Hist. Phil. Life Sci.

, 34 (2012), 391-406

The Place of Viruses in Biology in Light of the Metabolismversus-replication-first Debate

Purificacin Lpez-Garca
Unit dEcologie, Systmatique et Evolution CNRS UMR8079, Universit Paris-Sud 91405 Orsay, France
Abstract - The last decade has seen a revival of old virocentric ideas. These concepts are heterogeneous, extending from proposals that consider viruses functionally as living beings and/or as descendants of viral lineages that preceded cell evolution to other claims that consider viruses and/or some viral families a fourth domain of life. While the debates about whether viruses are alive or not and whether some virus-like replicators preceded the first cells fall under the long-lasting dichotomous view on the nature and origin of life (metabolism- versus replication-first), the claim that some giant viruses form a fourth domain in an organismal tree of life is not consistent with current evidence and can be falsified. Keywords - Tree of life, metabolism, self-replication, origin of life, definition of life, giant viruses, horizontal gene transfer, evolution

Introduction At the beginning of the twentieth century, the conditions for a scientific investigation into the origin of life on Earth were established. The rebuttal of continuous spontaneous generation by Louis Pasteur in the 1860s and the publication of On the Origin of Species in 1859 by Charles Darwin, led inevitably to the question of how the first life forms emerged. At the same time, immense progress in organic chemistry, biochemistry, cytology, and, among other advances, the discovery of the crucial importance of the cell nucleus, made it possible to approach a question that had remained until then too complex and intractable (Fry 2006). From very early on, however, two clear ideological currents emerged. One current gave primacy to self-replication (making copies of itself) as the crucial starting point for life and the other gave primacy to metabolism or self-maintenance. This persistent chicken-and-egg dichotomy corresponded, in the terminology of the time, to a nucleus
2012 Stazione Zoologica Anton Dohrn

392

PURIFICACIN LPEZ-GARCA

versus cytoplasm debate. Accordingly, hypotheses on the origin of life subscribed either to nucleocentric or cytoplasmic views of life. Among the important discoveries due to microscopy and other technological advances at the onset of the twentieth century was the discovery of viruses. Viruses were first discovered at the end of the nineteenth century when the Russian botanist Dmitri Ivanovsky (1892) observed that suspensions of plant tissues afflicted with mosaic tobacco disease were still infectious after passage through ceramic filters that retained bacteria. This observation was confirmed in 1898 by one of the spiritual founders of the so-called Delft school of microbiology, Martinus Beijerinck, who popularized the term virus to refer to the filterable infectious agents (reviewed in Podolsky 1996). A few years later, Frederick Twort (1915) and Felix DHrelle (1917) discovered viruses infecting bacteria, which were subsequently called bacteriophages. It is not surprising that at the time many researchers considered the mysterious viruses, with their infective capacities and their small sizes, the simplest living entities. As such, they were intermingled in the debate on the origin of life for several decades with different connotations: the virus as a metaphor for the simplest form of life, the virus as a functional model (an independent existing gene) and, collectively, the viruses as a phylogenetic lineage with historical continuity that could be placed between the chemical world and the first cells (Podolsky 1996). The importance of viruses for models on the origin of life and on the concept of what is life has vacillated over time. As reviewed in Podolsky (1996), until the mid-1930s the idea of a virus-centered origin-of-life was gaining credence. As early as 1914, the American psycho-physiologist Leonard Troland had envisaged that the first life form might have been an enzyme or organic catalyst (Troland 1914), although he later spoke of a genetic enzyme, and identified it with nucleic acids and proteins in the nucleus (Troland 1917). Subsequently, Herman Muller adopted and simplified Trolands ideas, replacing genetic enzyme with gene (Fry 2006). In 1922, Muller made a clear conceptual link between virus and gene, saying that there is no distinction between genes and them [viruses] (Muller 1922) and, in 1929, he openly proposed that the first living organism was a primitive gene (Muller 1929). The same year, John B.S. Haldane, in his essay on the origin of life, extended that operational view to a more phylogenetic view, asserting that life may have remained in the virus stage for many millions of years before a suitable assemblage of elementary units was brought together in the first cell (Haldane 1929). Along the same line of thought, Alexander and Bridges conceived of self-copying entities such as genes and viruses as the simplest components necessary to life, even dividing living beings into two

