Origins and evolution of viruses of eukaryotes

25 Pages·2015·4.01 MB·English

by  Dolja, Valerian V.

Origins and evolution of viruses of eukaryotes: The ultimate modularity
Koonin, E. V., Dolja, V. V., & Krupovic, M. (2015). Origins and evolution of viruses
of eukaryotes: the ultimate modularity. Virology, 479, 2-25.
doi:10.1016/j.virol.2015.02.039
10.1016/j.virol.2015.02.039
Elsevier
Version of Record
http://cdss.library.oregonstate.edu/sa-termsofuse
Virology479-480(2015)2–25
ContentslistsavailableatScienceDirect
Virology
journal homepage: www.elsevier.com/locate/yviro
Review
Origins and evolution of viruses of eukaryotes:
The ultimate modularity
Eugene V. Koonina,n, Valerian V. Doljab, Mart Krupovicc
aNationalCenterforBiotechnologyInformation,NationalLibraryofMedicine,NationalInstitutesofHealth,Bethesda,MD20894,USA
bDepartmentofBotanyandPlantPathology,OregonStateUniversity,Corvallis,OR97331,USA
cInstitutPasteur,UnitéBiologieMoléculaireduGènechezlesExtrêmophiles,DepartmentofMicrobiology,Paris75015,France
a r t i c l e i n f o a b s t r a c t
Articlehistory: Virusesandotherselfishgeneticelementsaredominantentitiesinthebiosphere,withrespecttoboth
Received27January2015 physicalabundanceandgeneticdiversity.Variousselfishelementsparasitizeonallcellularlifeforms.
Returnedtoauthorforrevisions Therelativeabundancesofdifferentclassesofvirusesaredramaticallydifferentbetweenprokaryotes
19February2015 and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA
Accepted20February2015
genomes,withasubstantialminorityofsingle-stranded(ss)DNAvirusesandonlylimitedpresenceof
Availableonline12March2015
RNAviruses. In contrast, in eukaryotes, RNAviruses account for the majority of the virome diversity
Keywords: althoughssDNAanddsDNAvirusesarecommonaswell.Phylogenomicanalysisyieldstangiblecluesfor
Evolutionofviruses the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes.
Transposableelements Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been
Polintons
assembled de novo from genes derived from prokaryotic retroelements and bacteria although a
Bacteriophages
primordialoriginofthisclassofvirusescannotberuledout.Differentgroupsofdouble-strandedRNA
Recombination
Functionalgenemodules virusesderiveeitherfromdsRNAbacteriophagesorfrompositive-strandRNAviruses.Theeukaryotic
ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating
plasmidsandpositive-strandRNAviruses.DifferentfamiliesofeukaryoticdsDNAvirusesappeartohave
originatedfromspecificgroupsofbacteriophagesonatleasttwoindependentoccasions.Polintons,the
largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the
evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA
viruses including the proposed order “Megavirales” that unites diverse families of large and giant
viruses.Strikingly,evolutionofallclassesofeukaryoticvirusesappearstohaveinvolvedfusionbetween
structuralandreplicativegenemodulesderivedfromdifferentsourcesalongwithadditionalacquisi-
tionsofdiversegenes.
PublishedbyElsevierInc.ThisisanopenaccessarticleundertheCCBYlicense
(http://creativecommons.org/licenses/by/4.0/).
Contents
Introduction.............................................................................................................. 3
Thecontrastingviromesofprokaryotesandeukaryotes........................................................................... 3
Evolutionaryscenariosfortheoriginofeukaryotesandtheirimpactonthereconstructionofvirusevolution............................... 4
Originsofthemajorclassesofeukaryoticvirusesandevolutionaryrelationshipsbetweenvirusesofprokaryotesandeukaryotes............... 5
AgeneralperspectiveonRNAvirusevolution:OutoftheprimordialRNAworld?.................................................. 5
Positive-strandRNAviruses:Assemblyfromdiverseprokaryoticprogenitorsandgeneexchangesleadingtoenormousdiversification....... 6
dsRNAviruses:Multipleoriginsfrompositive-strandRNAviruses .............................................................. 9
Negative-strandRNAviruses:Theemergingpositive-strandconnection......................................................... 10
SynopsisoneukaryoticRNAvirome...................................................................................... 10
Retroelementsandretroviruses:Virusesasderivedforms.................................................................... 10
nCorrespondingauthor.
E-mailaddresses:[email protected](E.V.Koonin),
[email protected](V.V.Dolja),[email protected](M.Krupovic).
http://dx.doi.org/10.1016/j.virol.2015.02.039
0042-6822/PublishedbyElsevierInc.ThisisanopenaccessarticleundertheCCBYlicense(http://creativecommons.org/licenses/by/4.0/).
E.V.Kooninetal./Virology479-480(2015)2–25 3
Synopsisoneukaryoticretroelements.................................................................................... 14
OriginsofssDNAvirusesofeukaryotes:MultiplecrossesbetweenplasmidsandRNAviruses ....................................... 14
SynopsisonssDNAvirusorigins......................................................................................... 17
OriginsandprimarydiversificationofeukaryoticdsDNAviruses:Thebacteriophageandtransposableelementconnections .............. 17
SynopsisofdsDNAvirusevolution....................................................................................... 20
Conclusions............................................................................................................. 20
Acknowledgments........................................................................................................ 21
AppendixA. Supportinginformation...................................................................................... 21
References.............................................................................................................. 21
Introduction
virusesandencompassmultipletransitionsfromcapsid-lesselements
A major discovery of environmental genomics over the last to bona fide viruses and vice versa (Koonin and Dolja, 2013, 2014).
decadeisthatthe mostcommonand abundantbiologicalentities Thus, any reconstruction of virus evolution that fails to take into
on earth are viruses, in particular bacteriophages (Edwards and accounttheevolutionaryrelationshipswithnon-viralselfishelements
Rohwer, 2005; Rohwer, 2003; Rohwer and Thurber, 2009; Suttle, isboundtobesubstantiallyincomplete.Thecapsid-lesselementsas
2005, 2007). In marine, soil and animal-associated environments, wellasmanyvirusesdifferintheirextentofintegrationwiththehost
virusparticlesconsistentlyoutnumbercellsbyonetotwoordersof cells: some insert into the cell genome and are transmitted mainly
magnitude.Virusesaremajorecologicalandevengeologicalagents verticallythroughthehostgenerations,othersarelargelyautonomous,
thatinlargepartshapesuchprocessesasenergyconversioninthe andmanycombinebothstrategiesmixedindifferentproportions.
biosphere and sediment formation in water bodies by killing off Viruses and other selfish elements certainly have not evolved
populationsofabundant,ecologicallyimportantorganismssuchas from a single common ancestor: indeed, not a single gene is
cyanobacteria or eukaryotic algae (Fuhrman, 1999; Rohwer and conserved across the entire “greater virus world” or even in the
Thurber,2009;Suttle,2007).Withthepossibleexceptionofsome majority of selfish elements (Holmes, 2011; Koonin et al., 2006).
