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The Virophage Family Lavidaviridae

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The Virophage Family Lavidaviridae The Virophage Family Lavidaviridae Matthias G. Fischer1* 1Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.040.001 Abstract Introduction Double-stranded (ds) DNA viruses of the family Virophages are a recently discovered class of dou- Lavidaviridae, commonly known as virophages, ble-stranded (ds) DNA viruses that have evolved a are a fascinating group of eukaryotic viruses that dependency on complex dsDNA viruses of eukary- depend on a coinfecting giant dsDNA virus of otes, so-called giant viruses. Te discovery of giant the Mimiviridae for their propagation. Instead of viruses was therefore a prerequisite for the isolation replicating in the nucleus, virophages multiply and characterization of virophages (see Fig. 12.1), in the cytoplasmic virion factory of a coinfecting as shall be reviewed here briefy (See also Reteno giant virus inside a phototrophic or heterotrophic et al., 2018). protistal host cell. Virophages are parasites of giant In 1992, following a pneumonia outbreak in viruses and can inhibit their replication, which Bradford, England, an intra-amoebal parasite was may lead to increased survival rates of the infected isolated by the team of T.J. Rowbotham and given host cell population. Te genomes of virophages the name ‘Bradford coccus’. Tis microorganism are 17–33 kilobase pairs (kbp) long and encode was initially assumed to be a bacterium because of 16–34 proteins. Genetic signatures of virophages its size and positive Gram-stain reaction; however, can be found in metagenomic datasets from various atempts to amplify and analyse its 16S riboso- saltwater and freshwater environments around the mal DNA sequences failed. A decade later in the planet. Most virophages share a set of conserved laboratory of Didier Raoult in Marseille, electron genes that code for a major and a minor capsid microscopy revealed that Bradford coccus was in fact protein, a cysteine protease, a genome-packaging a giant virus with a fbre-studded, 0.75 µm-diameter ATPase, and a superfamily 3 helicase, although the particle (La Scola et al., 2003). Te serendipitous genomes are otherwise diverse and variable. Lavi- discovery of Acanthamoeba polyphaga mimivirus daviruses share genes with other mobile genetic (family Mimiviridae, genus Mimivirus, species Acan- elements, suggesting that horizontal gene transfer thamoeba polyphaga mimivirus) and the analysis of and recombination have been major forces in shap- its 1.2 million base pair dsDNA genome have pro- ing these viral genomes. Integrases are occasionally foundly changed our view of the viral world (Raoult found in virophage genomes and enable these DNA et al., 2004). Tis virus exhibited a particle size and viruses to persist as provirophages in the chromo- genome length that exceeded those of the smallest somes of their viral and cellular hosts. As we watch cellular organisms, blurring the boundary between the genetic diversity of this new viral family unfold viruses and cells. Te fnding that some mimivirus through metagenomics, additional isolates are still genes were homologous to genes that were previ- lacking and critical questions regarding their infec- ously known to occur only in cellular genomes, in tion cycle, host range, and ecology remain to be particular four aminoacyl-tRNA synthetases and answered. four translation factors, spurred evolutionary sce- narios in which giant viruses were hypothesized to caister.com/cimb 1 Curr. Issues Mol. Biol. Vol. 40 Fischer Figure 12.1 Historical time line of virophage-related publications. be descendants of a cellular ancestor (Boyer et al., presence of Sputnik also elicited a morphological 2010; Nasir et al., 2012; Raoult et al., 2004). Such phenotype in mamavirus, with visible deforma- hypotheses, however, have been widely criticized tions such as partial capsid thickening in many of and the origin of giant viruses remains a mater of the newly synthesized virions. Te yield of mama- ongoing debate (Williams et al., 2011; Yutin et al., virus progeny from coinfected cells was reduced by 2014). Akin to poxviruses (Broyles, 2003), mimi- ≈70% (La Scola et al., 2008). Sputnik thus acted as virus and related giant viruses replicate solely in a parasite of mimiviruses and the term ‘virophage’ the cytoplasm of their unicellular eukaryotic host was coined to refect the relationship as a ‘virus of a (Mutsaf et al., 2010), which is made possible by virus’. However, the parasitic interaction appears to hundreds of virus-encoded proteins that provide be restricted to the intracellular phase of the virus nuclear functions to the virion factory (VF), such life cycle, when the biochemical complexity of giant as DNA replication and transcription. For instance, viruses unfolds in the form of the VF organelle. the mimivirus-encoded transcription apparatus In the years following the discovery of Sputnik, consists of at least eight