in the capsid volume. The distinct herpesviruses. It also supports the idea that
internal radius of the capsid was estimated using the although the three-dimensional structures of the
peak from the radial density plot which corresponds capsid proteins are similar at the gross level, we can
to the floor of the shell (HCMV, 50 nm; HSV-1, 47.5 expect changes in the interactions between mono-
nm) because the edge of the shell density is harder to mers at the atomic level, giving rise to differences in
estimate. Assuming a sphere, this gives a volume spacing between capsomers.
ratio of 1.17 for HCMV compared with HSV-1. This is Dr. Hong Zhou is thanked for providing a reconstruction of
much smaller than the ratio of the genome lengths HSV-1 B capsids. Dr. Frazer Rixon is thanked for helpful discus-
(1.51) of the two virus strains used in this study sions. Dr. Stephen Fuller kindly provided his programs, as did
[HCMV AD169, 230 kb (Dargan et al., 1997); HSV-1 Felix deHaas and Ralph Heinkel. Ilaria Ferlenghi and Erica
Mancini are thanked for help with scanning of the micrographs.
strain 17, 152 kb (McGeoch et al., 1988)]. Interest- This work was funded by the U.K. Medical Research Council.
ingly, HCMV assembles this larger shell with pro-
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