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Diversity of replicative helicases domain organizations in dsDNA viruses. The number of representative sequences having specific domain organization is indicated on the left. The catalytic domain of the helicase is shown in green; primase, orange; polymerase, red; other domains, gray. αHD, α-helical domain; DUF, domain of unknown function; WH, winged-helix-turn-helix domain; ZnBD, Zn-binding domain; DBD, DNA-binding domain; Pol, DNA polymerase.
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Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and co...
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... replicative minichro- mosome maintenance (MCM) helicase of the SF6 super- family, typical of archaea, could not be identified. Instead, HVTV-1 encodes a divergent SF4 helicase (Supplementary Figure S2, gi: 443404669), the only apparent candidate for the replicative helicase. ...
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... 3 (41% of all replicative helicases) is nearly as abundant among viruses as SF4, but more diverse with respect to both sequence similarity (Supplementary Figure S3) and domain composition ( Figure 2). SF3 is represented by well-studied polyoma-and papillomavirus replicative he- licases, large T antigen (Tag) and E1, respectively. ...
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... of these groups is similar to the VirE family (PF05272) and mainly includes phage sequences. Another group corresponds to the DUF927 family (Supple-mentary Figure S3 and Figure 2). In both groups, the puta- tive helicase domains are often fused with DnaG-or AEP- like primase domains, strongly suggesting their involvement in phage DNA replication. ...
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... interesting case is repre- sented by the putative primase-helicase proteins from the Phaeocystis globosa virus virophage and Sputnik virophage (gis: 509141013 and 195982544, respectively). These pro- teins have the C-terminal D5-like helicase module and an N-terminal domain (Figure 2 and Supplementary Figure S3) identified as a novel A-family polymerase implicated in both polymerase and primase activities (30). Superfamily 6 is exemplified by extensively studied ar- chaeal and eukaryotic replicative MCM helicases as well as RuvB proteins (23). ...
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... the N4 phage protein dns (gi: 119952220), which is essen- tial for replication (34) features a non-typical fusion. Un- like in most of primase-helicase fusions, the AEP domain is C-terminal to the helicase domain (Figure 2). In gen- eral, proteins from the DUF3987 family are often associ- ated with AEP or DnaG primases either as fusions or as separate proteins encoded immediately upstream of the he- licase. ...
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... gen- eral, proteins from the DUF3987 family are often associ- ated with AEP or DnaG primases either as fusions or as separate proteins encoded immediately upstream of the he- licase. Furthermore, similarly to known replicative SF6 he- licases, DUF3987 proteins possess the C-terminal winged helix-turn-helix domain (Figure 2). These observations sup- port the notion that DUF3987 proteins act as replicative helicases in phage replication. ...
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... 2 has the fewest members assigned as replicative helicases (Figure 1), despite being one of the most abundant protein groups in all prokaryotic viruses (37,38). SF2 members from phages N15 and PY54 (gi: 9630494 and 33770544, respectively) have the DnaG pri- mase domain fused to their N-termini ( Figure 2) and their function as replicative helicases has been experimentally confirmed (39,40). Another likely candidate for the role of a replicative helicase is phage PAU protein gp68 (gi: 435844571), which has an AEP primase domain (Figure 2). ...
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... members from phages N15 and PY54 (gi: 9630494 and 33770544, respectively) have the DnaG pri- mase domain fused to their N-termini ( Figure 2) and their function as replicative helicases has been experimentally confirmed (39,40). Another likely candidate for the role of a replicative helicase is phage PAU protein gp68 (gi: 435844571), which has an AEP primase domain (Figure 2). The assignment of viral SF2 members as replicative heli- cases in the case of archaeal virus AFV6 and phage Ma- LMM01 is less certain. ...
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... of them comprises proteins encoded by Lactococcus and Rhodococcus phages and exemplified by gp55 of Lac- tococcus phage 1706 (gi: 182637532), which encompasses SF3 helicase, AEP primase and PolB. Another case is exem- plified by the Pas55 protein of Actinoplanes phage phiAsp2 (gi: 48697456) featuring SF3 helicase fusion with DnaG pri- mase and PolA (Figure 2). Nevertheless, there are several notable cases of primases being absent, including phiKZ- like phages, halovirus HGTV-1 and Pseudomonas phage 119X (Supplementary file 1). ...
