Review Article Diversity of the DNA Replication System in the Archaea Domain

16 Pages·2015·1.31 MB·English

Hindawi Publishing Corporation
Archaea
Volume 2014, Article ID 675946, 15 pages
http://dx.doi.org/10.1155/2014/675946
Review Article
Archaea
Diversity of the DNA Replication System in the Domain
FelipeSarmiento,1FengLong,1IsaacCann,2andWilliamB.Whitman1
1DepartmentofMicrobiology,UniversityofGeorgia,541BiologicalScienceBuilding,Athens,GA30602-2605,USA
23408InstituteforGenomicBiology,UniversityofIllinois,1206WGregoryDrive,Urbana,IL61801,USA
CorrespondenceshouldbeaddressedtoWilliamB.Whitman;[email protected]
Received21October2013;Accepted16February2014;Published26March2014
AcademicEditor:YoshizumiIshino
Copyright©2014FelipeSarmientoetal. This is an open access article distributed under the Creative Commons Attribution
License,whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperly
cited.
Thepreciseandtimelyduplicationofthegenomeisessentialforcellularlife.ItisachievedbyDNAreplication,acomplexprocess
thatisconservedamongthethreedomainsoflife.Eventhoughthecellularstructureofarchaeacloselyresemblesthatofbacteria,
theinformationprocessingmachineryofarchaeaisevolutionarilymorecloselyrelatedtotheeukaryoticsystem,especiallyforthe
proteinsinvolvedintheDNAreplicationprocess.WhilethegeneralDNAreplicationmechanismisconservedamongthedifferent
domainsoflife,modificationsinfunctionalityandinsomeofthespecializedreplicationproteinsareobserved.Indeed,Archaea
possessspecificfeaturesuniquetothisdomain.Moreover,eventhoughthegeneralpatternofthereplicativesystemisthesamein
allarchaea,agreatdealofvariationexistsbetweenspecificgroups.
1.Introduction components of the replicative apparatus and the overall
processcloselyresembleasimplifiedversionoftheeukaryotic
Archaeaareadiversegroupofprokaryoteswhichareunited DNAreplicationsystem[6,7].However,afewcharacteristics
byanumberofuniquefeatures.Manyofthesemicroorgan- of the archaeal information processing system are shared
ismsnormallythriveunderextremeconditionsoftempera- only with Bacteria, such as the circular topology of the
ture,salinity,pH,orpressure.However,somealsocoexistin chromosome, the small size of the genome, and the pres-
moderateenvironmentswithBacteriaandeukaryotes[1,2]. enceofpolycistronictranscriptionunitsandShine-Dalgarno
Likewise,awiderangeoflifestyles,includinganaerobicand sequences in the mRNA instead of Kozak sequences [8, 9].
aerobicrespiration,fermentation,photo-andchemoautotro- TheseobservationssuggestthatarchaealDNAreplicationis
phy, and heterotrophy, are common among this group. In aprocesscatalyzedbyeukaryotic-likeproteinsinabacterial
spiteofthisdiversity,membersoftheArchaeadomainpossess context [10]. In addition, there are specific features which
specific physiological characteristics that unite them, such belong only to the domain Archaea, such as the DNA
as the composition and structure of their membrane lipids polymerase D, which add another level of complexity and
[3]. uniqueness to these microorganisms. While a number of
Archaea, for the most part, resemble Bacteria in size evolutionary hypotheses have been proposed to account
andshape,buttheypossessimportantdifferencesatgenetic, for the mosaic nature of this process [11, 12], comparative
molecular,andmetaboliclevels.Remarkabledifferencesare genomicsandultrastructuralstudiessupporttwoalternative
present in the machinery and functionality of the infor- scenarios. The archezoan scenario holds that an archaeal
mation processing systems. For example, the histones in ancestor developed a nucleus and evolved into a primitive
some Archaea [4], the similarity of proteins involved in archezoan, which later acquired an 𝛼-proteobacterium to
transcriptionandtranslation,andthestructureoftheribo- form the mitochondrion and evolved into the eukaryotes.
some are more closely related to those of eukaryotes than The symbiogenesis scenario holds that an archaeal ancestor
Bacteria[5].ThemoststrikingsimilaritiesbetweenArchaea plus an 𝛼-proteobacterium formed a chimeric cell, which
andeukaryotesareobservedinDNAreplication,oneofthe then evolved into the eukaryotic cell [12]. A major differ-
most conserved processes in living organisms, where the ence between these hypotheses is the time when the first
2 Archaea
eukaryotesevolved.Inthearchezoanscenario,theancestors 3.DNAReplicationComponents
oftheearlyeukaryotesareasancientasthetwoprokaryotic
lineages, the Bacteria and Archaea. In the symbiogenesis 3.1. Preinitiation (Origin of Replication and Origin Recogni-
scenario, the eukaryotes evolved relatively late after the tion). The number of origins of replication in a genome is
diversification of the ancient archaeal and bacterial line- correlated with phylogeny and varies among the different
ages. domains [19]. Members of the Bacteria domain usually
The cultivated Archaea are taxonomically divided into possessonlyonereplicationorigin,buteukaryoticchromo-
five phyla. Crenarchaeota and Euryarchaeota are best char- somes contain multiple replication origins. This difference
acterized,andthistaxonomicdivisionisstronglysupported was generally accepted as a clear divisor in DNA repli-
by comparative genomics. A number of genes with key cation of eukaryotes and prokaryotes. However, members
roles in chromosome structure and DNA replication are of the Archaea domain display either one or multiple ori-
present in one phylum but absent in the other. Crenar- gins of replication. The origins of replication in archaea
chaeotesalsoexhibitavastphysiologicaldiversity,including are commonly AT-rich regions which possess conserved
aerobesandanaerobes,fermenters,chemoheterotrophs,and sequencescalledoriginofrecognitionboxes(ORB)andare
chemolithotrophs[2].Themajorityofthecultivatedcrenar- well conserved across many archaeal species. Also, smaller
chaeotes are also thermophiles [13]. Euryarchaeotes exhibit versionsoftheORBs,calledmini-ORBs,havebeenidentified
anevenlargerdiversity,withseveraldifferentextremophiles [20].MembersoftheCrenarchaeotaphylumdisplaymultiple
amongtheirranksinadditiontolargenumbersofmesophilic originsofreplication.Forexample,speciesbelongingtothe
microorganisms. Interestingly, all the known methanogens Sulfolobalesordercontainthreeoriginsofreplication[20,21].
belongtothisphylum.Additionally,environmentalsequenc- Likewise,twoandfouroriginsofreplicationhavebeenfound
ing,16SrRNAanalysis,andcultivationeffortsprovidestrong in members of the Desulfurococcales (Aeropyrum pernix)
evidenceforthreeadditionalphyla:Thaumarchaeota,Korar- andThermoproteales(Pyrobaculumcalidifontis),respectively
chaeota, and Aigarchaeota [14–16]. A sixth phylum has also [22, 23]. In addition to shortening the time required for
been proposed previously, the Nanoarchaeota. This phy- replication,multipleoriginsmayplayaroleincounteracting
lumincludestheobligatesymbiontNanoarchaeumequitans, DNA damage during hyperthermophilic growth [24]. In
which has a greatly reduced genome [17]. However, a more contrast,mostmembersoftheEuryarchaeotaphylumseem
complete analysis of its genome suggests that N. equitans topossessonlyoneoriginofreplication.Forexample,species
corresponds to a rapidly evolving euryarchaeal lineage and belonging to the Thermococcales (Pyrococcus abyssi) and
notanearlyarchaealphylum[18]. Archaeoglobales(Archaeoglobusfulgidus)orderscontainonly
one origin of replication [25–27]. However, members of
2.GeneralOverviewof the order Halobacteriales (e.g., Halobacterium sp. NRC-1,
Haloferaxvolcanii,andHaloarculahispanica)possessnumer-
theDNAReplicationProcess
ous origins of replication that may be part of an intricate
replicationinitiationsystem[28–30].Infact,arecentreport
ThegeneralprocessofDNAreplicationisconservedamong
demonstrated that the different origins of replication in
the three domains of life, but each domain possesses some
Haloarculahispanicaarecontrolledbydiversemechanisms,
functional modifications and variations in key proteins.
