Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus.
ABSTRACT Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging. The extensive structural similarity revealed by such portals in diverse viruses, as well as their invariable positioning at a unique icosahedral vertex, led to the consensus that a particular, highly conserved vertex-portal architecture is essential for viral DNA translocations. Here we present an exception to this paradigm by demonstrating that genome delivery and packaging in the virus Acanthamoeba polyphaga mimivirus occur through two distinct portals. By using high-resolution techniques, including electron tomography and cryo-scanning electron microscopy, we show that Mimivirus genome delivery entails a large-scale conformational change of the capsid, whereby five icosahedral faces open up. This opening, which occurs at a unique vertex of the capsid that we coined the "stargate", allows for the formation of a massive membrane conduit through which the viral DNA is released. A transient aperture centered at an icosahedral face distal to the DNA delivery site acts as a non-vertex DNA packaging portal. In conjunction with comparative genomic studies, our observations imply a viral packaging pathway akin to bacterial DNA segregation, which might be shared by diverse internal membrane-containing viruses.
- SourceAvailable from: David Gil-Carton[Show abstract] [Hide abstract]
ABSTRACT: In internal membrane-containing viruses, a lipid vesicle enclosed by the icosahedral capsid protects the genome. It has been postulated that this internal membrane is the genome delivery device of the virus. Viruses built with this architectural principle infect hosts in all three domains of cellular life. Here, using a combination of electron microscopy techniques, we investigate bacteriophage PRD1, the best understood model for such viruses, to unveil the mechanism behind the genome translocation across the cell envelope. To deliver its double-stranded DNA, the icosahedral protein-rich virus membrane transforms into a tubular structure protruding from one of the 12 vertices of the capsid. We suggest that this viral nanotube exits from the same vertex used for DNA packaging, which is biochemically distinct from the other 11. The tube crosses the capsid through an aperture corresponding to the loss of the peripentonal P3 major capsid protein trimers, penton protein P31 and membrane protein P16. The remodeling of the internal viral membrane is nucleated by changes in osmolarity and loss of capsid-membrane interactions as consequence of the de-capping of the vertices. This engages the polymerization of the tail tube, which is structured by membrane-associated proteins. We have observed that the proteo-lipidic tube in vivo can pierce the gram-negative bacterial cell envelope allowing the viral genome to be shuttled to the host cell. The internal diameter of the tube allows one double-stranded DNA chain to be translocated. We conclude that the assembly principles of the viral tunneling nanotube take advantage of proteo-lipid interactions that confer to the tail tube elastic, mechanical and functional properties employed also in other protein-membrane systems.PLoS Biology 09/2013; 11(9):e1001667. · 12.69 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increasing frequency. These large viruses (often called giruses) can encode up to 900 proteins and also many tRNAs. Consequently, these viruses have more protein-encoding genes than many bacteria, and the concept of small particle/small genome that once defined viruses is no longer valid. Giruses infect bacteria and animals although most of the recently discovered ones infect protists. Thus, genome gigantism is not restricted to a specific host or phylogenetic clade. To date, most of the giruses are associated with aqueous environments. Many of these large viruses (phycodnaviruses and Mimiviruses) probably have a common evolutionary ancestor with the poxviruses, iridoviruses, asfarviruses, ascoviruses, and a recently discovered Marseillevirus. One issue that is perhaps not appreciated by the microbiology community is that large viruses, even ones classified in the same family, can differ significantly in morphology, lifestyle, and genome structure. This review focuses on some of these differences than on extensive details about individual viruses.Annual review of microbiology 01/2010; 64:83-99. · 12.80 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last 20 years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide.Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 06/2010; Chapter 7:Unit 7.13.
Distinct DNA Exit and Packaging Portals
in the Virus Acanthamoeba polyphaga mimivirus
Nathan Zauberman1, Yael Mutsafi1, Daniel Ben Halevy1, Eyal Shimoni2, Eugenia Klein2, Chuan Xiao3, Siyang Sun3,
1 Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel, 2 Electron Microscopy Center, The Weizmann Institute of Science, Rehovot, Israel, 3
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging. The extensive
structural similarity revealed by such portals in diverse viruses, as well as their invariable positioning at a unique
icosahedral vertex, led to the consensus that a particular, highly conserved vertex-portal architecture is essential for
viral DNA translocations. Here we present an exception to this paradigm by demonstrating that genome delivery and
packaging in the virus Acanthamoeba polyphaga mimivirus occur through two distinct portals. By using high-resolution
techniques, including electron tomography and cryo-scanning electron microscopy, we show that Mimivirus genome
delivery entails a large-scale conformational change of the capsid, whereby five icosahedral faces open up. This
opening, which occurs at a unique vertex of the capsid that we coined the ‘‘stargate’’, allows for the formation of a
massive membrane conduit through which the viral DNA is released. A transient aperture centered at an icosahedral
face distal to the DNA delivery site acts as a non-vertex DNA packaging portal. In conjunction with comparative
genomic studies, our observations imply a viral packaging pathway akin to bacterial DNA segregation, which might be
shared by diverse internal membrane–containing viruses.
Citation: Zauberman N, Mutsafi Y, Ben Halevy D, Shimoni E, Klein E, et al. (2008) Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus.
PLoS Biol 6(5): e114. doi:10.1371/journal.pbio.0060114
The prevailing model for genome translocations in
icosahedral viruses entails a molecular motor that is localized
at a single vertex and comprises a packaging ATPase and a
portal complex [1–5]. The particular structural features
revealed by the vertex-portal assembly have been argued to
facilitate both genome delivery  and genome encapsidation
[3,6,7]. Although the functional implications of these features
have been recently challenged [8,9], their apparent conserva-
tion led to the paradigm that a single vertex-portal system
plays a crucial and general role in both genome injection and
packaging in icosahedral viruses .