THE PLACE OF VIRUSES IN BIOLOGY

393

taxonomic categories, Cytobiontia (cellular organisms) and Ultrabiontia (viruses) (Alexander and Bridges 1928). The syllogism, smallest = virus, smallest = first, so that virus = first (Beutner 1938), was readily accepted during those early years; the nucleocentric view of the origin of life was also virocentric. This view, however, soon fell out of favor largely due to the cytoplasmist Alexander I. Oparins extensive work on the origin of life. Oparin conceived the origin of life from a biochemical or colloidal chemistry perspective, placing the emphasis on metabolism (Oparin 1938). For Oparin, life was a self-regulating system of catalytic reactions. In addition to Oparins influential model for the origin of life, several investigators called into question the progressivist view of viruses. Robert G. Green perceived viruses as products of the most extensive retrogradation and parasitization (Green 1932). This regressive view of viral evolution, shared by Andr Lwoff (Lwoff 1943; 1957), was increasingly accepted. Furthermore, Haldane affirmed that most evolutionary change has been degenerative (Haldane 1932). Haldanes position became, however, increasingly conciliatory to Oparins views. Although Haldane identified life with molecular self-reproduction, he pointed out that in a true living system the function of any part, including genes, depended on the cooperation of all other parts (Fry 2006). Nucleocentric views of life regained credence after the discovery that DNA was the genetic material (Avery et al. 1944) and, most importantly, after determination of the DNA structure, which suggested an elegant self-copying mechanism (Watson and Crick 1953). It was also shown that the nucleic acid component of viruses was the infectious component (Hershey and Chase 1952). Consequently, the association of virus - nucleic acid - gene was easy to make. Even so, the initial notion that viruses were phylogenetically the most primitive organisms on Earth was abandoned in the 1950s in favor of an operational view according to which viruses were seen as metaphors for living genes (Podolsky 1996). Virocentric ideas on the origin of life were largely abandoned in the 1960s and throughout the remainder of the twentieth century. This was due to two major factors. First, advances in biochemistry and molecular biology led to the recognition that viruses were strict molecular parasites. Since then, viruses have been considered biological entities able, like genes, to evolve but unable to self-replicate and to self-sustain, a position still held by the International Committee on Taxonomy of Viruses (van Regenmortel 2000; 2008). Second, the discovery was made that some RNAs have catalytic activity and, thus, display dual functions as informative polymers and catalysts. This and the discovery that the highly conserved ribosome is a ribozyme, led to the development of the

394

PURIFICACIN LPEZ-GARCA

RNA world as a powerful model of early life evolution (for a review, see Orgel 2004; Robertson and Joyce 2010). RNA replaced viruses in origin-of-life thinking: nucleocentric views on the origin of life were no longer virocentric. Renaissance of old virocentric ideas: whats new in the viral world? At the beginning of the twenty-first century, a renaissance of old virocentric ideas has taken place. Interestingly, this revival is taking place at both an operational level, with viruses seen functionally as living beings (Raoult and Forterre 2008), and at a phylogenetic level, with viruses viewed as descendants of viral lineages that preceded cell evolution (Bamford et al. 2005; Koonin et al. 2006). Additional claims assert more strongly that viruses and/or some viral families form a fourth domain of life (Raoult et al. 2004; Raoult and Forterre 2008). Some authors even consider viruses as capsid-encoding organisms, a renovated version of the Ultrabiontia, as opposed to ribosomeencoding organisms (cells) (Raoult and Forterre 2008). Collectively, these proposals are heterogeneous and, as we will see in the following, while some of these ideas fall under the two rival views on the nature and origin of life (metabolism versus genetic information), others are not consistent with current evidence and can be falsified (Lpez-Garca and Moreira 2009; Moreira and Lpez-Garca 2009). Why have these virocentric proposals been revived? The reasons are to be found in the considerable progress that is being made in viral research at various levels, from molecular and structural biology to ecology and evolution. A vast amount of knowledge about the structure and infectious cycles of viruses from very different families has been acquired in the past decades. The development of genomics has made it possible to sequence and compare RNA and DNA viral genomes, and also to compare those sequences to the host genomes. Contrary to recent virocentric claims asserting that viruses have been neglected by evolutionary biologists (Raoult and Forterre 2008), viruses have served for decades as models in population genetics often from an epidemiological standpoint because they evolve fast and have large population sizes. These factors allow for the testing of predictions based on different hypotheses (e.g. Gojobori et al. 1990; Lauring and Andino 2010). In recent years, it has also become clear through comparative genomics and phylogenetic analyses that viruses are active vehicles for horizontal gene transfer (HGT). Viral genomes or genome fragments (DNA