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... two proteins are often fused together into the same polypeptide chain (41% of replica- tive helicases) or are encoded nearby. Almost universally (94% of cases) the primase domain appears N-terminal to the helicase module (Supplementary file 2). We observed that phages with replicative helicases of the SF4 super- family more often code for a DNA primase as a separate gene (similarly to DnaB and DnaG in bacteria) rather than as a primase-helicase fusion (like in phage T7). ...
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... might be explained by the fact that replicative helicases are the first of the replication fork proteins loaded onto origins of replication (75). Furthermore, helicases might also be involved in recognition of replication origins (76) through the fusion with DNA-binding domains (Figure 2). Thus, it appears that a replicative helicase represents an optimal solution for efficient assembly of the whole repli- some on the viral DNA template. ...
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Nucleo-cytoplasmic large DNA viruses are doubled stranded DNA viruses capable of infecting eukaryotic cells. Since the discovery of Mimivirus and Pandoravirus, there has been no doubt about their extraordinary features compared to “classic” viruses. Recently, we reported the expansion of the proposed family Pithoviridae, with the description of Ced...
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... Mriyaviruses encode a small but unusual set of proteins implicated in viral genome replication. As noticed also for other large dsDNA viruses (28,29), the replication machinery compo nents are not strongly conserved among the members of "Mriyaviricetes," with several ancestral genes apparently replaced with genes of different origins encoding proteins with the same functions. Mriyaviruses lack the DNA-dependent DNA polymerase that is encoded by all other members of the Nucleocytoviricota, with the obvious implication that the replication of mriyavirus genomes relies on a host DNA polymerase. ...
... In particular, HUH endonucleases are also encoded by varidnaviruses of at least two families, Corticoviridae (30,31) and Simuloviridae (32,33), in which they apparently were acquired independently (22). The combination of primase and HUH endonuclease, proteins associated with different modes of genome replication, to our knowledge, so far has not been observed in any viruses or plasmids (28). By contrast, eukaryotic monodnaviruses typically encode both a HUH endonuclease and an SF3 helicase as a fusion protein (22), indicating a functional coupling. ...
The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35–45 kb that appear to be related to the Nucleocytoviricota . In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCPs) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of the Nucleocytoviricota and accordingly would comprise a class which we propose to name “ Mriyaviricetes ” (after Ukrainian “mriya,” dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of the Nucleocytoviricota . In the phylogenetic trees, mriyaviruses split into two well-separated branches, the family Yaraviridae and proposed new family “ Gamadviridae. ” The previously characterized members of these families, yaravirus and Pleurochrysis sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of the Nucleocytoviricota , and RNA polymerase subunits encoded by all cytoplasmic viruses among the Nucleocytoviricota , suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism.
IMPORTANCE
The origin of giant viruses of eukaryotes that belong to the phylum Nucleocytoviricota is not thoroughly understood and remains a matter of major interest and debate. Here, we combine metagenome database searches with extensive protein sequence and structure analysis to describe a distinct group of viruses with comparatively small genomes of 35–45 kilobases that appear to comprise a distinct class within the phylum Nucleocytoviricota that we provisionally named “ Mriyaviricetes .” Mriyaviruses appear to be the closest identified relatives of the ancestors of the Nucleocytoviricota . Analysis of proteins encoded in mriyavirus genomes suggests that they replicate their genome via the rolling circle mechanism that is unusual among viruses with double-stranded DNA genomes and so far not described for members of Nucleocytoviricota .
... The mobilome and virosphere provide for further variation and may give us some insight on the evolutionary emergence of organismal replisomes [293,297]. Various viral DNA replication machineries are diverse enough to warrant meaningful statistical analyses, and numerical correlations appear relevant in two different contexts [298]. Above all, the complexity of virus-encoded DNA replication machineries is positively correlated with increasing genome size, and the non-random patterns of co-occurrence for several key components may reflect step-wise, coevolutionary emergences of structurally interactive sub-modules within the composite replisome. ...