highlydegradedintracellularparasiticbacteria,virusesand/orother However, these elements form a dense evolutionary network in
selfishelements,suchastransposonsandplasmids,parasitizeonall whichgenomesarelinkedthroughdifferentsharedgenes(Koonin
cellularorganisms.Complementarytotheirphysicaldominancein andDolja,2014;KrupovicandKoonin,2015;Yutinetal.,2013).This
thebiosphere,virusescollectivelyappeartoencompassthebulkof typeofevolutionaryrelationshipresultsfromextensiveexchangeof
the genetic diversity on earth (Hendrix, 2003; Kristensen et al., genes and gene modules, in some cases betweenwidely different
2010,2013).Theubiquityofvirusesintheextantbiosphereandthe elements,aswellasparallelcaptureofhomologousgenesfromthe
resultsoftheoreticalmodelingindicatingthatemergenceofselfish hosts by distinct elements. Viruses with large genomes possess
genetic elements is intrinsic to any evolving system of replicators numerous genes that were acquired from the hosts at different
together imply that virus-host coevolution had been the mode of stages of evolution; such genes typically are restricted in their
theevolutionoflifeeversinceitsorigin(SzathmaryandDemeter, spreadtoanarrowgroupofviruses.However,asmallgroupofviral
1987;TakeuchiandHogeweg,2007,2012;Takeuchietal.,2011). hallmark genes that encode key proteins involved in genome
All cellular life forms possess genomes consisting of double- replicationandvirionformationandaresharedbyoverlappingsets
stranded(ds)DNAandemploythesame,standardschemeforrepl- of diverse viruses ensures the connectivity of the evolutionary
ication and expression. In contrast, viruses and other selfish network in the virus world (Holmes, 2011; Koonin and Dolja,
elements exploit all theoretically conceivable inter-conversions of 2014; Koonin et al., 2006). Virus hallmark genes have no obvious
nucleicacids,withthegenomerepresentedbyeitherRNAorDNA ancestorsincellularlifeforms,suggestingthatvirus-likeelements
thatcan be either single-stranded ordouble-stranded,eithercirc- evolvedatapre-cellularstageoftheevolutionoflife.
ularorlinear,andconsistsofeitherasingleormultiplemolecules The viromes and mobilomes (i.e. the supersets of viruses and
(Agol,1974;Baltimore,1971;Koonin,1991a).Typicalviralgenomes otherselfishelements)ofthethreedomainsofcellularlife(bacteria,
aresmallcomparedtogenomesofcellularlifeformsbutoverthe archaea and eukaryotes) are fundamentally different. Although
pastfewyearsthediscoveryofseveralgroupsofgiantviruseshas several families of dsDNA viruses are represented in both bacteria
dramaticallyexpandedtheviralgenomesizerangethatnowspans andarchaea,novirusesareknowntobesharedbyeukaryoteswith
3ordersofmagnitude,fromabout2kilobases(kb)toover2mega- any of the other two cellular domains, even at the family or order
bases(Mb).Thegenomesofgiantvirusesarelargerthanthegeno- level (King et al., 2011). The evolutionary connections between
mes of numerous bacteria and archaea, obliterating the gulf virusesofeukaryotesandthosethatinfectbacteriaandarchaeaare
betweencellsandvirusesintermsofgenomesizeandcomplexity distant and complex. In this review article, we quantify the differ-
(Claverie and Abergel, 2009; Claverie et al., 2006; Legendre et al., ences betweenthe prokaryotic and eukaryotic viromes, summarize
2014;Philippeetal.,2013;Raoultetal.,2004). theexistingevidenceonputativeprokaryoticancestryofthemajor
Given the fundamental differences in the reproduction strategy classes of eukaryotic viruses and virus-like elements, and delineate
betweenvirusesandcellularorganisms,alongwiththeprominenceof thelikelykeyeventsintheevolutionofeachclass.
virusesinthebiosphere,ithasbeenproposedthatallorganismsbe
classifiedintotwoprimary“empires”,theribosome-encoding(cellu-
lar) organisms and the capsid-encoding organisms (viruses) (Raoult Thecontrastingviromesofprokaryotesandeukaryotes
and Forterre, 2008). This division captures some of the essential
distinctionsbetweencellsandvirusesbut,duetothefocusoncapsids The high levelclassification of viruses that was introduced by
asapositive,definingtraitofthevirusempire,failstoreflectthefull Baltimore in 1971 (largely inspired by his co-discovery, with
complexity of the evolutionary relationships among selfish genetic Temin, of reverse transcription in animal tumor viruses) is based
elements.Indeed,comparativegenomicanalysesmakeitincreasingly on the replication-expression strategies and in particular on the
clearthattheevolutionaryconnectionsbetweenvirusesandvarious form of nucleic acid that is incorporated into virions (obviously,
capsid-less elements are multifarious, involve all major groups of this criterion is only applicable to bona fide viruses) (Baltimore,
4 E.V.Kooninetal./Virology479-480(2015)2–25
1971). The following 7 classes have been delineated under this ofthetrueimpactofthisclassofgenomicparasites.Thus,theactual
approach(Koonin,1991a):(i)positive-strandRNAviruses(virions discrepancybetweentheprokaryoticandeukaryoticviromesislikely
contain RNA of the same polarity as mRNA), (ii) negative-strand tobeevengreaterthansuggestedbythedatainFig.1.
RNAviruses(virionscontainRNAmoleculescomplementarytothe Thebiologicalcausesofthedramaticdifferenceinthecompo-
mRNA), (iii) dsRNAviruses, (iv) reverse-transcribing viruses with sitionof theviromebetweeneukaryotesandprokaryotesremain
positive-strand RNA genomes, (v) reverse-transcribing viruses unclear. It stands toreasonthat the emergence of theeukaryotic
with dsDNA genomes (these were characterized subsequent to nucleusseverelyshrunkthenichefordsDNAvirusreproductionby
the seminal publication of Baltimore), (vi) ssDNA viruses, (vii) creating a barrier for the access of viral DNA to the sites of host
dsDNAviruses. genome replication and transcription, and complicating the pro-
Theviromesofprokaryotesandeukaryotesdramaticallydiffer cessofvirusmaturation.Notably,themajorityofdsDNAvirusesof
withrespecttothecontributionofthedifferentBaltimoreclasses eukaryotesreplicateinthecytoplasm(seebelow)suggestingthat
totheoverallviraldiversity(Fig.1).Inbothbacteriaandarchaea, those few groups of dsDNA viruses that replicate in the nucleus
the vast majority of the viruses possess dsDNA genomes, mostly have evolved specific adaptations to overcome the barriers. Con-
withintherangeof10to100kb.Thesecondmostcommonclass versely, the cytosolic compartment of eukaryotic cells, with its
includes small ssDNA viruses. Positive-strand RNA and dsRNA elaborate intracellular membrane system, might provide a fertile
viruses are extremely rare, and no retroviruses are known nicheforthereproductionofRNAviruses(Belov,2014;denBoon
(reverse-transcribingelementsexistbutarenothighlyabundant) and Ahlquist, 2010; Greninger, 2015; Nagy and Pogany, 2012).
(Fig.1). With respect to the dramatic proliferation of retroelements, an
In contrast to bacteria and archaea, eukaryotes host numerous, accommodatingnichecouldhavebeenprovidedbytheexpanding
highlydiverseRNAviruses(particularlyofthepositive-strandclass) genomesofeukaryotesandtheirgreatertolerancetoinsertionof
as well as reverse-transcribing elements and retroviruses that mobile elements compared to genomes of prokaryotes (Lynch,
typically integrate into the host genome and are extremely abun- 2007;LynchandConery,2003).
dant, comprising a substantial fraction of the genome in many Regardless of theunderlying causes,reconstruction of theevo-
groupsofeukaryotes(GoodierandKazazian,2008;Kazazian,2004). lutionoftheeukaryoticvirome,withitsdramaticdifferencesfrom
Collectively,thediversityandabundanceofRNAvirusesandretro- the viromes of bacteria and archaea and comparatively greater
virusesineukaryotesexceedsthediversityandabundanceofDNA diversity,isamajorchallengeinthestudyofvirusevolution.Inthe
viruses (Fig. 1; in this comparison, we refer to bona fide viruses following sections of this article, we discuss the evolutionary
because the prevalence of capsid-less elements is much more scenarios that have been developed for different classes of eukar-
difficulttoquantify). yotic viruses over the last few years and how the evolutionary
ThecomparisoninFig.1thatusesthenumberofrecognizedviral relationships between viruses of prokaryotes and eukaryotes bec-
generafromeachoftheBaltimoreclassesinfectingprokaryotesand omeapparentinthesescenarios.
