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Journal of Virology, July 2000, p. 6546-6555, Vol. 74, No. 14
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Trypsin-Induced Structural Transformation in
Aquareovirus
Emma L.
Nason,1
Siba K.
Samal,2 and
B. V.
Venkataram
Prasad1,3,*
Verna and Marrs McLean Department of
Biochemistry and Molecular Biology1 and
W. M. Keck Center for Computational
Biology,3 Baylor College of Medicine, Houston,
Texas 77030, and VA-MD Regional College of Veterinary
Medicine, University of Maryland, College Park, Maryland
207422
Received 5 January 2000/Accepted 12 April 2000
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ABSTRACT |
Aquareovirus, a member of the family
Reoviridae, is a large virus with multiple capsid layers
surrounding a genome composed of 11 segments of double-stranded RNA.
Biochemical studies have shown that treatment with the proteolytic
agent trypsin significantly alters the infectivity of the virus. The
most infectious stage of the virus is produced by a 5-min treatment
with trypsin. However, prolonged trypsin treatment almost completely
abolishes the infectivity. We have used three-dimensional electron
cryomicroscopy to gain insight into the structural basis of
protease-induced alterations in infectivity by examining the structural
changes in the virion at various time intervals of trypsin treatment.
Our data show that after 5 min of trypsinization, projection-like
spikes made of VP7 (35 kDa), associated with the underlying trimeric
subunits, are completely removed. Concurrent with the removal of VP7,
conformational changes are observed in the trimeric subunit composed of
putative VP5 (71 kDa). The removal of VP7 and the accompanied
structural changes may expose regions in the putative VP5 important for
cell entry processes. Prolonged trypsinization not only entirely
removes the outer capsid layer, producing the poorly infectious core
particle, but also causes significant conformational changes in the
turret protein. These changes result in shortening of the turret and narrowing of its central channel. The turret, as in orthoreoviruses, is
likely to play a major role in the capping and translocation of mRNA
during transcription, and the observed conformational flexibility in
the turret protein may have implications in rendering the particle
transcriptionally active or inactive.
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INTRODUCTION |
Aquareovirus, a member of
the family Reoviridae, is a double-stranded RNA (dsRNA)
virus. The Reoviridae includes pathogens that can infect a
wide variety of organisms including vertebrates, invertebrates, and
plants. Several of these viruses have large and complex icosahedral
structures with diameters around 1,000 Å. Most have multiple layers of
protein enclosing multiple segments of dsRNA. The inner protein layers
are involved in facilitating the endogenous transcriptional activity,
whereas the outer capsid layers are important for facilitating cell
entry. While significant structural and biochemical information is
known about several members of the family such as
Rotavirus (25), Orthoreovirus (21, 26), and Orbivirus (9, 27), the
Aquareovirus genus is not as well characterized. In common
with rotaviruses, aquareoviruses have 11 segments of dsRNA
(30). However, earlier structural studies have shown that
architecturally, aquareoviruses more strongly resemble the
orthoreoviruses (29).
In contrast to rotaviruses and orthoreoviruses, which infect mammals
including humans, aquareoviruses cause infection in aquatic organisms
like bony fish, shellfish, and crustaceans. Currently, more than 50 aquareoviruses have been isolated worldwide. These viruses have been
isolated from fish with obvious diseases, such as hemorrhagic disease,
hepatitis, and pancreatitis, but the majority have been isolated during
routine examination of seemingly healthy fish and shellfish
(18).
Biochemical studies have shown that the aquareovirions contain seven
structural proteins: VP1 (~130 kDa), VP2 (~127 kDa), VP3 (~126
kDa), VP4 (~73 kDa), VP5 (~71 kDa), VP6 (~46 kDa), and VP7 (~35
kDa) (30). Structural studies using electron cryomicroscopy (cryo-EM) and computer image-processing techniques of the intact virion
have revealed that each particle is made of multiple capsid layers with
an overall diameter of ~800 Å (29). The structural organization of the outer capsid layers, like other members of the
Reoviridae, is based on a T=13 icosahedral lattice with a left-handed skew. In aquareovirus, the lattice is an incomplete T=13,
since it is punctuated at each fivefold axis by a large turret as seen
in orthoreoviruses. In electron micrographs of aquareovirus particles,
the outer layers are often seen clearly separated from the innermost
layer, which is ~600 Å in diameter, by an electron-lucent ring. One
of the interesting differences between aquareoviruses and
orthoreoviruses is that aquareovirus particles lack the slender spikes
at the fivefold vertices seen in orthoreovirus particles. In
orthoreoviruses, these spikes are made of
1 protein, which mediates
virus binding to the host cell receptor(s) (15). Another
noticeable difference is in the innermost T=1 capsid layer.
Aquareovirus particles have 120 nodules instead of 150 as seen in
orthoreovirus particles.