which suggest a high level of coordination between the
DNA replication may be divided into four main steps.
multiple origins [31]. In contrast, the deletion of a single
Step1(Preinitiation)startswhenspecificproteinsrecognize
originofreplicationinHaloferaxvolcaniiaffectsreplication
and bind the origin of replication, forming a protein-DNA
dynamics and growth, but the simultaneous deletion of all
complex. This complex recruits an ATP-dependent helicase
four origins of replication accelerated growth compared to
to unwind the double-stranded DNA (dsDNA). The single-
thewildtypestrain[32].Theseresultssuggestthatinitiation
strandedDNA(ssDNA)formedisthenprotectedbyssDNA-
of replication in Haloferax volcanii may be dependent of
bindingproteins(SSB).Step2(Initiation)correspondstothe
homologous recombination, as it is in some viruses, and
recruitmentoftheDNAprimaseandDNApolymerase.Step
generate questions about the purpose of the replication
3(Elongation)correspondstotheduplicationofbothstrands
origins [32]. With the exception of Methanothermobacter
ofDNAatthesametimebythesameunidirectionalreplica-
thermautotrophicus,theDNAreplicationoriginhasnotbeen
tionmachine.BecauseoftheantiparallelnatureoftheDNA,
experimentallydemonstratedinthemethanogens[33].How-
the leading strand is copied continuously, and the lagging
ever,bioinformaticsanalysisbyGC-skewinMethanosarcina
strandiscopieddiscontinuouslyasOkazakifragments[10].
acetivorans[34]and𝑍-curveanalysisforMethanocaldococcus
During replication, a sliding-clamp protein surrounds the
jannaschiiandMethanosarcinamazeisuggestasingleorigin
DNA and binds to the polymerase to increase processivity
of replication. A similar analysis of M. maripaludis S2 was
or the number of nucleotides added to the growing strand
inconclusive [35]. The fact that the order Halobacteriales is
before disassociation of the polymerase from the template.
Step 4 (Maturation) corresponds to the completion of the theonlyeuryarchaeotethatdisplaysmultipleoriginofrepli-
discontinuousreplicationinthelaggingstrandbytheactions cation suggests that there may have been a lineage-specific
ofRNase,DNAligase,andFlapendonuclease.Thevariability duplicationinthisgroup.Moreover,thenumberoforiginsis
oftheplayersinvolvedineachoftheseprocessesbetweenthe nothighlyconservedevenwithinasinglearchaealphylum.
threedomainsoflifeandmorespecificallywithintheArchaea Theoriginofreplicationisrecognizedbyspecificproteins
domainisdiscussedinfurtherdetailbelow. that bind and melt the dsDNA and assist in the loading of
Archaea 3
Number of homologs for replication genes
Order Phylum Number of ORC/CDC6 GINS15 GINS23 RPA MCM RFCS PCNA PolB DP1 DP2
genomes
Nitrosopumilales Thaumarchaeota 2 1 0 or 1 0 or 1 1 1 1 1 1 1 1
Thermoproteales 14 1∗ 0 0 0∗ 1 1 to 3 1 to 3 2∗ 0 0
Desulfurococcales Crenarchaeota 9 2 0 1∗ 0 or 1 1 1∗ 3∗ 2∗ 0 0
Sulfolobales 15 3 1 1 1 1 1 2∗ 3 0 0
Not named Korarchaeota 1 2 0 0 0 1 1 1 2 1 1
Nanoarchaeota 1 1 0 0 1 1 1 1 1 1 1
Thermococcales 11 1 1 1∗ 3 1∗ 1 1∗ 1 1 1
Methanopyrales 1 0 0 0 0 1 1 1 1 1 1
Methanobacteriales 7 1 or 2 0 or 1 0 1∗ 1 1 1 2 1 1
Methanococcales Euryarchaeota 15 0 0 0 2 to 4 2 to 8 1 1∗ 1 1 1
Thermoplasmatales 4 1∗ 0∗ 0 1 1 1 1 1 1 1
Archaeoglobales 4 2 or 3 0 0 0∗ 1 or 2 1 1 1∗ 1 1
Halobacteriales 15 3 to 15 0 0 1 1 or 2 2∗ 1 1∗ 1 1
Methanomicrobiales 6 2∗ 0 0 1 1 2 1 1 or 2 1 1
Methanocellales 1 2 0 0 1 1 1 1 3 1 1
Methanosarcinales 9 2∗ 0 0 3 1∗ 1∗ 1 1∗ 1∗ 1
Figure1:HomologsforsomekeygenesinvolvedinarchaealDNAreplication.Archaealordersarephylogeneticallyorganizedfollowing
a rooted maximum likelihood tree of Archaea based on 53 concatenated ribosomal proteins [36]. The homology search was performed
by RAST v4.0 (Rapid Annotation using Subsystem Technology), and the annotated data was viewed through the SEED viewer
(http://www.theseed.org/).Atotalof115archaealgenomesequenceswereobtainedfromNCBIanduploadedintotheRASTserver.RAST
annotation was performed using default parameters with the genetic code for Bacteria and Archaea. The replication proteins homologs
werecheckedthroughtheSEEDsubsystemDNAreplication.HomologyresultsofThermococcuskodakaraensisKOD1,Pyrococcusfuriosus
DSM3638,andThermofilumpendensHrk5weresearchedforreplicationproteinhomologsusingBLAST(blastxv2.2.28+).Resultswith
homology coverage of >80% and 𝐸-values less than 0.001 were considered as real homologs. The results were also supplemented with
data from literature reviews and BLAST searches. When indicated in the figure, zero (0) homologs means that no homolog was found
for a specific gene by using the described methodology. Asterisks indicate that one or two of the analyzed microorganisms possess
an exception for that specific feature. Exceptions noted are (feature/order) ORC1/CDC6/Thermoproteales, Thermofilum pendens Hrk5 (3
homologs),andThermosphaeraaggregansDSM11486(2homologs);ORC1/CDC6/ThermoplasmatalesandPicrophilustorridusDSM9790
(1homolog);ORC1/CDC6/MethanomicrobialesandMethanoplanuspetroleariusDSM11571(4homologs);ORC1/CDC6/Methanosarcinales
andMethanosalsumzhilinaeDSM4017(4homologs);GINS15/ThermoplasmatalesandThermoplasmaacidophilumDSM1728(1homolog);
GINS23/Desulfurococcales, Staphylothermus hellenicus DSM12710 (no homolog), and Staphylothermus marinus F1 (no homolog);
GINS23/Thermococcales, Pyrococcus horikoshii OT3 (2 homologs), RPA/Thermoproteales, Thermofilum pendens Hrk5 (3 homologs),
and Thermosphaera aggregans DSM11486 (1 homolog); RPA/Methanobacteriales and Methanothermus fervidus DSM2088 (no homolog);
RPA/Archaeoglobales and Archaeoglobus fulgidus DSM4304 (1 homolog); MCM/Thermococcales and Thermococcus kodakaraensis KOD1
(3 homologs); MCM/Methanosarcinales and Methanosarcina acetivorans C2A (2 homologs); RFCS/Desulfurococcales and Hyperthermus
butylicusDSM5456(2homologs);RFCS/HalobacterialesandHaloquadratum walsbyiDSM16790(1homolog);RFCS/Methanosarcinales,
Methanosaeta concilii CG6 (2 homologs), and Methanosaeta thermophila PT (2 homologs); PCNA/Desulfurococcales and Ignisphaera
aggregans DSM17230 (1 homolog); PCNA/Sulfolobales and Metallosphaera cuprina Ar-4 (1 homolog); PCNA/Thermococcales, Pyrococcus
horikoshiiOT3(2homologs),andThermococcuskodakaraensisKOD1(2homologs);PCNA/Methanococcales,Methanococcusmaripaludis
S2 (2 homologs), and Methanotorris igneus Kol5 (2 homologs). PolB/Thermoproteales, Caldivirga maquilingensis IC-167 (3 homologs),
and Pyrobaculum calidifontis JCM 11548 (3 homologs); PolB/Desulfurococcales, Staphylothermus hellenicus DSM12710 (3 homologs), and
Staphylothermus marinus F1 (3 homologs); PolB/Archaeoglobales, Archaeoglobus fulgidus DSM4304 (2 homologs); PolB/Halobacteriales,
HalorhabdusutahensisDSM12940(2homologs);PolB/Methanosarcinales,MethanosaetaconciliiGP6(2homologs);DP1/Methanosarcinales,
MethanococcoidesburtoniiDSM6242(2homologs).