eukaryotes as the measure of diversity most likely fails to pay full
justicetotheactualprevalenceofthedominantclasses,inparticular
dsDNA viruses, in the case of prokaryotes, and retroelements in Evolutionaryscenariosfortheoriginofeukaryotesandtheir
eukaryotes.Inthefirstinstance,thisappearstobethecasegiventhe impactonthereconstructionofvirusevolution
existence of numerous unclassified bacteriophages and undoubt-
edly an even much greater number of phages that remain to be Theoriginofeukaryotesisamajorprobleminevolutionarybiology
discovered. As a case in point, 39 new genera have been recently that is generally considered to be unresolved. It is now clear that
proposedwithinthebacteriophagefamilySiphoviridae(Adriaenssens nearly all extant eukaryotes possess membrane-bounded, energy-
et al., 2014). Despite the rapid accumulation of bacteriophage convertingorganelles,themitochondriaorpartiallydegradedderiva-
sequences,thediversityofphagegenesdoesnotshowanysignsof tives thereof (such as mitosomes or hydrogenosomes), and the few
saturation, suggestive of avast phage supergenome that so far has knowncasesofactuallossofmitochondriaaresecondary(Hjortetal.,
been barely tapped into (Kristensen et al., 2013). In the case of 2010; van der Giezen, 2009; van der Giezen and Tovar, 2005). Acc-
eukaryotes, the diversity of retroelements is not captured by the ordingly,theLastEukaryoticCommonAncestor(LECA)isbelievedto
existingclassificationofviruses,resultinginasevereunderestimate have been a typical, mitochondriate eukaryotic cell (Embley and
160
140
a 120
er
n
ge 100
s
u
vir 80
of
er 60
b
m
u 40
N
20
0
(+)RNA (-)RNA dsRNA Retro ssDNA dsDNA
Prokaryotes Eukaryotes
Fig.1. Representationofdifferent“Baltimoreclasses”ofvirusesinprokaryotesandeukaryotes.Thebarsshowthenumberofgeneraintherespectiveclassesaccordingto
thelatestICTVreport(Kingetal.,2011).Unclassifiedvirusesaredisregarded.ThenumbersforssDNAvirusesalsoincludethoseforpapillomavirusesandpolyomaviruses.
E.V.Kooninetal./Virology479-480(2015)2–25 5
Martin,2006;LaneandMartin,2010,2012).Anotherwellestablished, engulfment of bacteria and evolution of the compartmentalized
keypieceofinformationpertinentfortheoriginofeukaryotesisthe eukaryotic cell (Guy et al., 2014; Koonin and Yutin, 2014; Yutin
sharpsplitof theevolutionarilyconservedeukaryoticgenesintothe etal.,2009).
geneswithanarchaealevolutionaryaffinityandthosewithabacterial Inthefollowingsections,weexaminetheimplicationsofeach
affinity (along with some with no detectable prokaryotic homologs) ofthesescenariosoftheevolutionofeukaryotesfortheoriginof
(BrownandDoolittle,1997;Esseretal.,2004;Yutinetal.,2008).The differentclassesofeukaryoticviruses.
archaeal ancestry is apparent primarily for genes encoding compo-
nentsofinformationalsystemsalongwithsomekeycomponentsof
the cytoskeletonandthe celldivisionmachinery(KooninandYutin, Originsofthemajorclassesofeukaryoticvirusesand
2014),whereasoperationalgenes,suchasmetabolicenzymes,appear evolutionaryrelationshipsbetweenvirusesofprokaryotesand
tobelargelyofbacterialorigin. eukaryotes
Withintheconstraintssetbythesekeyobservations,twodistinct
classes of scenarios for the origin of eukaryotes are currently AgeneralperspectiveonRNAvirusevolution:Outoftheprimordial
considered; the scenarios within each class differ in detail but the RNAworld?
classes are sharply differentiated by the postulated nature of the
organism thatplayed hosttothe protomitochondrial endosymbiont According to the widely accepted RNA world hypothesis, the
(EmbleyandMartin,2006).Thehistoricallyfirstscenariopostulatesa RNA-onlyreplicationcycleantedatesreversetranscriptionandDNA-
lineage of primary amitochondrial eukaryotes (sometimes called basedreplication(Bernhardt,2012;Gilbert,1986;Neveuetal.,2013;
archaezoa) that are perceived to have evolved as a sister group of RobertsonandJoyce,2012).Underthispremise,theRNAvirusesand
archaea or possibly as a sister group of one of the major archaeal relatedselfishelementswhosereplicationreliesonRNA-dependent
branches, such as the ‘TACK (Thaumarchaeota–Aigarchaeota–Cre- RNA-polymerase (RdRp), are the only major group of organisms
narchaeota–Korarchaeota)superphylum’(Guyetal.,2014).Underthis (apartfromsmall,non-codingparasiticRNAssuchasviroidsDiener,
scenario, the hypothetical amitochondrial ancestor of eukaryotes 1989) that could be direct descendants of RNA world inhabitants.
possessedtheprincipalfeaturesoftheeukaryoticcellulararchitecture Because RdRpisthe only viralhallmark protein thatisuniversally
such as the advanced cytoskeleton and endomembrane system conservedinRNAviruses(KamerandArgos,1984;KooninandDolja,
includingthenucleus(Kurlandetal.,2006;Pooleetal.,1999;Poole 1993;Kooninetal.,2006),thisenzymeisthekeytoreconstructing
andPenny,2007).Thesefeatureswouldfacilitateengulfmentofthe their evolutionary histories. Together with distantly related RNA-
protomitochondrialendosymbiont(andbacteriaingeneral)whichis dependent DNA polymerases or reverse transcriptases (RT), viral
conceivably the strongest aspect of the primary amitochondrial RdRps represent a deeply branching lineage within the ancient
scenario(hereinafterprotoeukaryotescenario).Theobviousweakest superfamilyofpalmdomain-containingpolymerasesandprimases
pointofthisscenarioisthelackofanyevidenceoftheexistenceof (Iyeretal.,2005).Asistypicalofviralhallmarkgenes(Kooninetal.,
primary amitochondrial eukaryotic forms despite intensive search. 2006),cellularorganismsencodenohomologsofviralRdRpswith
Theproponentsoftheprotoeukaryoticscenariothushavetopostu- the same enzymatic activity. The only known family of RdRps
late that such forms are either extinct or exceedingly rare. Further- encoded in cellular genomes, those involved in the amplification
more, there is no precedent for the evolution of large, internally ofsmallinterferingRNAsineukaryotes,arehomologsoftheDNA-
compartmentalizedcellsamongprokaryotes,andithasbeenargued dependentRNApolymerases(Iyeretal.,2003;Salgadoetal.,2006).
