Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories

Abstract

The recent discovery of multiple giant double-stranded DNA (dsDNA) viruses blurred the consensual distinction between viruses and cells due to their size, as well as to their structural and genetic complexity. A dramatic feature revealed by these viruses as well as by many positive-strand RNA viruses is their ability to rapidly form elaborate intracellular organelles, termed "viral factories," where viral progeny are continuously generated. Here we report the first isolation of viral factories at progressive postinfection time points. The isolated factories were subjected to mass spectrometry-based proteomics, bioinformatics, and imaging analyses. These analyses revealed that numerous viral proteins are present in the factories but not in mature virions, thus implying that multiple and diverse proteins are required to promote the efficiency of viral factories as "production lines" of viral progeny. Moreover, our results highlight the dynamic and highly complex nature of viral factories, provide new and general insights into viral infection, and substantiate the intriguing notion that viral factories may represent the living state of viruses. IMPORTANCELarge dsDNA viruses such as vaccinia virus and the giant mimivirus, as well as many positive-strand RNA viruses, generate elaborate cytoplasmic organelles in which the multiple and diverse transactions required for viral replication and assembly occur. These organelles, which were termed "viral factories," are attracting much interest due to the increasing realization that the rapid and continuous production of viral progeny is a direct outcome of the elaborate structure and composition of the factories, which act as efficient production lines. To get new insights into the nature and function of viral factories, we devised a method that allows, for the first time, the isolation of these organelles. Analyses of the isolated factories generated at different times postinfection by mass spectrometry-based proteomics provide new perceptions of their role and reveal the highly dynamic nature of these organelles.A n exciting recent development in cellular biology is the realization that intracellular organelles previously considered to be randomly organized are in fact exquisitely ordered and that this order crucially affects their function. A prominent example is provided by replication cycles of positive-strand RNA [(ϩ)RNA] viruses, which were shown to involve massive reorganization of the host cytoskeleton and membrane networks into well-defined cytoplasmic platforms, termed "viral factories" (VFs), within which genome replication and virion assembly are effectively coordinated (1-4). An additional example of highly ordered virus-generated intracellular organelles is the replication cycle of nucleocytoplasmic large DNA viruses (NCLDVs), which include Poxviridae, Phycodnaviridae, Iridoviridae, Asfarviridae, Mimiviridae, and Marseilleviridae (5-7). Specifically, these viruses were shown to partially or exclusively replicate within large and elaborate cytoplasmic ...

Filling Knowledge Gaps for Mimivirus Entry, Uncoating, and Morphogenesis

“…This hypothesis was strengthened when we systematically observed the reduction of the fibrillar area after release of viral particles from the VF, suggesting that a fibrillar matrix is continuously consumed as the particles pass through it. Curiously, fibril proteins were not detected in isolated VF analyzed via proteomic approaches (14). It is possible that a large fraction of that region was lost during the purification process of the factories, thus hampering the detection of fibrils by this method.…”

“…A typical viral eclipse phase is then established, during which viral particles are not visible in the cell (11,13). The viral seed releases the DNA, promoting a reorganization of the host cytoplasm with further formation of viral factories (VF), where the virus genome is replicated and transcribed and new particles are assembled (13,14). Based on atomic force microscopy, Kuznetsov and colleagues proposed a model for morphogenesis of mimivirus particles (15).…”

Kinetics of Mimivirus Infection Stages Quantified Using Image Flow Cytometry

“…Many of these proteins, including translation initiation factors, amino‐acyl transfer RNA synthetases, and DNA repair enzymes, are associated with cellular life and were not previously detected in viruses . Unlike smaller viruses, whose replication relies almost entirely on host‐cell factors, Mimivirus uses hundreds of its own genes to orchestrate host cell takeover and virion production . Although the complexity of Mimivirus approaches that of bacteria and small eukaryotic cells, Mimivirus is nevertheless an obligate parasite.…”

“…Much of our current knowledge on Mimivirus and its infection cycle have been derived from two research directions: bioinformatics and structural studies. The bioinformatics research has provided information on Mimivirus gene content, offered putative functional annotations, and explored gene expression throughout the infection cycle (5)(6)(7)13). In addition, bioinformatics analyses yielded a phylogenetic overview of the relationship among the known members of the giant viruses and their relationship to the tree of life (5,(13)(14)(15)(16).…”

First evidence of host range expansion in virophages and its potential impact on giant viruses and host cells

“…Virophage multiplication was clearly correlated with a progressive degradation of Tupanvirus viral factories. Isolation and characterization of these structures have previously shown that they are composed of an arsenal of virus-encoded proteins involved in virus replication and assembly 36 . Therefore, there is some overlap between our observations and previous studies reporting that virophages hijack their giant virus-encoded machinery to express and probably replicate their genomes 35,37 .…”