the replicative helicases. In Bacteria this protein is DnaA, S. solfataricus binds to ORB elements from other crenar-
which binds to the DnaA boxes [37]. In eukaryotes, a chaeotes and euryarchaeotes in vitro, suggesting that these
proteincomplexknownasORC(originrecognitioncomplex) proteins recognize sequences conserved across the archaeal
composed of 6 different proteins (Orc1-6) binds at the domain [20]. The crystal structures of these proteins from
replicationoriginandrecruitsotherproteins[38].InArchaea, Pyrobaculum aerophilum [41] and Aeropyrum pernix [42]
thecandidateforreplicationinitiationisaproteinthatshares havebeensolved,contributingtotheoverallunderstanding
homologywiththeeukaryoticOrc1andCdc6(celldivision oftheiractivityduringtheinitiationofreplication(reviewed
cycle 6) proteins and is encoded by almost all archaeal in [43]). In general, the number of Orc1/Cdc6 homologs
genomes[39].Theirgenesarecommonlylocatedadjacentto found in archaeal genomes varies between one and three
theoriginofreplication.Theseproteins,termedOrc1/Cdc6 (Figure1). However, there are some interesting exceptions.
homologs,havebeenstudiedindetailinrepresentativesofthe MembersoftheorderHalobacterialespossessbetween3and
Euryarchaeota (Pyrococcus) and Crenarchaeota (Sulfolobus) 15Orc1/Cdc6homologs,whichmayreflectthelargenumber
and have been shown to bind to the ORB region with high oforiginsofreplication.Interestingly,likeothermembersof
specificity[20,26,40].Inaddition,purifiedOrc1/Cdc6from theMethanosarcinales,theextremelyhalophilicmethanogen
4 Archaea
Methanohalobium evestigatum Z-7303 only possesses two MCM system is suggested to form homologous multimeric
Orc1/Cdc6homologs.Thus,theabilitytogrowatextremely complexes [64]. A recent study proposed that two of the
highconcentrationsofsaltandtomaintainhighintracellular MCMhomologsthatareconservedamongrepresentativesof
salt concentrations does not necessarily require a large the order Methanococcales are a consequence of an ancient
numberofOrc1/Cdc6homologs.Althoughmostmembersof duplication that occurred prior to the divergence of this
theorderMethanomicrobialespossesstwocopiesofthisgene, group[59].Ithasalsobeenproposedthatthelargenumber
MethanoplanuspetroleariusDSM11571possessesfourcopies. of MCM homologsin the order Methanococcales is a direct
Thus, the number of Orc1/Cdc6 homologs varies consider- consequence of mobile elements, which may have taken
ably among the euryarchaeotes. In an extreme case, repre- advantage of the ancient duplication of the MCM genes to
sentativesoftheordersMethanococcalesandMethanopyrales take over the replication system by forming cellular MCM
donotpossessanyrecognizablehomologsfortheOrc1/Cdc6 heterocomplexes[58].Inanycase,thelargenumberofMCM
protein[7,44],andthemechanicsofreplicationinitiationin homologsintheorderMethanococcalesmaybeaproductof
thesearchaearemainanintriguingunknownofthearchaeal an intricate and complex evolutionary history. Whether or
replicationprocess. not it is related to the absence of the replication initiation
proteinOrc1/Cdc6isaninterestingpossibility[58].
3.2.Initiation(DNAUnwindingandPrimerSynthesis). After In eukaryotes the MCM complex is not active on its
Orc1/Cdc6 proteins bind to the origin of replication, a own and requires the association of two accessory factors,
helicase is recruited to unwind the dsDNA. In Bacteria the the heterotetrameric GINS complex (from the Japanese go-
replicativehelicaseisthehomohexamerDnaB.Ineukaryotes ishi-ni-san meaning 5-1-2-3, after the four subunits Sld5,
themostlikelycandidateforthereplicativeDNAhelicaseis Psf1, Psf2, and Psf3) and the Cdc45 protein. This complex,
theMCM(minichromosomemaintenance)complex,which calledCMG(Cdc45-MCM-GINS),isthoughttobetheactive
is a heterohexamer that is activated when associated with replicative helicase [47]. Homologs for GINS subunits have
otherreplicativeproteins,formingtheCMG(Cdc45-MCM- been identified in Archaea by bioinformatics analysis. One
GINS) complex [45–48]. As in eukaryotes, in Archaea the homolog is most similar to the eukaryotic proteins Psf2
most probable candidate for the replicative helicase is the and Psf3 (GINS23) and is common in the crenarchaeotes.
MCMcomplex.Intriguingly,theMCMcomplexesineukary- Another homolog is most similar to the eukaryotic pro-
󸀠 󸀠
otesandarchaeapossessa3 -5 unwindingpolarity,butthe teins Psf1 and Sld5 (GINS15) and is found largely in the
bacterialDnaBhelicaseunwindsduplexDNAontheopposite euryarchaeotes [65]. The GINS complex is expected to be
󸀠 󸀠
directionwithadistinct5 -3 polarity[49–51]. essential for DNA replication, but the distribution of these
MostarchaealgenomesstudiedsofarencodeoneMCM two different GINS homologs suggests that the presence of
homolog. Its helicase activity has been demonstrated in oneofthemissufficientforarchaealDNAreplication.Some
vitro for several archaea, including Methanothermobacter Crenarchaeota (S. solfataricus) and some Euryarchaeota (P.
thermautotrophicus ΔH, where the MCM protein forms a furiosus and T. kodakaraensis) possess both homologs and
dimerofhexamers[52,53].Theinvivointeractionbetween formheterotetramerssimilartotheonesfoundineukaryotes
the MCM complex and the Orc1/Cdc6 proteins has been with a ratio 2:2 [66–68]. To find homologs of GINS15 and
demonstratedinotherArchaea[54–56].Indeed,throughan GINS23 in Archaea, two known GINS15 (from Sulfolobus
invitrorecruitingassay,Orc1/CDC6fromP.furiosushasbeen solfataricus P2 and Thermococcus gammatolerans EJ3) and
demonstratedasthepossiblerecruiteroftheMCMcomplex threeknownGINS23(fromSulfolobussolfataricusP2,Pyro-
to the origin of replication [57]. A recent study identified coccusyayanosiiCH1,andThermococcusgammatoleransEJ3)
thirteenspeciesofarchaeawithmultiplemcmgenesencoding were used for homology searches. These analyses failed to
the MCM complexes (Figure1, [58]). The number of mcm identifyGINShomologsinseveralarchaealgroups(Figure1).