... Viruses with primases and DNA polymerases of the latter category are numerous in all three domains of life, whereas the bacterial counterparts are confined to rather few bacteriophages. A similar trend is also observed for the accessory proteins of sliding 30 clamps and clamp loaders [298]. These fundamental differences indicate that virus hallmark replication genes descended from primordial replicators well before the consolidation of cellular organismal lineages [299]. ...
The main objective is to offer a functionally coherent counter-narrative to the polarized views prevailing now about the complex ‘Eukaryogenesis problem’ versus the “primitive” nature ascribed to so-called “Prokaryotes” (termed Akaryotes herein). The paradigm shift presented aims at bridging the conceptual gap between the rudimentary beginnings of biomolecular cooperativity on a pristine Earth (the Origins of Life or OoL) and the beginnings of lineage-wise diversification toward Darwinean speciation in the Tree of Life (or ToL). Although the research field as a whole is not aware of a corresponding ‘Prokaryogenesis problem’, the evolutionary process resulting in the partly independent archaeal and bacterial cell types is not fully understood. The present paper provides an explanation for these problems based on coevolutionary complementarity at multiple levels. The unconventional model connects various stages from “neighborhood selection” in film-like layers of unbounded “surface protoplasm” based on short “statistical proteins”, via a closely knit “peptide/RNA partnership” in the “making of genes”, toward the “making of genomes” in several RNA-to-DNA transitions. Three virus-related plasmids carrying different DNA replicases may have initiated the vertical stability of hereditable lineages that led to the three “domains” of organismal life, with a fourth lineage ending in eukaryotic organelles. These partly independent transitions established DNA as a late-comer of fundamental biomolecules.
... implicated in viral genome replication. As noticed also for other large dsDNA viruses (27,28), the 293 replication machinery components are not strongly conserved among the members of "Mriyaviricetes", 294 ...
... independently (21). The combination of primase and HUH endonuclease, proteins associated with 307 different modes of genome replication, to our knowledge, so far has not been observed in any viruses or 308 plasmids (27). By contrast, eukaryotic monodnaviruses typically encode both an HUH endonuclease and 309 a SF3 helicase as a fusion protein (21). ...
The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35-45 kb that appear to be related to the Nucleocytoviricota. In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCP) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of the Nucleocytoviricota and accordingly would comprise a class which we propose to name Mriyaviricetes (after Ukrainian Mriya, dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of the Nucleocytoviricota. In the phylogenetic trees, mriyaviruses split into two well-separated branches, the family Yaraviridae and proposed new family Gamadviridae. The previously characterized members of these families, Yaravirus and Pleurochrysis sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of the Nucleocytoviricota, and RNA polymerase subunits encoded by all cytoplasmic viruses among the Nucleocytoviricota, suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism.
... The proposed family "Kunpengviridae" was detected in hydrothermal vents (Fig. 2) Table S4), indicative of (at least, partially) autonomous genome replication [58]. Notably, unlike in other tailed viruses, the proofreading DEDDy 3 -5 exonuclease (gene Kenpengvirus_45) and the family B DNA polymerase domains are encoded by two distinct genes. ...
Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family “Fuxiviridae” harbor an atypical type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family “Chiyouviridae” encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.
... The existence of domain mosaicism in phages is not a new phenomenon as some functions analysed here have been previously linked with mosaic domain architectures 51,52 . We thus next enquired which cases of ECOD-based mosaicism are ancient (i.e., represent ancestral domain shuffling underlying functional diversification) and which cases of ECOD-based mosaicism are contemporary (i.e., are the result of an evolutionarily recent reshuffling of domains). ...
Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While genomic modularity in phages has been extensively studied, less attention has been paid to protein modularity—proteins consisting of distinct building blocks that can evolve and recombine, enhancing functional and genetic diversity. Here, we use a set of 133,574 representative phage proteins and highly sensitive homology detection to capture instances of domain mosaicism, defined as fragment sharing between two otherwise unrelated proteins, and to understand its relationship with functional diversity in phage genomes. We discover that unrelated proteins from diverse functional classes frequently share homologous domains. This phenomenon is particularly pronounced within receptor-binding proteins, endolysins, and DNA polymerases. We also identify multiple instances of recent diversification via domain shuffling in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery, often transcending distant taxonomic and ecological boundaries. Our findings suggest that ongoing diversification via domain shuffling is reflective of a co-evolutionary arms race, driven by the need to overcome various bacterial resistance mechanisms against phages.