The major focus of the present paper is to investigate trypsin-induced
structural changes in aquareoviruses and to correlate them with changes
in infectivity. These studies may have an in vivo relevance, since
trypsin is present in the pancreatic tissues, which are susceptible to
aquareovirus infection. Protease-induced enhancement of infectivity is
well documented in two of the members of the Reoviridae,
Rotavirus and Bluetongue virus (BTV), although the precise molecular mechanism is not known. In rotavirus, trypsin cleaves the spike protein VP4 and this cleavage increases the infectivity significantly (7). In BTV, after proteolytic
treatment, the particles, called intermediate subviral particles
(ISVPs), have a selective enhanced infectivity for insect cells but not for mammalian cells (20). In contrast, treatment of
orthoreoviruses with proteases is not known to result in enhanced
infectivity (11). In fact, ISVPs of the T3D strain are less
infectious than are native virions. Although these particles lack an
outer capsid protein (
3) and have a cleaved spike protein (
1),
the loss of viral infectivity is associated with cleavage of the
1
protein (22). Prolonged protease treatment of orthoreovirus
removes the outer protein layers completely, and the resulting core
particles become transcriptionally active. The complete removal of the
outer protein shell and the subsequent opening of a channel at the
fivefold axis support the hypothesis that mRNA molecules exit through
the channels of the
2 turrets (5).
Biochemical studies have shown that proteolytic treatment of
aquareoviruses for short (5-min) periods with either trypsin or
chymotrypsin serves to activate the virus and results in significantly enhanced infectivity for susceptible cells. Trypsin results in a
greater increase and so has been the focus of previous studies (19) as well as this study. Prolonged periods of
trypsinization, greater than 20 min, result in a level of infectivity
significantly lower than that of native virions. In this study, using
cryo-EM techniques, we have observed the trypsin-induced structural
changes at different times and have interpreted these changes in the
light of the biochemical data. Although the protease-induced structural changes in aquareoviruses are generally similar to those seen in
orthoreoviruses, there are significant and intriguing differences, particularly in the turrets. We have compared and contrasted our structural results with the published data on the chymotrypsin treatment of orthoreoviruses (5).
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MATERIALS AND METHODS |
Native virion preparation.
The SBR strain of aquareovirus
was originally obtained from diseased striped bass (Morone
saxatilis) (1). The aquareovirus virions were
propagated and purified in the same way as previously reported, with a
particle-to-PFU ratio of 100:1 (19).
Subviral-particle preparation.
Purified native aquareovirus
virions (100 µg) were treated with 10 µg of trypsin (Worthington
Biochemical Corp., Lakewood, N.J.) per ml in 1 ml of phosphate-buffered
saline and incubated for 5 min, 15 min, or 2 h at 37°C with
gentle agitation. The incubation was terminated by placing the
particles on ice. Digested proteins were then immediately separated
from the particles, and the particles were concentrated by gently
pelleting the core particles at 12,400 × g overnight.
The pellet was resuspended in phosphate-buffered saline for the 5-min
and 15-min trypsinized preparations, but the 2-h preparation was
resuspended in core buffer (1 M NaCl, 100 mM MgCl2, 25 mM
HEPES [pH 8.0]) (5). This buffer resulted in far better
distribution of the particles, as confirmed by cryo-EM. The protein
composition of the particles before and after trypsinization was
examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis immediately prior to structural analysis. The
protein profiles of the particles at various times during trypsinization were identical to those reported earlier (19) and hence are not shown.
Cryo-EM.
Specimen preparation for cryo-EM was carried out
using standard procedures (6). The specimen suspension,
native aquareovirus or trypsin-treated aquareovirus, at a concentration
of ~1.3 mg/ml (4-µl aliquot), was applied to one side of a holey
carbon grid. This grid was then blotted and plunged into a bath of
liquid ethane (
180°C). The frozen-hydrated sample was transferred
to a precooled GATAN cryoholder and observed in a JEOL 1200 transmission electron microscope operated at 100 kV and maintained at a
specimen temperature of
163°C. Regions of interest were imaged at
×30,000 magnification with an electron dose of 5 electrons/Å2. From each region, a focal pair was recorded
with intended defocus values of 1.2 and 2.4 µm. The electron images
were recorded with 1-s exposure on Kodak SO-163 films. These films were
developed in Kodak D-19 developer for 12 min at 21°C and fixed in
Kodak fixer for 10 min.
Three-dimensional structural analysis.
Micrographs were
selected based on particle concentration, quality of ice, and
appropriate defocus. The images were digitized on a Zeiss SCAI
microdensitometer (Carl Zeiss, Inc., Englewood, Colo.), using a 7-µm
step size. The pixels were then averaged to give a 14-µm step size
that corresponded to 4.67 Å/pixel in the object. Intact particles were
boxed with a pixel area of 256 by 256, and core particles were boxed
with a box size of 192 by 192. The determination of the orientational
parameters, their refinement, and the three-dimensional reconstructions
were carried out using the ICOS Toolkit software suite (13).
Orientations of the particles were determined using the common-lines
approach (2), and their refinement was carried out using the
cross-common-lines method (8). Three-dimensional
reconstruction, from a set of particles (native full virions [NV],
105 particles; naturally degraded [ND], 322 particles; 5-min
trypsinized [5MT], 61 particles; 15-min trypsinized [15MT], 24 particles; and 2-h trypsinized, 109 particles) which adequately
represented the icosahedral asymmetric unit, was computed using
cylindrical expansion methods (2). The further-from-focus
micrograph in each focal pair was processed first to obtain a
low-resolution reconstruction, and this was then used to assist in
finding correct orientations for the particles imaged in the
corresponding closer-to-focus micrograph.