homologs is especially high in the order Methanococcales, These results suggest that there are other unknown GINS
where different representatives possess from 2 to 8 copies homologs in archaea or that the sequences have diverged
[59, 60]. For instance, Methanococcus maripaludis S2 pos- enough between genera not to be recognized by homology
sesses four homologs of the MCM protein [44]. Through a searches.Inanycase,amorecomprehensiveanalysisofGINS
shotgun proteomic study, peptides for three of them have proteinsisnecessarytofullyunderstandtheirfunctionand
been detected [61], suggesting that multiple MCMs are distributioninArchaea.
expressed and functional. However, a genome-wide survey ThedetailedinteractionsoftheGINSandMCMproteins
of gene functionality in M. maripaludis demonstrated that in archaea appear to be highly variable. Although the S.
onlyoneofthesegenes,MMP0030,waslikelytobeessential solfataricus GINS and MCM proteins physically interact
for growth [62]. In addition, coexpression of recombinant in vitro, MCM helicase activity was not stimulated in the
MCMs from M. maripaludis S2 allowed copurification of complex [66]. In contrast, the MCM helicase activity of T.
all four proteins [59], suggesting that M. maripaludis may kodakaraensis and P. furiosus is clearly stimulated by their
form a heterologous multimeric MCM complex. However, GINScomplexes[64,67].ThecrystalstructureoftheGINS
because MMP0030 protein is the only mcm gene essential complex of T. kodakaraensis was recently determined. The
for growth, a homologous multimeric complex may also backbone structure and the assembly are similar to the
be possible. Similar results have been found in Thermo- humancomplexwithsomenotabledifferences[68].Interest-
coccus kodakaraensis, in which three MCM homologs are ingly,manyothereuryarchaeotespossessonlythehomolog
present but only one is essential [63]. The T. kodakaraensis toGINS15.Oneofthose,Thermoplasmaacidophilum,forms
Archaea 5
ahomotetramericcomplex[68,69].Moreover,invitrotheT. the genomes of many members of the closely related order
acidophilum MCM helicase activity was not affected by the Thermoprotealeswithsomefewexceptions(Figure1)[81].
GINScomplex[69].Theseresultssuggestthatotherproteins RPAs have been studied from different representatives
maybeinvolvedintheformationofastablehelicaseinmany oftheeuryarchaeotes,revealingadditionaldiversity.M.jan-
Archaea.M.maripaludisS2possessesahypotheticalprotein naschiiandM.thermautotrophicuspossessasingleRPAsub-
which may correspond to the gene encoding for GINS15, unit,whichsharesaminoacidsimilaritywiththeeukaryotic
whichisprobablyessentialforgrowth[60,62].Nohomologs RPA70andpossessesfourandfiveOB-folds,respectively[82,
ofGINS23arepresentinthegenomeofM.maripaludis. 83].P.furiosuspossessesthreedifferentRPAsubunits,which
The replication related Cdc45 protein is ubiquitous in form a stable heterotrimer that is involved in homologous
eukaryotes, but its exact role has not yet been elucidated. recombination in vitro [84]. The P. furiosus RPA, therefore,
Interestingly,homologsoftheCdc45proteinarenotpresent issimilarinsubunitorganizationtotheeukaryoticRPA.The
inArchaea.However,abioinformaticsanalysisrevealedthat other members of the Thermococcales genera also possess
the eukaryotic Cdc45 and the prokaryotic RecJ, which is a three RPA homologs, which likely form the homotrimeric
󸀠 󸀠
conserved 5 -3 exonuclease in most bacteria and archaea, complexdescribedforP.furiosus(Figure1).Methanosarcina
possess a common ancestry and share a homologous DHH acetivoransalsopossessesthreedifferentRPAproteins(RPA1-
domain [70]. These results suggest that the archaeal RecJ 3),withfour,two,andtwoOB-folds,respectively.However,
maysubstitutefortheeukaryoticCdc45duringreplication. theydonotinteractwitheachotherandappeartofunction
Circumstantialevidencesupportsthisconclusion.InS.solfa- as homodimers [85]. This arrangement is common among
taricus,ahomologoftheDNAbindingdomainofRecJwas theMethanosarcinalesbutisnotfoundinthecloselyrelated
purified together with a GINS protein [66]. Similarly, in T. methanogen orders such as the Methanocellales (Figure1).
kodakaraensis,theRecJhomolog(TK1252p)copurifiedwith Members of the order Methanococcales possess two to four
proteinsoftheGINScomplex[71]andformedastableinvitro RPA homologs. The genome of M. maripaludis S2 contains
associationwiththeGINScomplex[72].TwoRecJhomologs three possible RPA homologs (MMP0122, 0616, and 1032)
arefoundinM.jannaschii(MJ0977and0831),andtheypar- [60].OnlyMMP0616and1032werelikelytobeessentialfor
tiallycomplementarecJmutationinE.coli.Therecombinant growth[62],suggestingapossibledifferentcomplexconfigu-
MJ0977 also possesses high levels of thermostable single- rationforRPAproteinsinthisarchaeon.Ithasbeenhypoth-
strandedDNAdegradingactivitysimilartoRecJ[73].InM. esizedthatthediversityinOB-foldsinthearchaealRPAsisa
maripaludisS2,fourproteinspossesstheDHHdomainwith directconsequenceofhomologousrecombination[86].
similarity to the M. jannaschii RecJ homologs (MMP1682, DNA synthesis starts with the production of a RNA
0547, 1078, and 1314). However, none of them was essential primer, since the DNA polymerases that replicate genomes
forgrowth,suggestingthattheactivitieswereredundant[62]. are incapable of de novo DNA synthesis. The RNA primer
Alternatively, another protein, which has a low similarity is synthesized by a DNA-dependent RNA polymerase or
withM.jannaschiiRecJhomolog(MMP0285)butpossesses primase. DnaG, a single subunit protein, is the primase in
the DHH domain, was possibly essential for growth [62]. Bacteria.Ineukaryotes,atwo-subunitprimase,consistingof
However, this protein possesses other domains related to a small catalytic subunit (PriS) and a large subunit (PriL),
transport, which make it an unlikely candidate for RecJ. is found in a complex with DNA polymerase 𝛼 and its
Theseresultsarenotdefinitive,andmoreexperimentaldata accessoryBsubunit[87].InArchaea,thefirstbiochemically
isneededtoassignafunctiontothisprotein. characterizedprimasewastheeukaryoticprimase-likesmall
As soon as the DNA is unwound, ssDNA is protected subunit PriS in M. jannaschii [88]. Later, homologs of the
fromnucleases,chemicalmodification,andotherdisruptions PriS and PriL subunits were described in several Pyrococ-
byssDNAbindingproteins.Theseproteinsarepresentinall cus species [89–93]. The eukaryotic-like DNA primase has
three domains of life and are called SSB in Bacteria, where also been characterized in the crenarchaeote S. solfataricus
theyformhomotetramersorhomodimers[74,75],andRPA [94, 95], where it has been shown to interact with MCM
(replication protein A) in eukaryotes, where they form a through GINS23 [66]. A unique polymerization activity
stableheterotrimercomposedof70,32,and14kDaproteins acrossdiscontinuousDNAtemplateshasbeencharacterized
[76]. Although all ssDNA binding proteins contain dif- in the PriSL of S. solfataricus, suggesting that this primase
ferent combinationsof the oligonucleotide/oligosaccharide- maybeinvolvedindouble-strandedbreakrepairinArchaea
bindingfoldorOB-fold[77],thesequencesimilarityislow [96]. So far the eukaryotic-like primases found in archaea
among RPA and the bacterial SSBs [43]. In Archaea, differ- exhibit similar properties. PriS functions as the catalytic
ent types of ssDNA binding proteins have been reported. subunit and PriL modulate its activity [87]. In addition,
In crenarchaeotes, an ssDNA binding protein is only well the archaeal eukaryotic-like primase has the unique ability
characterized in S. solfataricus. The S. solfataricus ssDNA to synthesize both DNA and RNA in vitro. Indeed, the
bindingproteincontainsonlyoneOB-foldandcanadopta P. furiosus PriS synthesizes long DNA fragments, but the
heterotetramerconformation[78].However,theproteinalso addition of PriL regulates the process by decreasing the
appearstoexistasamonomer[79].Thisproteinappearsto DNA polymerase activity, increasing the RNA polymerase
bemoresimilartothebacterialproteinsinsequence,butits activity,anddecreasingtheproductlength[90].Additionally,
structureismoresimilartothatoftheeukaryoticRPAs[43, studies of the P. abyssi enzyme suggest that DNA primase
80]. While homologs are recognizable in other members of may also be involved in DNA repair because of the DNA
theSulfolobalesandmostotherArchaea,theyareabsentfrom polymerase, gap filling, and strand displacement activities
6 Archaea
alsopresentinvitro[93].Interestingly,thearchaealprimase characterized in S. solfataricus [108] and the Methanosarci-
small subunit resembles DNA polymerases from the Pol X nales, in which several species harbor two homologs [109].