DNA-dependent RNA pol- additional virophages such as mavirus (Fischer and ymerase subunits, a trifunctional mRNA capping Sutle, 2011) and Zamilon (Gaia et al., 2014) were enzyme, a polyadenylate polymerase, and several isolated, and more than a dozen putative virophage transcription factors. genomes were found in metagenomic datasets A targeted search for giant viruses was launched (Gong et al., 2016; Oh et al., 2016; Yau et al., 2011; following the characterization of mimivirus and Yutin et al., 2015a; Zhou et al., 2013, 2015) (see resulted in the isolation of dozens of new viral strains Table 12.1). Tese eukaryotic dsDNA viruses are (La Scola et al., 2010). One of the frst strains to be geographically widespread, genetically diverse, isolated was Acanthamoeba castellanii mamavirus, and appear to be commonly associated with giant a close relative of mimivirus that was recovered virus-infected protist populations. Te interested from a cooling tower in Paris. Electron microscopy reader is referred to previously published review analysis of mamavirus-infected amoebae revealed articles on this topic (Bekliz et al., 2016; Claverie the presence of a second, smaller icosahedral virus and Abergel, 2009b; Desnues and Raoult, 2010; that was named Sputnik (La Scola et al., 2008). Gaia et al., 2013a). Sputnik was unable to infect Acanthamoeba cells on its own, and replicated only when the cells were coinfected with mamavirus. In coinfected Virion structure cells, Sputnik colocalized to the mamavirus VF, Only few virophage representatives (Sputnik, mavi- providing the frst evidence that Sputnik uses giant rus, and Zamilon) have been isolated in laboratory virus-encoded enzymes for its propagation. Te culture and are thus amenable to structural studies. caister.com/cimb 2 Curr. Issues Mol. Biol. Vol. 40 Virophages Te virophage particles that have been examined Te capsid proteins of diferent virophages show so far are 50–75 nm in diameter and possess ico- low levels of conservation on the amino acid level sahedral symmetry (Fig. 12.2). A 3.5 Å resolution (e.g. ~40% for the MCPs of Sputnik and mavirus) cryo-electron microscopy (cryo-EM) reconstruc- (Krupovic et al., 2016). Te mCP in particular is tion of the 75 nm wide Sputnik particle suggested highly diverse, which hinders sequence similarity- the lack of a membrane component (Zhang et al., based identifcation of novel virophages. Despite 2012), contradicting earlier reports that assumed a the high sequence divergence, all MCPs and mCPs lipid component in the Sputnik particle (Desnues are assumed to adopt the double and single jelly- et al., 2012a; Sun et al., 2010). Te Sputnik capsid roll folds, respectively, and preliminary data shows structure is composed of the major capsid protein that the three-dimensional structure of the mavirus (MCP) encoded by the V20 gene, and the minor MCP is very similar to that of Sputnik (D. Born, capsid protein (mCP) encoded by the V18/V19 L. Reuter, U. Mersdorf, M. Mueller, M.G. Fischer, gene. Te MCP contains a double jelly-roll fold and A. Meinhart and J. Reinstein, under review). How- forms trimeric capsomers (hexons) with pseudo- ever, since most of the sequence space occupied hexagonal symmetry that build the 20 faces of the by virophages remains unknown, the existence of icosahedral particle (Fig. 12.2C), whereas the mCP diferent capsid architectures cannot be excluded. is a single jelly-roll protein that forms pentameric For instance, the virophage genomes assembled capsomers (pentons) occupying the 12 vertices. from a sheep rumen metagenome apparently lack Te mature capsid consists of 260 hexons and 12 a penton gene (Yutin et al., 2015a). In addition to pentons that are arranged in a latice with a trian- the main capsid components (MCP and mCP), gulation (T) number of 27 (h = 3; k = 3) (Sun et al., other virophage-encoded proteins may be present 2010; Zhang et al., 2012). in the mature virion, such as the mavirus MV13 Figure 12.2 The structure of lavidavirus capsids. A) Negative stain electron micrograph of a Sputnik particle (courtesy of M. Gaia and B. La Scola, Univ. Aix-Marseille, France). B) Negative stain EM image of CsCl gradient- purifed mavirus particles (U. Mersdorf and M. Fischer, Max Planck Institute for Medical Research, Germany). C) Cryo-EM reconstruction of the Sputnik virion at 3.5 Å resolution with a magnifed major capsid protein trimer (PDB entry 3J26). Modifed from (Zhang et al., 2012). caister.com/cimb 3 Curr. Issues Mol. Biol. Vol. 40 Fischer protein, which could have lipase activity (Fischer et viruses, e.g. mimivirus (28% G+C), CroV (23%), al., 2014). PgV-16T (32% G+C), and OLPV-1 (30% G+C) (Fischer et al., 2010; Raoult et al., 2004; Santini et al., 2013; Yau et al., 2011). In contrast, the G+C Virophage genomics contents of the nuclear genomes in the eukaryotic All virophages described so far possess dsDNA hosts are typically higher, e.g. 59% for Acantham- genomes ranging in size from 17 to more than 30 oeba polyphaga (GenBank Acc.
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