The reconstructions of the various particles were computed to a
resolution within the first zero of the contrast transfer function
(CTF) of the corresponding micrograph. The defocus values were
determined from CTF ring positions in the sum of particle Fourier
transforms. The defocus values of various specimens in the
closer-to-focus micrographs ranged from 1.2 to 1.48 µm. The reconstructions were corrected for the effects of the CTF using procedures described earlier (37). The final resolution for each reconstruction was determined by Fourier ring correlation analysis
(31). Since the resolution of the reconstruction of 5-min-trypsinized particles was 23 Å, all the other reconstructions used for comparative analysis, such as native and other trypsinized particles, were recomputed to this resolution. The structure of the
empty particles, from 17 particles, was computed to a nominal resolution of 26 Å. Contour levels in each reconstruction were chosen
to represent equal volume between the radii of ~234 and ~294 Å (which contains mass common to all the reconstructions) and represented
all core proteins in their assumed quantities except for the turret
protein. Any magnification differences between different images were
taken into account by using rotavirus double-layered particles (DLPs)
as an internal standard. Rotavirus DLPs were mixed with either native
aquareovirus virions or the cores just before cryofreezing of the
specimen for microscopy. The peaks of density for the VP2 and VP6
layers of the DLPs were found to be invariant among the micrographs of
the two preparations. The reconstructions were viewed on a Silicon
Graphics Workstation using IRIS Explorer v3.5 (Numerical Algorithms
Group, Inc.).
 |
RESULTS |
Cryo-EM.
Trypsinization of aquareovirus over time resulted in
the removal of proteins in a specific and reproducible manner.
Micrographs of unstained, frozen hydrated aquareovirus at different
stages of trypsinization, along with the images of NV, are given in
Fig. 1. Included in these are NV which
were kept at 4°C for approximately 14 days before being prepared for
cryo-EM. These are ND particles, since reconstructions of such
particles clearly showed some degradation with respect to virions that
had been prepared for microscopy immediately after purification.
Although NV (Fig. 1A), ND, and 5MT particles (Fig. 1B) appear similar
to each other, a close examination of the NV particles indicates the
presence of small additional density at the periphery (Fig. 1A). NV,
ND, and 5MT particles all have a diameter of ~800 Å and show a
well-defined electron lucent boundary between the inner and outer
layers. The 15MT virions were in the process of being uncoated (Fig.
1C). These particles have a nonuniform morphology with disorganized and
fuzzy outer layers. The diameters of these partially uncoated particles
ranged from ~600 to ~800 Å. After 2 h of incubation with
trypsin, the particles were all of a similar size (Fig. 1D). These
particles, referred to hereafter as cores, are ~600 Å in diameter
and exhibit distinct looped features that are attached to the particle.
In the close-to-focus images, whorl-like patterns are observed; we
attribute these to dsRNA (Fig. 1D, inset). In each preparation, empty
particles that did not contain genomic RNA were also observed.

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FIG. 1.
Images of frozen-hydrated aquareovirus (SBR strain)
particles examined by cryo-EM. (A) Native aquareovirus (NV). The
asterisk indicates particles devoid of dsRNA (empty particles). The
arrows indicate the additional mass density at the periphery of the NV
particles. (B) The left panel shows ND aquareovirus particles, and the
right panel shows 5MT aquareovirus particles. Arrowheads in panels A
and B indicate the electron-lucent boundary. (C) 15MT aquareovirus
particles. Arrowheads indicate the disordered outer capsid layer. (D)
Cores. Arrowheads indicate pentonal turrets. In the inset,
close-to-focus images of the cores show whorl-like patterns
representing the genome. All images were taken at an electron dose of 5 Å/electron2 and at a magnification of ×30,000, except for
the inset in panel D, which was taken with an electron dose of 5 Å/electron2 and a magnification of ×40,000. Bars, 1,000 Å, except for the inset (600 Å).
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Image processing.
The digitized micrographs for each
preparation were used for image reconstructions. We found that 95% of
the inverse eigenvalues were below 0.1, indicating that there was
adequate sampling for the computed resolutions. To take into
consideration any magnification differences that may have been present
during microscopy of various specimens, rotavirus DLPs were used as an
internal calibration standard. Rotavirus DLPs were mixed with samples
of NV and cores. Independent reconstructions of the DLPs from the two
preparations gave identical radial density profiles. The radial density
profiles for NV and for the core structure from these two preparations were compared. The NV had a major peak at a radius of 257 Å,
corresponding to the inner capsid layer, that was directly
superimposable onto the radial density profile for the core (Fig.
2). The radial density profiles for the
NV, ND, and 5MT structures, which were determined in the absence of
rotavirus DLPs, used in this study have been radially scaled between 93 and 410 Å with respect to the NV, using rotavirus DLP as an internal
control. Likewise, the core structure was radially scaled with respect
to the core structure imaged in the presence of rotavirus DLP.

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FIG. 2.
Radial density profiles computed from NV. ND, 5MT, and
core reconstructions. A horizontal line represents averaged radial
density of zero. Possible locations of aquareovirus structural proteins
with respect to radius are indicated.