family in sequence and structure, suggesting a similarity in Even though the activity of DNA polymerases belonging
theircatalyticmechanism[96]. to the Y family in archaea is not fully understood, they are
HomologsofthebacterialDnaGprimasearealsofound suggestedtoplayanimportantroleinDNArepair[109].
in archaea. However, in vitro studies of the P. furiosus Representatives of the DNA polymerase family B have
enzymefailedtodetectprimersynthesisactivity,andtheT. beenidentifiedinallArchaea.Thecrenarchaeotespossessat
kodakaraensisDnaGwascopurifiedwithproteinsoftheexo- least two family B DNA polymerases (PolB I and PolB II,
some[71].Also,inS.solfataricus,DnaGprimasewasfoundto andinsomecasesPolBIII)[102,110,111].Therecombinant
beacoreexosomesubunitinvolvedinRNAdegradation[97, S.solfataricus,Pyrodictiumoccultum,andA.pernixenzymes
98].However,recentstudiesdemonstratedthattheS.solfa- have been characterized [102]. In contrast, euryarchaeotes
taricusDnaGhomologhaslimitedprimersynthesisactivity, only contain PolB I. The recombinant P. furiosus enzyme
andadualprimasesystemwithPriSLhasbeenproposedto has been characterized [112]. The PolB I enzymes have
functionduringDNAreplication[99].Huetal.hypothesized similaraminoacidsequenceandoverallstructure,andthey
󸀠 󸀠
aninterestingtheorywhichsuggeststhatLUCAemployeda possessapotent3 -5 exonucleaseproofreadingactivity[102].
dual-primasesystemcomprisingDnaGandPriSL,whichalso AuniquepropertyofthearchaealfamilyBDNApolymerase
served roles in RNA degradation and the nonhomologous is the ability to stall DNA polymerization in the presence
endjoining(NHEJ)pathway.Thesystemwasinheritedbyall of uracil or hypoxanthine deaminated bases [113, 114]; this
threedomains.IntheArchaeadomain,itretaineditsoriginal propertyhelpstopreventthecopyoftemplate-stranduracil
functions. However, in the Bacteria domain DnaG became and the transmission of fixed mutations to progeny [115].
themajorreplicativeprimaseandPriSLevolvedintothePol Commonly, cytosine deamination converts G:C base pairs
domainofLigDinvolvedintheNHEJpathway.Incontrast, into the promutagenic G:U mismatches, which result in
DnaGwaslostintheEukaryotadomain,andPriSLbecame 50%oftheoffspringcontaininganA:Ttransitionmutation
theonlyreplicativeprimase.Inaddition,italsoevolvedinto afterreplication[116].Inaddition,whenA-Ubasepairsare
theDNAPolXfamilyinvolvedinNHEJ[96]. formed, the loss of the 5-methyl moiety upon replacement
LikeotherArchaea,M.maripaludisS2possessesboththe of thymine can exert a detrimental effect on protein DNA
eukaryotic-andbacterial-likeprimases.Anewgenome-wide interactions. Interestingly, in some crenarchaeotes and eur-
surveyofthismethanoarchaearevealedthatgenesencoding yarchaeotes, one of the B family DNA polymerase paralogs
bothsubunitsoftheeukaryoticlikeprimase,PriS,andPriL possesses disrupted versions of the sequence motifs that
(MMP0009 and MMP0071) were likely to be essential for are essential for catalysis. Possibly, these enzymes possess a
growth,whichisconsistentwitharoleinreplication.Similar structuralrole[117].
observationshavebeendemonstratedinotherArchaea,such DNApolymerasefamilyD(PolD)isanovelenzymethat
asHalobacteriumsp.NRC-1andHaloferaxvolcanii[93,100]. was originally discovered in P. furiosus [118]. It has since
IncontrasttheDnaGprimase(MMP1286)wasnonessential, then been identified in all euryarchaeotes [119]. For a long
whichwouldbeconsistentwitharoleintheexosome[62]. time, this enzyme was considered a euryarchaeote-specific
These results suggest that in M. maripaludis and probably polymerase, but the three newly discovered archaeal phyla
other euryarchaeotes, a dual primase system is not pre- were also found to possess genes for PolD [14–16]. PolD is
sent. aheterodimerwithasmallsubunit(DP1)andalargesubunit
(DP2). It has been proposed that the large subunit harbors
3.3. Elongation (Replicative DNA Polymerase). The primer thepolymeraseactivity,althoughitssequenceisverydifferent
synthesizedbytheprimaseisfurtherextendedbyareplicative fromotherhithertodescribedDNApolymerases.Thesmall
DNA polymerase. DNA polymerases have been classified subunit possesses high similarity with the noncatalytic B-
into seven families based on their amino acid sequence subunitsoftheeukaryoticDNApolymerases𝛼,𝛿,and𝜀[120].
similarity(A,B,C,D,E,X,andY)[101–105].InBacteria,E. Studies of the M. jannaschii enzyme demonstrated that the
󸀠 󸀠
colipossessesfiveDNApolymerases,PolI–V,wherethefirst small subunit possesses a strong 3 -5 exonuclease activity,
threebelongtofamiliesA,B,andC,respectively,andthelast suggesting that it may be involved in proofreading activity
twobelongtotheYfamily.ThemajorreplicativeDNApoly- [7,121].Efficientpolymeraseandproofreadingactivityhave
meraseinE.coliisPolIII,amemberoftheCfamily,which also been detected from a purified PolD of P. furiosus, and
synthesizes DNA with high processivity when functioning the residues Asp-1122 and Asp-1124 are essential for the
withintheholoenzyme[106].Ineukaryotes,agreatdiversity polymerization reaction in P. horikoshii [122, 123]. Every
of DNA polymerases is also found, but DNA replication euryarchaeoteexaminedpossessedonehomologforDP1and
requires three replicative DNA polymerases which belong DP2,exceptforMethanococcoidesburtoniiDSM6242,which
to family B (Pol𝛼, Pol𝛿, and Pol𝜀) [107]. In Archaea, fewer possessestwohomologsforDP1(Figure1).
types of DNA polymerases are present, but they have an Because the crenarchaeotes only possess family B DNA
interestingevolutionarydivision.RepresentativesoftheDNA polymerases,oneofthemmustbethereplicativepolymerase.
polymeraseBfamilyarefoundinallArchaea.TheDfamily However, in euryarchaeotes it was not clear which enzyme
DNA polymerase is present in every phyla studied so far was involved in replication. Studies in Halobacterium sp.