... Some of these proteins are capsids in which newly replicated dsDNA is packaged. Once packaged, the packaged virion is released outside the cell to infect other cells (Figure 4) (Kazlauskas et al., 2016;Kazlauskas and Venclovas, 2011;Rao and Feiss, 2015). A well-known example of dsRNA motif mimicry is the PxLTXP motif in the HADC serotype 5 E1 protein interacting with the human BS69 protein MYND domain. ...
The virus interacts with its hosts by developing protein-protein interactions. Most viruses employ protein interactions to imitate the host protein: A viral protein with the same amino acid sequence or structure as the host protein attaches to the host protein's binding partner and interferes with the host protein's pathways. Being opportunistic, viruses have evolved to manipulate host cellular mechanisms by mimicking short linear motifs. In this review, we shed light on the current understanding of mimicry via short linear motifs and focus on viral mimicry by genetically different viral subtypes by providing recent examples of mimicry evidence and how high-throughput methods can be a reliable source to study SLiM-mediated viral mimicry.
... The 5A SSB contains an oligosaccharide/oligonucleotide binding (OB)-fold, a structural domain common to most SSBs, as well as the acidic C terminus found in many phage SSBs. [65][66][67][68] Phage SSBs may activate Hna's Abi response by promoting certain unwinding or nuclease activities; such alteration or stimulation of biochemical activities by SSBs has been reported for numerous pairs of SSB and helicase proteins, including Gp32 and UvsW in phage T4, Gp2.5 and Gp4 in phage T7, SSB and PriA in E. coli, and RPA and Dna2 in Saccharomyces cerevisiae. [69][70][71][72][73] If this is the case the cell must presumably have a method of distinguishing between foreign and host SSBs. ...
There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
... For example, related viruses can encode nonhomologous or distantly related DNA polymerase genes of families A, B, or C that are interspersed with cellular counterparts. Some may lack DNA polymerase genes altogether and instead encode diverse replication initiators that facilitate the recruitment of the host replisome [25,27]. ...
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
... In that case, the Topo IIA from a Caudoviricetes present in this putative bacterial endosymbiont would have been transferred to an ancestor of Nucleocytoviricota, potentially with other components of the DNA replication machinery shared between Caudoviricetes and Nucleocytoviricota, including NAD-dependent DNA ligase (Yutin and Koonin 2009). Notably, a comparison of DNA replication machinery of all dsDNA viruses revealed a strong evolutionary and likely functional coupling between DNA topoisomerases and DNA ligases, with 96 per cent of viruses encoding DNA topoisomerases also carrying a gene for a ligase (Kazlauskas, Krupovic, and Venclovas 2016). To explain the great divergence between the Topo IIAs encoded by Caudoviricetes and those encoded by Nucleocytoviricota in terms of sequences and structure, this scenario entails that the rate of Topo IIA evolution increased dramatically following the transfer of the Caudoviricetes version into the lineage leading to the LNCA, with the fusion of the three Topo IIA subunits of Caudoviricetes Topo IIA into a single polypeptide. ...
Type II DNA topoisomerases of the family A (Topo IIAs) are present in all Bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation, and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologs and have no orthologs in Archaea. Interestingly, eukaryotic Topo IIAs have close homologs in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses. Topo IIAs are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses on a dataset combining viral and cellular Topo IIA homologs. Topo IIAs encoded by Bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both Bacteria and Caudoviricetes from the data set, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long-branch attraction artifact. The topologies of our trees suggest that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.
... In the cellular world, the RdRp and the RT perform very specialized functions, but are not involved in genome replication. It is striking that both enzymes share with DNA-dependent DNA polymerases a structural folding located in the main catalytic domain (Iyer et al., 2005;Kazlauskas et al., 2016), which seems Spigelman's Monster. In this experiment published in 1967, the RNA from phage Qβ (red lines) and the enzyme responsible for its copy (blue pentagons) were incubated in the presence of nucleotides, and subjected to in vitro replication. ...
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