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Figure
2 shows the density distribution profiles for the four
reconstructions of aquareovirus. The inner capsid shell in all
cases
lies between 240 and 290 Å in radius. A second capsid shell
is
observed in NV, ND, and 5MT structures. The radial density
profile
reveals this shell as having two peaks of density, one
at ~315 Å and
one at ~380 Å. Immediately inside the inner capsid
shell of all the
particle types is a series of regularly spaced
peaks that are 26 Å
apart.
Structures of NV, ND, and 5MT particles.
The NV, ND, and 5MT
structures have many similar characteristics (Fig.
3A to C). All three structures are
composed of two capsid shells, as seen in the radial density profiles
computed from the respective three-dimensional reconstructions (Fig. 2A to C). These radial density profiles (Fig. 2) indicate that NV, with a
diameter of ~820 Å, is slightly larger than ND and 5MT, which have
diameters of ~800 and ~785 Å, respectively. The outer capsid is
arranged on an incomplete T=13 lattice with a left-handed configuration. The fivefold axis of aquareoviruses at all stages of
proteolytic cleavage contains a turret. In NV, ND, and 5MT, this
structure is recessed inward compared with the outer shell of the
particle. The radius at the fivefold axis is ~383 Å. A more detailed
analysis of the turret structure is given below.

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FIG. 3.
Surface-shaded representations of the NV (A), ND (B),
5MT (C), and core (D) structures viewed along the icosahedral threefold
axis. The capsids are radially depth-cued as shown in the color chart
(top left of figure). The same coloring scheme is used in other figures
unless mentioned otherwise. (A) Finger-like projections protrude from
the surface of the virion. Three projections attach to each of the
underlying trimeric subunits. At the fivefold axes is a depression, in
which sits a turret. At the top of each turret is a petal-like
structure surrounding the central channel. (B) The ND particle shows
the remnants of the finger-like projections. (C) The triangular
subunits onto which the projections attach are more visible in the 5MT
structure. The turrets retain the same basic morphology. (D) The
removal of the outer capsid reveals a core, which possesses 120 nodules
closely associated with the underlying capsid layer and turrets at all
the fivefold axes. Each icosahedral asymmetric unit contains two
nodules, labeled a and b. The a nodules surround the fivefold axis with
mass extending up the turret, whereas the b nodules surround the
threefold axis. Bar, 200 Å.
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Loss of projection densities.
In NV, 600 knobby protrusions
were observed attached to the outer capsid (Fig. 3A). A major
difference between the NV and 5MT structures was apparent, since these
protrusions were completely absent in the 5MT structure (Fig. 3C).
SDS-PAGE of 5MT particles has shown that these particles do not contain
VP7 (35 kDa) (19). In NV, these densities protruded above
the surface of the particle, resulting in a particle diameter of ~820
Å at the threefold axes (Fig. 3A). A difference map between the NV and
5MT structures clearly showed the locations and morphology of the extra
density. The volume occupied by these densities was sufficient to
accommodate 600 copies of a 35-kDa protein, indicating that these
densities are due to VP7. Each protrusion was roughly cylindrical and
is referred to below as a projection. Figure
4A and C clearly show that three
projections clamp onto the three sides of a trimeric subunit in the
outer capsid. Each projection is composed of a bulbous projection head
(Ph in Fig. 4C) that protrudes ~17 Å above the capsid surface. The
body of the projection (Pb in Fig. 4C) interacts with the side of the
trimeric subunit.

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FIG. 4.
Trypsin-induced structural changes in the trimeric
subunit. (A and B) The trimeric subunit at the threefold axis is
excised from NV (A) and 5MT (B) maps. The arrow in panel A indicates
the position of the threefold axis. (C) The native map is colored red
and is superimposed onto the 5MT subunit. Note the cylindrical
morphology of the projection. The projection head (Ph) and projection
body (Pb) are labeled. (D) The 5MT subunit is colored green and is
superimposed onto the native map. The asterisk denotes the lateral
"horn-like" extension.
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The ND particle was formed without the addition of exogenous trypsin
and appears to be an intermediate form between the NV
and 5MT
structures (Fig.
3B). Small pieces of density were observed
in the
place of the projections. By SDS-PAGE, the presence of
a band at 35 kDa
was observed in purified, pelleted ND particles.
It is possible that
these ND particles still have VP7 attached
in some positions but in the
process of being removed. The major
portion of VP7 is likely to be
oriented differently within the
particle and between the particles and
hence is averaged out.
The pieces of density that we see may represent
a small portion
of VP7 attached to the ND virion that is coherently
contributing
to the
reconstruction.
In NV, at the base of some projections, weak connections are made with
the projections from neighboring subunits related by
local twofold axes
(arrow in Fig.
3A). As the projections are
removed, these connections
are lost and are absent in both ND
and 5MT structures. Concurrent with
the removal of the projections,
structural changes are observed in the
upper part of the trimeric
subunit (Fig.
4).
Structural changes in trimeric subunits.
The projections
attach to underlying trimeric subunits. These subunits span a radius
from ~294 to ~392 Å. The upper part of the trimeric subunit
between radii of ~369 and ~392 Å forms triangular proteins. These
are most easily observed in the 5MT structure (Fig. 3C). The lower part
of the trimeric subunit (between a radius of ~294 and ~369 Å)
forms a network of proteins, as previously seen (29).
Simultaneous with the removal of the projections, additional structural
changes are made in the upper layer of the trimeric subunit.
