COMMENTARY Virophages go nuclear in the marine alga Bigelowiella natans Matthias G. Fischer1 particles can be seen under a light micro- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, scope and contain DNA genomes that 69120 Heidelberg, Germany code for more than 1,000 proteins (5). As it turns out, giant viruses are rather com- The virus world in which we live will never affect biodiversity and community structures mon in the environment, infecting freshwa- ter amoebae as well as marine heterotrophic cease to amaze us. Historically, viruses were of their hosts [for which they can even act and photosynthetic protists (6). Another un- studied primarily from medical and eco- as symbionts (2)], and perhaps most pro- expected finding was that giant viruses in nomic perspectives; however, the last decades foundly, viruses have influenced all cellular the family Mimiviridae were associated with have shown that viruses play roles far more life from its very beginning and they continue a previously unknown group of smaller versatile than we could have imagined. Being to leave their footprints in cellular genomes double-stranded DNA (dsDNA) viruses the most abundant biological entities on the (3, 4), including our own. One of biggest that acted as parasites of the former. Dubbed ∼ 10 planet (there are 10 virus particles in surprises in recent virological history was “virophages,” these icosahedrally shaped every liter of seawater), viruses drive biogeo- the discovery of Acanthamoeba polyphaga viruses with 20- to 30-kilobase-pair (kbp) ge- chemical cycles on a global scale (1), they mimivirus and other giant viruses, whose nomes replicate in the cytoplasmic virus fac- tories of their giant viruses, where they exploit the transcriptional machinery of their viral host (7). To replicate, virophages must therefore infect a susceptible host cell that is coinfected with a permissive giant virus, i.e., a virus that has the capacity to support gene expression of the virophage. Virophages ap- pear to have evolved multiple strategies to track down their viral and cellular hosts. The Sputnik virophage can adhere to long fibers on the surface of the mimivirus capsid, and it is assumed that Sputnik hitches a ride when mimivirus is phagocytosed by the amoebal host cell (8). By contrast, the mavi- rus virophage enters the host cell indepen- dently of its giant virus CroV, which lacks an external fiber coat (9). Another mecha- nism by which a virophage can stay in touch with its host cell or giant virus is to insert its genome into either host genome. Whereas Sputnik integration into the mimivirus genome has been described (10), no provirophages (i.e., integrated virophage genomes) in a eukaryotic genome have been found so far. In PNAS, Blanc et al. (11) now report such a case. The authors searched through more than 1,000 eukaryotic genomes for signatures of virophages, and they struck gold in the unicellular alga Bigelowiella natans. B. natans belongs to a group of mixotrophic protists called chlorarachniophytes that have trod- den an interesting evolutionary path. Their Fig. 1. A model for the protective effect of provirophages on their host cells. Modified from ref. 11. Shown is a schematic B. natans cell (A), which can be infected and lysed by a large dsDNA virus (B). Blanc et al. (11) propose that Author contributions: M.G.F. wrote the paper. a virophage could integrate into the nuclear genome of a host cell in the absence of a large dsDNA virus. The pro- The author declares no conflict of interest. virophage-carrying cell (C) does not produce virophage particles until the cell is infected by a large dsDNA virus, which is then inhibited in its infection cycle by the reactivated virophage (D). As a result, the host population may survive the See companion article on page E5318. viral infection and disseminate the provirophage (E). N, nucleus; P, plastid; VF, virus factory. 1Email: [email protected]. 11750–11751 | PNAS | September 22, 2015 | vol. 112 | no. 38 www.pnas.org/cgi/doi/10.1073/pnas.1515142112 Downloaded by guest on September 28, 2021 – plastids are derived from secondary endo- would be removed from the constant race (9, 14 16). These endogenous elements are COMMENTARY symbiosis, i.e., their heterotrophic ancestor against decay by adverse environmental widely distributed in the eukaryotic domain engulfed a eukaryotic cell (a green alga in conditions such as UV light, before it en- and stand out from most other DNA trans- this case) that already possessed a chloro- counters a new giant virus-infected host. posons due to a set of conserved genes with plast of cyanobacterial origin (12). Remark- Upon superinfection with a permissive giant undeniable virus-like properties. Two of these ably, not only did chlorarachniophytes retain virus, the provirophage would become active genes were recently found to be distant ver- the envelopes of those enslaved organisms again and interfere with the production of sions of the jelly-roll capsid