THE PLACE OF VIRUSES IN BIOLOGY

395

or retrotranscribed RNA) can recombine with host DNA, sometimes being inserted into host genomes and remaining latent in a proviral state until they are activated and enter an active replicative and infectious phase. Fragments of viral DNA can also be incorporated between short palindromic sequences in regions known as CRISPRs, which provide immunity to bacteria and archaea against specific viruses (Horvath and Barrangou 2010). By recombining with host genomes, viruses can pick up genes from cells or insert genes of foreign origin (either from viral or from distant cellular donors) into cell genomes. Therefore, they can affect and promote host evolution by transferring genes among cellular lines, an important phenomenon in evolution (Gogarten and Townsend 2005), or by promoting recombination of cellular genes (Zeidner et al. 2005). Some cellular genes, occasionally leading to innovations, appear to come from viruses, such as the telomerase enzyme (Eickbush 1997; Nakamura et al. 1997), or syncytin (of possible retroviral origin), found in placental mammals (Dupressoir et al. 2009). However, genes associated with viral genomes evolve fast, so that determining whether viral genes are truly viral or whether they correspond to fast-evolving cellular genes is extremely difficult. The contrary is certainly true: cellular genes are captured by viral genomes. This may happen accidentally, but occasionally the genes are nonetheless retained by selection. For instance, genes encoding elements of photosystems II (Sullivan et al. 2006) and I (Sharon et al. 2009) have been found in many cyanophages. These genes are expressed and appear to confer an advantage during phage infection. Another important element contributing to the renovated virocentric debate is the realization that viruses are extraordinarily diverse and abundant. This diversity has been revealed by classical studies on viruses infecting divergent cellular lineages and also by the development of new approaches, notably metagenomic analysis of viral fractions in various environments. Thus, studies on viruses infecting hyperthermophilic archaea revealed an unsuspected variety of new viral families, including new morphotypes. Some of these viruses can even experience morphological changes that render them infective when exposed to high temperatures (Prangishvili et al. 2006). A landmark discovery in recent years was that of giant viruses with very large genomes infecting amoeba. Some of these genomes exceed the size of some parasitic bacterial genomes and possess some homologues to cellular genes involved in typical cellular processes, including translation (Colson et al. 2011; Raoult et al. 2004). Some of these giant viruses can even be parasitized by other viruses (La Scola et al. 2008). At the same time and at the ecosystem level, DNA-staining of ultra-filtrates supposed to be free of bacteria suggested that viral particles (virions) can be up to an order of magnitude

396

PURIFICACIN LPEZ-GARCA

more abundant than cells in ocean plankton. These studies prompted the metagenomic analysis of such cell-free fractions by direct DNA or retrotranscribed-DNA sequencing, and revealed immense viral genetic diversity (Culley et al. 2003; Edwards and Rohwer 2005). Since then, metagenomic analyses of viruses are expanding and, with them, the discovery of novel groups of viruses and virus-like agents (Kristensen et al. 2010). Collectively, viruses constitute a huge genetic reservoir and are important engines of cellular evolution (Rohwer and Thurber 2009; Suttle 2007). Not only are they vehicles for HGT between cells and contribute to the acceleration of gene evolutionary rates (leading potentially to the evolution of novel functions in cells), they also impact cell evolution via their regulatory effect on cell populations. Viruses regulate populations by inducing cell lysis, contributing to both biogeochemical cycles and the maintenance of biodiversity via a kill-the-winner mechanism (Rodriguez-Valera et al. 2009; Suttle 2007). They also contribute to cellular evolution by Red Queen effects; i.e., generating an arms race involving the continuous evolution of resistance by hosts to novel virus variants. Recently, they have even been shown to influence cell cycle changes in the photosynthetic picoeukaryote Emiliania huxleyi, promoting a change from a diploid non-motile to a haploid motile and virus-resistant phase, a so-called Cheshire cat escape strategy (Frada et al. 2008). Dissecting current controversies on the place of viruses in biology The accumulated knowledge about virus diversity and their undeniable role in cellular evolution have revived virocentric debates. These are various, but can be generally classed into two types. The first is conceptual and relates to the definition of viruses and whether or not they can be considered alive from an operational point of view. The second is phylogenetic and relates to the actual possibility of placing viruses in the tree of life. Epistemological considerations: are viruses alive? Biologists work on living organisms but do not generally define life and do not feel comfortable with the task. This is largely due to the difficulty in delimiting barriers to some kind of natural continuum. Defining life, as with defining species, is therefore problematic. However, this should not prevent biologists from reaching a consensus on what is life (Morange 2011). Indeed, when some biologists say that viruses are alive,