"Horn-like" mass densities extend laterally from the side of the
subunits to interact with neighboring subunits. Figure 4B and D show
the location of these additional features in 5MT compared with the NV.
These ~24-Å bridges of mass connect neighboring subunits across the
local twofold axes surrounding the strict threefold axes (Fig. 3C).
The trimeric subunits appeared to be completely disordered after a
15-min trypsinization. A reconstruction of the 15MT particles
was
attempted, although the orientational parameters of only a
few
particles could be determined. The structure showed a disordered
outer
layer, but the features of the core were well
preserved.
Structure of inner core.
Prolonged trypsinization of the
virion (2 hour) resulted in the complete removal of the outer protein
layers (Fig. 3D). These particles strongly resemble the orthoreovirus
cores produced by proteolytic cleavage (5). Two features
that are common to both orthoreovirus and aquareovirus cores are the
turrets found at the icosahedral vertices and the nodules present on
the inner capsid layer surrounding the threefold and fivefold axes. The turrets extend out to a radius of ~365 Å. The nodules surrounding the fivefold axes are connected to the turrets by extensions that continue upward from the nodule and appear to support the turret on the
surface of the core like the legs of a five-legged stool. The nodules
are ~19 Å high and ~63 Å long by ~42 Å wide. They are very
similar in size to the nodules on the surface of the orthoreovirus
core. However, while 150 nodules are present in orthoreoviruses, only
120 are found in aquareoviruses. Nodules are absent from all twofold
axes in aquareoviruses. In both viruses, the upper surface of the
nodules makes weak connections with the protein layer above.
Conformational changes in the turret.
A view down the fivefold
axis of NV, 5MT, and core particles shows the top of the turret to have
two concentric layers of protein surrounding a central channel (Figs.
5A to C). In NV, the lower ring (Fig.
5A), at a radius of 365 Å, is composed of five bilobed structures that
are connected to one another. Five petal-like features arranged with a
right-handed skew form the upper ring, at a radius of 383 Å (Fig. 5A).
These petals, ~66 Å long, form a lid narrowing the opening of the
central channel to 34 Å wide. They not only are attached to one
another but also are attached to one piece of the bilobed density of
the lower ring. Although the overall structure of the turret remains
the same, significant structural changes are observed in the top
portion of the turret, particularly after prolonged trypsinization. In the core, the opening of the central channel is reduced to ~20 Å (Fig. 5C). The point of contact between the petals and the bilobed features has been shifted to a more central position, making the petals
in the core appear shorter. A comparison of thin sections through the
turrets of NV and the core (bottom panel of Fig. 5) shows that the
petals undergo a large movement during trypsinization. The appearance
of a change in the volume of the sections in this figure is because
these sections do not incorporate equivalent volumes as a result of the
movement. Mass volume calculations of the entire turret portions of the
NV and the core structures in fact show no significant change in
volume. The "lid" of the turret is positioned at a higher radius in
the NV than in the core structures (Fig. 5D to F). Petals that project
toward the center of the channel appear to be able to pivot on a hinge
upward and outward to give the large ~34-Å channel observed in the
native virion. After 2 h of trypsinization, the petals apparently
rotate inward and downward, decreasing the channel opening to ~20 Å and shortening the height of the turret by ~18 Å. In contrast to
large-scale structural changes seen between the turrets of NV and the
core, subtle differences along the same lines are seen between the
turrets of NV, ND, and the 5MT structures. Both the ND and the 5MT
structures have turrets that are slightly shorter than that of the NV
but taller than that of the core.

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FIG. 5.
Structural differences between the turret of native and
trypsin-treated particles. (A to C) View of the turret, along the
fivefold axis, in NV (A), 5MT (B), and core (C). In panel A, petal-like
features are indicated by an asterisk, the bilobed pieces of mass are
denoted by a solid diamond, and the "link" joining the bilobed
pieces of density is shown by the arrow. A dashed line indicates the
location of the section extracted for panels D to F. The channel at the
center of the fivefold axis decreases considerably in size from the NV
to the core (A to C). (D to F) A thin slice, as indicated in panel A,
across the turret perpendicular to the fivefold axis extracted from NV
(D) and core (E) structures. A superimposition of NV (shown as a
transparent surface) and core slices is shown (F). The downward
movement of the petals in the core is clearly demonstrated. An asterisk
marks the possible location of a pivot point about which the petal can
rotate.
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Internal features.
Fingerprint-like whorls of density were
observed in some of the close-to-focus negatives (Fig. 1D, inset). The
inner protein-dsRNA interface of the virus was previously determined to
be at a 235-Å radius (29). Examination of the interior of
the NV, ND, 5MT, and core structures showed concentric layers of mass
separated by ~26-Å intervals directly beneath the inner capsid
layer. The internal features of the NV are shown in Fig.
6A. This was in contrast to the
"empty" particles, in which no concentric rings of mass were
observed, suggesting that these most probably are dsRNA. Similarly
arranged shells of mass are seen in other members of the same family,
including Rotavirus (24),
Orthoreovirus (5), BTV (9), and
Cytoplasmic polyhedrosis virus (CPV) (10, 36).

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FIG. 6.
Internal features of the virus. (A) A 23-Å thick
equatorial slice of the NV perpendicular to the fivefold axis, showing
the concentric layers of mass ~26 Å apart beneath the inner capsid
layer. (B) A conical cutaway of the mass density at the fivefold axis,
showing a large flower-shaped structure (pink) directly beneath
the turret.
