93710.2217/FVL.13.79 © 2013 Future Medicine Ltd ISSN 1746-0794

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Future Virol. (2013) 8(10), 937–939

We are used to thinking of viruses as the ulti-mate parasites, the tiny infectious agents that reproduce within cells. Although this attribute of the obligate intracellular parasitism remains, the distinction between viruses and cellular life forms in terms of size and genomic complexity is gone thanks to the discovery of giant viruses infecting unicellular eukaryotes [1]. The isola-tion and genome sequencing of the mimivirus, which encompasses more than 1000 genes with a 1-Mb genome, squarely put viruses within the range of genome sizes characteristic of cellular life forms [2]. Subsequent studies have shown that mimiviruses represent an expansive, widespread family of giant viruses [3]. The recent isolation of the colossal pandoraviruses, with their 2.5-Mb genomes, larger than the genome of numerous bacteria and Archaea, and even some parasitic eukaryotes [4], implies that there might be vir-tually no limit to virus genome growth beyond perhaps physically fitting multiple virus particles into the host cell.

The pandoraviruses appear to be distantly related to other viruses; the comprehensive ana lysis of the genomes of these ‘superviruses’ remains to be performed, but the mimivirus genomes have been explored in detail. The mimi-viruses are bona fide members of a large group of eukaryotic viruses known as the nucleocyto-plasmic large DNA viruses (NCLDV), or the proposed Megavirales order [5–7]. In addition to the mimiviruses, the NCLDV include six other families of much smaller viruses, namely poxvi-ruses, asfarviruses, phycodnaviruses, iridoviruses, ascoviruses and marseilleviruses. These viruses share multiple conserved genes, approximately 50 of which were mapped to their putative common ancestor by a maximum-likelihood reconstruc-tion method [6]. These putative ancestral genes encode the key virus proteins that are responsible

for viral genome replication and virion assembly, and so comprise the essential core of the NCLDV. The mimiviruses retain an almost full comple-ment of the ancestral NCLDV genes. Thus, these giants of the virus world appear to have evolved from much simpler, even if still large, viruses. The mimiviruses also possess a suite of very dif-ferent genes that are not commonly found in viruses, including genes encoding components of the translation system such as aminoacyl-tRNA synthetases. These genes provide for the formal possibility of including mimiviruses into the ‘tree of life’, which is traditionally constructed by compara tive ana lysis of universally conserved genes. In the resulting tree the mimiviruses do not show unequivocal affinity with any group of cellular life forms, fueling the speculation that these viruses might bear relics of a fourth domain of cellular life [2,8]. However, considering the shared evolutionary history of the mimiviruses and the other NCLDVs, it appears most likely that the universal ‘cellular’ genes were acquired piecemeal during the evolution of the mimivi-rus lineage [6,9]. Under this scenario, the mimi-viruses, all their complexity notwithstanding, remain typical viruses rather than remnants of a vanished fourth domain of cellular life.

Remarkably, the giant mimiviruses have been shown to harbor several classes of parasites of their own that together comprise a complex, highly dynamic mobilome, the compendium of mobile, selfish elements that parasitize on the giant viruses [10]. The first to be discovered were self-splicing introns and inteins that are inserted into several genes of the mimiviruses. These are the simplest, selfish genetic elements that use enzymes encoded within them to jump into new positions in the host genome; they are relatively common in bacteria and eukaryotic organelles. Subsequently, mimiviruses have been

A flea has smaller fleas that on him prey: giant viruses, their parasites and evolutionary networks

“…the distinction between viruses and cellular life forms … is gone thanks to the discovery of

giant viruses…”

Eugene V KooninNational Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA n koonin@ncbi.nlm.nih.gov

Edito

rial

Keywords

n giant viruses n transposable elements n transpovirons n virophages n virus evolution

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Future Virol. (2013) 8(10)938 future science group

shown to harbor a unique class of parasites, small viruses that became known as virophages and infect giant viruses rather than cells [11,12]. The three well-characterized virophages possess small isocahedral virions and genomes of 20–25 kb (i.e., almost three orders of magnitude smaller than the host giant virus) encoding 21–26 pro-teins each [11,13,14]. Analysis of metagenomic sequences allowed the assembly of several addi-tional virophage genomes, suggesting that the virophages are rather common in various habitats [15]. The virophages replicate within the factories of the host giant virus; that is, the specifically structured sites in the cytosol of the infected cells that harbor all the stages of giant virus reproduc-tion. Numerous particles of the virophage then accumulate within the giant virus capsid.