Vertex-portal assemblies were, however, characterized only
in herpesviruses that contain an external lipid membrane
[3,4,10], and in tailed double-stranded DNA (dsDNA) bacter-
iophages in which membranes are absent [1,5–7,11]. This
point is noteworthy in light of recent studies, which implied
that DNA packaging machinery in viruses containing an
inner membrane layer is fundamentally different from the
vertex-portal apparatus of herpesviruses and bacteriophages
[12–14]. Specifically, inner membrane–containing viruses
were shown to contain putative DNA-packaging ATPases
that, in addition to the regular Walker A and B motifs, carry a
conserved motif that might act as a membrane anchor [12–
14]. The structural aspects that underlie genome trans-
location mechanisms deployed by these viruses remain,
however, largely unknown .
The amoeba-infecting virus Acanthamoeba polyphaga mimivi-
rus is a member of the nucleocytoplasmic large DNA viruses
(NCLDV) clade that comprises several eukaryote-infecting
viral families such as the Phycodnaviridae, Iridoviridae, and
Asfarviridae . As in all members of NCLDVs, the Mimivirus
is composed of a core containing a dsDNA genome, which is
surrounded by a lipid membrane that underlies an icosahe-
dral capsid [17–19]. The capsid is, in turn, covered by closely
packed 120-nm-long fibers that form a dense matrix at their
attachment site [17–19]. The closely packed fibers and the
dense layer at the base of these fibers represent a unique
feature of the Mimivirus. In addition, a single modified vertex
has been detected in mature particles .
With a 1.2–mega base pair (Mbp) dsDNA genome and a
particle size of ;750 nm, the Mimivirus represents the largest
virus documented so far, blurring the established division
between viruses and single-cell organisms [17,18,20]. Promp-
ted by these unique features, we conducted high-resolution
studies of the Mimivirus life cycle within its amoeba host,
focusing on genome delivery and packaging stages that
remain poorly understood in all members of the NCLDV
clade. By performing cryo-scanning electron microscopy and
electron tomography on cryo-preserved host cells at different
post-infection time points, we demonstrate that DNA exit
occurs in phagosome-enclosed viral particles through a
massive opening of five icosahedral faces of the capsid. This
large-scale capsid reorganization, which occurs at a unique,
Academic Editor: Bill Sugden, University of Wisconsin, Madison, United States of
Received December 4, 2007; Accepted March 25, 2008; Published May 13, 2008
Copyright: ? 2008 Zauberman et al. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
Abbreviations: cryo-SEM, cryogenic scanning electron microscopy; dsDNA,
double-stranded DNA; NCLDV, nucleocytoplasmic large DNA virus; TEM, trans-
mission electron microscopy
* To whom correspondence should be addressed. E-mail: avi.minsky@weizmann.
PLoS Biology | www.plosbiology.org May 2008 | Volume 6 | Issue 5 | e1141104
P PL Lo oS S BIOLOGY
structurally modified icosahedral vertex, allows for the fusion
of the internal viral membrane with the membrane of the
host phagosome. The fusion leads, in turn, to the formation
of a massive membrane conduit through which DNA delivery
occurs. In conjunction with single-particle reconstruction
studies that indicated the presence of two successive
membrane layers underlying the Mimivirus protein shell
, these observations raise the possibility that the Mim-
ivirus genome is released into the host cytoplasm and is
translocated toward the host nucleus enclosed within a vesicle
that is derived from the viral inner membrane.
We further show that DNA packaging into preformed
Mimivirus procapsids proceeds through a non-vertex portal,
transiently formed at an icosahedral face distal to the DNA
delivery site. Along with comparative genomic studies [12,13],
these results imply a viral packaging pathway reminiscent of
DNA segregation in bacteria, a pathway that might be
common to internal-membrane–containing viruses. Taken
together, the observations reported here may indicate that
Mimivirus and potentially other large dsDNA viruses have
evolved mechanisms that allow them to effectively cope with
the exit and entry of particularly large genomes.
Massive 5-Fold Assembly on the Mimivirus Capsid
Extracellular Mimivirus particles were sectioned following
cryo-fixation and examined by transmission electron micro-
scopy (TEM). Notably, all TEM specimens in the current study
were preserved through the high-pressure freezing technique
that, in sharp contrast to conventional chemical fixation
protocols, allows for instantaneous immobilization of all
structures in their native morphology. As such, this preser-
vation method is generally considered to be highly reliable
and hence optimal for electron tomography studies .
The extracellular particles reveal an unprecedented 5-fold
star-shaped structure that is localized at a single icosahedral
vertex and extends along the whole length of the five
icosahedral edges that are centered around this unique
vertex (Figure 1A). Geometric considerations of an icosahe-
dron structure modified along five icosahedral edges that is
randomly sliced indicate that if all viral particles include such
a massive assembly, parts of this structure should be
discerned in 75%–80% of the sections used for TEM analysis,
depending on the thickness (70–80 nm) of the sections. In
;500 extracellular viruses examined, the 5-fold assembly or
parts thereof were detected in ;400 particles (80%), thus
demonstrating that all viral particles contain this structure.
None of the examined extracellular viral particles or of the
intracellular particles (see below) revealed more than one
star-shaped structure per particle, a finding fully consistent
with single-particle cryo-TEM studies in which a single
modified vertex was detected .
The presence of the star-shaped assembly was further
confirmed by cryo-TEM studies conducted on whole extra-
cellular Mimivirus particles that were vitrified in their
hydrated state. Due to the interference of the extremely
dense fiber layer that surrounds the viral capsids , the 5-
fold structure could not be detected in mature particles, but
was clearly and consistently discerned in immature, fiber-less
viruses that constitute a small yet significant (;10%)
population of the viruses that are released upon lysis of the
amoeba cells at the completion of the infection cycle (Figure
To ascertain that the 5-fold assembly represents a general
and genuine feature, .500 extracellular Mimivirus particles
were analyzed by cryo-scanning electron microscopy (cryo-
SEM). These studies corroborate the presence of a massive 5-
fold structure at a unique vertex of the particle. The assembly
is detected in fiber-covered Mimivirus where it appears as
crevices, but is particularly conspicuous and consistently
revealed in immature fiber-less particles, where it takes the
form of prominent ridges (Figure 1C and 1D, respectively).