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In empty NV particles (i.e., those that do not contain a dsRNA genome),
a flower-shaped feature was observed. This feature
is attached to the
inside of the inner capsid layer directly beneath
the fivefold axis
(Fig.
6B). A similar feature is also present
in the particles
containing dsRNA, but due to the surrounding
density it was not easy to
identify. This flower-shaped structure
is very similar to a feature
seen along the fivefold axes of a
recombinant rotavirus DLP
(
24) and was proposed to be the transcription
complex
composed of the RNA polymerase and/or the guanylyl transferase.
Similar
features have also been observed in
Orthoreovirus
(
4)
and CPV (
36).
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DISCUSSION |
It is established that at least two members of the
Reoviridae family, Rotavirus and BTV, require
proteolytic treatment in order to achieve optimal infectivity. However,
it is less clear how the enhancement of infectivity is caused by
proteolysis. For aquareoviruses, it has been shown that trypsinization
causes a significant increase in infectivity (19). We have
used three-dimensional cryo-EM to investigate the effect of trypsin on
the structure of aquareoviruses, to gain insight into the molecular
mechanism of protease-enhanced infectivity. The observed capsid
undressing caused by proteolysis as a function of time, combined with
published biochemical analysis, has also allowed us to infer
topographical locations of the various proteins in the aquareovirus
structure. The overall architecture of Aquareovirus is
clearly more similar to orthoreoviruses than to any other member in the
Reoviridae. The proteolytic degradation of the aquareovirus
structure presented here also parallels that of the orthoreoviruses in
several ways and yet there are also interesting differences,
particularly in the turret regions. It is possible that, as with
orthoreoviruses (21), the observed disassembly stages in
aquareoviruses may mimic the process that occurs during the initial
stages of infection, and the structural information presented here may
have relevance for understanding the process of aquareovirus infection.
Unlike orthoreoviruses, detailed functional studies of the
aquareovirus proteins are still lacking. However, a careful
comparison between the two viruses, particularly with respect to their
protease-induced structural changes, has allowed us to propose
functional and structural equivalents between aquareoviruses
and orthoreoviruses (Table 1).
Effect of trypsin on the outer-layer proteins.
Comparative
SDS-PAGE analysis of native and trypsin-treated aquareoviruses clearly
indicates that VP7 (35 kDa), VP4 (73 kDa), and VP5 (71 kDa) are present
in the outer coat of the virion (19). All three proteins are
removed upon prolonged and complete trypsinization, resulting in the
core particles. However, biochemical studies indicate that VP7 (35 kDa)
is the most external protein, since it is the first protein to be
removed during trypsinization and also since it is glycosylated
(28, 30).
A major structural difference between the NV and the 5MT structure is
the loss of projections in the 5MT structure. The NV
has a full
complement of 600 projections extending from the trimeric
subunits,
whereas the 5MT structure lacks these projections and
thus has a
smoother surface. The volume calculations, assuming
a density of 1.30 g/cm
3, indicate that each of these projections can
accommodate a 35-kDa
protein. Therefore, the projections seen in the
native structure
are most probably composed of VP7. In orthoreoviruses,
a similar
phenomenon occurs with 1-h chymotrypsin treatment. In the
native
orthoreoviruses, 600 copies of

3 (41 kDa) form
projection-like
spikes on the outer surface of the particle. After
protease treatment,

3 is removed from the particle, leaving a
smoother surfaced virion
known as an ISVP. It therefore appears that
aquareovirus VP7 is
structurally analogous to orthoreovirus

3,
although there is
no amino acid sequence similarity between the two
proteins (
17).
It is to be noted that the previously published aquareovirus structure
(
29) does not show the projections that we have seen
in the
NV. This earlier structure is very similar to the ND or
the 5MT
structure presented here. We reckon that in the structure
published by
Shaw et al. (
29), projections may have fallen off,
perhaps
because of residual proteases present in the virus preparations.
In the
present studies we have been careful to freeze the NV samples
for
cryo-EM studies immediately after virus purification. These
studies
clearly indicate that VP7 is highly sensitive to proteases
and can
easily become disassociated from the virion. In line with
this
suggestion are the conclusions from very early biochemical
studies on
aquareoviruses, suggesting that VP5 was the outermost
protein; none of
the aquareovirus proteins were observed to be
glycosylated in that
study (
28). It is quite likely that the
virus particles used
in the earlier studies had already lost
VP7.
The other major structural feature of the outer layer, apart from the
projections, is the trimeric subunit. One of two currently
unassigned
outer layer proteins, VP5 or VP4, which have very similar
molecular
weights, should account for this density. Two pieces
of evidence
suggest that VP5 is the better candidate. Biochemical
studies have
shown that VP5 is trypsinized before VP4, suggesting
that it is the
next most accessible protein after VP7 (
19,
28).
Also, the
intensity of the protein band for VP5 is noticeably
greater than that
of the band for VP4, suggesting that VP5 is
present in greater number
in each virion. Assignment of VP5 to
the trimeric subunits requires
that this protein be present in
600 copies per virion, and therefore
such a protein would show
up as an intense band in the gel. We
hypothesize that VP5 constitutes
the trimeric subunits in the protein
layer that lies between the
projections and the core. Comparison of the
NV and 5MT structures
shows a noticeable structural change in the
trimeric subunits
(Fig.
