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Journal of Virology, December 2003, p. 13036-13041, Vol. 77, No. 24
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.24.13036-13041.2003
Copyright © 2003, American
Society for
Microbiology. All Rights Reserved.
Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 2QH,1 Veterinary Sciences Division, Department of Agriculture and Rural Development for Northern Ireland, Stormont, Belfast BT4 3SD, United Kingdom2
Received 30 June 2003/ Accepted 4 September 2003
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CAV causes disease in young chickens which is characterized by anemia, lymphoid depletion, and hemorrhaging, with associated increased mortality. The capsid of CAV consists of a single type of protein VP1, which encapsidates a negative-strand genome of about 2,300 bases (19). VP1, which has a molecular mass of 50 kDa, has an extremely basic N-terminal region of about 50 amino acids that is likely to interact with the packaged DNA. The C-terminal region of the protein carries motifs associated with rolling circle replication (RCR) of DNA (10), suggesting that VP1 has both structural and functional roles.
The first identified PCV, now known as PCV type 1 (PCV-1), was isolated as a contaminant of cultured pig kidney cells (17) but was later found to be widespread, although it apparently caused no symptoms in pigs. More recently, a clear disease association was demonstrated between a second PCV (PCV-2) and an economically important disease of pigs known as postweaning multisystemic wasting syndrome (4). The capsid of PCV-2 consists of a single type of protein, encoded by open reading frame 2 (ORF2), which encapsidates an ambisense genome of approximately 1,767 bases. The ORF2-encoded capsid proteins of PCV-1 and PCV-2 are 66% identical (12). Like VP1 of CAV, the ORF2-encoded capsid protein has a very basic N-terminal region expected to interact with the packaged DNA; however, with a molecular mass of only 28 kDa, it lacks a region containing RCR motifs. Instead, the replication function in PCVs is carried out by a separate protein. BFDV has a genomic organization similar to that of PCVs, and the ORF2-encoded capsid protein of BFDV shows 26% identity to that of PCV-2, as determined by use of published sequence alignments (2, 12).
The present study was undertaken to analyze the detailed structures of these recently characterized viruses and to determine their morphological relationships. An earlier study of negatively stained preparations of the three viruses showed CAV to have a larger diameter (19.1 to 26.5 nm) than PCV-1 (16.8 to 20.7 nm) or BFDV (14 to 20.7 nm) (20). CAV also has a more distinctive surface morphology, which was interpreted visually to indicate a T=3 surface lattice with 32 hexamer-pentamer clustered morphological units (8, 11). Here we calculated three-dimensional maps from unstained cryopreserved specimens of CAV and PCV-2 and from a negatively stained specimen of BFDV. We showed that all three viruses have an icosahedral T=1 structure containing 60 capsid protein molecules arranged in 12 pentamer clustered units. Whereas PCV-2 and BFDV have very similar appearances with relatively flat capsomeres, in CAV each capsomere has a very striking pentagonal trumpet-shaped appearance. The results indicate that viruses in the genera Gyrovirus and Circovirus are not structurally related.
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The 1010 isolate of PCV-2 was grown in a continuous porcine kidney cell line (PK/15) (1, 18). The virus was initially purified by lysis of the cells with Triton X-114 and differential centrifugation as described previously (21). Following sucrose density gradient centrifugation, peak virus-containing fractions were identified by an antigen capture enzyme-linked immunosorbent assay and then dialyzed in 0.01 M phosphate-buffered saline (pH 7.2) prior to storage at -80°C until required for electron microscopic studies.
Cryomicroscopy. The virus samples had a particle concentration of about 109 per ml, which is adequate for conventional negative staining, where the particles are allowed to adsorb to a carbon support. However, cryomicroscopic methods mostly use "in-solution" imaging, where concentrations 1 or 2 orders of magnitude higher are required. Different methods of concentrating the specimens were attempted. High-speed centrifugation resulted in a loss through aggregation in a pellet that could not be resuspended; a 100-kDa-cutoff Microcon concentrator adsorbed the particles even after preblocking with bovine serum albumin (BSA). It was possible to concentrate CAV with a collodion thimble, although contaminating protein was concentrated with the virus.
For CAV, 4-µl samples were applied to air glow-discharged holey carbon films, blotted with Whatman no. 1 filter paper, and frozen in liquid ethane. PCV-2 was applied to holey carbon films with thin carbon across the holes. This method allowed adsorption, as with negative staining, and most of the water was blotted away before freezing. This procedure left virus particles embedded in amorphous ice over thin carbon films supported by the thicker carbon of the holey grid. Low-dose (about 1,000 electrons/nm2) images of CAV were taken with an FEI Tecnai F30 FEG microscope operating at 300 kV in the defocus range of 2.5 to 3.5 µm. Images of PCV-2 were taken with an FEI Tecnai T12 microscope operating at 120 kV in the defocus range of 1 to 4 µm. The grids were kept at liquid nitrogen temperature with side-entry Gatan 626 cold stages. Kodak SO163 film was developed in D19.
