Structural Studies of the Giant Mimivirus

Abstract

Mimivirus is the largest known virus whose genome and physical size are comparable to some small bacteria, blurring the boundary between a virus and a cell. Structural studies of Mimivirus have been difficult because of its size and long surface fibers. Here we report the use of enzymatic digestions to remove the surface fibers of Mimivirus in order to expose the surface of the viral capsid. Cryo-electron microscopy (cryoEM) and atomic force microscopy were able to show that the 20 icosahedral faces of Mimivirus capsids have hexagonal arrays of depressions. Each depression is surrounded by six trimeric capsomers that are similar in structure to those in many other large, icosahedral double-stranded DNA viruses. Whereas in most viruses these capsomers are hexagonally close-packed with the same orientation in each face, in Mimivirus there are vacancies at the systematic depressions with neighboring capsomers differing in orientation by 60°. The previously observed starfish-shaped feature is well-resolved and found to be on each virus particle and is associated with a special pentameric vertex. The arms of the starfish fit into the gaps between the five faces surrounding the unique vertex, acting as a seal. Furthermore, the enveloped nucleocapsid is accurately positioned and oriented within the capsid with a concave surface facing the unique vertex. Thus, the starfish-shaped feature and the organization of the nucleocapsid might regulate the delivery of the genome to the host. The structure of Mimivirus, as well as the various fiber components observed in the virus, suggests that the Mimivirus genome includes genes derived from both eukaryotic and prokaryotic organisms. The three-dimensional cryoEM reconstruction reported here is of a virus with a volume that is one order of magnitude larger than any previously reported molecular assembly studied at a resolution of equal to or better than 65 Å.

mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus

“…However, a closer inspection of the genes clustered in the same expression class indicates that their individual transcription profiles are not superimposable ( The biological relevance of the three main classes of transcription profiles was confirmed by examining the expression pattern of several genes of known function. The ''late'' expression class, for instance, includes genes encoding structural components of the Mimivirus particles (such as the main capsid protein L425 or the core protein L410) or genes encoding enzymes carried by the particle (such as the glucose-methanol-choline [GMC]-type oxydoreductase R315) or enzymes most likely involved in the biosynthesis of the lipopolysaccharide (LPS)-like outer layer of the virus particle Claverie et al 2009a;Xiao et al 2009) (L136, R689, L780) ( Accordingly, the proportion of genes from this class, the products of which were also detected in the particle proteome (Renesto et al 2006;Claverie et al 2009a), is much higher than in the other expression classes (Fig. 4E).…”

“…The nondetection of these proteins-as well as of the minor capsid proteins-in the particle proteome might be due to extensive post-translational modifications or to their covalent association with an insoluble LPS-like moiety (Raoult et al 2004;Claverie and Abergel 2009;Claverie et al 2009a;Xiao et al 2009) conferring its exceptional solidity to the Mimivirus particle.…”

“…The unique features of Mimivirus revived the debate about the evolution of DNA viruses (Claverie 2006;Claverie et al 2006;Iyer et al 2006) and their position in the Tree of Life (Brüssow 2009;Claverie and Ogata 2009;Moreira and Lopez-Garcia 2009). The complex Mimivirus particle has been the object of detailed proteomic (Renesto et al 2006) and ultrastructural studies (Zauberman et al 2008;Xiao et al 2009), and several individual gene products have been characterized (for review, see Claverie and Abergel 2009); however, a systemic description of the molecular processes at work during the intracellular Mimivirus replication cycle (in particular the eclipse phase) is missing. During this phase, the Acanthamoeba cells are instructed by the infecting Mimivirus to build up a giant organelle-like ''virion factory'' that appears to centralize most of the metabolic processes leading to the synthesis of new Mimivirus particles (Suzan-Monti et al 2007;Claverie and Abergel 2009;Claverie et al 2009b).…”

Future challenges for x-ray microscopy

“…These are intruiging results; however, given the scaling of scattered signals with resolution, it is not yet clear whether these approaches can be extended towards or beyond the resolution obtained in single particle cryo electron microscopy. In addition, both carboxysomes [40,41,42] and mimivirus [43,44] are imaged as individual samples (rather than as an ensemble average structure via single particle imaging) today at higher resolution using cryo electron microscopy (EM). Thus the greatest potential for single particle x-ray imaging may be for objects thicker than the sub-micrometer thickness that EM can tackle, but a challenge may be the increasing structural variability associated with increasing object size (Fig.…”

“…As one gets to larger structures, one can find a greater range of conformational variations in macromolecules; one can sort for a number of these variations in single particle electron microscopy [52,53,54,55]. Individual variations are seen in the interiors of larger viruses (see for example [43,44]), and by the time one reaches the length scale of bacteria and especially with eukaryotic cells, one has a large degree of structural heterogeneity.…”