Abstract: A distinct class of infectious agents, the virophages1 that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome2 of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements3, the transpovirons4. The transpovirons are linear DNA elements of ∼7 kb [kilobases]5 that encompass six to eight protein-coding genes, two of which are homologous6 to virophage genes. Fluorescence7 in situ hybridization8 showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate9 in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns10 and inteins11 constitute the complex, interconnected mobilome12 of the giant viruses and are likely to substantially contribute to interviral gene transfer.[Full Text PDF] and two explanations in English
Mobile genetic elements (MGEs) that are collectively referred to as the “mobilome” are key players in the genome evolution of prokaryotes (*1*) and eukaryotes (*2*, *3*) and are considered “genetic engineers” of biological innovation (*1*). MGEs can be roughly grouped into four major classes: transposable elements (TEs), plasmids, viruses, and self-splicing elements such as group I and II introns and inteins (*4*). The mobilomes of many bacteria, archaea, and unicellular eukaryotes include all of these elements in a free or integrated form. Given that viruses constitute a part of the mobilome, they are not normally considered to possess mobilomes of their own. However, some large viruses contain retrovirus sequences integrated into their genomes (*5*, *6*), whereas others, including members of the Mimiviridae family, harbor self-splicing introns and/or inteins (*7*, *8*, *9*). Furthermore, many viruses support the reproduction of satellite viruses1 (*10*). The discovery of the Sputnik virophage in 2008 added a new twist to the existing understanding of the relationships between different mobile elements by demonstrating for the ﬁrst time that a giant virus could be infected by another, much smaller virus in a manner similar to the viral infection of cells (11). The Sputnik virophage is a small icosahedral virus (74 nm in diameter) that parasitizes on Mamavirus, a member of the Mimiviridae family (12, 13). Sputnik replicates inside Mamavirus or Mimivirus viral factories when the host giant virus is grown in amoebae such as Acanthamoeba castellanii or A. polyphaga (11). An in-depth analysis of the Sputnik proteins has suggested an evolutionary connection between this virophage and a distinct class of TEs (14). The second virophage, the Mavirus (15), was isolated as a parasite of a distinct member of the Mimiviridae family, Cafeteria roenbergensis virus (CroV) [Previously on Metafilter] (16). At least four Mavirus proteins, including the major capsid protein13, are homologous6 to proteins of Sputnik. In addition, the Mavirus genome encodes a retroviral-type integrase and a protein-primed DNA polymerase B; these proteins are homologous to the respective proteins of Maverick/polinton DNA transposons, which insert into genomes of diverse eukaryotes, suggesting an evolutionary link between the Mavirus and the polintons (15). The third complete virophage genome sequence has been identiﬁed in the metagenome of the hypersaline Organic Lake in Antarctica (*17*). This Organic Lake virophage (OLV) is thought to parasitize on phycoDNAviruses that infect green algae. The OLV genome encodes seven proteins with homologs in Sputnik (*17*), including two key proteins, the major capsid protein and the DNA-packaging ATPase, that are shared by all three virophages. Thus, the virophages apparently share a common origin, although each underwent multiple gene replacements. The virophages are likely to be common parasites of nucleocytoplasmic large DNA viruses that infect diverse eukaryotes, and show multiple evolutionary connections to other mobile elements (*18*). Here we present ﬁndings that substantially expand the complexity of the giant virus mobilome through the description of an integrated form of the virophage and of a distinct class of MGEs, the transposovirons.Discussion:
The discovery of the Mimivirus and subsequent identiﬁcation of other giant viruses revealed unexpected complexity of viral genomes that, with over 1,000 protein-coding genes, are more complex than many parasitic and symbiotic bacteria and are comparable to the most compact genomes of free-living bacteria and archaea (*7*). The present work shows that giant viruses are associated with a commensurately complex mobilome that encompasses three of the four major classes of mobile elements, namely self-splicing elements, transposable elements or linear plasmids (transpovirons), and viruses (virophages that can form provirophages after integration into the host giant virus genome). Different components of the giant virus mobilome share homologous genes, and genomic comparisons point to DNA transfer between the mobilome components and the host virus but also within the mobilome itself. Thus, the giant virus mobilome is a network that potentially could provide routes and vehicles for gene exchange and might make substantial contributions to the shaping of mosaic viral genomes. The giant viruses and their mobilomes together are part of even more expansive, dynamic genetic networks: the amoebae with their diverse bacterial parasites and symbionts and their own viruses (30).Glossary of Terms Used in the Abstract, Introduction, and Discussion:
Of special note is the transpoviron, a distinct plasmid that depends on giant viruses for its replication and spread. Substantial analogies can be found between the transpovirons and virus-associated plasmids present in bacteria and archaea. In particular, the well-studied bacteriophage P4 (also known as a “phasmid”) is a plasmid that replicates episomally in the absence of the helper bacteriophage P2 but is encapsidated into virions and thus can infect new bacterial cells in the presence of the helper (*31*, *32*). A similar replication strategy has been described for the archaeal virus plasmid pSSVx that depends on the fuselloviruses SSV1 or SSV2 and appears to have acquired genes from a fusellovirus (33). The discovery of the transpoviron shows that virus-associated plasmids exist in all three domains of cellular life.
