Mimivirus unveiled

Alan Cann blogged on May 13th 2008 on mimivirus structure, in “Mimivirus and the Stargate“, following publication of a PLoS Biology paper on “Distinct DNA Exit and Packaging Portals in the Virus Acanthamoeba polyphaga mimivirus by Abraham Minsky’s group at the Weizman Institute in Israel.  This paper has some stunning EM images and cryoEM reconstructions, which prompt their summary statement:

“…we identified a large tunnel in the Mimivirus capsid that is formed shortly after infection, following a large-scale opening of the capsid [which they term the “stargate”]. 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.”

Given that PLoS Biology has an Open Access policy which  “…allow[s] anyone to download, reuse, reprint, modify, distribute, and/or copy articles in PLoS journals, so long as the original authors and source are cited”,  I HAVE to share these pictures with you.


Mimivirus Stargate

Mimivirus Stargate

(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.
(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, respectively.
(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).

Schematic Representation of a Mimivirus Particle at Its Final Uncoating Stage

Zauberman N, Mutsafi Y, Ben Halevy D, Shimoni E, Klein E, et al. (2008) Distinct DNA exit and packaging portals in the virus PLoS Biol 6(5): e114.   doi:10.1371/journal.pbio.0060114


Schematic Representation of a Mimivirus Particle at Its Final Uncoating Stage

Schematic Representation of a Mimivirus Particle at Its Final Uncoating Stage


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.

Zauberman N, Mutsafi Y, Ben Halevy D, Shimoni E, Klein E, et al. (2008) Distinct DNA exit and packaging portals in the virus PLoS Biol 6(5): e114.   doi:10.1371/journal.pbio.0060114



 I commented at the time of Alan’s blog that:

“It is becoming apparent to me – especially now as I do a 10-year revision of my Web teaching material – that there is a hitherto unsuspected level of complexity in the way big viruses get their genomes into cells – and back out into virions. Phycodnaviruses may emulate phages in dissolving their way through cell walls AND injecting DNA; now mimiviruses have special mechanisms for both loading virions and getting their DNA out.

Watch this space: a major growth area in structural biology and virology.”

And, of course, it has come to pass: Michael Rossmann’s group at Purdue University and their collaborators have just published a paper entitled “Structural Studies of the Giant Mimivirus” , also in PLoS Biology, in which they explore in greater detail aspects of the structure, particularly as this is related to getting DNA out of the particles.

Their paper has the most stunning images and reconstructions, including images which show that the “starfish” shaped portal seems to be detachable – and that the unique stargate-associated 5-fold rotational axis of symmetry also has associated with it a depression in the inner nucleocapsid, which is undoubtedly associated with delivery of the DNA within.


(A–C) Surface-shaded rendering of cryoEM reconstruction of untreated Mimivirus. (A) Looking down the starfish-shaped feature associated vertex, (B) looking from one side, and (C) looking from the opposite side of the “starfish”-associated vertex.

(D) The “starfish”-associated vertex was removed to show the internal nucleocapsid with its concave surface facing the special vertex.

(E) Central slice of the reconstruction looking from the side of the particle showing the concave face of the nucleocapsid and the low density space beneath the “starfish”-associated vertex. A perfectly icosahedral particle is outlined in gray to show the extension of the unique vertex.

(F) Central slice of the reconstruction looking along the 5-fold axis from the starfish-shaped feature showing the enveloped nucleocapsid surrounded by a lower density space. The coloring is based on radial distance from the center of the virus. Gray is from 0 to 1,800 Å, red from 1,800 to 2,100 Å, and rainbow coloring from red to blue between 2,100 and 2,500 Å.

The scale bars in all panels represent 1,000 Å.