The crevices that characterize the 5-fold structure in mature
particles (Figure 1C) imply that this particular structure is
depleted of fibers, in contrast to all other regions of the
Electron tomography (Figure 1E and Video S1) and
volume-reconstruction analyses (Figure 1F–1H) were per-
formed on viral particles within infected amoeba cells at final
infection stages (12 hours post-infection), where cells are
crammed with mature viruses. The analyses indicate that the
Mimivirus capsid is composed of two superimposed shells
characterized by conspicuously different densities. This
observation, obtained from three tomography analyses
conducted on different intracellular viral particles, is
consistent with single-particle reconstruction studies, which
indicated the presence of a protein shell surrounded by a
distinct layer that corresponds to a dense base of fibers .
In addition to the two shells, a prominent star-shaped
structure is discerned in the intracellular Mimivirus particles
(Figure 1E). Volume-reconstruction analysis of the star-
shaped structure indicates that the outer shell adopts a
partially open configuration (corresponding to the dark star-
shaped region in Figure 1F). This open region is, however,
completely sealed by the underlying inner shell (Figure 1G),
an observation compatible with the ridges that delineate the
5-fold star-shaped structure in immature fiber-less particles
(Figure 1D). Figure 1H, which represents a superposition of
the two shells, demonstrates the perfect match between the
PLoS Biology | www.plosbiology.orgMay 2008 | Volume 6 | Issue 5 | e114 1105
Mimivirus: A Tale of Two Portals
Two fundamental events in viral life cycles are the delivery of viral
genomes into host cells and the packaging of these genomes into
viral protein capsids. In bacteriophages and herpesviruses, these
processes occur linearly along the genome, base pair after base pair,
through a single portal located at a unique site in the viral capsid.
We have addressed the question of whether such a linear
translocation through a single portal also takes place for viruses
harboring very large genomes, by studying genome delivery and
packaging in the amoeba-infecting virus Acanthamoeba polyphaga
mimivirus. With 1.2 million base pairs, this double-stranded DNA
genome is the largest documented viral genome. By using electron
tomography and cryo-scanning electron microscopy, we identified a
large tunnel in the Mimivirus capsid that is formed shortly after
infection, following a large-scale opening of the capsid. The tunnel
allows the whole viral genome to exit in a rapid, one-step process.
DNA encapsidation is mediated by a transient aperture in the capsid
that, we suggest, may promote concomitant entry of multiple
segments of the viral DNA molecule. These unprecedented modes
of viral genome translocation imply that Mimivirus—and potentially
other large viruses—evolved mechanisms that allow them to cope
effectively with the exit and entry of particularly large genomes.
ridges at the inner shell and the regions in which the outer
shell is missing.
The Stargate: A 5-Fold Structure That Acts as a Genome
A recent study implied that the initial stages of Mimivirus
infection occurs by phagocytosis . Our observations
support this notion by demonstrating the presence of
phagosomes containing one or several viral particles within
infected amoeba cells at early (2–3 h) post-infection time
points (Figures 2 and 3).
The different morphological aspects revealed by the
phagosome-enclosed viral particles are straightforwardly
interpreted as a result of sectioning the viruses along
different planes, as clarified in the inset in Figure 2A and
demonstrated in Video S2. Specifically, in a randomly sliced
section that contains the star-shape assembly and is parallel
to field of view depicted in the inset, a star-shape structure is
detected, as demonstrated in Figure 1A, 1E–1H, and in Figure
2A. If, on the other hand, the TEM section is sliced along a
plane parallel to that illustrated in the inset yet located below
the star-shape assembly, only unmodified vertices will be
detected, as indeed is the case for the viral particle shown in
Figure 2B. Sections perpendicular to a single star-like
assembly should reveal either one or two modified vertices,
which correspond to slices along the blue and red lines in the
inset, respectively. These two morphological aspects are
indeed manifested by the viral particles shown in Figure 2C
and in Figure 3A (particle 2), which reveal a single modified
vertex, and by particle 1 in Figure 3A, in which two modified
vertices (marked by red arrowheads) are visible. Such two
modified icosahedral edges that belong to the same star-
shaped assembly are particularly evident in thick sections that
are sliced along the red line in the inset, as indeed shown in
Figure 3B and in Video S2. In conjunction with the geometric
considerations described above, a statistical analysis con-
ducted on more than 100 phagosome-enclosed viral particles
(which basically represent mature virions) indicate that all
intracellular Mimivirus particles contain a modified, star-
shaped vertex, and that this vertex is unique, as is the case for
the extracellular Mimivirus particles.
Figure 3A shows a tomographic slice of a phagosome in
which three viral particles were captured at three successive
uncoating stages. Volume reconstruction of the particle 1
(early uncoating) reveals that in this virus, both the outer
(red) and inner (orange) capsid layers are opened at the star-
shaped assembly (Figure 3B). The opening of both shells is in
contrast with the morphology revealed by extracellular
viruses (Figure 1), as well as by intracellular particles during
early phagocytic stages (Figure 2C), in which the inner shell
appears to be completely sealed. This opening allows for the
lipid layer underlying the capsid shell (blue layer in Figure
3B) to protrude and extend towards the phagocytic mem-
brane. This stage is represented by the viral particle 2 in
Figure 1. Mimivirus Star-Shaped Structures
(A) TEM image of cryo-fixed sectioned and stained extracellular Mimivirus particles revealing a star-shaped structure at a unique vertex.
(B) Cryo-TEM image of a whole vitrified fiber-less Mimivirus.
(C) SEM image of the star-shaped structure in a mature extracellular Mimivirus particle.