4). This observation correlates with the
biochemical studies
which show that the putative VP5 protein becomes
cleaved after
5 min of trypsin treatment, resulting in a 52-kDa
fragment which
stays associated with the particle (
19). The
remaining fragment
has not been visualized by SDS-PAGE, and so the size
of the fragment
is unknown, but the fragment is presumably no longer
attached
to the particle. If VP5 is assigned to the trimeric
subunit, a
relevant question is where VP4 is located in the virion
structure.
Further structural studies using monoclonal antibodies
against
VP4 and/or VP5 are necessary to address this
question.
Removal of VP7 and the concurrent cleavage of the putative VP5
correlates with increased infectivity in aquareoviruses. The
infectivity of the 5MT particles is 4.4 × 10
9 PFU
compared with 1.8 × 10
7 PFU for the native virion
(
19). It is likely that the 52-kDa
cleavage product has
relevance for cell entry, possibly in the
same way that µ1 of
orthoreoviruses has been implicated in membrane
insertion
(
23). Orthoreovirus µ1 is located beneath the

3
projection,
which is analogous to the location of VP5 beneath the VP7
projection
in aquareoviruses. It is also possible that the removal of
the
VP7 in aquareoviruses may expose some regions of the putative
VP5
critical for efficient entry into cells. It is not clear if
the removal
of VP7 is necessary for the cleavage of
VP5.
More than 5 min of trypsinization results in particles that have a
significant decrease in infectivity (
19). We have shown
that
after a 15-min incubation, the outer layer of the majority
of particles
is clearly being disordered and/or disassembled (Fig.
1C). At this time
point, the infectivity is low (between 1.5 ×
10
6 and
2.9 × 10
8 PFU), indicating that the structural
integrity of the trimeric
subunit is essential for optimal
infectivity.
Lack of a
1 equivalent in aquareoviruses.
Treatment of
orthoreoviruses with chymotrypsin also causes
1, a spike-like
protein emanating from the fivefold axes, to adopt a more extended
conformation. This protein mediates the capacity of the virions to
agglutinate red blood cells (3) and is also the receptor
recognition protein (15). We have not seen any evidence of
an equivalent structural feature at the fivefold axes, either in the
native or in the trypsin-treated aquareovirus. It is likely that
aquareovirus has no
1-equivalent protein, in agreement with
biochemical studies indicating that aquareoviruses do not exhibit
hemagglutinating activity (33).
Effect of prolonged trypsinization.
A 2-h treatment of
aquareoviruses with trypsin produces core particles, which retain
the turrets at the fivefold axes. The four distinct structural
features of the core are the turrets, the nodules, a shell of density
beneath the nodules (Fig. 3D), which encloses the genome, and the
inwardly protruding flower-shaped feature at the fivefold axis
(Fig. 6B). Except for the large conformational changes in the
turret regions (Fig. 5), the structure of the core particles derived
from prolonged trypsinization remains essentially similar to that of
the core region in the native particles. The interactions between
the core and the outer-layer particles were described earlier
(29). SDS-PAGE of the core particles shows that these
particles are composed of four proteins, VP1, VP2, VP3, and VP6
(19). It is possible that each of these proteins can be
associated with one of the four distinct structural features of the
core. Treatment of orthoreoviruses with chymotrypsin for 3 h
produces architecturally similar core particles (5).
However, in orthoreoviruses, these particles are formed from five
proteins. The major distinction between the cores of these two viruses
is that aquareoviruses have only 120 nodules, in contrast to 150 nodules in the orthoreovirus cores. The nodules at the icosahedral twofold axes are absent in the aquareovirus structure. In combination with the observed structural features of the core particles and the
relative intensities of the core proteins in SDS-PAGE, we have ascribed
possible locations to the aquareovirus proteins that compose the core.
Core proteins and their locations.
On SDS-PAGE (12%
polyacrylamide), the three largest aquareovirus proteins, VP1, VP2, and
VP3 migrate very close together; however, they are separated on a 6%
polyacrylamide gel with 4% bisacrylamide cross-linkage
(19). As judged by the intensities of the bands in SDS-PAGE,
VP3 (~126 kDa) and VP6 (46 kDa) are more abundant than VP1 and VP2.
VP1 is present in larger copy numbers than VP2. Based on their
molecular weights and the volume calculations from the structure, VP6
and VP3 would be suitable candidates for the nodules and the spherical
shell of the core, respectively. In orthoreoviruses, the capsid shell
of the core is composed of two proteins,
2 (47 kDa) and
1 (137 kDa), having molecular masses similar to those of VP6 and VP3,
respectively. The structural organization of 150
2 molecules, which
form the nodules, and 120
1 molecules, which constitute the shell in
the core of orthoreoviruses is now known from recent X-ray
crystallographic studies (26). It is likely that the
molecular interactions between the proposed VP6 and VP3 molecules in
the aquareovirus core are very similar to those seen between
2 and
1 in orthoreoviruses.