that emergence of such cells is unfeasible without highly efficient Basedonthestructureof theencapsidatedgenomeandgenome
cellular energetics that is provided by the multiple mitochondria replication/expression cycles, the ‘RNA only’ viruses are divided into
residingwithinasinglecell(LaneandMartin,2010,2012). threeBaltimoreclasses:positive-strand,double-strandandnegative-
The alternative, symbiogenetic scenario (Embley and Martin, strand (þRNA, dsRNA and (cid:2)RNA, respectively). All non-defective
2006; Martin et al., 2007), obviously fueled by the ubiquity of viruses from each of these classes employ virus-encoded RdRps for
mitochondriaandrelatedorganellesineukaryotes,postulatesthat genome replication and often for the distinct process of genome
the host of the proto-mitochondrial endosymbiont was not a transcriptiontogenerateviralsubgenomicmRNAs.Earlycomparative
protoeukaryote endowed with the key features of the eukaryotic analyses identified 6 signature amino acid sequence motifs that are
cellular organization, including the nucleus, but rather a regular conservedinRdRpsofdiverseþRNAvirusesinfectingbacteria,plants
archaeon, most likely a mesophilic form that could comprise a andanimals,suggestingtheirmonophyleticorigin(KamerandArgos,
deep branch within the TACK superphylum or possibly a sister 1984;Koonin,1991b;XiongandEickbush,1990).Ithasbeenfurther
group thereof (Koonin and Yutin, 2014). The symbiogenetic sce- demonstrated that similar motifs were present in RdRps of dsRNA
nario implies a plausible succession of events leading to the key virusesandtheRTs(KamerandArgos,1984;Kooninetal.,1989;Xiong
innovations of the eukaryotic cell such as the endomembrane andEickbush,1990).AlthoughtheRdRpsofthe–RNAvirusespossess
system including the nucleus, the cytoskeleton, the ubiquitin- certain motifs resembling those conserved in þRNA and dsRNA
centeredsignalingsystemandpre-mRNAsplicing(Koonin,2006; viruses (Tordo et al., 1988; Xiong and Eickbush, 1990), the overall
Martin and Koonin, 2006). The weakness of the symbiogenetic levelofsimilarityisextremelylow,makingtheevolutionaryconnec-
scenario is the extreme rarity of endosymbiosis among prokar- tionbetweenthe (cid:2)RNAvirusesandtherestofRNAvirusestenuous
yotes (although bacteria living inside other bacteria have been atbest.
described Husnik et al., 2013; von Dohlen et al., 2001) and the In addition to protein sequence analysis, reconstruction of the
apparent absence of mechanisms, such as phagocytosis, that RdRp evolution is substantially aided by the comparisons of their
would facilitate engulfment of bacteria. The proponents of this atomicstructures.IthasbeenfoundthatRdRpsfromdiverseþRNA
scenariothereforeareforcedtopostulatea(extremely)rareevent and dsRNAviruses of bacteria and animalspossessa characteristic
at the root of eukaryogenesis. However, the recent discovery of ‘right-handed’ fold, comprising palm, fingers, and thumb domains
archaealhomologs(andputativeancestors)ofkeyelementsofthe (ChoiandRossmann,2009;Ferrer-Ortaetal.,2006;Kidmoseetal.,
eukaryotic cytoskeleton, cell division systems and ubiquitin 2010;Monttinenetal.,2014).Along-awaitedfirstatomicstructure
machineryprovideforanamendedsymbiogeneticscenario.Under of the RdRp of a (cid:2)RNA virus, bat influenza A virus, helped to
this hypothesis, the archaeal ancestor of eukaryotes, the host of demystify the origins of these viruses by revealing a high level of
theprotomitochondrialendosymbiont,couldhavepossessedrela- structural similarity to RdRps of both þRNA and dsRNA viruses
tively complex intracellular organization that would facilitate (Pflugetal.,2014).Thus,thethreeclassesofRNAvirusessharethe
6 E.V.Kooninetal./Virology479-480(2015)2–25
homologous core enzyme that is responsible for their replication superfamily.Furthermore,allthesevirusesexpresstheirgenomes
and,byimplication,relatedorigins. via polyprotein processing (in some groups, there are two poly-
Under the symbiogenetic scenarioforthe origin of eukaryotes, it proteins,oneencompassing thestructuralproteinsandtheother
seemsnaturaltoassumethatRNAvirusesofeukaryotesoriginatefrom one proteins involved in replication) and package the genomic
eitherRNAbacteriophagesorRNAvirusesofArchaea.Thisassumption, RNA into characteristic icosahedral virions with a pseudo-T¼3
however,ischallengedbythestrikingscarcityofbacterialandarchaeal symmetry.Notably,Picornaviralesincludevirusesinfectingabroad
RNA viruses compared to the flourishing genomic and ecological range of hosts from three supergroups of eukaryotic organisms,
diversity of their eukaryotic counterparts (see above). Indeed, there Unikonts (vertebrates, insects), Plantae (angiosperms) and Chro-
areonlyahandfuloftheþRNAbacteriophagesallofwhichbelongto malveolates (diatomes, raphidophytes, thraustrochytrids), as well
the family Leviviridae infecting primarily enterobacteria and some asvirusesfrommarineenvironmentswithunidentifiedhosts(Le
otherproteobacteria(BollbackandHuelsenbeck,2001).Likewise,only Galletal.,2008).
a few dsRNA bacteriophages of the family Cystoviridae that infect ThefamilyofvertebratevirusesCaliciviridaeiscloselyrelatedto
γ-proteobacteria of the genus Pseudomonas are currently known Picornavirales, sharing a conserved S3H-VPg-3CPro-RdRp-JRC gene
(Mindich,2004)althougheffortsonnewvirusisolationmightexpand array and differing only in the structure of their true T¼3 capsid.
this range (Mantynen et al., 2015). The targeted search for extant Strikingly, in the phylogenetic tree of the RdRp, caliciviruses con-
archaeal RNA viruses so far has netted only a single þRNA virus fidentlyclusterwiththemembersofTotiviridae,afamilyofdsRNA
candidate that appears to represent a novel virus family but whose viruses that infect fungi (Unikonts) as well as Kinetoplastids,
hostrangeremainstobevalidated(Bolducetal.,2012).Thus,thevery Trichomonads and Diplomonads, all of which belong to a distinct
existenceofarchaealRNAvirusesremainsanopenquestion.Finally, supergroup of unicellular eukaryotes, the Excavates. Because the
thereisnoevidenceof(cid:2)RNAvirusesinfectingprokaryotes.Theproto- clade that unites Caliciviradae and Totiviridae is lodged inside the
eukaryoticscenariowouldimplyadifferentnarrativeontheoriginsof picornavirus-likeRdRptree,itseemslikelythatthisfamilyofdsRNA
the RNA viruses of eukaryotes whereby the remarkable diversity of virusesisahighlyderivedoff-shootofthepicornavirus-likesuper-
thesevirusesevolvedwithintheancientprotoeukaryoticlineagedue family of þRNAviruses. The viruses in the remaining three major
tothe features of the (proto)eukaryoticcell organization,such as an evolutionarylineagesofpicornavirus-likeviruses(Fig.2)encompass
intracellularmembranesystem,thatmightbeconducivetoRNAvirus onlysubsetsofthefivepicornaviralsignaturegenesor,inthecaseof
reproduction. Should that be the case, the search for bacterial or the family Partitiviridae, only the picornavirus-type RdRp. Each of
archaealancestrywouldbefutileinprinciple.Belowwediscusshow thesegroupsalsoincludesvirusesinfectinghoststhatbelongtotwo
theavailabledataontheoriginsofdifferentgenesofRNAvirusesbear orthreeeukaryoticsupergroups(Kooninetal.,2008).