Electron microscopic images of negatively stained preparations of mixed CAV and BFDV particles were prepared as described previously (20).
Image processing. Micrographs (magnification, x39,000) of CAV were scanned at a sampling of 7 µm on a Z/I SCAI film scanner and then binned to 14 µm, giving a sampling of 0.359 nm/pixel for the specimen. Micrographs (magnification, x52,000) of PCV-2 were treated similarly, giving a sampling of 0.269 nm/pixel for the specimen. In each case, particles were selected manually by using Ximdisp (6) and then boxed, floated, and scaled to a common mean and standard deviation. Initial orientations and origins were found by self-common lines with icosahedral symmetry (5). Once a preliminary three-dimensional map was available, all further processing was carried out by using cross-common lines against a computed set of projections from the present best three-dimensional map (7). The maps were improved iteratively by these methods.
For CAV images taken with the F30 microscope, there were sufficient particles per micrograph to compute maps uncorrected for defocus to a high resolution for each micrograph. Preliminary estimates of the defocus of each micrograph were made from the positions of the rings of intensity in the incoherent sum of transforms from all of the particles on a particular micrograph. Using these preliminary estimates, maps with different defocus values could be combined to make an initial corrected map (3). Defocus values were then refined by calculating Fourier shell correlations between an uncorrected map from a particular micrograph and the corrected map calculated from all the other micrographs, excluding the particular one under consideration. The resolution of the final map was estimated by computing Fourier shell correlations between defocus-corrected maps computed from two half data sets. The absolute handednessof the CAV structure was determined with previously described computer programs (16) by comparing particle orientations in two images of the same area of specimen, one untilted and the other with the specimen tilted by 10° in a known direction.
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FIG. 1. Micrographs
of various circoviruses. (A) Cryomicrograph of CAV.
(B) Cryomicrograph of PCV-2. (C) Micrograph of a
negatively stained preparation of a mixture of CAV and BFDV. The
larger, rough particles are CAV, and the smaller, smoother particles
are BFDV. Scale bar, 50
nm.
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FIG. 2. Fourier
shell correlations. (A) Fourier shell correlation between a
map not corrected for defocus and a map combining data from 10 other
micrographs corrected for defocus (solid line). The computed
phase-contrast transfer function (broken line) for the appropriate
level of defocus of the uncorrected map, in this case, 3,500 nm, was
calculated on the assumption of 5% amplitude contrast. Note the
good agreement between the zero-crossing positions. (B)
Fourier shell correlation between maps computed from two half data
sets, showing good agreement out to spacings of about 1.2
nm.
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FIG. 3. Determination
of the absolute handedness of CAV. Average phase residuals for 45
particle images recorded at a tilt of 10° were determined by
using the three-dimensional model (see Fig.
4A) and tilt-transformed
orientation parameters of the corresponding untilted particle images.
The contours show phase residuals for tilt transformations up to
15° along the x and y axes. At any point in
the plot, the tilt angle (x2+
y2)1/2 is the distance from the origin,
and the direction of the tilt axis is arctan(y/x).
The direction of the known tilt axis of the goniometer is shown as a
diagonal line. The minimum phase residual (54.6°) at a tilt of
about -10° around the known tilt axis indicates that
the map (see Fig. 4A) is
of the correct handedness. The residual (67.6°) at the point
corresponding to the opposite handedness is considerably higher,
indicating the degree of confidence in the
determination.
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FIG. 4. Three-dimensional
maps of circoviruses. (A) CAV computed from cryomicrographs.
The capsid is formed from 12 pentagonal trumpet-shaped capsomeres,
indicating a T=1 surface lattice containing 60
subunits. (B) PCV-2 computed from cryomicrographs. (C) BFDV
computed from a micrograph of a negatively stained preparation. The
structures in panels B and C are very similar, showing flat pentamer
units making contacts across the twofold positions and around the
threefold positions and indicating a T=1 surface lattice
containing 60 protein subunits in each structure. All maps are viewed
along a twofold axis.
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5°). The cavities on the
fivefold axes extend inward for about 3.5 nm from the plane of the
outermost pentagonal surface. Their pentagonal shape means that the
wall of the trumpet is about 1.5 to 2.0 nm thick, although modulated
into domain-like features. The inner surface of the protein shell is
not well defined and appears to merge with disorganized material in the
interior of the capsid, as shown in the central section of the map
(Fig.