withtheexceptionoftheCrenarchaeota(Figure1).Lastly,a NRC-1 showed that both PolB and PolD were essential for
memberoftheYfamilyhasbeenidentifiedandbiochemically viability, and it was proposed that they could be working
Archaea 7
togetheratthereplicationfork,synthesizingtheleadingand kodakaraensisdemonstratedthatbothhomologsstimulatein
lagging strand, respectively [100, 124]. However, in other vitrotheprimerextensionactivityofPolB,butonlyPCNA1
Euryarchaeota, PolB does not appear to be essential. For and not PCNA2 stimulates the same activity of PolD [138].
instance,arecentreportdemonstratedthatbothsubunitsof Also, the same report showed that the pcna2 gene can be
PolDwereessential,butPolBwasnonessentialforthegrowth disruptedwithoutcausinggrowthdeficiencies,butitwasnot
of M. maripaludis S2 [62]. Likewise, in T. kodakaraensis possible to isolate mutants of pcna1. These results suggest
PolDcanbecoisolatedwithdifferentproteinsofthearchaeal thatPCNA1butnotPCNA2isessentialforDNAreplication
replicationfork,butPolBwasmainlycoisolatedwithproteins [138]. It has been proposed that one of the PCNA genes
of unknown function [71]. A deletion of the PolB in T. was acquired by lateral gene transfer [139]. Members of the
kodakaraensis also had no detectable effect on cell viability orderMethanococcalespossessonePCNAhomologwithtwo
[125]. Interestingly, T. kodakaraensis PolB mutants have exceptions.M.maripaludisS2possessestwoPCNAhomologs
increasedsensitivitytoUVradiation.Theseresultstogether (MMP1126and1711)[60].Bothgenesappearedtobeessential
suggestthatPolDistheessentialreplicativeDNApolymerase for growth, suggesting that they both play an important
in these euryarchaeotes and not a PolB family polymerase. role in replication [62]. The gene MMP1711 possesses high
Inthisscenario,PolBmayhavesomeothercrucialfunction similarity to both T. kodakaraensis genes and is likely the
in Halobacteriumandpossiblyothercloselyrelatedspecies, truemethanococcalPCNA.Incontrast,MMP1126possesses
which it is not conserved throughout the phylum. Finally, only low similarity to the T. kodakaraensis genes and also
it has been demonstrated that purified PolD from P. abyssi contains an S-adenosylmethionine-dependent methyltrans-
is able to perform strand displacement and RNA primer ferasesdomain.Thus,itislikelytopossesssomealternative
extensioninvitro.PurifiedPolB,onitsown,cannotperform function. Methanotorris igneus Kol 5 also possesses two
theseactivitiesinvitro,butinthepresenceofPCNAstrand PCNAhomologs.
displacementactivityisstimulated[124,126].Arecentinvitro For PCNA to assemble around DNA, a specific loading
studyinP.abyssidemonstratedthatRNaseHIIisrequiredto factor is required. In Bacteria the loading factor is known
initiatestranddisplacementDNAsynthesisbyPolB[127]. as 𝛾-complex and comprises three different subunits in
a 𝛾3-𝛿-𝛿󸀠 stoichiometry [140]. In eukaryotes, the loading
3.4. Elongation (Other Accessory Proteins). Purified DNA factor is known as Replication Factor C (RFC) and is a
polymerases possess low processivity; however, the addi- heteropentamericcomplexcomprisingonelargesubunitand
tion of an accessory factor, the sliding clamp, gives DNA fourdifferentsmallsubunits[141].Incontrast,inArchaeathe
polymerasestherequiredprocessivitytoreplicategenomes. RFCconsistsoftwodifferentproteins,asmallsubunitRFCS
Thisfactor,whosestructureresemblesadoughnut,functions andalargesubunitRFCL.Theyalsoformaheteropentameric
as a molecular platform which recruits several replication- complex in a 4:1 ratio (RFCS:RFCL). Interestingly, many
associated enzymes and act together with DNA and the crenarchaeotes possess one homolog of RFCL and two or
polymerase to stabilize their interactions during replication threehomologsofRFCS.Alternatively,mosteuryarchaeotes
[128]. The structure of sliding clamps is conserved in the possessonlyoneRFCLandRFCShomolog.Theexceptions
three domains of life. In Bacteria, the sliding clamp or 𝛽- aresomemembersoftheordersHalobacteriales,Methanomi-
subunit is a homodimeric ring [129]. In eukaryotes, the crobiales, and Methanosarcinales, which possess two RFCS
sliding clamp or proliferating cell nuclear antigen (PCNA) homologs (Figure1). Structural and biochemical studies of
is a homotrimeric ring [128]. In Archaea, the majority of RFChavebeenconductedinseveraleuryarchaeotes,suchas
crenarchaeotes have multiple PCNA homologs which form ArchaeoglobusfulgidusandPyrococcusspecies[142–144].An
heterotrimeric rings [130, 131] (Figure1). In contrast, most interesting case is observed in Methanosarcina acetivorans.
euryarchaeotes possess a single PCNA homolog (Figure1). This RFC possesses three subunits (RFC1, 2, L) found in
Interactions of DNA polymerase with the sliding clamp a ratio 3:1:1 [145]. Homologs for these three subunits are
are mediated through a common motif, called the PCNA also present in most of the genomes of the haloarchaea
Interacting Protein (PIP) box [132]. The three dimensional [145].ItisinferredthatthistypeofRFCcomplexrepresents
structuresofPCNA-PolBandthePolB-PCNA-DNAcomplex an intermediary form transitional between the canonical
from P. furiosus have been solved, shedding light on the archaealRFCcomplexofonesmallandonelargesubunitand
interactionsbetweenthesemolecules[133,134].Inaddition, theeukaryoticRFCcomplexoffourdifferentsmallandone
astudydemonstratedthatthePolD/PCNAandPolB/PCNA largesubunit[146].Theorganizationandspatialdistribution
interactions require two and one PIP boxes, respectively exhibitasimilaritytotheE.coliminimal𝛾-complex,butthe
[135]. Recently, through a protein-interaction network of P. functionofthesubunitsisprobablynotconserved[145].
abyssi, a previouslyunknown proteinwith nuclease activity
(Pab0431) and a PIP canonical motif was discovered to 3.5.Maturation. DuringDNAreplication,thelaggingstrand
interact with PCNA, suggesting a possible involvement in isdiscontinuouslysynthesizedbyextendingtheRNAprimers
DNA replication [136]. T. kodakaraensis is the only well- or Okazaki fragments. This discontinuously synthesized
documentedexampleofaneuryarchaeotewithtwohomologs DNAstrandrequiresmaturationtoformasingle,covalently
forPCNA,TK0535(PCNA1),andTK0582(PCNA2).Recent closed strand to end the replication process. In Archaea,
workdemonstratedbothproteinsformstablehomotrimeric Okazaki fragments were first demonstrated during replica-
ringsthatinteractwithT.kodakaraensis PolBinvitro[137]. tioninP. abyssiandSulfolobusacidocaldarius[147].During
A more detailed study of the two homologs of PCNA in T. replication,theseRNAprimersarereplacedwithDNA.The
8 Archaea
removaloftheprimersisperformedbytheenzymeRNaseH, coupled DNA synthesis, RNA primer removal, and DNA
which is ubiquitous in the three domains of life. According ligation. In this model a single PCNA (heterotrimericring)
to their sequence similarity, in prokaryotes the RNase H coordinates the activities of PolBI, FEN-1, and DNA ligase
proteinsareclassifiedintothreegroups:RNaseHI,HII,and into an efficient maturation complex [157]. A different in
HIII.Ineukaryotes,theyareclassifiedasRNaseH1andH2 vitrostudyinP.abyssihasdemonstratedtwodifferentmodels
[148].However,phylogeneticanalysessuggestthattheRNase forOkazakifragmentsmaturation,whichdifferintheRNA
H proteins can also be classified into two different groups: primer removal process. In the first model RNA primer
Type1(prokaryoticRNaseHI,eukaryoticRNaseH1,andviral eliminationisexecutedbycontinuousPolDstranddisplace-
󸀠
RNaseH)andType2(prokaryoticRNaseHIIandHIIIand ment DNA synthesis and 5 RNA flap cleavage by FEN-1.
