Entrevista 10

After discussing the difficulties of defining the concept of a virus, its status as living organism, and its taxonomic classification, we next look in more detail at viral evolution in order to establish from where these difficulties originate. In particular, we will review the relationship between viruses and the three domains of cellular life and highlight the importance of viruses as gene transfer vehicles; last, a bold theory on the origin of cellular life is introduced that features viruses as protagonists.

Viruses and the three domains of life

All cellular life present today, as categorized into the three domains Bacteria, Archaea, and Eukarya, has descended from a single ances- tor (LUCA: last universal cellular ancestor),(1)a complex life form with complete, protein-based ribosomal machinery(2)_{that already} used the universal genetic code.(3) _{Based on sequence similarity of} ribosomal proteins and rRNA-components, it is possible to assign to each cellular organisms a position within a single tree of life, a common representation of ancestry and speciation.(4),(5)

As briefly touched upon before, families of giant viruses such as mimiviruses, marseilleviruses, and mamaviruses(6)were identified that possess genomes and physical dimensions rivaling that of bacteria. The genomes of these and other viral families contain genes for carbon-, energy-, and cellular metabolism(7)– functions that are more characteristic for cellular than of viral life(8). These findings have lead to the proposition of an additional, fourth domain of life consisting of giant viruses,(9)a notion that was later found to be invalid due to erroneous phylogenetic assumptions.(10)

Since novel genes cannot appear in viral particles de novo, it is very likely that genes of giant viruses are homologs of cellular genes from either current or long extinct cellular lines, possibly reaching back before the LUCA. These genes may then have been manipulated by gene duplication, recombination, and frameshift mutations and thus repurposed by selection and divergent evolu- tion while also being subject to frequent horizontal gene transfer between viruses and their hosts. The latter may have occurred to an extent resulting in more novel genes having been transferred from viruses to cellular life than vice versa(11)(a notion that is, however, contested).(12)

36 from basic research to clinical applications

(13)_{Forterre(2006a),Forterre and}

Prangishvili(2009b)

(14)_{Koonin et al.(2006)} (15)_{Forterre(2005)}

(16)_{Koonin et al.(2006)}

(17)_{Forterre and Prangishvili(2009b),}

Holmes(2011)

(18)_{Forterre(2006a),Gorbalenya et al.}

(1990),Hansen et al.(1997)

(19)_{Koonin and Dolja(2006)} (20)_{Mira et al.(2001)}

(21)_{Kindt et al.(2001)} (22)_{Koonin et al.(2001)}

(23)_{Casjens(2003),Edwards and Rohwer}

(2005)

(24)_{Lindell et al.(2005)}

Established and novel theories on the origin of viruses

Several conflicting hypotheses for the origin of viruses have been proposed; these include notions that viruses are remnants of pre- cellular life forms (virus-first hypothesis), that viruses are reduced forms from cellular life that either escaped the cellular environ- ment and adapted to a parasitic style of life (escape hypothesis), or that viruses are parasites of evolutionary more competent rivals (one of whose descendants developed to be the LUCA instead of becoming extinct (reduction hypothesis ). Newer investigations have re-evaluated these hypotheses based on the current data and con- firm an ancient origin of viruses(13)_{that probably goes back to a} primordial environment, termed the RNA-world, in which viruses either preceded cellular life(14)_{or existed concurrently with it.}(15)

These arguments pertaining to the origin of viruses are based on the observation that viral genes originally involved in DNA and RNA replication are structurally more similar between viruses infecting all three domains of life than between viruses and cellu- lar organisms.(16) Similarly, specific protein folds of viral capsids are also present in RNA and DNA viruses and in viruses infect- ing the three domains of life, thus strongly suggesting that these viruses predate the LUCA and may have significantly shaped the emergence of cellular life.(17) Further insights derived from the comparison of protein structures suggest that the world of viruses may have been split from the beginning: while RNA viruses origi- nated by escape or reduction, DNA viruses may have evolved only later from RNA viruses, possibly due to an evolutionary arms race between RNA-based viral and RNA-based cellular life in which viruses changed the chemical implementation of their genomes in order to protect themselves against host nucleases.(18)