This latest paper makes summary comments as follows:

“The enveloped genome within the larger viral capsid, perhaps supported by fibers …, has some similarity to eukaryotic cells. In contrast, the external peptidoglycan component mimics bacterial cell walls …. In addition, the existence of a unique vertex in Mimivirus, possibly for genome delivery …, is reminiscent of tailed bacteriophages. These observations are consistent with other results …, implying that Mimiviruses and some other large icosahedral dsDNA viruses have gathered genes from eukaryotic, prokaryotic, as well as archaeal origins [my emphasis].

The three-dimensional cryoEM reconstruction reported here, which was made possible in part by relaxing the icosahedral symmetry, is of a virus whose volume is an order of magnitude larger than has previously been reported. Thus, the detection of a unique vertex may have been missed in other structural studies in which strict icosahedral symmetry had been imposed [my emphasis].”

There are two important points here – one of which may be wrong.

The first is that mimiviruses et alia “…have gathered genes from eukaryotic, prokaryotic, as well as archaeal origins”: given the evolutionary speculations published by Susan-Monti et al. (Virus Research 117 (2006) 145–155), who say:

“Our current hypothesis is that DNA viruses are of deep evolutionary origin close to the origin of the other domains of life.”,

and point out the virus does not seem to have exchanged much DNA (=horizontal gene transfer) with its host despite a presumably ancient association.  This builds on Suhre et al. (PNAS 102 : 14689-14693, 2005), who say:

“Our bioinformatics and comparative genomics study revealed a unique feature of Mimivirus among the eukaryotic domain [sic]: the presence of a highly conserved AAAATTGA motif in the immediate 5′ upstream region of 50% of its protein-encoding genes. By analogy with the known promoter structures of unicellular eukaryotes, amoebal organisms in particular, we propose that this motif corresponds to a TATA box-like core promoter element. This element, and its conservation, appears to be specific of the Mimivirus lineage and might correspond to an ancestral promoter structure predating the radiation of the eukaryotic kingdoms ….

Mimivirus genes exhibiting this type of promoter might be ancestral as well. [my emphasis].”

Thus, it is possibly more likely that eukaryotes and possibly prokaryotes have garnered genes from mimi- and other viruses, rather than the converse!

The second point, given that they ARE a structural biology group, is much more likely: missing unique non-icosahedral capsid structures because of averaging could mean there is a whole world of specialised machinery in large DNA viruses which has simply been missed up till now.

I reiterate, watch this research space….  Anyone interested in mimivirus basics would also be well advised to look here.

6 Responses to “Mimivirus unveiled”

  1. Viruses as nanomachines! Or: what you can believe from YouTube « ViroBlogy Says:

    […] However, there is more to viruses and nanotechnology than phages with contractile tails, whether or not they have been around for billions of years: mimiviruses too have both nanoscale DNA loading and rapid-delivery systems, as previously discussed here. […]

  2. Dankzij virussen een celkern? « Visionaire berichten Says:

    […] enzymen: een eigen machinerie om zichzelf te kopiëren dus. Veel onderzoekers denken daarom dat het mimivirus misschien ten grondslag lag aan de celkern. Als een bacterie werd overgenomen door een mimivirus-achtig organisme, zou deze misschien in de […]

  3. Virus origins: from what did viruses evolve or how did they initially arise? « ViroBlogy Says:

    […] as cell-derived subcomponents is not as obvious.  In fact, the largest viruses yet discovered – mimiviruses, with a genome size of greater than 1 million base pairs of DNA – have genomes which are larger […]

  4. Goodbye, Mimi – we got Mega! « ViroBlogy Says:

    […] have blogged earlier on Mimivirus structure and evolution – see “Mimivirus unveiled” – and it is nice to see that an important speculation from those earlier […]

  5. Linda Pifer, Ph.D. Says:

    Absolutely remarkable work! I think we will see wonders within wonders in these fascinating little “machines”!

  6. jonas Says:

    wow this is awesome and i am a 8 year old boy! and a virologist i have been searching at a bunch of viruses like that bacteriophage T4 virus at the top of the page on the left

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