(D) Cryo-SEM of an immature, fiber-less particle.
(E) Tomographic slice of a mature intracellular Mimivirus particle captured at a late (12 h post infection) infection stage. As shown in Video S1, at this
late stage the host cell is packed with mature viral particles.
(F and G) Volume reconstruction of the particle shown in (E), revealing the presence of an outer (red) and inner (orange) capsid shells. The star-shaped
structure is present in both shells but adopts partially open (dark, star-like region), and completely sealed configurations in the outer and inner shells,
(H) Superposition of the two shells in (F) and (G).
Scale bars, 100 nm in (A, B, D, and E), and 200 nm in (C).
PLoS Biology | www.plosbiology.orgMay 2008 | Volume 6 | Issue 5 | e1141106
Mimivirus: A Tale of Two Portals
Figure 3A. The final uncoating stage is demonstrated by the
particle 3 (Figure 3A). Surface rendering analysis of this virus
demonstrates a massive opening of five triangular icosahedral
faces that occurs at the star-shaped vertex and results in a
fusion of the viral (light blue) and phagocytic (dark blue)
membranes (Figure 3C). The three uncoating stages are
visible in the tomogram shown in Video S2.
We interpret these observations as indicating that the star-
shaped structure, which we coin ‘‘stargate’’, represents a
device that mediates a large-scale capsid opening, thus
allowing for the protrusion of the inner viral membrane
and a subsequent viral-phagosome membrane fusion. This
fusion results in the formation of a massive membrane tube
through which the genome core is released into the host
cytoplasm. The notion that DNA delivery occurs following
the formation of a membrane conduit is supported by the
presence of empty capsids within phagosomes (our observa-
tions and ). The large-scale capsid opening at the stargate
site, and the membrane tube are depicted in a schematic
model (Figure 4), which is based on the tomography (Figure
3A and Video S2) and surface rendering (Figure 3C) of
particle 3 in Figure 3A.
To identify the factors that promote the stargate opening
within the host phagosome, and in light of extensive fusion of
lysosomes with phagosomes in which viral uncoating occurs
(Figure 3A and Video S2), isolated Mimivirus particles were
exposed to acidic conditions (pH 6.5, 5.5, and 4.5) in the
absence or presence of lysozyme. None of these treatments
triggered stargate opening, implying that other or additional
factors are involved in effecting this structural reorganiza-
tion. Exposure of particles to elevated temperature (838C) for
30 min resulted in a release of membranal structures that
specifically occurred at the stargate site in ;10% of the
particles (Figure 5A). While physiologically irrelevant, this
finding implies that the stargate represents a structurally
susceptible site, a conjecture further supported by the
observation that a small population (,1%) of extracellular
particles reveals a conspicuous 5-fold opening (Figure 5B).
These capsids might represent faulty viral particles, or
particles that have ejected their genome and then released
to the medium upon viral-induced lysis of the host cells at the
completion of the infection cycle.
Viral Factories and DNA Packaging
Following release, the Mimivirus genome is imported into
the host nucleus and then translocated to a cytoplasmic viral
factory where viral assembly occurs . TEM studies of
infected and cryo-fixed amoeba cells reveal that already at 8 h
post-infection, viral factories are studded with empty, fiber-
less procapsids that are only partially assembled, as well as
with icosahedral procapsids undergoing DNA packaging
(Figures 6 and 7) . The occurrence of DNA packaging
into procapsids at the periphery of the factories (green
arrowheads in Figures 6 and 7) was supported by specific
DNA staining and Br-dU experiments (unpublished data).
Intriguingly, in some particles, the genome appeared to be
translocated at a vertex (Figure 6A) , whereas in others,
DNA translocation proceeds through an aperture located at
an icosahedral face (Figure 6B and 6C). A statistical survey of
a large number (.50) of intracellular viral factories indicated
that at any thin section of the factory analyzed in TEM, 20–25
viral particles are present at various stages of assembly. Out
of these assembling virions, 4–5 particles were captured at the
stage of DNA packaging, and within this population, pack-
aging through a face-located aperture, as shown in Figure 6B
and 6C, was consistently detected in 2–3 virions. Thus, in
more than 200 analyzed particles that undergo DNA pack-
aging, a face-centered rather than a vertex-centered pack-
aging is visible in more than 120 (;60%) particles.
Projection images derived from TEM studies of thin
Figure 2. Morphological Aspects of Phagosome-Enclosed Mimivirus Particles
(A) TEM projection of a phagosome-enclosed particle sectioned along a plane that contains the whole star-shaped structure. The observed features are
similar to those characterizing extracellular Mimivirus particles (Figure 1A) and mature intracellular particles (Figure 1E), thus indicating that the star-
shape assembly is present in the capsid throughout the life cycle of the Mimivirus. The inset provides the various possibilities for random sectioning of
the Mimivirus particle.
(B) TEM projection of a phagosome-enclosed particle sectioned along a plane that does not contain the star-shaped assembly, thus revealing only
(C) TEM projection of a phagosome-enclosed Mimivirus particle, revealing the star-shape structure (blue arrowhead) sliced in its center along the plane
depicted by a blue line in the inset in (A).
Scale bars, 100nm.
PLoS Biology | www.plosbiology.orgMay 2008 | Volume 6 | Issue 5 | e114 1107
Mimivirus: A Tale of Two Portals
sections cannot provide, however, unequivocal data on the
precise site of the packaging process, as such data can be
masked or incorrectly interpreted due to the angle of the site
within the TEM section relative to the electron beam. To
obtain deeper insights into the DNA packaging process in
Mimivirus, we performed electron tomography and volume
reconstruction analyses on three randomly chosen procapsids
during their assembly on the periphery of the viral factories.