Virus-like gene transfer agents (GTAs) are hypothesized to be major drivers in the development of complexity in early evolu- tion.(19) While prokaryotes are under constant selective pressure to maintain small genomes,(20)many viruses are less constrained in this regard due to the need for a certain minimal genome size in or- der to ensure high-pressure capsid-packing required for successful infection.(21) Horizontal gene transfer events are a common mode of genomic exchange between viruses and prokaryotes:(22) _more than 60% of the sequenced bacterial genomes contain at least one integrated viral genome (a provirus) and up to 3% of the nucleotide content of all bacterial genomes may consist of such proviruses.(23) The widespread use of horizontal transfer may confer selective ad- vantages to the host and thus increase metabolic resources for the virus: this case is illustrated by marine phages that infect Prochloro- coccus and Synechococcus, the most abundant photosynthetic organ- isms in oceanic ecosystems, and supplement the host repertoire of photosynthesis genes, thereby increasing host fitness.(24)

the origins of viruses 37

(25)_{Angly et al.(2006)}

(26)_{Forterre(2002)}

(27)_{Mushegian and Koonin(1996)}

(28)_{Leipe et al.(1999)}

(29)_{Forterre and Philippe(1999)}

(30)_{Gray and Lang(1998)}

(31)_{Filée et al.(2003),Shutt and Gray}

(2006)

(32)_{Lazcano et al.(1988)}

(33)_{Wintersberger and Wintersberger}

(1987)

(34)_{Forterre(2006b)} (35)_Warren(1980)

(36)_{Takahashi and Marmur(1963)}

Viruses as midwifes of the tree of life

Due to the high abundance of viruses and other virus-like gene transfer agents, the virosphere forms a gigantic reservoir of genes that can be transferred to cellular organisms, in principle.(25) In- terestingly, it is therefore at least conceivable that DNA replication may have originated first in the virosphere, for example as a re- sult of gene duplication of existing RNA polymerases, followed by divergent evolution. More daring hypotheses even suggest that components of the cellular DNA replication machinery could have been transported by horizontal gene transfer from the first DNA viruses to cellular life, thereby aiding in the emergence of the first DNA cellular life forms.(26) _{Indeed, there is strong evidence for the} fact that while DNA was invented before the LUCA,(27)_{it was not} yet replicated by that time. Instead, data suggest that replication mechanisms were invented by Bacteria and Archaea independently after the divergence of these domains.(28)

This hypothesis is compatible with the proposed introduction of DNA replication systems into RNA-based cellular life by DNA viruses.(29) While certainly a provocative theory, a similar event also demonstrates large-scale intercellular innovation originating from viruses at later evolutionary times: it is now well established by comparative genomics data that eukaryotic mitochondria orig- inated from a free-living a-Proteobacterium.(30) However, it is less commonly known that the bacterial RNA and DNA polymerases of the proto-mitochondria have been replaced by more efficient viral homologs of T-odd bacteriophages at the time of endosymbiosis, an event that is conceptually similar to the proposed introduction of DNA replication in bacteria.(31)

Interestingly, viral invention and the proposed transfer of viral DNA replication mechanisms into cellular organisms solves an ap- parent evolutionary paradox: DNA is more stable than RNA and protects genetic information against oxidization and cytosine-uracil mutations, thus providing a necessary precondition for the evolu- tion towards larger genome sizes.(32) However, it is unclear what a viable RNA-DNA intermediate that is required for evolving such a transition may look like, or how the future potential for encod- ing a larger genome may confer an immediate selective advantage to a cell that has just transitioned to a DNA-based genome. The proposed stepwise origin of DNA replication that makes use of an RNA template(33)_{may explain the diversity of proteins replicat-} ing DNA in the three domains of life,(34)_{provides an immediate} benefit to DNA viruses due to the protection of their genome from host RNA nucleases,(35)and is further supported by evidence for a potential RNA-DNA intermediary that has been identified in phages.(36)