eukaryotic RNase H2) [149]. These two types of RNase H The resulting nicks are closed by DNA ligase. Alternatively,
possessdifferentspecificactivities,metalionpreferences,and the second model proposes that RNase HII cleaves the
cleavage sites [150]. Originally it was thought that Archaea RNA primer, followed by the action of FEN-1 and strand
onlypossesstype2RNaseH[149],butseveraltype1archaeal displacement DNA synthesis by polB or polD. The nick is
RNaseHenzymeshavesincethenbeendiscovered[151,152]. then sealed by DNA ligase [127]. Testing these models in
Interestingly,ineukaryotes,RNaseH1andH2tendtocoexist, vivoisofgreatinteresttocompletethepictureofhowthese
anddifferentcombinationsofthethreeprokaryoticRNasesH processesbehaveinthecell.Inaddition,otherfactorsthatcan
(I,II,andIII)arefound,exceptforthecombinationofRNases modulatetheseprocessesmayberequiredforcoordinationof
HI and HIII. This mutually exclusive evolution of some of theinvivomaturationprocess.
the prokaryotic RNases seems to be related to functional
redundancy[148]. 4.Conclusions
Another enzyme involved in primer replacement in
DNA replication is the Flap endonuclease I (FEN-1), which DNA replication in archaea possesses a dual nature, where
󸀠
recognizesdouble-strandedDNAwithanunannealed5-flap, themachineryisstructurallyandfunctionallysimilartothe
and cleaves it. A eukaryotic homolog of FEN-1 is found in eukaryotic replication system, but it is executed within a
every archaeal member analyzed, and one member of the bacterial context [11, 25]. Additionally, unique archaeal fea-
Thermoproteales, Thermofilum pendens Hrk5, possesses two turesdemonstratethecomplexityofthisprocess,anditdoes
homologs. not appear to be just a simplified version of the eukary-
M. maripaludis S2 possesses genes for the prokaryotic otic system. For example, the archaeal specific DNA poly-
RNase HI and HII, and for FEN-1, but none are essential, merase D is conserved across the Archaea domain with the
suggesting that they may be redundant in their functions exceptionoftheCrenarchaeotaphylum.Therecentdiscovery
[44, 62]. Possibly, both RNase H proteins persist and are thatitistheessentialreplicativepolymeraseintwodifferent
evolutionary stable in the genome. The gene products may euryarchaeotic species demonstrates an unanticipated vari-
performthesamefunctionbutoneislessefficientthanthe abilityinarchaealDNAreplicationandafundamentaldiffer-
other[153]. ence in the replication mechanism between crenarchaeotes
After the Okazaki fragments are replaced by DNA in and euryarchaeotes. Interestingly, the absence of PolD in
the lagging strand, the nick between the newly synthesized crenarchaeotes is not the only difference in DNA repli-
and the elongated DNA is repaired by a DNA ligase. This cation. These differences include the absence of histones
enzymeusesanucleotidecofactortocatalyzetheformation in crenarchaeotes [4], the presence of multiple origins of
ofthephosphodiesterbondinthreewell-characterizedsteps replication in crenarchaeotes and a single origin of repli-
[154].Theenzymeiscommontoallthreedomainsbutcanbe cation in most euryarchaeotes, the absence of GINS23 in
groupedintotwofamiliesbasedoncofactorspecificity(ATP most euryarchaeotes, the absence of RPA protein in many
+
orNAD ).TheDNAligasesfromseveralcrenarchaeotesand crenarchaeotes,thepresenceofmultipleMCMhomologsin
euryarchaeotes have been further characterized (reviewed Methanococcales,andthepresenceofonehomologofPCNA
in [43]). Many archaeal DNA ligases possess dual cofactor in euryarchaeotes compared to the multiple homologs in
+
specificity (ATP/NAD or ATP/ADP), but every archaeal crenarchaeotes.Thesedistinctivecharacteristicsbetweenthe
DNA ligase characterized so far uses ATP. A thermophilic phylahighlightthecomplexityofarchaealDNAreplication
DNAligasefromM.thermautotrophicuswhichusesATPas andsuggestacomplexevolutionaryhistory(Table1).
solecofactorwascharacterizedinvitro[155].Acharacterized AmongtheEuryarchaeota,theordersHalobacterialesand
DNAligasefromthecrenarchaeoteSulfophobococcuszilligii Methanococcales possess differences in the DNAreplication
+
displayed specificity for three cofactors (ATP/NAD /GTP) system that make them unique. For instance, Halobac-
[156].Majorstructuralworkinthisenzymehasbeenachieved teriales possess many more origin recognition proteins
inP.furiosusandS.solfataricus,andthefindingshavebeen (Orc1/Cdc6) compared to the rest of the archaea. On the
reviewedindetail[43].InM.maripaludisS2,theDNAligase other hand, Methanococcales and Methanopyrales lack rec-
islikelytobeessentialforgrowth[44,62]. ognizable homologs for the Orc1/Cdc6 proteins, suggesting
Understanding the maturation process in archaea has the presence of a very different mechanism forinitiationof
becomeafocusofincreasingresearchinrecentyears.Anin replication.Inaddition,theMethanococcalespossessalarge
vitro study reconstituted the Okazaki fragment maturation number of MCM protein homologs. It has been proposed
usingproteinsderivedfromthecrenarchaeoteS.solfataricus. thatthesedistinctivefeaturesareconnected,andbecauseof
They demonstrated that only six proteins are necessary for the absence of the Orc1/Cdc6 proteins, MCM proteins may
Archaea 9
)
Archaeadomain.Modifiedfrom[43]. ArchaeaCrenarchaeotaEuryarchaeotaaMultipleSinglebOrc1/Cdc6Orc1/Cdc6MCMcomplexMCMcomplex cGINS23/GINS15GINS15 RecJhomolog?RecJhomolog? DNAprimaseDNAprimase(PriSLd(PriSL)/DnaGFamilyDDNAFamilyBDNApolymeraseepolymeraseRFC(clamploader)RFC(clamploader)PCNA(clamp)PCNA(clamp)Fen1Fen1RNaseHRNaseHDNAligaseDNAligase oninthisandcloselyrelatedorganisms.
e ati
h c
a,andthetwomajorphylaoft Eukaryota MultipleORCcomplex(ORC1-6)MCMcomplex(MCM2-7)Cdc6Cdt1GINScomplex(Sld5,Psf1-3)Cdc45 𝛼Pol/primasecomplex 𝛿𝜀ol,andPol(FamilyBDNApolymerase)RFC(clamploader)PCNA(clamp)Fen1/Dna2RNaseHDNAligase ed,itmightalsoplayaroleinrepli
ryot P cidat
a u
Table1:DNAreplicationproteinsandfeaturesinthedomainsBacteria,Euk DNAreplicationstageProcessBacteria OriginofreplicationSinglePreinitiationOriginrecognitionDnaADNAunwinding(Helicase)DnaB DNAunwindingInitiationDnaC(Accessoryproteins) PrimersynthesisDnaG DNAsynthesisPolIII(FamilyCDNApolymerase)(polymerase)Elongation𝛾DNAsynthesis-complex(clamploader)𝛽(Processivityfactors)-clamp(clamp)PolI(familyADNApolymerase)Maturation(OkazakiMaturationRNaseHfragmentprocessing)DNAligaseaException,theorderHalobacteriales.bNotknownformembersoftheEuryarchaeotaordersMethanococcalesandMethanopyrales.cGINS23hasbeenfoundedonlyintheorderThermococcalesoftheEuryarchaeota.dSulfolobussolfataricusdidshowprimaseactivityinvitro.eFamilyBDNApolymeraseisalsoessentialinHalobacterium.Becauseitsfunctionhasnotbeenclearlyel
10 Archaea
interact with other unknown initiation enzymes, resulting [8] S.GribaldoandC.Brochier-Armanet,“Theoriginandevolu-
in a complex phylogeny of the MCM homologs [49]. Pre- tionofarchaea:astateoftheart,”PhilosophicalTransactionsof
sumably, these differences also account for the inability to theRoyalSocietyB,vol.361,no.1470,pp.1007–1022,2006.