Figure 3. Mimivirus Uncoating and Membrane Fusion
(A) Tomographic slice of a late phagosome enclosing three Mimivirus particles at early, advanced, and final uncoating stages (particles 1, 2, and 3,
respectively). At the early uncoating stage, a partial opening of the inner protein shell at the stargate assembly is initiated. The red arrowheads highlight
the star-shaped structure sectioned along the plane depicted by a red line in the inset in Figure 2A. The opening of the stargate allows for the extrusion
of the viral membrane towards the phagosome membrane, a stage characterizing particle 2. In the final uncoating stage, fusion between viral and
phagosome membranes occurs, as revealed in particle 3. The lysosomes surrounding the phagosome should be noted. The reconstructed volume of
the tomographic slice is shown in Video S2. Scale bar, 100nm.
(B) Volume reconstruction of particle 1 in (A), showing the outer (red) and inner (orange) capsid shells and the closely apposed inner membrane (light
blue). The opening of the star-shaped structure in the inner shell (in contrast to its closed configuration in extracellular particles or in particles enclosed
in early phagosomes) should be noted.
(C) Surface rendering of particle 3 in (A), showing fusion of the viral and phagosome membranes (light and dark blue, respectively) at the site of the
opened star-shaped structure. The boundary between the viral and phagosome membranes is arbitrary.
PLoS Biology | www.plosbiology.orgMay 2008 | Volume 6 | Issue 5 | e1141108
Mimivirus: A Tale of Two Portals
A slice of a tomogram obtained from one of these assembling
procapsids (Figure 7A; the whole tomogram is shown in Video
S3) demonstrates that DNA packaging proceeds through an
aperture that spans the outer and inner capsid shells, as well
as the internal membrane, and is located at the center of an
icosahedral face. The aperture, which is sealed following
completion of DNA packaging as implied by the structure of
mature particles, adopts a cone shape with diameters of 35
nm and 20 nm at the outer and inner shells, respectively.
These features, clearly discernible in the reconstructed
volume of the particle (Figure 7B), are detected in all three
tomograms of assembling procapsids. Notably, whenever
stargates are discerned in electron microscopy sections of
assembling viral particles, they are invariably detected at the
distal site of the factory, pointing away from the replication
center (Figures 6 and 7). This finding, which is consistent with
earlier observations , is particularly evident in tomograms
obtained from relatively thick sections (Figure 7 and Video
To substantiate our TEM results, we have isolated viral
factories by gentle lysis of infected amoeba cells at 8–10 h
post-infection, thus capturing successive assembly stages.
SEM studies of factories isolated at 8 h post-infection show
immature viral particles that abut on the periphery of the
factories and reveal conspicuous stargates (Figure 8A and 8B).
Due to the dense fiber layer, stargates are hardly discernible
in SEM analysis of mature particles, which are located further
away from the periphery. Notably, in viral factories isolated at
a 10 h post-infection (Figure 8C), only mature particles, which
presumably cover and mask the immature particles, can be
detected. Thus, the SEM results, obtained from .50 isolated
viral factories, corroborate the TEM studies conducted on
intracellular factories, and strongly imply that the stargate
structures represent an early stage of the viral assembly.
The observations reported here imply that in contrast to all
viral genome translocation processes heretofore character-
ized, DNA exit and packaging in the amoeba-infecting virus
Acanthamoeba polyphaga mimivirus proceed through different
portals, both revealing unparalleled features.
The Stargate Assembly
Mimivirus infection is initiated by phagocytosis , and
genome delivery occurs upon exposure of the virus to cues
within the host phagosome. While the nature of these cues
remains unknown, detection of multiple lysosomes under-
going fusion with the phagosomes (Figure 3A and Video S2)
may imply that lysosomal activity promotes the opening of
the viral capsid. The observations reported here indicate that
this opening entails a unique portal, the stargate, which is
located at a single icosahedral vertex (Figures 1–5), in keeping
with previous single-particle studies , in which a single
modified vertex has been identified. These studies, as well as
our electron tomography observations (Figure 1E–1H) re-
vealed that the Mimivirus is composed of a protein shell
surrounded by an outer layer corresponding to a dense base
Our cryo-TEM (Figure 1B), cryo-SEM (Figure 1C and 1D),
and electron tomography of cryo-fixed specimens (Figure 1E–
1H) indicate that the stargate is located within the protein
shell, extending along the whole length of five icosahedral
edges that are centered around a single icosahedral vertex,
thus forming an assembly of unprecedented morphology and
dimensions. The icosahedral edges appear as prominent
ridges in the protein shell, which are clearly discerned in
immature, extracellular viral particles that lack the dense
fiber layer (Figure 1D). Our observations further indicate that
while the outer shell surrounds most of the inner protein
shell, it is absent along the icosahedral edges that constitute
the stargate (Figure 1F). This fiber-less region is likely to
enable the cues that trigger the opening of the stargate to
reach their specific target in the inner protein shell. Notably,
the stargate is detected in extracellular Mimivirus particles, in
phagosome-enclosed virions, in mature intracellular viral
particles present within the amoeba host cells at the final
infection stage (Figures 1 and 2 and Video S1), as well as in
assembling virions (Figures 6–8), thus indicating that this
prominent assembly is present in the Mimivirus capsid
throughout the virus life cycle.
Genome Exit: Potential Vesicle-Mediated DNA Release and
The large-scale conformational change of the capsid
whereby the five icosahedral faces centered on the unique
stargate vertex open up, allows the extrusion of the viral
membrane that underlies the viral protein shell. This
extrusion is followed by the fusion of the viral membrane
with the phagosome membrane, thus resulting in the
formation of a large membrane conduit (Figures 3–5 and
Video S2) through which the Mimivirus genome is presum-
ably released into the host cytoplasm. The actual mode of
DNA release remains unclear, as in all virus-containing
Figure 4. Schematic Representation of a Mimivirus Particle at Its Final
The capsid (red) is opened at the stargate, allowing for fusion of the viral
and phagosome membranes (light and dark blue, respectively), thus
forming a star-shaped membrane conduit (See Video S2 for the
tomogram from which the model was derived).