onthesedistinctoriginscenarios. Thus,theevolutionaryscenariobestcompatiblewiththesuper-
impositionofthephylogenetictreesofeukaryotesandpicorna-like
Positive-strandRNAviruses:Assemblyfromdiverseprokaryotic viruses involves early diversification antedating the divergence of
progenitorsandgeneexchangesleadingtoenormousdiversification eukaryotic supergroups. The alternative, i.e. emergence of the
ancestors of each of the 6 lineages of the picornavirus-like super-
Large-scalephylogenomicanalysisofthe þRNAvirusesofeukar- familyinoneoftheeukaryoticsupergroupsfollowedbyhorizontal
yoteswasinitiatedovertwodecadesagoandyieldedconclusionsthat virustransfer(HVT)tohostsfromothersupergroups,appearstobe
withstood the test of time remarkably well (Goldbach and Wellink, decidedlylessparsimoniousbecausesuchascenariowouldrequire
1988; Koonin, 1991b; Koonin and Dolja, 1993). These studies have numerous HVT events involving organisms with widely different
identifiedthree majorevolutionarylineagesthatcollectivelyencom- lifestylesandecologicalniches(Kooninetal.,2008).However,HVT
pass the vast majority of the þRNA viruses infecting eukaryotes: couldhaveplayedanimportantroleinthesubsequentevolutionof
picornavirus-like, alphavirus-like and flavivirus-like superfamilies thepicorna-likeviruses(DoljaandKoonin,2011).Onecaseinpoint
(Fig.2).Thisclassificationisbasedonacombinationofevidencefrom isthephylogenyofpartitivirusesinwhichfungalandplantviruses
theRdRpphylogenywithsignaturegenesandgenearrangementsthat intermix, pointing to multiple occurrences of HVT between two
have been identified for the picornavirus-like and alphavirus-like widely different host taxa (Nibert et al., 2013). Another example
superfamilies(seebelow).Thecongruencebetweenthetwolinesof involvesthecloselyrelatedplantPotiviridaeandfungalHypoviridae
evidenceiscrucialbecausethehighsequencedivergenceoftheRdRp (Kooninetal.,1991a).TheHVTbetweenplantsandfungiappearsto
that is dictated by the overall high mutation rate of RNA viruses, beparticularlyplausiblegivencloseassociationsbetweenplantsand
despitetheessentialityofthepolymerase,hamperstheconstruction theirubiquitousfungalpathogensandsymbionts.
offullyreliablephylogenetictrees(Zanottoetal.,1996). Incontrasttothepicornavirus-likesuperfamily,thealphavirus-like
The picornavirus-like superfamily is by far the largest, most andflavivirus-likesuperfamiliesexhibitmuchlessdiversityintermsof
diverse and most widely represented across the diversity of the boththenumbersofincludedfamiliesandevenmoresotheirglobal
eukaryotichosts.Inadditiontoadistinct RdRp lineage,thepico- ecologies (Dolja and Koonin, 2011). The alphavirus-like superfamily
rnavirus-likesuperfamilyisdefinedbythepresenceofaconserved includes the order Tymovirales along with several other families of
array of signature genes, which encode a superfamily 3 helicase plantvirusesandtwofamiliesofanimalviruses(SupplementaryTable
(S3H), a small genome-linked protein (VPg), a distinct chymot- S1 and Fig. 2). All these viruses are unified bya conserved array of
rypsin-likeprotease3CProandasinglebeta-barreljelly-rollcapsid replication-associated genes which encode capping enzyme, super-
protein(JRC),andarerepresented,somelossesandreplacements family1helicaseandtheRdRp(KooninandDolja,1993).Arecentin-
notwithstanding, in most members of this superfamily (Koonin depthcomparativeanalysisofviralproteinsequenceshasrevealeda
andDolja,1993;Kooninetal.,2008). highlyderivedvariantofthecappingenzymeinthenodaviruses,an
Theglobalecologyofthepicornavirus-likesuperfamily,which abundantfamilyofanimal þRNAviruseswithsmallgenomes(Ahola
spans a broad range of multicellular and unicellular eukaryotic andKarlin,2015).TheRdRpofnodavirusesdoesnotshowanaffinity
hosts(SupplementaryTableS1)pointstoanearlyoriginofthese withthealphavirus-likesuperfamilybutratherhadbeententatively
viruses antedating the radiation of the eukaryotic supergroups. included in the picorna-like superfamily on the basis of limited
Thecoreofthepicornavirus-likesuperfamilyisrepresentedbythe conservation of some sequence motifs (Koonin, 1991b; Koonin and
order Picornavirales that encompasses 5 families, several floating Dolja,1993;Kooninetal.,2008).However,thereisnostrongobjective
genera and many unclassified viruses (Le Gall et al., 2008). The supportforthisaffinity.Althoughnodaviruses,similartoother þRNA
viruses within this order share all the signature genes of the viruses with small genomes, lack a helicase, the presence of the
E.V.Kooninetal./Virology479-480(2015)2–25 7
Fig.2. OriginofthemajorgroupsofRNAvirusesofeukaryotes.Thedepictedevolutionaryreconstructionispredicatedonthesymbiogeneticscenarioofeukaryogenesis.The
hostrangesofviralgroupsarecolor-codedasshownintheinset.Iconsofvirionstructuresareshownforselectedgroups.Ancestor-descendantrelationshipsthatare
consideredtentativeareshownwithdottedlines,andparticularlyweaklinksareadditionallyindicatedbyquestionmarks(seetextfordetails).Keyhorizontalgenetransfer
eventsareshownbygray,curvedarrows.Abbreviations:CIIFP,ClassIIfusionprotein;CP,capsidprotein;CPf,capsidproteinoffilamentousviruses;JRC,jellyrollcapsid
(protein);MP,movementprotein;RT,reversetranscriptase;S2H,Superfamily2helicase;S3H,Superfamily3helicase.
predictedcappingenzymesuggeststheirinclusioninthealphavirus- tetravirusesandbirnavirusesthatappeartoshareacommonancestor
likesuperfamilyasadeep,perhapsbasalbranch(Fig.2).Thisaffiliation and are included in the alphavirus-like superfamily on the basis of
is compatiblewiththe observationthatnodaviruses share a distinct the RdRp phylogeny (Wang et al., 2012a). Unlike the picorna-like
variant of the JRC containing an autoprocessing domain with viruses, the great majority of which possess JRC-based icosahedral
8 E.V.Kooninetal./Virology479-480(2015)2–25
capsids(withtheexceptionoffilamentouspotyvirusesandcapsid-less requirement of a helicase for the replication of (relatively) large
hypoviruses),capsidarchitecturesofalphavirus-likevirusesareextre- RNAgenomes.Theexistenceofsucharequirementissuggestedby
melydiverse.Thesearchitecturesinclude:(i)icosahedralvirionsbuilt theclearthresholdforthepresenceofthehelicasegenewhichis
ofeitherJRCorunrelatedproteins;(ii)helicalrod-shapedorflexible found in all þRNA viruses with genomes larger than approxi-
filamentous virions formed bya distinct family of four-helix bundle mately6kbbutnotinviruseswithsmallergenomes(Gorbalenya
capsid proteins; (iii) membrane-enveloped virions. The host ranges andKoonin,1989).Strikingly,however,boththehelicasesandthe
of alpha-like viruses are limited almost exclusively to plants, where proteases in the three viral superfamilies belong to different
thesevirusesreachremarkablediversity,andanimals.Onlythefamily proteinfamilies(KooninandDolja,1993andseeabove).Whether
Endornaviridaethatconsistsofcapsid-lesselementshasabroaderhost these analogous designs of the viral genomes evolved in parallel
rangeincluding“viruses”ofplantsandfungi,andasingle“virus”ofa fromacommonancestorthatlackedthehelicaseandtheprotease
plant-parasiticoomycete,potentially,aresultofHVTfromahostplant orthroughdisplacementofthecorrespondingancestraldomains,
(KooninandDolja,2014;Roossincketal.,2011). isdifficulttoascertain.