THE PLACE OF VIRUSES IN BIOLOGY

397

they implicitly apply a definition of life. There are many definitions of life and/or living organisms that incorporate more or less long lists of properties (Luisi 1998). However, when reduced to essentials, they can be aligned along the two historically opposed views on the origin of life, metabolist (cytoplasmist) versus geneticist (nucleocentric). For metabolist views more popular among biochemists and physicists the essential property of life is self-maintenance. Obviously, viruses do not conform to such a definition of life because they lack any form of metabolism. Despite all the recent fascinating discoveries about the extent of viral diversity and their role in cellular evolution mentioned above, none of these discoveries actually challenges the basic essence of viruses: they are strict molecular parasites unable to transform energy and matter. They are unable to "create order from disorder" and actively keep the system far from thermodynamic equilibrium. Nonetheless, some authors have recently tried to accommodate viruses within this type of definition by using a conceptual trick. According to them, viruses would be quasi-autonomous entities whose true state is the "cell factory" or the "virocell"; i.e., the transformed infected cell actively replicating the virus. Virions, they say, should not be confounded with viruses, just as fish eggs should not be confounded with fish, or human spermatozoids with humans (Claverie 2006; Claverie and Abergel 2010; Forterre 2010). Using this artifice, the properties intrinsic to life (cells) are transferred to the virus. However, for a scientist, there is no doubt that a fish egg of a given species is a member of that species just as the adult fish is; they are both part of the life cycle of that species. The same applies to viruses: virions are viruses just as the viruses being actively replicated within the cell are viruses; they are both part of the infective viral cycle (Moreira and Lpez-Garca 2009; Van Regenmortel 2010). Defining an entity (a virus) in terms of itself plus a portion of another entity (a cell) is alien to logic and can be considered as epistemological cheating. Viruses, unlike cells (including obligatory parasitic cells), are devoid of metabolic capabilities and cannot be deemed alive if self-maintenance is considered as the irreducible property of life. For geneticist views, the essential properties of life are self-replication and evolution. Evolution is a consequence of imperfect replication generating variants upon which drift or natural selection can act. Viruses do evolve, but are unable to self-replicate. Consequently, this definition of life does not accommodate viruses either. A self-replicating ribozyme would be alive (Robertson and Joyce 2010), but a virus would not be. Yet, many biologists consider viruses alive because they do evolve. However, viruses, like genes, do not evolve by themselves because they cannot self-replicate; they are evolved by cells, because they are replicated

398

PURIFICACIN LPEZ-GARCA

by cells (Moreira and Lpez-Garca 2009). Similarly, cultural traits such as language, art, or technology (memes according to Dawkins 1976), do not evolve by themselves; they are evolved by humans. At this point, we face two different possibilities if we want to consider viruses alive according to the geneticist view. Either anything that can evolve or be evolved is alive, which would include genes and memes in general, or the term virus is extended to accommodate a hypothetical capacity for selfreplication. The latter is precisely the option that some authors defend, namely those who maintain that viruses historically predate cells. Thus, Koonin and co-workers proposed the existence of a "Virus World" preceding cells that were composed of self-replicating virus-like genetic elements (Koonin et al. 2006). Modern viruses would derive from these virus-like entities. Similarly, others speak of self-replicating proto-viruses at the origin of cells (Jalasvuori and Bamford 2008). These proposals invite ambiguity and introduce confusion because viruses as we know them do not self-replicate. The term "virus" is being used not only as current non-self-reproducing viruses, but also as more generic genetic elements having properties that viruses actually lack. Despite the ambiguity, these models, which propose that self-replicating virus-like entities pre-date cells and are at the origin of modern viruses (Bamford et al. 2005; Jalasvuori and Bamford 2008; Koonin et al. 2006), are fully comprehensible under a pure geneticist view of life and its origin. Methodological considerations: can viruses be placed in a phylogenetic tree of life? The unquestionable importance of viruses in biological evolution does not necessarily authorize their inclusion in the tree of life. In addition to logical issues of the kind, if viruses are alive, they should be included in the tree of life; if they are not alive, they should excluded, there are other issues that prevent any practical attempt to place viruses in the tree of life. The first issue has to do with the meaning of the tree of life and how to reconstruct it in practice. A tree of life may be defined as a conceptual representation of organismal history. Since organisms and cells form from pre-existing organisms/cells, this tree would proceed basically by successive branch bifurcation. Based on biochemical grounds and the universality of the genetic code, there is little doubt that extant life derives from a common ancestor. Therefore, a universal organismal tree of vertical descent must exist because, physically, cells derive from cells. However, how to reconstruct such a tree from contemporary traits is far