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Mimivirus: A Tale of Two Portals
phagosomes inspected in this study (.100), only mature
viruses, viruses at various uncoating stages, or empty viral
particles could be discerned (Figures 2 and 3).
In light of the size of the Mimivirus genome, the failure to
capture genome release is intriguing. On the basis of cryo-
TEM studies of Mimivirus particles  that implied the
presence of two successive membrane layers underlying the
protein shell (as is the case for at least one additional member
of the NCLDV clade, the African Swine Fever Virus [22,23]), it
can be hypothesized that the Mimivirus genome is released
into the host cytoplasm enclosed within a vesicle. Such a
vesicle might be derived from the inner membrane layer,
whereas the outer membrane forms a conduit for this DNA-
containing vesicle by fusing with the phagosome. This
conjecture provides a rationale to the need for the massive
opening of the capsid that is reported here, a possible reason
for the failure to capture DNA release (as a vesicle-mediated
release would likely be a fast process), as well as a plausible
answer to the question how is the viral genome protected
against host nucleases during its transport to the host
nucleus. Moreover, the notion of a vesicle-mediated exit
and transport of the Mimivirus genome provides a potential
and highly attractive solution to the question of how is a 1.2-
Mbp DNA molecule translocated through the extremely
crowded cytoplasm of the host, which has been shown to
present a supreme barrier for translocation of long DNA
molecules . The notion of genome release and trans-
portation within a vesicle that is derived from internal viral
membranes is, to the best of our knowledge, unprecedented
and is being currently investigated.
Notably, while DNA injection and packaging in the
internal-membrane–containing tail-less bacteriophage PRD1
appear to occur through a unique vertex , in vitro studies
implied that PRD1 delivers its genome through a membrane
tube . For this to occur, the PRD1 capsid must open up in
a yet uncharacterized process that might be similar to the
genome release process occurring in Mimivirus. High-
resolution structural studies of PRD1 life cycle will be
required to address this intriguing possibility.
Mimivirus assembly occurs in cytoplasmic viral factories
. DNA is packaged into preformed procapsids located at
the periphery of factories (Figure 6). Studies of intra-
cellular factories (Figures 6 and 7) as well as of viral factories
isolated at various post infection time points (Figure 8)
indicate that the formation of the stargate structure occurs at
a very early stage of the viral assembly. These observations
imply that in addition to acting as a DNA release portal, the
stargate might be involved in the initiation of Mimivirus
particles assembly. Such an initiation role is in keeping with
the fact that capsids incorporate only one portal that is
located at a unique vertex, and this symmetry-breaking step
can only be rationalized in terms of a singular event, as is the
initiation stage. Indeed, previous studies indicated that
portals are involved in the initiation of capsid assembly in
herpesviruses and several bacteriophages such as T4 and
(A) SEM image depicting the release of membranal structures following exposure of mature, extracellular Mimivirus particles to 83 8C for 30 min.
Membrane release consistently occurs at the stargate (arrows pointing to the fiber-less edges of the stargate).
(B) Extracellular Mimivirus particle revealing a conspicuous 5-fold opening. Such open stargates were detected in a small population of extracellular
particles, and may represent empty viral particles released upon the viral-induced lysis of the host cells.
Scale bars, 100nm.
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Mimivirus: A Tale of Two Portals
Genome Packaging through a Face-Located Portal
Our electron tomography and volume reconstruction
analyses, supported by TEM and SEM studies, demonstrate
that DNA packaging in Mimivirus proceeds through a
transient aperture located at a distal site of the stargate site.
These studies further indicate that in contrast to all
heretofore-characterized viruses, Mimivirus genome pack-
aging occurs at an icosahedral face rather than at a vertex
(Figures 4–6 and Video S3). Notably, 3-nm-wide pores
detected on the 3-fold axes in ‘‘open’’ procapsids of the a3
bacteriophage of the Microviridae family were proposed as
possible DNA entry sites [29,30]. In the current study, such a
face-centered, non-vertex, DNA packaging site is directly
demonstrated. The functional significance of this finding
becomes apparent in light of recent biochemical and
comparative genomic studies, which indicated that inner-
membrane–containing viruses such as bacteriophage PRD1
and members of the NCLDV clade (including Mimivirus) code
for proteins that are closely homologous to ATPases of the
FtsK/SpoIIIE/HerA superfamily [12–14]. These ATPases were
proposed to act as membrane-anchored motors that pump
DNA through a closing membranal septum during bacterial
and archaean division [31,32]. On the basis of these findings
and considerations, it has been suggested that viruses
containing inner membranes package their genomes through
a pumping mechanism akin to the DNA segregation pathway
deployed in bacteria and archaea [12–14].
Our observations complement this conjecture. Since FtsK/
SpoIIIE/HerA ATPases mediate a strictly unidirectional mode
of DNA translocation [31,32], this system is unlikely to be
responsible for both exit and packaging of viral genomes. In
keeping with this notion, we identify distinct exit and entry
portals in Mimivirus. Moreover, whereas a vertex-centered
motor for DNA packaging in bacteriophages and herpesvi-
ruses represents a thermodynamically sensible solution,
because it minimizes vertex-portal interactions, such a setting
would be incompatible with a pumping system that must rely
on robust motor–membrane interactions. Such interactions
can, however, be maximized when the packaging motor is
located within an icosahedral face (rather than on an
icosahedral vertex). In addition, our conjecture that the
DNA entry portal is sealed once packaging is concluded is
Figure 6. Intracellular Viral Factories and DNA Packaging
(A) TEM of an intracellular viral factory, revealing Mimivirus particles at various assembly stages. Empty, fiber-less particles at initial assembly stages,
appearing at close vicinity to the periphery of the viral factory (purple arrowheads); partially assembled empty, fiber-less particles (blue); and mature,
fiber-covered particles located further away from the viral factory than immature particles (yellow). A stargate that is consistently located at the distal
site of the factory can be discerned in several particles (red arrowheads). VF and Cyt stand for viral factory and cytoplasm.