proteins found in (their plastid is surrounded by four mem- new giant virus particles (Fig. 1). Indeed, many DNA viruses such as pox- and adeno- branes), but they still contain remnants of this scenario would describe a mutualistic viruses, as well as virophages (17). The ’ the green algal endosymbiont snucleus,which relationship between a virus and a host cell Maverick/Polinton transposons can there- is referred to as a nucleomorph. B. natans (2): the host cell provides an opportunity to fore be viewed as endogenous viruses, and therefore harbors four distinct genomes that the virophage to persist and spread vertically these “polintoviruses” may even have played arelocatedinthenucleus,themitochon- within the host population, and, in return, a pivotal role in the evolution of several drion, the plastid, and the nucleomorph. Fol- the virophage protects the host cell from families of eukaryotic DNA viruses, includ- lowingtheuptakeofthegreenalgal lysis by giant viruses (9, 11). ing giant viruses and their virophages (18). endosymbiont, substantial gene transfer The fact that no giant viruses infecting The Bigelowiella provirophages could repre- to the host nucleus occurred, which left Bigelowiella have been described to date does sent an intermediate form between freely the plastid and nucleomorph genomes not weaken this hypothesis. Remarkably, not replicating virophages and the endogenous with mere 57 and 284 protein-coding only does the B. natans genome harbor viro- Maverick/Polinton elements and may shed genes, respectively. Amid the resulting phage-like elements, it also contains pieces of more light on the flow of mobile genetic mosaic nuclear genome of B. natans putative large DNA virus genomes (11). The elements in the microbial world. (13), Blanc et al. identified 38 virophage- largest such fragment is 165 kbp long and Overall, the findings by Blanc et al. raise like elements. Although these elements contains 83 genes, most of which are un- ranged from extremely truncated gene known, but some display clear phylogenetic several interesting questions, such as how snippets of just 100 bp to presumably affinities to large algal viruses. In contrast to frequently and under which conditions a complete virus genomes of more than 30 the virophage-like elements, the large virus virophage can stably integrate into a host kbp, they were highly similar at the nucleo- insert was found to be transcriptionally silent genome. Unclear is also whether genome tide level, indicating that they derived from a and had a G+Ccontentsimilartothatofthe integration is a dead end for the virophage, or common ancestral virophage. It is difficult to host nuclear genome (11). This algal lineage whether the provirophage can be triggered estimate how much time has passed since the has apparently witnessed multiple encounters to resume active replication by an incoming B. natans genome was invaded by these viral with DNA viruses of various sizes. Blanc et al. giant virus. The most interesting question in elements, but the fact that the viral sequences demonstrate how paleovirology can reveal this context may be whether provirophages display a lower G+C content than the flank- stories of long ago battles between viruses play a role in defending protist populations ing host sequences implies that the inte- and their hosts, even between different viruses. from giant virus infections. The discovery gration events happened recently enough There is yet another, more far-reaching of provirophages in the B. natans genome to prevent complete assimilation to the twist to the story. Some virophages have strongly suggests the existence of chlorarach- host nucleotide composition. strong genetic ties with 15- to 25-kbp-long niophyte-specific giant viruses. Isolation of Blanc et al. then analyzed gene expression insertion elements, which have been named such a virus in laboratory culture may pro- data of several B. natans strains and found Maverick or Polinton DNA transposons vide answers to at least some of these riddles. most of the ∼300 virophage genes to be transcribed—a surprising finding because virophages are thought to rely on the tran- 1 Suttle CA (2007) Marine viruses—major players in the global 11 Blanc G, Gallot-Lavallée L, Maumus F (2015) Provirophages in the scription enzymes of a coinfecting giant vi- ecosystem. Nat Rev Microbiol 5(10):801–812. Bigelowiella genome bear testimony to past encounters with giant 2 Roossinck MJ (2011) The good viruses: Viral mutualistic symbioses. viruses. Proc Natl Acad Sci USA 112:E5318–E5326. rus. Whether this transcriptional activity is Nat Rev Microbiol 9(2):99–108. 12 Keeling PJ (2010) The endosymbiotic origin, diversification and indicative of a biological mechanism that 3 Aiewsakun P, Katzourakis A (2015) Endogenous viruses: fate of plastids. Philos Trans R Soc Lond B Biol Sci 365(1541): – Connecting recent and ancient viral evolution. Virology 479-480: 729 748. might benefit virophage or host cell remains 13 26–37.