THE PLACE OF VIRUSES IN BIOLOGY

399

from trivial, because few traits are universally shared. In the late 1970s, Carl R. Woese had the idea of using universally conserved genes and, in particular, ribosomal RNA genes to build such a tree, which incidentally resulted in the discovery of the archaea (Woese and Fox 1977). The use of other conserved markers confirmed that initial topology. Subsequently, however, the important development of genomics and molecular phylogeny has revealed conflicting tree topologies for different gene markers. This is due to a number of reasons, among which one of the most important is the significant level of horizontal gene transfer, especially among prokaryotes (Dagan and Martin 2006). This has led to the proposal that a tree of life does not exist and that it should be replaced by a network of genes and genomes (Dagan and Martin 2009; Doolittle and Bapteste 2007), or by a forest of individual gene trees (Puigbo et al. 2010). This controversy reflects again the dichotomous view of life. More metabolist views conceive of life in terms of organisms whose history can be reconstructed using a core of conserved gene markers and can be represented in the form of a tree of life. By contrast, pure geneticist views conceive of life in terms of genes and they deny the existence of a tree of life, because organisms are seen as mixtures of genes from different origins. Can viruses be placed in the tree of life? Paradoxically, under a pure geneticist view, which would be the only one that could accommodate viruses as living beings, a tree of life does not exist, making artificial the placement of viruses in such a tree. Independently of that theoretical consideration, can viruses be actually placed in the tree of life? Here, we need again to differentiate between two types of hypotheses. As mentioned, some hypotheses propose that viruses derive from an ancient virus world that preceded the evolution of cells (Koonin et al. 2006). They recognize that viruses cannot be placed in a tree of life because, among other things, they are polyphyletic, evolve fast, and the genes that they share with cells were mostly acquired by HGT from cells. Yet, they propose that there is a series of largely distributed hallmark viral genes and/or protein folds that are not present in cells and that could attest to ancient virus-specific genes (Bamford et al. 2005; Koonin et al. 2006). However, since viruses are indeed polyphyletic, there is not a single gene actually shared by all viruses, which impedes any attempt to construct a universal phylogeny of all viruses (this is, however, possible for independent viral families). Furthermore, the conclusion that particular viral capsid folds attest to a common origin (Bamford et al. 2005) ignores alternative explanations of the presence of common viral features in very different viral families or of viruses infecting very distant organisms. These include HGT, which is

400

PURIFICACIN LPEZ-GARCA

extremely frequent in viruses, but also host shifts (the capacity to infect distant hosts) and even convergence, which is relatively easy for simple structures such as icosahedral capsid proteins (Moreira and Lpez-Garca 2009). Therefore, that similar capsid protein folds occur in distant viral families infecting distant hosts is not compelling evidence for those specific folds and viruses to actually predate cells. Current data do not allow verifying or falsifying this hypothesis. By contrast, the last type of hypotheses to be considered here proposes that homologous genes shared by cells and viruses either were transferred to cells from viruses (Forterre 1999; 2006; Villarreal and De Filippis 2000) or indicate a common descent that allows placing viruses in the tree of life. This latter claim has been most specifically made for the giant Mimivirus and related nucleo-cytoplasmic large DNA viruses (NCLDV) which, based on the presence of homologues of cellular genes involved in typical cellular housekeeping functions such as translation, would constitute a fourth domain of life branching at the base of eukaryotes (Boyer et al. 2010; Raoult et al. 2004). These hypotheses can be tested using phylogenetic analyses. However, to make meaningful phylogenetic analyses, it is very important to apply appropriate models of sequence evolution, because viral genes evolve fast and are particularly prone to phylogenetic reconstruction artifacts such as long branch attraction, which would tend to place them at the base of the phylogenetic tree (Philippe et al. 2000). It is also very important to incorporate sequences that will result in a good taxonomic sampling, a sampling that includes, among other elements, representatives from the viruss hosts. Taking those precautions into consideration, it can be shown that the vast majority of homologues to cellular genes present in giant viruses correspond to transfers from the host (or from bacteria co-infecting the same host) to its virus. NCLDV genes do not form a monophyletic group at the base of eukaryotes, but appear dispersed within the eukaryotic tree close to their respective hosts (Lpez-Garca and Moreira 2009; Moreira 2000; Moreira and BrochierArmanet 2008; Moreira and Lpez-Garca 2005; 2009; Williams et al. 2011). Therefore, the hypothesis can be refuted that NCLDV giant viruses form a fourth domain of life, which can be placed in an organismal tree of life (Boyer et al. 2010; Raoult et al. 2004). The inconsistencies of claims proposing giant viruses as a fourth domain of life have also been revealed by the ambivalent positions of the proponents of such hypotheses as a response to criticism based on indepth phylogenetic analyses. Thus, after having proposed a fourth domain for viruses based on the reconstruction of an organismal tree of life using conserved genes (Raoult et al. 2004), Raoult first denied the exis-