(B and C) TEM of Mimivirus particles undergoing DNA packaging through a non-vertex face-centered site (green arrowheads). Two edges of a stargate
located at the opposite site of the DNA packaging site are indicated with red arrowheads. Approximately 60% of viral particles undergoing DNA
packaging (;120 particles out of ;200 analyzed in this study) reveal a face-centered DNA packaging site, while in other virions the packaging site is
unclear. As discussed in the text, the reason for this apparent ambiguity in the packaging site results from intrinsic constraints in the interpretation of
data derived from projection TEM studies of thin sections. More inclusive data on this issue can, however, be obtained from electron tomography
analyses of thick sections, as demonstrated in Figure 7 and in Video S3.
Scale bars: 500 nm in (A), 200 nm in (B), 100 nm in (C).
PLoS Biology | www.plosbiology.orgMay 2008 | Volume 6 | Issue 5 | e1141111
Mimivirus: A Tale of Two Portals
consistent with recent studies that indicated that the DNA
translocating ATPase SpoIIIE promotes membrane fusion
following completion of bacterial DNA segregation .
Interestingly, the cone-shaped aperture through which DNA
is packaged is characterized by a diameter of 20 nm at the
inner shell, thus capable of accommodating more than a
single DNA duplex, as indeed is implied by TEM studies
(Figures 6 and 7). Of note in this context is the conjecture
that several SpoIIIE rings might fuse to form a larger ATPase
The size and genome complexity of the Mimivirus call into
question the conventional division between viruses and
single-cell organisms. Our findings, which support the
conjecture that the DNA packaging mechanism deployed by
internal-membrane–containing viruses might share structur-
al and functional patterns with bacterial DNA segregation
[12–14], further substantiate the notion that the conventional
division between viruses and single-cell organisms should be
re-examined. Moreover, the observations concerning the
stargate and its massive opening, the DNA packaging
machinery, as well as the possibility raised here that the exit
and transportation of the genome occur within a vesicle
derived from a viral internal membrane, may indicate that
Mimivirus and potentially other large dsDNA viruses have
evolved mechanisms that allow them to effectively cope with
the exit and entry of particularly large genomes.
Because structure, rather than genomic sequence, repre-
sents the most reliable determinant for viral lineage , the
structural features underlying the Mimivirus replication cycle
raise intriguing questions. The presence of distinct portals
for genome exit and entry, as well as the shape of the stargate
and the unprecedented face-centered location of the pack-
aging portal, may indicate that Mimivirus represents a unique
specimen. It is, however, enticing to suggest that these
features, along with their functional and evolutionary
implications, are shared by diverse viruses containing
internal membranes. This conjecture, which is consistent
with comparative genomic studies [12,13,16,34], as well as
with the notion that an inner membrane represents a key
factor for viral evolution and classification [35,36], is being
currently tested by high-resolution studies of the replication
cycles of various inner membrane-containing viruses. Finally,
for only a small fraction of the open reading frames in
Mimivirus, genome function has been attributed . The
observations reported here may stimulate further studies on
the Mimivirus that will focus on heretofore uncharacterized
structural features, including the stargate, its putative role in
Mimivirus assembly, and its massive opening, as well as the
face-centered DNA packaging apparatus. Such studies are
likely to provide deeper insights into the unusually complex
genome of this virus and into the factors that directed and
dictated its evolution.
Material and Methods
Sample preparation for TEM and electron tomography. Acantha-
moeba polyphaga were cultivated and infected by Mimivirus as
previously described . Infected cells at various post infection
time points were cryo-immobilized by the high-pressure freezing
technique , using an HPM high-pressure freezer (BAL-TEC).
Samples were then freeze-substituted (Leica EM AFS) in dry acetone
containing 2% glutaraldehyde and 0.1% tannic acid for 60 h at ?90
8C, and warmed up to room temperature over 24 h. Following
acetone rinses, samples were incubated in 0.1% uranyl acetate (UA)
and 1% OsO4for 1 h, infiltrated with increasing concentrations of
(A) Tomographic slice of a procapsid undergoing DNA packaging. The DNA-loaded packaging gateway and the stargate are highlighted (green and red
arrowheads, respectively). Scale bar, 100 nm.
(B) Volume reconstruction of the particle depicted in (A) showing the orifice through which DNA (green) is packaged, which spans the outer and inner
capsid shells, and the internal membrane (red, orange, and blue, respectively). The protein core underlying the membrane is shown in gray (See Video
S3 for the whole tomogram).
Electron Tomography of a DNA Packaging Site
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Mimivirus: A Tale of Two Portals
Epon over 6 d, and polymerized at 60 8C. Thin sections (50–70 nm),
obtained with an Ultracut UCT microtome (Leica) were post-stained
with 1%–2% uranyl acetate and Reynold’s lead citrate and examined
using FEI Tecnai T12 TEM operating at 120 kV. Images were
recorded on a MegaView III CCD (SIS). Preparation of vitrified
Mimivirus and cryo-TEM studies were as described in .
For electron tomography, semi-thick sections (170–200 nm)
decorated on both sides with 12-nm colloidal gold markers were
prepared as described above, and post-stained with 2% UA. Double-
tilted image series were acquired in FEI Tecnai F-20 TEM operating
at 200 kV. Images were recorded on a 4kx4k TemCam CCD camera.
Acquisition was performed at 18 intervals over a range of 6688, using
SerialEM program . Alignment and 3D reconstruction were
performed with IMOD image-processing package . IMOD and
Amira 4.1 packages were used for modeling.