It is unlikely that the present study exhausts the diversity of the giant virus mobilome; additional virophages and transpovirons, and perhaps distinct classes of mobile elements, are likely to be discovered. Indeed, the transpoviron had not been detected until the isolation of Lentille virus from a human sample described here. Furthermore, we failed to detect closely related homologs of transpoviron genes in the available databases of environmental sequences, although close homologs of many Mimivirus and Sputnik genes were readily detectable (11). Thus, speciﬁc conditions and/or habitats could be required for accumulation of transpovirons and probably other elements comprising the giant virus mobilome. Characterization of such conditions will likely lead to the discovery of additional genetic elements associated with giant viruses and facilitate elucidation of their replication mechanisms and the relationships between different mobilome components.
1Virophage: A subviral agent composed of nucleic acid that depends on the co-infection of a host cell with a helper or master virus for its multiplication. When a satellite encodes the coat protein in which its nucleic acid is encapsidated it is referred to as a satellite virus. A satellite virus of mimivirus that inhibits the replication of its host has been termed a virophage. However, the usage of this term remains controversial due to the lack of fundamental differences between virophages and classical satellite viruses.References from the Introduction and Discussion:
2Integrated Genome: A prophage is a phage (viral) genome inserted and integrated into the circular bacterial DNA chromosome. A prophage, also known as a temperate phage, is any virus in the lysogenic cycle; it is integrated into the host chromosome or exists as an extrachromosomal plasmid. Technically, a virus may be called a prophage only while the viral DNA remains incorporated in the host DNA. This is a latent form of a bacteriophage, in which the viral genes are incorporated into the bacterial chromosome without causing disruption of the bacterial cell. Upon detection of host cell damage, such as UV light or certain chemicals, the prophage is excised from the bacterial chromosome in a process called prophage induction. After induction, viral replication begins via the lytic cycle. In the lytic cycle, the virus commandeers the cell's reproductive machinery. The cell may fill with new viruses until it lyses or bursts, or it may release the new viruses one at a time in a reverse endocytotic process. The period from infection to lysis is termed the latent period. A virus following a lytic cycle is called a virulent virus. Prophages are important agents of horizontal gene transfer, and are considered part of the mobilome.
3Mobile genetic elements: Mobile genetic elements (MGE) are a type of DNA that can move around within the genome. They include Transposons (also called transposable elements including Retrotransposons, DNA transposons, and Insertion sequences), Plasmids, Bacteriophage elements like Mu (which integrates randomly into the genome), and Group II introns. The total of all mobile genetic elements in a genome may be referred to as the mobilome.
4Transpoviron: This is a new term that the authors are proposing to refer to mobile genetic elements within viruses.
5Kb or Kilobasepairs: A measurement of the length of a stretch of DNA equivalent to 1,000 base pairs
6Homology: Homologous traits of organisms are due to sharing a common ancestor, and such traits often have similar embryological origins and development. This is contrasted with analogous traits: similarities between organisms that were not present in the last common ancestor of the taxa being considered but rather evolved separately. An example of analogous traits would be the wings of bats and birds, which evolved separately but both of which evolved from the vertebrate forelimb and therefore have similar early embryology. Whether or not a trait is homologous depends on both the taxonomic and anatomical levels at which the trait is examined. For example, the bird and bat wings are homologous as forearms in tetrapods. However, they are not homologous as wings, because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods. By definition, any homologous trait defines a clade—a monophyletic taxon in which all the members have the trait (or have lost it secondarily); and all non-members lack it
7Fluorescence: The emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation. However, when the absorbed electromagnetic radiation is intense, it is possible for one electron to absorb two photons; this two-photon absorption can lead to emission of radiation having a shorter wavelength than the absorbed radiation. The emitted radiation may also be of the same wavelength as the absorbed radiation, termed "resonance fluorescence".
8In situ hybridization: A type of hybridization that uses a labeled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ)
9Viral Integration: A superpower possessed by Eukaryotic retroviruses (like HIV and Human T-lymphotropic virus) and temperate bacteriophages, where the virus integrates its genome into its host's genome and shuts off ll of its host lethal genes in order to hide - indefinitely - until conditions become better for an active infection.
10Intron: An intron is any nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation. The word intron is derived from the term intragenic region; i.e., a region inside a gene. Although introns are sometimes called intervening sequences, the term "intervening sequence" can refer to any of several families of internal nucleic acid sequences that are not present in the final gene product, including inteins, untranslated sequences (UTR), and nucleotides removed by RNA editing, in addition to introns.
11Intein: An intein is a segment of a protein that is able to excise itself and rejoin the remaining portions (the exteins) with a peptide bond. Inteins have also been called "protein introns".
12Mobilome: The total of all mobile genetic elements in a genome; a play on the word Genome.
13Major Capsid Protein: A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic material of the virus.
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