THE PLACE OF VIRUSES IN BIOLOGY

401

tence of a tree of life from which viruses were out (Raoult 2009) and then made an ambiguous proposal for a fuzzy rhizome of life (Raoult 2010). In other words, to escape criticism, Raoult shifted from a metabolist view to a pure geneticist view to something undefined in between, thus adding much confusion to the debate. Claverie, another proponent of giant viruses as a fourth domain of life (Raoult et al. 2004), modified his opinion in order to claim that giant viruses are degenerated cells (Arslan et al. 2011). This implies a departure from the previous idea that these viruses constitute a fourth domain on the same footing as cellular domains, because now they would derive from within a cellular domain. There is no doubt that these giant viruses are very interesting and attest to a variety of mechanisms involved in genome evolution. However, the available data do not support their origin as an independent domain of life or as a line of degenerated cells. On the contrary, thorough genome comparative analyses suggest that these NCLDVs evolved from an ancestral virus having a core of proteins involved in viral replication and capsid formation after the recruitment of many eukaryotic and some bacterial genes via HGT, as well as many mobile genetic elements followed by massive lineage-specific duplications (Filee 2009; Koonin and Yutin 2010). Conclusion Old virocentric debates that considered viruses as alive and/or predating cells have been revived due to the accumulation of genomic and metagenomic analyses showing that viruses are extremely diverse, represent a huge genetic reservoir that interferes with the cellular reservoir via HGT (Brussow 2009), and play an important role in organismal ecology and evolution. However, despite their extraordinary diversity, no novel properties can be attributed to viruses, which remain strict genetic parasites lacking carbon and energy metabolism. Therefore, claims that viruses are alive and predate cellular evolution can be understood only within the framework of a strict geneticist view of life based exclusively on the property of evolution and the use of the term virus as a relaxed metaphor for self-replicating entities something which viruses, strictly speaking, are not. From a metabolist perspective, although it is conceivable that viruses emerged very early in evolution (i.e. right after cells or during cell evolution), they could not have evolved prior to cells or pre-cellular stages that could be parasitized by them. By contrast, claims that giant viruses form a fourth domain in the

402

PURIFICACIN LPEZ-GARCA

tree of life based on genes shared by cells involved in typical cellular functions can be refuted by proper molecular phylogenetic analyses and need to be removed from this debate. Acknowledgments I am grateful to Michel Morange and Ute Deichman for having invited me to participate in the Workshop on The Origin of Life at the Jacques Loeb Centre for the History and Philosophy of Life Sciences, Ben Gurion University, in June 2011. I also thank David Moreira for stimulating discussions and John Herrick for revising the English. This work was supported by the Centre National de la Recherche Scientifique through its interdisciplinary program, Environnements plantaires et origines de la vie. References
Alexander J. and Bridges C.B., 1928, Some physico-chemical aspects of life, mutation and evolution, in: Alexander J. (ed.), Colloid Chemistry, Theoretical and Applied, New York: Reinhold, 1-17. Arslan D., Legendre M., Seltzer V., Abergel C. and Claverie J.M., 2011, Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae, Proceedings of the National Academy of Sciences USA., 108: 1748617491. Avery O.T., MacLeod C.M. and McCarty M., 1944, Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from Pneumococcus type III, Journal of Experimental Medicine, 79: 137-158. Bamford D.H., Grimes J.M. and Stuart D.I., 2005, What does structure tell us about virus evolution?, Current Opinion in Structural Biology, 15: 655-663. Beutner R., 1938, Lifes beginning on the Earth, Baltimore: Williams & Wilkins. Boyer M., Madoui M.A., Gimenez G., La Scola B. and Raoult D., 2010, Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses, PLoS ONE, 5: e15530. Brussow H., 2009, The not so universal tree of life or the place of viruses in the living world, Philosophical Transactions of the Royal Society of London B, Biological Sciences, 364: 2263-2274. Claverie J.M., 2006, Viruses take center stage in cellular evolution, Genome Bioloby, 7: 110. Claverie J.M. and Abergel C., 2010, Mimivirus: the emerging paradox of quasiautonomous viruses, Trends in Genetics, 26: 431-437. Colson P., Yutin N., Shabalina S.A., Robert C., Fournous G., La Scola B., Raoult D. and Koonin E.V., 2011, Viruses with more than 1,000 genes: Mamavirus, a