“…the mimiviruses, all their complexity notwithstanding, remain typical viruses

rather than remnants of a vanished fourth domain of cellular life.”

Despite the similar genome size and struc-ture, all virophages share only five conserved genes. The rest of the genes show diverse phy-logenetic affinities suggestive of chimeric ori-gins of the virophages, including some genes apparently acquired from the host giant viruses. The virophages are generally similar to satellite viruses, which have been known for many years and are viruses with small genomes that depend on other, more complex, viruses for their repro-duction [16]. Examples include adeno-associated viruses, which are small animal viruses depend-ent on the much larger adenoviruses, and numer-ous plant RNA viruses, some of which possess extremely reduced genomes that do not encode any protein at all. However, although it appears legitimate to view the virophages as a special case of satellite viruses, they nevertheless possess unique features with an uncanny resemblance of regular viruses infecting cellular hosts, such as the accumulation of hordes of virophage particles within a single giant virus capsid.

Genomic ana lysis of one of the virophages, known as the Mavirus, which parasitizes on the giant Cafeteria roenbergensis virus, a distant rela-tive of the mimiviruses [17], unexpectedly showed the conservation of five genes involved in genome replication and virion maturation in the Mavirus and the large, self-replicating eukaryotic transpos-able elements known as Mavericks (aka polintons) [13]. The Mavericks are present, in highly variable numbers, in the genomes of diverse eukaryotes,

reaching high abundance in some protists. They are considered as ‘virus-like’ transposons thanks to their large size (typically more than 20 kb) and the presence of several genes that are oth-erwise typical of viruses rather than transpos-able elements [18]. Among the currently known viruses, the Mavirus shows the closest similarity to the Mavericks, leading to the hypothesis that the Mavericks evolved from the virophages [13]. However, phylogenetic ana lysis of the genes that are shared by the Mavirus and the Mavericks appear to be telling a different story. The Mavirus genes are embedded inside the Maverick tree, sug-gesting the opposite direction of evolution, from a particular branch of Mavericks, to Mavirus, conceivably via recombination with another virophage or an as yet unidentified virus [19].

In addition to the virophages, the giant viruses have been shown to harbor novel linear plas-mids that have been dubbed transpovirons [10]. Numerous transpoviron copies are associated with several giant viruses of the Mimiviridae family. The transpovirons encompass only six to eight genes, and two of these are homologous to virophage genes, suggestive of multiple gene exchanges within the giant virus mobilome.

“…[a] network of evolutionary connections is emerging as the key

feature of the virus world…”

Exhaustive comparative ana lysis of the genomes of the giant viruses, the components of the associated mobilome, and related viruses and mobile elements reveals a complex network of evolutionary relationships that is knit together through small sets of widespread virus genes [19]. This type of network of evolutionary connec-tions is emerging as the key feature of the virus world in which genome fluidity reaches extremes such that no single core of conserved genes exists, although diverse types of selfish elements are linked via partially overlapping gene sets.

At a fundamental level, the discovery of the diverse mobilomes of the giant viruses illus-trates a key principle of biology: any complex life form spawns genomic parasites; that is, viruses and/or virus-like mobile elements, and virus–host interactions are an inalienable, essen-tial driver of the evolution of life [20]. The study of the giant viruses and their mobilomes is still in its infancy, and numerous fascinating questions remain unanswered. In particular, are certain types of parasites, for example, virophages and transpovirons, ubiquitous in giant viruses? For

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instance, should one expect that pandoraviruses are infested with these and perhaps other, novel types of parasites? What is the role of mobile elements in the gene transfer between giant viruses? What is the exact history of the rela-tionships between virophages and polintons? Do giant viruses encode dedicated means of defense against their parasites? The answers to these and other related questions will illuminate one of the most remarkable corners of the virus world.

Financial & competing interests disclosureThe author has no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the sub-ject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.

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