Theflavivirus-likesuperfamilyisthesmallestofthethreemajor Elucidation of the exact evolutionary relationships among the
groups of the þRNA viruses of eukaryotes and encompasses only threesuperfamiliesof þRNAvirusesofeukaryotesrequiresin-depth
two families that appear to be rather odd bedfellows (Fig. 2). The phylogeneticanalysesoftheirRdRpswhichisadauntingtaskgiven
Flaviviridae are enveloped animal viruses that encode a specific thehighsequencedivergenceofthisproteinoutsidetheconserved
lineageofRdRp,asuperfamily2helicaseaswellasaproteaseanda motifs.ExpansionofthecollectionofRdRpstructuresandrefinement
capping enzyme that are distinct from the functionally analogous of methods for structure-based phylogeny could lead to progress.
proteins of the picornavirus-like and alphavirus-like superfamilies, Nonetheless, the available evidence seems to support evolutionary
respectively (Koonin and Dolja,1993). None of these genes except primacyof thepicornavirus-likesuperfamily.Mostimportantly,the
forRdRpisconservedinTombusviridae,viruseswithsmallicosahe- host ranges of alphavirus-like and flavivirus-like superfamilies are
dral capsid built of JRC that infect plants (with the exception of a limited almost exclusively to vertebrates, their arthropod parasites,
singlemarinevirusthatpresumablyinfectsaunicellulareukaryotic and flowering plants, that is, only three groups of multicellular
host) (Culley et al., 2006; Dolja and Koonin, 2011). Thus, the organisms. These narrow host ranges could point to relatively late
flavivirus-likesuperfamilyisheldtogetheronlybythephylogenetic evolutionary origins of the viruses of these superfamilies, perhaps
affinity of the RdRPs. Although this association is consistently concomitant with the emergence of the respective host groups.
observed in multiple, independent phylogenetic analyses (Koonin Furthermore,HVT,inparticularviainsectvectors,couldhaveplayed
andDolja,1993),thelackofadditionalsupportfromsignaturegenes an important role in the evolution of these viral superfamilies. In
makesthissuperfamilyatenuousgroup.Itisnotinconceivablethat contrast, the broad host range of picorna-like viruses encompasses
Flaviviridae and Tombusviridae would be best treated as separate four eukaryotic supergroups and a great varietyof both unicellular
superfamiliesof þRNAviruses. andmulticellularorganisms.Furthermore,multiplehost-specificand
Inaccordancewithamajor,generaltrendofvirusevolution(see metagenomicstudiesofmarineRNAviruses(mostofthemdemon-
alsobelow),thehistoriesofthethreesuperfamiliesof þRNAviruses strated or thought to infect diverse unicellular eukaryotes) have
werenotcompletelyindependentbutratherinvolvedmultiplegene recoveredalargenumberofnovelpicorna-likevirusesbutonlyone
exchanges.AstrikingcaseinpointisthefamilyPotiviridae,thelargest tombus-likevirusandnoalpha-likeviruses(Culleyetal.,2006,2014;
familyofplantviruses(GibbsandOhshima,2010)thatareconfidently CulleyandSteward,2007;Kooninetal.,2008).
included in the picornavirus-like superfamily on the basis of a Thethree-superfamilyclassificationof þRNAvirusesdoesnot
combination of several features including the RdRp phylogeny, the readilyaccommodatethedistinctorderNidoviraleswhichincludes
presenceoftwoadditionalsignaturegenes,namelythepicornavirus- viruseswiththelargestknownRNAgenomesandseveralunique
likeproteaseandVPg,andthemodeofproteinexpressionviapoly- genomicfeatures.Notably,noneof theseviruses encodeJRCand,
protein processing. However, two other signature genes of the consistently,donotformicosahedralvirions.Instead,membersof
picornavirus-likesuperfamily,namelytheS3HandtheJRC,arerepl- the Nidovirales have enveloped virions which vary from roughly
acedinthepotyviruses,respectively,byaSuperfamily2helicasemost spherical to rod-shaped, depending on the organization of the
closely related to the homologous helicase of flaviviruses and by a helical nucleocapsids (Gorbalenya et al., 2006; Koonin and Dolja,
four-helixbundlecapsidproteinrelatedtothatoffilamentousplant 1993). However, certain evolutionary affinity between RdRps of
viruses in the alphavirus-like superfamily (e.g. potexviruses) (Dolja picornavirus-like viruses and nidoviruses, together with the pre-
et al., 1991; Koonin and Dolja, 1993; Koonin et al., 2008). Thus, sence of distantly related proteases responsible for polyprotein
evolutionofthepotyvirusesinvolvedsubstantialmodificationofthe processinginbothofthesevirusgroups(Gorbalenyaetal.,2006;
picornavirus-like scaffold (and consequently, the virion structure) KooninandDolja,1993),suggeststhatnidovirusescouldbehighly
through contributions from the other two superfamilies of þRNA derivedoff-shootsofthepicornavirus-likesuperfamily.
viruses(Fig.2).Othernotablecasesofintersuperfamilygeneexchange Thus, the extreme diversity of the picorna-like viruses, with
include the apparent transfer of the serine protease gene between respecttoboththehostrangeandthegenomearchitecture,sugg-
flaviviruses and togaviruses in which, strikingly, the protease was ests that picornaviralancestors haveevolved concomitantly with
recruited for the capsid protein function (Gorbalenya et al.,1989b); or shortly after the emergence of eukaryotes, rapidly diversified
spreadofthegenesformovementproteinsbetweenplant-infecting and spawned the ancestors of the alphavirus-like and flavivirus-
viruses from all three superfamilies (Mushegian and Koonin,1993); like superfamilies as well as the Nidovirales (that are known to
andspreadofclassIIfusionproteinsamongflaviviruses,togaviruses infect only vertebrates, insects and crustaceans), perhaps later in
andbunyaviruses(Modis,2014;VaneyandRey,2011). evolution(Fig.2).
A notable complementary trend in the evolution of þRNA Ifthepicornavirus-likesuperfamilyindeedrepresentstheances-
virusesistheparallelismbetweenthedesignsoftheviralgenomes tral viral reservoir from which the rest of the eukaryotic þRNA
inthethreesuperfamilies.Indeed,apartfromtheRdRpandtheCP, viruses evolved (with some notable exceptions discussed below),
most of the viruses in the picorna-like and alpha-like super- then, the problem of the origin of eukaryotic þRNA viruses boils
families and the animal viruses in the flavi-like superfamily downtotheoriginoftheancestralpicorna-likevirus.Thisquestion
encode proteins with two types of functionality, helicases and has been addressed through a focused search for potential prokar-
proteases(KooninandDolja,1993).Thepresenceofthesedomains yoticrootsofpicorna-likeviruses(Kooninetal.,2008).Inadditionto
most likely is dictated by functional requirements such as the validatingthetightrelationshipbetweenthethreesuperfamiliesof
E.V.Kooninetal./Virology479-480(2015)2–25 9
theeukaryoticpositive-strandRNAviruses,in-depthsequence ana- movement and possibly capsid proteins are related to respective
lysisoftheRdRpsofthepicornavirus-likesuperfamilyhasrevealed proteins of tombusviruses, it has beenproposed thatourmiaviruses
remarkably highsimilarityof picornavius-like RdRps tothe reverse evolvedviarecombinationbetweenanarnavirus-likeelementfroma
transcriptases (RTs) of the bacterial group II retroelements (self- plant-pathogenicfungusandatombusvirus(Rastgouetal.,2009).