38 from basic research to clinical applications

(37)_{Forterre(2005)}

(38)_{Forterre(2006b)}

(39)_{Woese et al.(1990)}

(40)_{Forterre and Philippe(1999)} (41)_Woese(1987)

(42)_Gupta(2000)

(43)_{López-Gar´cia and Moreira(1999)}

(44)_{Forterre(2011)}

(45)_{Which are of viral origin (Coronaviridae)}

and are about 32 kbp long; cf.Lauber et al.(2013) for a recent discussion on the relation of replication fidelity, genome size, and genetic complexity of RNA genomes in general and Coronaviridae in particular.

(46)_{Forterre(2006a)}

(47)_{Forterre(2006a)}

(48)_Woese(2000)

By way of extending these provocative assumptions, an elegant theory of the origin of DNA-based life proposes that the three do- mains of life are the results of three independent fusion-events between viral DNA replication machinery and RNA-based cellu- lar life.(37) Depending on the phylogenetic data used for analysis, multiple conflicting scenarios for the evolutionary relation between the three domains of life are proposed, each of which fails to ex- plain all of the observed data(38): either two lineages diverged from the LUCA, giving rise to Bacteria and the common ancestor of Ar- chaea and Eukarya, respectively,(39)or two primordial lineages gave rise to Eukarya and the common ancestor of Archaea and Bacte- ria.(40) _{While the identity of the LUCA is argued to be either an} RNA-based cellular life form,(41)_{or a bacterium giving rise to the} Archaea,(42)_{the popular chimeric theory of eukaryotic evolution} suggests that eukaryotes are a product of extensive genome fusion event between archaeal and bacterial lineages.(43)

The ’three viruses, three domains’ theory, in contrast, suggests that the LUCA was RNA-based cellular life that gave rise to Bac- teria and the common ancestor of Archaea and Eukarya, the latter of which might have arisen by divergence or by fusion of Bacteria and Archaea,(44)resulting in the three accepted domains of life. Three independent fusions of a founder cell of each domains with a different DNA virus, respectively, may then have lead to a trans- formation of the RNA genomes into DNA genomes. As a result, the transformed cells and their descendants may have been able to sta- bilize their genomes with regard to mutations and afford genome sizes larger than the largest currently known RNA genomes.(45) Due to the higher genetic stability and functional versatility, these cells may have then been in a position to quickly outcompete other RNA-based life forms, which were consequently lost from evolu- tionary records.

This theory, while not falsifiable by available data, has consider- able explanatory power. First, it explains why there are only three domains of life: viral fusion is a rare event and RNA-based cells were outcompeted and removed from the biosphere, thus elimi- nating the basis for further fusion events. The three domains of life that originated before loss of RNA-based life specialized in differ- ent life styles (fast replicating Bacteria versus predatory Eukarya) or invaded environmental niches (Archaea).(46) _{Second, the theory} justifies why there are three different canonical versions of riboso- mal proteins, as well as extensive differences between components of the DNA replication machinery in the three domains of life.(47) Third, the hypothesis provides arguments for mutation rates in the time period between the LUCA and the origin of the three do- mains of life being in accordance with RNA-based life, while later evolutionary rates are suggestive of DNA-based life.(48) In sum- mary, these hypotheses suggest that viruses may play an influential role in the evolution of the three kingdoms of life. Whether viruses should be considered to be part of the tree of life or only act as mediators between its branches is open to debate.

(1)_{Rice et al.(2004)} (2)_{Levin and Moran(2011)}

(3)_{cf.Vasileva and Jessberger(2005)}

for a recent overview on the latter two processes.

(4)_{Feschotte and Gilbert(2012)}