recognizetheoriginofreplicationinthesemicroorganisms. [9] P. Londei, “Evolution of translational initiation: new insights
ThisuniquescenarioforinitiationofDNAreplicationmaybe fromthearchaea,”FEMSMicrobiologyReviews,vol.29,no.2,
adirectconsequenceofvariousprocessessuchasduplication, pp.185–200,2005.
mobilegeneticelements,andinteractionswithviruses[58]. [10] B. Grabowski and Z. Kelman, “Archaeal DNA replication:
The differences in DNA replication among archaeal eukaryal proteins in a bacterial context,” Annual Review of
highertaxademonstrateanunexpectedvariabilityandsug- Microbiology,vol.57,pp.487–516,2003.
gesttwoalternativeevolutionarymodels.Inthefirstmodel, [11] P.Forterre,J.File´e,andH.Myllykallio,“Originandevolution
DNA replication evolved late after the diversification of of DNA and DNA replication machineries,” in The Genetic
the archaeal lineages. Because the replicative system was CodeandtheOriginofLife,L.Ribas,Ed.,LandesBioscience,
Georgetown,Tex,USA,2007.
not fully formed, it was possible to develop differently
between the lineages. Once formed, replication would then [12] E. V. Koonin, “The origin and early evolution of eukaryotes
inthelightofphylogenomics,”GenomeBiology,vol.11,no.5,
be highly conserved. However, this model is not consistent
article209,2010.
with differences observed between lineages that must have
[13] M. Ko¨nneke, A. E. Bernhard, J. R. de la Torre, C. B. Walker,
formed relatively late, such as those between the orders or
J. B. Waterbury, and D. A. Stahl, “Isolation of an autotrophic
even, in some cases, within certain orders. The alternative
ammonia-oxidizing marine archaeon,” Nature, vol. 437, no.
model is that DNA replication has changed throughout the
7058,pp.543–546,2005.
evolutionofthearchaea.Thus,differencesinthereplicative
[14] C.Brochier-Armanet,B.Boussau,S.Gribaldo,andP.Forterre,
systemsmayrepresentancientaswellasmodernadaptations
“Mesophiliccrenarchaeota:proposalforathirdarchaealphy-
to changing environments. In this case, differences in the
lum,theThaumarchaeota,”NatureReviewsMicrobiology,vol.6,
replicative systems may provide importantinsights into the
no.3,pp.245–252,2008.
evolutionary pressures in play during different episodes of
[15] J. G. Elkins, M. Podar, D. E. Graham et al., “A korarchaeal
archaeal evolution. From this perspective, the differences
genome reveals insights into the evolution of the Archaea,”
betweentheeukaryoticandarchaealreplicativesystemsmay
Proceedings of the National Academy of Sciencesof the United
not be evidence for an ancient origin of the eukaryotes. StatesofAmerica,vol.105,no.23,pp.8102–8107,2008.
Instead, it is entirelyplausible that the replicative system in
[16] T. Nunoura, Y. Takaki, J. Kakuta et al., “Insights into the
eukaryotes could have evolved relatively late from a well- evolutionofArchaeaandeukaryoticproteinmodifiersystems
developedarchaealsystem. revealedbythegenomeofanovelarchaealgroup,”NucleicAcids
Research,vol.39,no.8,pp.3204–3223,2011.
ConflictofInterests [17] H.Huber,M.J.Hohn,R.Rachel,T.Fuchs,V.C.Wimmer,andK.
O.Stetter,“AnewphylumofArchaearepresentedbyananosized
The authors declare that there is no conflict of interests hyperthermophilicsymbiont,”Nature,vol.417,no.6884,pp.63–
regardingthepublicationofthispaper. 67,2002.
[18] C.Brochier,S.Gribaldo,Y.Zivanovic,F.Confalonieri,andP.
Forterre,“Nanoarchaea:representativesofanovelarchaealphy-
References
lumorafast-evolvingeuryarchaeallineagerelatedtoTherm-
ococcales?”GenomeBiology,vol.6,no.5,articleR42,2005.
[1] E. F. DeLong and N. R. Pace, “Environmental diversity of
[19] S.J.Aves,“DNAreplicationinitiation,”MethodsinMolecular
bacteriaandarchaea,”SystematicBiology,vol.50,no.4,pp.470–
Biology,vol.521,pp.3–17,2009.
478,2001.
[20] N. P. Robinson, I. Dionne, M. Lundgren, V. L. Marsh, R.
[2] B.Chaban,S.Y.M.Ng,andK.F.Jarrell,“Archaealhabitats—
Bernander, and S. D. Bell, “Identification of two origins of
fromtheextremetotheordinary,”CanadianJournalofMicro-
replicationinthesinglechromosomeofthearchaeonSulfolobus
biology,vol.52,no.2,pp.73–116,2006.
solfataricus,”Cell,vol.116,no.1,pp.25–38,2004.
[3] M. J. Hanford and T. L. Peeples, “Archaeal tetraether lipids:
[21] M. Lundgren, A. Andersson, L. Chen, P. Nilsson, and R.
uniquestructuresandapplications,”AppliedBiochemistryand
Bernander, “Three replication origins in Sulfolobus species:
BiotechnologyA,vol.97,no.1,pp.45–62,2002.
synchronous initiation of chromosome replication and asyn-
[4] K.SandmanandJ.N.Reeve,“Archaealhistonesandtheorigin chronoustermination,”ProceedingsoftheNationalAcademyof
ofthehistonefold,”CurrentOpinioninMicrobiology,vol.9,no. SciencesoftheUnitedStatesofAmerica,vol.101,no.18,pp.7046–
5,pp.520–525,2006. 7051,2004.
[5] O. Lecompte, R. Ripp, J.-C. Thierry, D. Moras, and O. Poch, [22] N.P.RobinsonandS.D.Bell,“Extrachromosomalelementcap-
“Comparativeanalysisofribosomalproteinsincompletegen- tureandtheevolutionofmultiplereplicationoriginsinarchaeal
omes:anexampleofreductiveevolutionatthedomainscale,” chromosomes,”ProceedingsoftheNationalAcademyofSciences
NucleicAcidsResearch,vol.30,no.24,pp.5382–5390,2002. oftheUnitedStatesofAmerica,vol.104,no.14,pp.5806–5811,
[6] D.R.EdgellandW.F.Doolittle,“Archaeaandtheorigin(s)of 2007.
DNArplicationpoteins,”Cell,vol.89,no.7,pp.995–998,1997. [23] E.A.Pelve,A.C.Lindas,A.Knoppel,A.Mira,andR.Bernan-
[7] E. R. Barry and S. D. Bell, “DNA replication in the archaea,” der, “Four chromosome replication origins in the archaeon
MicrobiologyandMolecularBiologyReviews,vol.70,no.4,pp. Pyrobaculumcalidifontis,”MolecularMicrobiology,vol.85,no.
876–887,2006. 5,pp.986–995,2012.