5A).
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FIG. 5. Central
sections of the three maps shown in Fig.
4. (A) CAV.
(B) PCV-2. (C) BFDV. The sections are
normal to a twofold axis. Protein or nucleic acid appears
white. Scale bar, 5
nm.
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As would be expected from the raw images, the computed three-dimensional map of PCV-2 (Fig. 4B) shows a much less strongly modulated surface than does that of CAV. The morphology can still be described in terms of 12 pentamer units, again indicating a T=1 lattice containing 60 subunits. However, in this case, the pentamer units protrude only slightly, giving an overall diameter of about 20.5 nm. The pentamers protrude sufficiently for projected views of the particle to have a polygonal outline, as noted in the raw images. Material extends from the pentamers to form bridges at an outer radius across the twofold axes and to produce Y-shaped features at the threefold axes. There appear to be small holes in the capsid between the twofold bridges and the threefold Y-shaped features. There also may be small holes at the fivefold axes at the centers sections of the pentamers. The inner surface of the protein shell at a radius of about 7.5 to 8 nm is more clearly delineated in PCV-2 than in CAV, and the capsid has a thickness of about 2.5 nm. There is an inner shell of material, likely to represent DNA, at a radius of about 6.5 nm, and the capsid appears to contact this inner shell under the threefold Y-shaped features (Fig. 5B).
Structure of BFDV. Negatively stained particles of BFDV (Fig. 1C) look rather smooth and featureless, with an approximately circular outline. Initial orientations and origin positions were found for a few particles by cross-common line refinement against appropriately scaled projections of the PCV-2 map. A map of BFDV was then computed, and the parameters of additional particles were determined by cross-common line refinement against this map. After iteration of this procedure, the final map (Fig. 4C) was made from 72 of the 100 particles initially selected from the micrograph, with data included to 2-nm spacings. The map of BFDV has an appearance very similar to that of PCV-2, with 12 flattened pentamer units making bridges at the twofold positions and Y-shaped contacts around the threefold positions. There appear to be holes in the capsid shell between the twofold bridges and the Y-shaped features and also on the fivefold positions. A small difference between the PCV-2 map and the BFDV map is that the material around the fivefold positions does not project from BFDV quite so much as it does from PCV-2. This finding was clear from the nature of the images, where the PCV-2 particles show a polygonal outline and the BFDV particles look circular, a point emphasized by comparison of the central sections of the two maps (Fig. 5B and C). However, whether this is a genuine difference between the particles or arises from staining of the BFDV preparation remains to be determined.
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The three-dimensional maps show PCV-2 and BFDV to have a diameter of about 20.5 nm, while the diameter of CAV is about 25 nm. In PCV-2 and BFDV, the capsids show very similar structures, consisting of 12 flat pentameric morphological units, whereas the capsid of CAV consists of 12 pentagonal trumpet-shaped units. Thus, all three viruses have a T = 1 structure containing 60 protein subunits. However, the capsids of the two Circovirus members (PCV-2 and BFDV) are very different from the capsid of the Gyrovirus member (CAV). Previous studies based on visual inspection of micrographs had interpreted images of negatively stained CAV in terms of a T=3 hexamer-pentamer structure (8, 11). The results presented here show that this interpretation was incorrect. Earlier images of BFDV and PCV-1 showed too little detail for interpretation by simple visual inspection to be attempted, but the more sophisticated analysis undertaken here has allowed details of the similar capsid structures of BFDV and PCV-2 to be established.
The capsid protein of CAV contains motifs for RCR in its C-terminal half, suggesting that it has a functional role in replication as well as a structural role in encapsidation. Since the basic N-terminal region of the capsid protein is likely to interact with the packaged DNA, this part of the protein will be inside the capsid. The next part of the polypeptide chain therefore is likely to form the inner shell of the capsid, where contacts between pentamers take place, and the C-terminal half of the polypeptide, containing replication motifs, is likely to form the outer part of the pentagonal trumpets. It would be interesting to know whether the replication function is carried out by polymeric forms of the capsid/replication protein or whether polymeric forms occur only during virion assembly.
The human TT viruses (TTV) also have been shown to possess circular single-stranded DNA genomes (13, 14). The genomic organization of TTV appears to be similar to that of CAV, although very little sequence homology is detectable. As in CAV, the capsid and replication functions of TTV appear to be combined in a single polypeptide which is considerably larger than the corresponding CAV protein but still has a very basic N-terminal region. TTV sizes have been estimated to be in the range of 30 to 50 nm (14). It is thus possible that the capsid of TTV is organized in the same way as that of CAV but with the larger capsid/replication protein yielding a virion with a larger diameter.
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