Sample preparation for SEM and cryo-SEM. Viruses purified by
filtration were fixed with 2% gluteraldehyde in Cacodylate buffer for
1 h. Viruses were deposited on poly-L-lysine–treated formvar-coated
200-mesh Ni grids, post-fixed with 1% OsO4, 1% tannic acid, and 1%
uranyl acetate. Dehydration in increasing ethanol concentrations was
followed by critical point drying using CPD30 (BAL-TEC). Samples
were sputter-coated with 2-nm Cr and visualized in the high-
resolution SEM FEG Ultra 55 (Zeiss). For cryo-SEM experiments,
samples were fixed in 2% gluteraldehyde for 1 h, washed with DDW
and deposited on Aclar disk (EMS). Samples were frozen by plunging
in liquid ethane, freeze-dried for 1 h at ?100 8C in a BAF60 freeze-
fracture device (BAL-TEC) and rotary shadowed at 458 with 2-nm
platinum-carbon and 5-nm carbon at ?120 8C. Samples were
transferred to Ultra 55 SEM using a VCT100 vacuum-cryo-transfer,
and observed at ?120oC.
Replication factories were isolated using the spheroplast method-
ology [39,40]. Specifically, Acanthamoeba polyphaga were cultivated and
infected by Mimivirus. The infected cells were washed with ice-cold
20 mM potassium phosphate buffer, pH 6.5, at different times post
infection, and transferred into a glass tube at a concentration of 105
cells/ml. The cells were diluted with two volumes of ice-cold DDW,
and incubated for 10 min on ice. The swollen cells were then
incubated in ice-cold 0.3 M NaCl in 20 mM potassium phosphate
buffer, pH 6.5 for 10 min. Aliquots of 10 ll were deposited on top of
40 ll fixative 1 (4% paraformaldehyde in 20 mM potassium
phosphate, 0.2 M sucrose, pH 6.5) and spun onto poly-L-lysine-
treated silicon chips at 4000g in a swing out rotor for 5 min. The
samples were further fixed in fixative 2 (2% glutaraldehyde, 0.2%
tannic acid in 20 mM potassium phosphate, 0.2 M sucrose, pH 6.5) for
10 min. The chips were washed in DDW and treated with 1% OsO4
(DDW) for 10 min, washed with DDW and stained with 1% UA (DDW)
for 10 min. Samples were then prepared for SEM analysis by ethanol
dehydration followed by critical point drying. The dried samples were
coated with 2-nm chromium in a stage-rotation mode. The 535 mm
silicon chips were pre-treated with 0.1% poly-L-lysine (in DDW) and
incubated in a humid chamber over-night at 4 8C.
Video S1. Electron Tomogram of an Infected Amoeba Host Cell at
Late Infection Stage
The tomogram includes a large number of mature, intracellular
Mimivirus particles at a late (12 h post infection) stage of the
infection cycle. At this stage, the virions are crammed within the host
cytoplasm. All morphological aspects of the stargates can be
discerned in the various viral particles, as function of the sectioning
plane. Each frame of the movie is an average of ten 0.9-nm slices of a
thick section of the amoeba host cell.
Found at doi:10.1371/journal.pbio.0060114.sv001 (6.50 MB MPG).
Video S2. Electron Tomogram of a Late Phagosome Enclosing Three
Mimivirus Particles at Early, Advanced, and Final Uncoating Stages
In the particle at the upper right side of the phagosome, the vertex
containing the stargate is clearly visible. The tomogram provides an
interpretation to the observation that two vertices appear to be
modified, by showing that these two sites actually belong to the same
vertex and correspond to the stargate edges. The extrusion of the
viral membrane towards the phagosome membrane is visible in the
particle at the bottom on the right side of the phagosome. The
opening of the stargate and formation of the membrane tube through
fusion of the viral and phagosomal membranes are indicated in the
particle at the left region of the phagosome. Note the fusion of
lysosomes with the phagosome. Each frame of the movie represents
an average of ten 0.9-nm slices of a thick section of a Mimivirus
Found at doi:10.1371/journal.pbio.0060114.sv002 (4.05 MB MPG).
Packaging at the Periphery of a Viral Factory (Figure 7A)
Note the stargate structure at the opposite site of the DNA packaging
site. Each frame of the movie is an average of ten 2.7-nm slices of a
thick section of a Mimivirus particle.
Found at doi:10.1371/journal.pbio.0060114.sv003 (2.02 MB MPG).
Electron Tomogram of a Procapsid Undergoing DNA
We thank M. Rossmann, J. Van Etten, A. Steven, D. Bamford, L.
Aravind, K. Suhre, and Y. Shaul for critically reading and comment-
ing on the manuscript. We would also like to thank J. Errington and
Figure 8. Isolated Viral Factories
(A) SEM of a viral factory within an amoeba cell lysed 8 h post infection. A high-magnification image of the site indicated by the yellow arrowhead
(inset) shows assembling fiber-less particles with stargates (red arrowheads), as well as mature fiber-coated particles.
(B) SEM of a viral factory isolated 8 h post infection. The factory is studded with viral particles at various assembly stages. Stargates are indicated with
(C) SEM of a viral factory isolated 10 hours post infection. Only mature, fiber-covered particles can be detected. Scale bars are 2 lm in (A), 300 nm in (B),
and 500 nm in (C).
PLoS Biology | www.plosbiology.orgMay 2008 | Volume 6 | Issue 5 | e1141113
Mimivirus: A Tale of Two Portals
D. Sherratt for insights on the SpoIIIE motor. The electron
microscopy studies were conducted at the Irving and Cherna
Moskowitz Center for Nano and Bio-Nano Imaging at the Weizmann
Institute of Science. AM dedicates this paper to the late Professor
Jeremy Knowles, a friend and revered mentor.
Author contributions. NZ, YM, and AM conceived and designed the
experiments. NZ, YM, DBH, and CX performed the experiments. NZ,
YM, AM, ES, and EK analyzed the data. NZ, ES, EK, and SS
contributed reagents/materials/analysis tools. AM wrote the paper.
Funding. The research was supported by the Minerva Foundation,
Competing interests. The authors have declared that no competing
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Mimivirus: A Tale of Two Portals