splicing introns), in contrast to the much lower similarity to the
RdRpsofRNAbacteriophages(Kooninetal.,2008).Consideringthe
wide spread of the group II retroelements in bacteria (Lambowitz dsRNAviruses:Multipleoriginsfrompositive-strandRNAviruses
and Zimmerly, 2004, 2011), in contrast to the scarcity of RNA
bacteriophages, it appears plausible that the prokaryotic RTs were ThedsRNAvirusesofeukaryotesappeartobemuchlessdive-
the ancestors of picornavirus-like RdRps. Search for the closest rse than þRNAviruses as follows fromthe numbers of currently
homologs of the 3CPro confidently identified bacterial and mito- recognized families (10 versus 31, respectively; Supplementary
chondrial proteases of the HtrA family (Gorbalenya et al., 1989a; Table S2). However, the recent accelerated pace of discovery of
Koonin etal., 2008), suggestingdirect descentof the viral protease new,diversedsRNAvirusesmightsoonchallengethisperception
frombacterialendosymbiontofemergingeukaryoticcell.Theexact (Liuetal.,2012a,2012b).EarlyphylogeneticanalysesoftheRdRps
originsoftheotherpicornaviralsignaturegenes,S3H,JRCandVPg, ledtotheconclusionthatthedsRNAvirusesoriginatedonmulti-
proved much more difficult to trace. Nevertheless, S3H is encoded ple occasions, mainly from different groups of þRNA viruses
insomedsDNAbacteriophagesandbacterialrolling-circleplasmids (Koonin,1992; Koonin et al.,1989). The inclusion of two families
(see below) whereas the single β-barrel JRC of the picorna-like of dsRNA viruses, Totiviridae and Partitiviridae, into the picor-
varietyispresentinssDNAbacteriophagesofthefamilyMicroviridae navirus-like superfamily is in full accord with this evolutionary
(McKenna et al.,1992; Roux et al., 2012). Additionally, the JRC-like scenario. The viruses in the family Birnaviridae share an unusual
β-barrel fold is found in various carbohydrate-binding proteins permutedRdRp,agenome-linkedproteinandadistinctvariantof
including those from bacteria (Norris et al., 1994; Wong et al., theJRCwithsomeofthetetraviruses(thefamilyTetraviridaehas
2000),andsomenon-viralβ-barrelproteins,suchastumornecrosis been recently split into three distinct families, namely Alphate-
factor,areevenknowntoformvirus-likeparticles(Liuetal.,2002). traviridae, Carmotetraviridae and Permutotetraviridae; Table S1),
Thesecellularjelly-rollproteinsareconsiderablymorecompactthan supportingacommonoriginofthesefamiliesofdsRNAandþRNA
CPsofmicrovirusesandthusmightbemorelikelytohavebeenthe viruses at an early stage of the evolution of the alphavirus-like
ancestors of JRC of RNAviruses. Consequently, bacterial origins for superfamily(Fig.2)(Gorbalenyaetal.,2002;Zeddametal.,2010).
these genes are conceivable as well, leading to an evolutionary Notably, the divergence of birnaviruses from tetraviruses has
scenario in which the ancestral picorna-like virus was assembled apparently occurred following the acquisition of the JRC protein
from diverse building blocks derived from the proto-mitochondrial gene by their common ancestor from a nodavirus (Wang et al.,
endosymbiont during eukaryogenesis (Koonin et al., 2008) (Fig. 2). 2012a). The family of capsid-less viruses Endornaviridae that is
Clearly,thisscenarioismostplausiblewithintheframeworkofthe currently classified with dsRNA viruses clearly evolved from an
symbiogenetic scenario for the origin of eukaryotes. Under the alphavirus-likeancestorasindicatedbytheconservationofasign-
protoeukaryote scenario, the ancestral picorna-like virus could be aturesetofcorereplicationgenes(KooninandDolja,2014).
construed asa directdescendantof the primordialRNAworld that Evolutionary scenarios based on the phylogenetic analysis of
survived and thrived in the protoeukaryotic lineage (Fig. 2). In this viralreplicationproteinsoftendeviatefromthosecenteredonthe
case, the RdRp of the picorna-like viruses would be viewed as the evolutionofotherfunctionalmodules,inparticularthoseofviral
primordial replicase, and S3H and JRC accordingly would be con- capsid proteins (Krupovic and Bamford, 2008, 2009). Thus, for
sidered ancestral forms of the respective proteins. The ancestral comprehensive reconstruction of virus evolution, that would
picorna-like virus thus could resemble the extant nodaviruses that reflect the intrinsic modularity of this process, it is essential to
possess a “minimal” genome within the picornavirus-like super- complementphylogeneticandcomparativegenomicanalyseswith
family encoding only the RdRp and the JRC. Incidentally, the only theanalysisofstructuraldata(Kooninetal.,2009).Theemerging
reported putative RNA virus of archaea shows a similar genome picture of the evolution of dsRNA viruses is among the best
architecture although it is premature to discuss its possible role in illustrationsofthisgeneralprinciple.
the evolution of the viruses of eukaryotes until the archaeal host StructuralanalyseshaveshownthateukaryoticdsRNAvirusesfrom
range is validated (Bolduc et al., 2012). The 3CPro, for which the the families Picobirnaviridae, Chrysoviridae, Totiviridae, Partitiviridae,
bacterial origin appears undeniable, could be a later acquisition ReoviridaeandbacteriophagesofthefamilyCystoviridaeemployrelated
concurrentwiththesymbiogenesis. capsidproteinstobuildtheiruniqueT¼1icosahedralcapsidsfrom60
Although the only known group of þRNA bacteriophages, the asymmetrical CP dimers (El Omari et al., 2013; Janssen et al., 2015;
leviviruses,apparentlyhavenotcontributedtotheoriginofthebulk Luqueetal.,2014;PoranenandBamford,2012).Basedoncomparisons
of the eukaryotic þRNA viruses, they did give rise to two distinct, of thevirionandCPstructures,ithasbeenproposedthatreoviruses
smalllineagesoftheeukaryoticviruses(Fig.2).Searchesforthemost are most closely related to cystoviruses whereas picobirnaviruses,
closelyrelatedhomologsoftheleviviralRdRpsidentifiedtheRdRpsof partitiviruses, and totiviruses form another, distant branch of dsRNA
thesetwonarrowgroups,fungalNarnaviridaeandplantOurmiavirus, viruses(ElOmarietal.,2013);additionally,theCPofchrysoviruseshas
as the eukaryotic descendants of the leviviruses. The narnaviruses beenconcludedtobemostcloselyrelatedtothatoftotiviruses(Luque
hardlymeetthenarrowdefinitionofvirusesbecausetheyareneither etal.,2014).Thus,bacterialcystovirusesappeartohavecontributedthe
infectious nor possess an extracellular encapsidated form (Hillman structuralgenestomostofthedsRNAvirusesinfectingeukaryotes.The
andCai,2013).Theentirereplicationcycleofthenarnavirusesofthe reoviruses, the largest family of dsRNA viruses that infect diverse
genus Mitovirus takes place within fungal mitochondria. Given the eukaryotic hosts (Fig. 2 and Supplementary Table S2), appear to be
origin of the mitochondria from an alphaproteobacterial endosym- directdescendantsofthecystoviruses.Incontrast,intheevolutionof
biont, it appears most likely that the ancestral narnavirus evolved picobirnaviruses, partitiviruses, totiviruses, chrysoviruses and the
from an RNA bacteriophage brought along by the protomitochon- related megabirnaviruses the pivotal event was recombination (or
drion, by losing the capsid and thus switching to the status of a morelikely,multiple,independentrecombinationevents)withmem-
mitochondrialRNAplasmid.Incontrast,plantourmiavirusesarefull- bersofthepicornavirus-likesuperfamilyofþRNAviruses,resultingin
fledged, infectious, encapsidated þRNA plant viruses. Because their chimeric genomes encoding cystovirus-derived capsid proteins and
RdRpsarerelatedtothoseofnarnaviruses,whereastheintercellular pricornavirus-likeRdRps(Fig.2).