THE PLACE OF VIRUSES IN BIOLOGY

403

new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes, Genome Biology and Evolution, 3: 737-742. Culley A.I., Lang A.S. and Suttle C.A., 2003, High diversity of unknown picornalike viruses in the sea, Nature, 424: 1054-1057. Dagan T. and Martin W., 2006, The tree of one percent, Genome Biology, 7: 118. Dagan T. and Martin W., 2009, Getting a better picture of microbial evolution en route to a network of genomes, Philosophical Transactions of the Royal Society of London B, Biological Sciences, 364: 2187-2196. Dawkins R., 1976, The Selfish Gene, New York: Oxford University Press. Doolittle W.F. and Bapteste E., 2007, Pattern pluralism and the Tree of Life hypothesis, Proceedings of the National Academy of Sciences USA, 104: 20432049. Dupressoir A., Vernochet C., Bawa O., Harper F., Pierron G., Opolon P. and Heidmann T., 2009, Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene, Proceedings of the National Academy of Sciences USA, 106: 12127-12132. Edwards R.A. and Rohwer F., 2005, Viral metagenomics, Nature Reviews Microbiology, 3: 504-510. Eickbush T.H., 1997, Telomerase and retrotransposons: which came first?, Science, 277: 911-912. Filee J., 2009, Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses, Journal of Invertebrate Pathology, 101: 169-171. Forterre P., 1999, Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins, Molecular Microbiology, 33: 457-465. Forterre P., 2006, Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain, Proceedings of the National Academy of Sciences USA, 103: 3669-3674. Forterre P., 2010, Defining life: the virus viewpoint, Origin of Life and Evolution of Biospheres, 40: 151-160. Frada M., Probert I., Allen M.J., Wilson W.H. and de Vargas C., 2008, The Cheshire Cat escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection, Proceedings of the National Academy of Sciences USA, 105: 15944-15949. Fry I., 2006, The origins of research into the origins of life, Endeavour, 30: 24-28. Gogarten J.P. and Townsend J.P., 2005, Horizontal gene transfer, genome innovation and evolution, Nature Reviews in Microbiology, 3: 679-687. Gojobori T., Moriyama E.N. and Kimura M., 1990, Molecular clock of viral evolution, and the neutral theory, Proceedings of the National Academy of Sciences USA, 87: 10015-10018. Green R.G., 1932, On the nature of the filterable viruses, Science, 82: 444. Haldane J.B.S., 1929, The origin of life, The Rationalist Annual: 3-10. Haldane J.B.S., 1932, The causes of evolution, London: Harper. Hershey A.D. and Chase M., 1952, Independent functions of viral protein and nucleic acid in growth of bacteriophage, Journal of General Physiology, 36: 39-56.

404

PURIFICACIN LPEZ-GARCA

Horvath P. and Barrangou R., 2010, CRISPR/Cas, the immune system of bacteria and archaea, Science, 327: 167-170. Jalasvuori M. and Bamford J.K., 2008, Structural co-evolution of viruses and cells in the primordial world, Origin of Life and Evolution of Biospheres, 38: 165-181. Koonin E.V., Senkevich T.G. and Dolja V.V., 2006, The ancient Virus World and evolution of cells, Biology Direct, 1: 29. Koonin E.V. and Yutin N., 2010, Origin and evolution of eukaryotic large nucleocytoplasmic DNA viruses, Intervirology, 53: 284-292. Kristensen D.M., Mushegian A.R., Dolja V.V. and Koonin E.V., 2010, New dimensions of the virus world discovered through metagenomics, Trends in Microbiology, 18: 11-19. La Scola B., Desnues C., Pagnier I., Robert C., Barrassi L., Fournous G., Merchat M., Suzan-Monti M., Forterre P., Koonin E. and Raoult D., 2008, The virophage as a unique parasite of the giant mimivirus, Nature, 455: 100-104. Lauring A.S. and Andino R., 2010, Quasispecies theory and the behavior of RNA viruses, PLoS Pathogens, 6: e1001005. Lpez-Garca P. and Moreira D., 2009, Yet viruses cannot be included in the tree of life, Nature Reviews in Microbiology, 7: 615-617, doi:10.1038/nrmicro2108-c7. Luisi P.L., 1998, About various definitions of life, Origin of Life and Evolution of Biospheres, 28: 613-622. Lwoff A., 1943, Lvolution physiologique: Etude des pertes de fonctions chez les microorganismes, Paris: Hermann et Cie. Morange M., 2011, Problems raised by a definition of life, in: Gargaud M., LpezGarca P. and Martin H. (eds), Origins and evolution of life, New York: Cambridge University Press, 3-13. Moreira D., 2000, Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages: implications for the origin of bacterial replication machinery, Molecular Microbiology, 35: 1-5. Moreira D. and Brochier-Armanet C., 2008, Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes, MC Evolutionary Biology, 8: e12. Moreira D. and Lopez-Garcia P., 2005, Comment on The 1.2-megabase genome sequence of Mimivirus, Science, 308: 1114. Moreira D. and Lpez-Garca P., 2009, Ten reasons to exclude viruses from the tree of life, Nature Reviews in Microbiology, 7: 306-311. Muller H., 1929, The gene as the basis of life, in: Duggar B.M. (ed.), Proceedings of the International Congress of Plant Sciences. George Banta, Menasha, WI, USA, 917-918. Muller H.J., 1922, Variation due to change in the individual gene, American Naturalist, 56: 32-50. Nakamura T.M., Morin G.B., Chapman K.B., Weinrich S.L., Andrews W.H., Lingner J., Harley C.B. and Cech T.R., 1997, Telomerase catalytic subunit homologs from fission yeast and human, Science, 277: 955-959. Oparin A.I., 1938, The origin of life, New York: Mac Millan. Orgel L.E., 2004, Prebiotic chemistry and the origin of the RNA world, Critical Reviews in Biochemistry and Molecular Biology, 39: 99-123.