The structural organization of the innermost shell, with 120 subunits,
appears to be a common theme among the members of the
Reoviridae. Such a unique organization, perhaps necessitated
by
the requirement to transcribe the dsRNA segments endogenously,
is
seen in BTV (
9),
Rotavirus (
14), and
Rice dwarf virus (RDV) (
16), in addition to
Orthoreovirus (
4), and CPV (
10,
36).
The core structures of
Orthoreovirus, CPV, and
Aquareovirus,
which may be called the "turreted
viruses," are distinguished
from those of
Rotavirus, BTV,
and RDV by having additional features
such as turrets and nodules. The
innermost layers of
Rotavirus,
BTV, and RDV, in contrast,
have a smooth
appearance.
Turret structure.
The turret is a large structure present at
the fivefold axes and, as in orthoreoviruses, may play an important
role during the transcription. Cryo-EM reconstruction of the actively
transcribing orthoreovirus cores has shown that the transcripts are
extruded through the central channel of the turret (34).
Even in Rotavirus, and very probably in BTV, nascent
transcripts exit through a channel at the fivefold axis
(12). In Aquareovirus, between VP1 and VP2, which
are the remaining proteins, VP1 is the most likely candidate for the
turret structure, since it is present in greater abundance than VP2. We
propose that each turret is composed of 5 copies of a protein, yielding
60 copies of the protein per virion. Such an assignment is well
supported by volume calculations from the structure. In
Orthoreovirus, the turret is composed of 60 copies of
2
(144 kDa). It is very likely that the function of VP1 in
Aquareovirus is analogous to
2 in
Orthoreovirus, which, as a part of the transcriptase
apparatus, mediates guanylyl transferase activity (32).
The remaining protein, VP2, with a molecular mass of ~127 kDa, has
the band of weakest intensity on the 6% PAGE and so is
likely to have
relatively few copies per virion. We propose that
the flower-shaped
density directly beneath the fivefold axis is
composed of VP2. In
orthoreoviruses, a similar structural feature
has been ascribed to

3
(142 kDa) (
4) and is thought to be
a part of the
transcriptase complex. Possibly like

3 in orthoreoviruses,
VP2 is
present in very small amounts (12 copies) per virion and
functions as a
viral polymerase. It appears that aquareoviruses
lack the equivalent of

2 (83 kDa), a minor core protein in orthoreoviruses,
which has been
suggested to be a cofactor for the viral polymerase
(
35).
Conformational change in turret structure.
Treatment of
aquareovirus virions with trypsin produces a large conformational
change in the turret structure. In the native virion, the turret is at
its tallest and the channel is at its widest. After trypsinization, the
turret protein (putative VP1) rearranges, resulting in a shorter turret
with a smaller channel aperture. In orthoreoviruses, treatment with
chymotrypsin produces the opposite effect. A conformational change in
the turret converts the short turret with a closed channel in the
virion to an extended turret with an open channel in the core. The
conformational differences in the turret observed between the
orthoreovirus and aquareovirus cores may be due to the higher salt
content of the buffer used with the aquareovirus cores. Such a buffer
was required to retain well-dispersed particles in ice.
In the aquareovirus NV, interactions were observed between the two
rings of density in the petal-like feature at the top of
the turret.
These perhaps serve to give some stability, enabling
the petals to
remain in an "open" channel configuration. After
a 2-h
trypsinization, this interaction appears to be relaxed somewhat,
so
that the petals are no longer as strongly held outward and
have moved
inward toward one another, resulting in a much smaller
channel. The
ability of this turret protein to rearrange under
various conditions
may have implications in the transcription
of the virus. Although the
transcriptional activity of the virions,
ISVP, or core of aquareovirus
has yet to be established, the observed
narrowing of the channel, in
contrast to the widening seen in
orthoreovirus, appears to be rather
counterintuitive. It is possible
that a different set of conditions is
required to establish transcriptional
activity in aquareovirus. All
trypsinization experiments shown
here were conducted at 37°C, as in
previous biochemical studies
(
19). However, the aquatic
animals that become infected by aquareoviruses
live at ~20°C,
and it is possible that this temperature would
reveal a different
conformation of the turret proteins. Nevertheless,
this study has
revealed a labile domain in the turret protein.
Its conformation is
most probably the determining factor in whether
the particle is able to
release the nascent
transcripts.
It is remarkable that despite differences in host specificity and in
the number of dsRNA segments, aquareoviruses and orthoreoviruses
exhibit such extensive similarity. These similarities may suggest
that
these viruses, while belonging to distinct genera in the
family
Reoviridae, may indeed have evolved from a common ancestor.
Despite similar protease-induced disassembly profiles, the
orthoreoviruses
do not exhibit any increased infectivity like
aquareoviruses.
Protease-enhanced infectivity in aquareoviruses may
have resulted
from their necessity to survive in protease-rich regions
of the
host
organisms.
 |
ACKNOWLEDGMENTS |
This work was supported by NIH grant AI36040 to B.V.V.P.
We thank J. A. Lawton for helpful discussions and critical reading
of the manuscript.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Biochemistry and Molecular Biology, Rm. N410, Baylor College of
Medicine, One Baylor Plaza, Houston, TX 77030. Phone: (713) 798-5686. Fax: (713) 798-1625. E-mail: vprasad{at}bcm.tmc.edu.
 |
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Journal of Virology, July 2000, p. 6546-6555, Vol. 74, No. 14
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