10 E.V.Kooninetal./Virology479-480(2015)2–25
The global ecology of the dsRNAviruses appears rather pecu- (cid:2)RNAvirusfamiliesthatincludemembersinfectingeitheranimals
liar.Unlikemostofthefamiliesof þRNAvirusesthatareconfined orplants.
toarelativelynarrow host ranges(e.g., arthropodsfor Iflaviridae, Amajorinsightintotheoriginof (cid:2)RNAvirusescamefromthe
vertebrates for Picornaviridae and plants for Secoviridae), extre- recentlysolvedcrystalstructureoftheInfluenzaAvirusRdRpthat
mely diverse hosts are often infected by the dsRNAviruses from has revealed striking similarity to the structure of the flavivirus
thesamefamily.Asacaseinpoint,thefamilyReoviridaeincludes RdRps (Pflug et al., 2014). This finding strongly suggests that
virusesthatinfectvertebrates,arthropods,mollusks,fungi,flower- (cid:2)RNA viruses evolved from a þRNA ancestor of the flavivirus-
ing plants and a unicellular green alga. Likewise, Partitiviridae like superfamily but diverged from the ancestral forms beyond
infect fungi, flowering plants and an apicomplexan unicellular recognition atthesequencelevelduetotheswitchtoaradically
eukaryote, whereas host range of Totiviridae includes fungi and differentreplicationcycle. AlthoughinfluenzaRdRp isalso struc-
several unicellular eukaryotic parasites from the Excavate super- turallysimilartotheRdRpofdsRNAbacteriophages(cystoviruses),
group(Kingetal.,2011).Suchecologicalpatternsincludingtwoor a direct evolutionary connection seems unlikely given the sig-
threesupergroupsofeukaryotichostsforeachofthethreelargest nificantlylowersimilarity thanthatwiththeflavivirusRdRpand
families of the dsRNAviruses point to their ancient origins from the apparent relatively late emergence of the (cid:2)RNAviruses (see
the dsRNA bacteriophage and picornavirus-like ancestors as dis- above). This reasoning is further buttressed by the recent identi-
cussedabove(Fig.2). ficationofanematode-infectingflavi-likevirus(Bekaletal.,2014)
TheroleofHVTintheevolutionof thedsRNAvirusesismost which suggests that nematodes could have played the role of a
apparentforthefamilyEndornaviridaewheretheplantandfungal melting pot in which the progenitor of the (cid:2)RNA viruses was
virus branches in the phylogenetic trees of viral RdRps often conceived and that also played a key role in the spread of these
intermingle within the same cluster (Roossinck et al., 2011). A virusestonewhosts.Further,in-depthphylogeneticandstructural
contribution of HVT appears likely also in the evolution of analysis of the proteins encoded by flavi-like viruses and (cid:2)RNA
reovirusesmanyofwhich,bothfromvertebratesandfromplants, viruses are required to develop the proposed evolutionary sce-
arealsocapableofinfectingtheirarthropodvectors(NgandFalk, narioinmoredetail.
2006; Quito-Avila et al., 2012) that could serve as HVT interme- Given the accumulating evidence of the origin of both dsRNA
diaries. Thus, phylogenetic, structural, and host range analyses viruses and (cid:2)RNAviruses from different groups of þRNAviruses,
converge in supporting the major theme in the evolution of the the ancestor of the picorna-like viruses appears to have been the
dsRNAviruses: ancient polyphyletic origin from dsRNA bacterio- ultimateprogenitorofthegreatmajorityofeukaryoticRNAviruses.
phagesordistinctgroupsof þRNAvirusancestors,orviarecom- Whether this ancestral picorna-like virus was assembled from
bination between these distinct types of ancestors. The current several distinct building blocks of bacterial origin during eukaryo-
spread of the dsRNAviruses, however, could have been substan- genesis (Fig. 2) or evolved as a continuous lineage from the
tiallyaffectedbymorerecentHVTevents. primordial gene pool, is an intriguing and important question. The
answercriticallydependsonthechoiceofthescenariofortheorigin
ofeukaryotesthathopefullywillbeinformedbythefurtheradvances
Negative-strandRNAviruses:Theemergingpositive-strand of archaeal and bacterial genomics. Regardless of the impending
connection solution to this key problem, a limited footprint of RNA bacterio-
phagesontheevolutionofeukaryoticRNAvirusesisapparentinthe
Negative-strand RNA viruses of eukaryotes include the order originofnarnavirusesandourmiavirusesfromleviviruses,andmost
Mononegavirales that consists of three related virus families with likely,reovirusesfromcystoviruses.
non-segmentedgenomesand5familiesofviruseswithsegmented
genomes(SupplementaryTableS3).Foralongtime,theevolution- SynopsisoneukaryoticRNAvirome
aryoriginof the (cid:2)RNAviruses had beenveiled inmysterydueto
the highly derived sequences of their RdRps (Tordo et al., 1988; TorecapitulatethekeypointsontheeukaryoticRNAvirome,the
XiongandEickbush,1990)andthelackofreadilyidentifiedhomo- enormous diversity of RNAviruses is a hallmark of the eukaryotic
logs for other proteins, with the exception of capping enzymes in partofthevirusworld.Wearefarfromafullunderstandingofthe
Mononegaviralesthatalsoisextremelydivergedfromallhomologs underlying causes of this remarkable bloom of RNA viruses but it
(Bujnicki and Rychlewski, 2002; Li et al., 2008). The narrow host stands to reason that the eukaryotic cytosol, with its extensive
ranges of (cid:2)RNA viruses, limited to animals and plants, imply endomembranesystemprovidesanichethatishighlyconduciveto
relatively recent evolutionary origin. Furthermore, it has been RNA replication. There is sufficient evidence to derive the great
proposedthat (cid:2)RNAvirusesofplantswereacquiredfromanimals majorityofeukaryoticRNAvirusesfromacommon,positive-strand
viaHVT(DoljaandKoonin,2011).Thisscenarioiscompatiblewith ancestorthatmighthavebeenassembledfromseveralcomponents
themarkedlyhigherdiversityandprevalenceoftheanimal (cid:2)RNA withdistinctrootsinprokaryotesincludingareversetranscriptase.
virusescomparedtotherelativescarcityofthesevirusesinplants. Incontrast,severalisolatedgroupsofeukaryoticRNAvirusesderive
Theproteinsequences,aswellasvirionandgenomearchitectures, directlyfrombacterialRNAviralancestors.Thestrikingdiversifica-
arehighlysimilarbetweenanimalandplantvirusesinthefamilies tionofRNAvirusesineukaryotes,inpart,dependedonswitchesin
RhabdoviridaeandBunyaviridae.Furthermore,arthropodparasitesof genome replication-expression strategies (from positive-strand to
animals and plants could have readily served as HVT vehicles double-stranded and negative-stranded genomes) and multiple
because both plant and animal rhabdoviruses and bunyaviruses exchangesofgenesbetweenfardivergedgroupsofviruses.
aretransmittedbyandreplicateintheirarthropodvectors(Ammar
eletal.,2009;Guuetal.,2012).Thediscoveryoffour–RNAviruses Retroelementsandretroviruses:Virusesasderivedforms
that infect soybean cyst nematodes further expands the ecological
reach of these viruses within animal lineage of evolution (Bekal Anextremelycommonandabundantclassofselfishelementsin
etal.,2011).Thisfindingsuggestsapotentialmajorrouteofanimal- eukaryotes consists of reverse-transcribing elements (or retroele-
to-plant HVTof (cid:2)RNAviruses given that the nematodes, many of ments for short), including retroviruses. Similar to the case of RNA
whichareplantparasites,arethemostnumerousanimalsonearth viruses,thesinglecommondenominatoroftheseextremelydiverse
(Blaxter et al.,1998). Notably, two of these novel viruses are most elementsisthepolymeraseinvolvedintheirreplication,inthiscase,
closely related to bunyaviruses,and one to rhabdoviruses,the two the reverse transcriptase (RT) which defines the key feature of the