THE PLACE OF VIRUSES IN BIOLOGY

405

Philippe H., Lopez P., Brinkmann H., Budin K., Germot A., Laurent J., Moreira D., Muller M. and Le Guyader H., 2000, Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions, Proceedings of the Royal Society of London B, Biological Sciences, 267: 1213-1221. Podolsky S., 1996, The role of the virus in origin-of-life theorizing, Journal of the History of Biology, 29: 79-126. Prangishvili D., Vestergaard G., Haring M., Aramayo R., Basta T., Rachel R. and Garrett R.A., 2006, Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle, Journal of Molecular Biology, 359: 1203-1216. Puigbo P., Wolf Y.I. and Koonin E.V., 2010, The tree and net components of prokaryote evolution, Genome Biology and Evolution, 2: 745-756. Raoult D., 2009, There is no such thing such as a tree of life (and of course viruses are out!), Nature Reviews in Microbiology, 7: 615. Raoult D., 2010, The post-Darwinist rhizome of life, Lancet, 375: 104-105. Raoult D., Audic S., Robert C., Abergel C., Renesto P., Ogata H., La Scola B., Suzan M. and Claverie J.M., 2004, The 1.2-megabase genome sequence of Mimivirus, Science, 306: 1344-1350. Raoult D. and Forterre P., 2008, Redefining viruses: lessons from Mimivirus, Nature Reviews in Microbiology, 6: 315-319. Robertson M.P. and Joyce G.F., 2010, The Origins of the RNA World, Cold Spring Harbor Perspectives in Biology. Rodriguez-Valera F., Martin-Cuadrado A.B., Rodriguez-Brito B., Pasic L., Thingstad T.F., Rohwer F. and Mira A., 2009, Explaining microbial population genomics through phage predation, Nature Reviews in Microbiology, 7: 828-836. Rohwer F. and Thurber R.V., 2009, Viruses manipulate the marine environment, Nature, 459: 207-212. Sharon I., Alperovitch A., Rohwer F., Haynes M., Glaser F., Atamna-Ismaeel N., Pinter R.Y., Partensky F., Koonin E.V., Wolf Y.I., Nelson N. and Beja O., 2009, Photosystem I gene cassettes are present in marine virus genomes, Nature, 461: 258-262. Sullivan M.B., Lindell D., Lee J.A., Thompson L.R., Bielawski J.P. and Chisholm S.W., 2006, Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts, PLoS Biology, 4: e234. Suttle C.A., 2007, Marine viruses major players in the global ecosystem, Nature Reviews in Microbiology, 5: 801-812. Troland L.T., 1914, The chemical origin and regulation of life, Monist, 24: 92133. Troland L.T., 1917, Biological enigmas and the theory of enzyme action, American Naturalist, 51: 321-350. Van Regenmortel M.H., 2010, Logical puzzles and scientific controversies: the nature of species, viruses and living organisms, Systematic and Applied Microbiology, 33: 1-6. van Regenmortel M.H.V., 2000, Introduction to the species concept in virus taxonomy, in: van Regenmortel M.H.V. et al. (eds), 7th Report of the International Committee on Taxonomy of Viruses, San Diego: Academic Press, 3-16.

406

PURIFICACIN LPEZ-GARCA

van Regenmortel M.H.V., 2008, The nature of viruses, in: Mahy B.W.J. and van Regenmortel M.H.V. (eds), Encyclopedia of Virology, Amsterdam: Elsevier/ Academic Press, 398-402. Villarreal L.P. and DeFilippis V.R., 2000, A hypothesis for DNA viruses as the origin of eukaryotic replication proteins, Journal of Virology, 74: 7079-7084. Watson J.D. and Crick F.H., 1953, The structure of DNA, Cold Spring Harbor Symposia on Quantitative Biology, 18: 123-131. Williams T.A., Embley T.M. and Heinz E., 2011, Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses, PLoS ONE, 6: e21080. Woese C.R. and Fox G.E., 1977, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proceedings of the National Academy of Sciences USA, 74: 5088-5090. Zeidner G., Bielawski J.P., Shmoish M., Scanlan D.J., Sabehi G. and Beja O., 2005, Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates, Environmental Microbiology, 7: 15051513.